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. 2017 Jun 9;14(6):1246E. doi: 10.2903/sp.efsa.2017.EN-1246

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Jan Paces 1, Miloslav Nic 2, Tomas Novotny 2, Petr Svoboda 1
PMCID: PMC7163844

The content is available as a PDF (7.6 MB).

Suggested citation: Pačes Jan, Nič Miloslav, Novotný Tomáš, Svoboda Petr 2017. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. EFSA supporting publication 2017: 14(6):EN‐1246. 314 pp. doi: 10.2903/sp.efsa.2017.EN-1246

Question number: EFSA‐Q‐2015‐00258

Disclaimer: The present document has been produced and adopted by the bodies identified above as author(s). This task has been carried out exclusively by the author(s) in the context of a contract between the European Food Safety Authority and the author(s), awarded following a tender procedure. The present document is published complying with the transparency principle to which the Authority is subject. It may not be considered as an output adopted by the Authority. The European Food Safety Authority reserves its rights, view and position as regards the issues addressed and the conclusions reached in the present document, without prejudice to the rights of the authors.

References

  1. Athanasiadis A, Rich A and Maas S, 2004. Widespread A‐to‐I RNA editing of Alu‐containing mRNAs in the human transcriptome. PLoS Biol, 2, e391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, Eachus R and Pasquinelli AE, 2005. Regulation by let‐7 and lin‐4 miRNAs results in target mRNA degradation. Cell, 122, 553–563. [DOI] [PubMed] [Google Scholar]
  3. Bartel DP, 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281–297. [DOI] [PubMed] [Google Scholar]
  4. Bernstein E, Caudy AA, Hammond SM and Hannon GJ, 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409, 363–366. [DOI] [PubMed] [Google Scholar]
  5. Brennecke J, Stark A, Russell RB and Cohen SM, 2005. Principles of microRNA‐target recognition. PLoS Biol, 3, e85. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Carmell MA, Xuan Z, Zhang MQ and Hannon GJ, 2002. The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev, 16, 2733–2742. [DOI] [PubMed] [Google Scholar]
  7. Cerutti H and Casas‐Mollano JA, 2006. On the origin and functions of RNA‐mediated silencing: from protists to man. Curr Genet, 50, 81–99. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Chen Y, Boland A, Kuzuoglu‐Ozturk D, Bawankar P, Loh B, Chang CT, Weichenrieder O and Izaurralde E, 2014. A DDX6‐CNOT1 complex and W‐binding pockets in CNOT9 reveal direct links between miRNA target recognition and silencing. Mol Cell, 54, 737–750. [DOI] [PubMed] [Google Scholar]
  9. Chera S, de Rosa R, Miljkovic‐Licina M, Dobretz K, Ghila L, Kaloulis K and Galliot B, 2006. Silencing of the hydra serine protease inhibitor Kazal1 gene mimics the human SPINK1 pancreatic phenotype. J Cell Sci, 119, 846–857. [DOI] [PubMed] [Google Scholar]
  10. Cogoni C and Macino G, 1999. Gene silencing in Neurospora crassa requires a protein homologous to RNA‐dependent RNA polymerase. Nature, 399, 166–169. [DOI] [PubMed] [Google Scholar]
  11. Dalmay T, Horsefield R, Braunstein TH and Baulcombe DC, 2001. SDE3 encodes an RNA helicase required for post‐transcriptional gene silencing in Arabidopsis . EMBO J, 20, 2069–2078. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Decker CJ and Parker R, 2012. P‐bodies and stress granules: possible roles in the control of translation and mRNA degradation. Cold Spring Harb Perspect Biol, 4, a012286. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Djuranovic S, Nahvi A and Green R, 2012. miRNA‐mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science, 336, 237–240. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Dlakic M, 2006. DUF283 domain of Dicer proteins has a double‐stranded RNA‐binding fold. Bioinformatics, 22, 2711–2714. [DOI] [PubMed] [Google Scholar]
  15. Doench JG, Petersen CP and Sharp PA, 2003. siRNAs can function as miRNAs. Genes Dev, 17, 438–442. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Du T and Zamore PD, 2005. microPrimer: the biogenesis and function of microRNA. Development, 132, 4645–4652. [DOI] [PubMed] [Google Scholar]
  17. Eichhorn SW, Guo H, McGeary SE, Rodriguez‐Mias RA, Shin C, Baek D, Hsu SH, Ghoshal K, Villen J and Bartel DP, 2014. mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Mol Cell, 56, 104–115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Faehnle CR and Joshua‐Tor L, 2007. Argonautes confront new small RNAs. Curr Opin Chem Biol, 11, 569–577. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE and Mello CC, 1998. Potent and specific genetic interference by double‐stranded RNA in Caenorhabditis elegans. Nature, 391, 806–811. [DOI] [PubMed] [Google Scholar]
  20. Friedman RC, Farh KK, Burge CB and Bartel DP, 2009. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res, 19, 92–105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Gantier MP and Williams BR, 2007. The response of mammalian cells to double‐stranded RNA. Cytokine Growth Factor Rev, 18, 363–371. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Geiss G, Jin G, Guo J, Bumgarner R, Katze MG and Sen GC, 2001. A comprehensive view of regulation of gene expression by double‐stranded RNA‐mediated cell signaling. J Biol Chem, 276, 30178–30182. [DOI] [PubMed] [Google Scholar]
  23. Geldhof P, Visser A, Clark D, Saunders G, Britton C, Gilleard J, Berriman M and Knox D, 2007. RNA interference in parasitic helminths: current situation, potential pitfalls and future prospects. Parasitology, 134, 609–619. [DOI] [PubMed] [Google Scholar]
  24. Grice LF and Degnan BM, 2015. The origin of the ADAR gene family and animal RNA editing. BMC Evol Biol, 15, 4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A, Ruvkun G and Mello CC, 2001. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell, 106, 23–34. [DOI] [PubMed] [Google Scholar]
  26. Hall IM, Shankaranarayana GD, Noma K, Ayoub N, Cohen A and Grewal SI, 2002. Establishment and maintenance of a heterochromatin domain. Science, 297, 2232–2237. [DOI] [PubMed] [Google Scholar]
  27. Hamilton AJ and Baulcombe DC, 1999. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science, 286, 950–952. [DOI] [PubMed] [Google Scholar]
  28. Higuchi M, Maas S, Single FN, Hartner J, Rozov A, Burnashev N, Feldmeyer D, Sprengel R and Seeburg PH, 2000. Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA‐editing enzyme ADAR2. Nature, 406, 78–81. [DOI] [PubMed] [Google Scholar]
  29. Himber C, Dunoyer P, Moissiard G, Ritzenthaler C and Voinnet O, 2003. Transitivity‐dependent and ‐independent cell‐to‐cell movement of RNA silencing. EMBO J, 22, 4523–4533. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Hunter T, Hunt T, Jackson RJ and Robertson HD, 1975. The characteristics of inhibition of protein synthesis by double‐stranded ribonucleic acid in reticulocyte lysates. J Biol Chem, 250, 409–417. [PubMed] [Google Scholar]
  31. Hutvagner G and Zamore PD, 2002. A microRNA in a multiple‐turnover RNAi enzyme complex. Science, 297, 2056–2060. [DOI] [PubMed] [Google Scholar]
  32. Huvenne H and Smagghe G, 2010. Mechanisms of dsRNA uptake in insects and potential of RNAi for pest control: a review. J Insect Physiol, 56, 227–235. [DOI] [PubMed] [Google Scholar]
  33. Jaskiewicz L and Filipowicz W, 2008. Role of Dicer in posttranscriptional RNA silencing. Curr Top Microbiol Immunol, 320, 77–97. [DOI] [PubMed] [Google Scholar]
  34. Jinek M and Doudna JA, 2009. A three‐dimensional view of the molecular machinery of RNA interference. Nature, 457, 405–412. [DOI] [PubMed] [Google Scholar]
  35. Kawahara Y, Zinshteyn B, Chendrimada TP, Shiekhattar R and Nishikura K, 2007a. RNA editing of the microRNA‐151 precursor blocks cleavage by the Dicer‐TRBP complex. EMBO Rep, 8, 763–769. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Kawahara Y, Zinshteyn B, Sethupathy P, Iizasa H, Hatzigeorgiou AG and Nishikura K, 2007b. Redirection of silencing targets by adenosine‐to‐inosine editing of miRNAs. Science, 315, 1137–1140. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Ketting RF, 2011. The many faces of RNAi. Dev Cell, 20, 148–161. [DOI] [PubMed] [Google Scholar]
  38. Kim VN, Han J and Siomi MC, 2009. Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol, 10, 126–139. [DOI] [PubMed] [Google Scholar]
  39. Kozomara A and Griffiths‐Jones S, 2014. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res, 42, D68–73. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Lee RC, Feinbaum RL and Ambros V, 1993. The C. elegans heterochronic gene lin‐4 encodes small RNAs with antisense complementarity to lin‐14. Cell, 75, 843–854. [DOI] [PubMed] [Google Scholar]
  41. Lehmann KA and Bass BL, 1999. The importance of internal loops within RNA substrates of ADAR1. J Mol Biol, 291, 1–13. [DOI] [PubMed] [Google Scholar]
  42. Lim LP, Lau NC, Garrett‐Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS and Johnson JM, 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature, 433, 769–773. [DOI] [PubMed] [Google Scholar]
  43. Lingel A, Simon B, Izaurralde E and Sattler M, 2003. Structure and nucleic‐acid binding of the Drosophila Argonaute 2 PAZ domain. Nature, 426, 465–469. [DOI] [PubMed] [Google Scholar]
  44. Lingel A, Simon B, Izaurralde E and Sattler M, 2004. Nucleic acid 3′‐end recognition by the Argonaute2 PAZ domain. Nat Struct Mol Biol, 11, 576–577. [DOI] [PubMed] [Google Scholar]
  45. Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, Song JJ, Hammond SM, Joshua‐Tor L and Hannon GJ, 2004. Argonaute2 is the catalytic engine of mammalian RNAi. Science, 305, 1437–1441. [DOI] [PubMed] [Google Scholar]
  46. Liu J, Valencia‐Sanchez MA, Hannon GJ and Parker R, 2005. MicroRNA‐dependent localization of targeted mRNAs to mammalian P‐bodies. Nat Cell Biol, 7, 719–723. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Ma JB, Ye K and Patel DJ, 2004. Structural basis for overhang‐specific small interfering RNA recognition by the PAZ domain. Nature, 429, 318–322. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Ma JB, Yuan YR, Meister G, Pei Y, Tuschl T and Patel DJ, 2005. Structural basis for 5′‐end‐specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature, 434, 666–670. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. MacRae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD and Doudna JA, 2006. Structural basis for double‐stranded RNA processing by Dicer. Science, 311, 195–198. [DOI] [PubMed] [Google Scholar]
  50. MacRae IJ, Zhou K and Doudna JA, 2007. Structural determinants of RNA recognition and cleavage by Dicer. Nat Struct Mol Biol, 14, 934–940. [DOI] [PubMed] [Google Scholar]
  51. Marques JT and Carthew RW, 2007. A call to arms: coevolution of animal viruses and host innate immune responses. Trends Genet, 23, 359–364. [DOI] [PubMed] [Google Scholar]
  52. Martinez J, Patkaniowska A, Urlaub H, Luhrmann R and Tuschl T, 2002. Single‐stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell, 110, 563–574. [DOI] [PubMed] [Google Scholar]
  53. Meins F, Jr , Si‐Ammour A and Blevins T, 2005. RNA silencing systems and their relevance to plant development. Annu Rev Cell Dev Biol, 21, 297–318. [DOI] [PubMed] [Google Scholar]
  54. Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G and Tuschl T, 2004. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol Cell, 15, 185–197. [DOI] [PubMed] [Google Scholar]
  55. Meister G and Tuschl T, 2004. Mechanisms of gene silencing by double‐stranded RNA. Nature, 431, 343–349. [DOI] [PubMed] [Google Scholar]
  56. Meurs E, Chong K, Galabru J, Thomas NS, Kerr IM, Williams BR and Hovanessian AG, 1990. Molecular cloning and characterization of the human double‐stranded RNA‐activated protein kinase induced by interferon. Cell, 62, 379–390. [DOI] [PubMed] [Google Scholar]
  57. Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L, Rappsilber J, Mann M and Dreyfuss G, 2002. miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev, 16, 720–728. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Mourrain P, Beclin C, Elmayan T, Feuerbach F, Godon C, Morel JB, Jouette D, Lacombe AM, Nikic S, Picault N, Remoue K, Sanial M, Vo TA and Vaucheret H, 2000. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell, 101, 533–542. [DOI] [PubMed] [Google Scholar]
  59. Murphy D, Dancis B and Brown JR, 2008. The evolution of core proteins involved in microRNA biogenesis. BMC Evol Biol, 8, 92. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Napoli C, Lemieux C and Jorgensen R, 1990. Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co‐Suppression of Homologous Genes in trans. Plant Cell, 2, 279–289. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Newmark PA, Reddien PW, Cebria F and Sanchez Alvarado A, 2003. Ingestion of bacterially expressed double‐stranded RNA inhibits gene expression in planarians. Proc Natl Acad Sci U S A, 100 Suppl 1, 11861–11865. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Nishihara T, Zekri L, Braun JE and Izaurralde E, 2013. miRISC recruits decapping factors to miRNA targets to enhance their degradation. Nucleic Acids Res, 41, 8692–8705. [DOI] [PMC free article] [PubMed] [Google Scholar]
  63. Nishikura K, Yoo C, Kim U, Murray JM, Estes PA, Cash FE and Liebhaber SA, 1991. Substrate specificity of the dsRNA unwinding/modifying activity. EMBO J, 10, 3523–3532. [DOI] [PMC free article] [PubMed] [Google Scholar]
  64. Nishikura K, 2010. Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem, 79, 321–349. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. Nykanen A, Haley B and Zamore PD, 2001. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell, 107, 309–321. [DOI] [PubMed] [Google Scholar]
  66. Orii H, Mochii M and Watanabe K, 2003. A simple “soaking method” for RNA interference in the planarian Dugesia japonica. Dev Genes Evol, 213, 138–141. [DOI] [PubMed] [Google Scholar]
  67. Palladino MJ, Keegan LP, O'Connell MA and Reenan RA, 2000. A‐to‐I pre‐mRNA editing in Drosophila is primarily involved in adult nervous system function and integrity. Cell, 102, 437–449. [DOI] [PubMed] [Google Scholar]
  68. Parker JS, Roe SM and Barford D, 2004. Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J, 23, 4727–4737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Muller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E and Ruvkun G, 2000. Conservation of the sequence and temporal expression of let‐7 heterochronic regulatory RNA. Nature, 408, 86–89. [DOI] [PubMed] [Google Scholar]
  70. Pham JW, Pellino JL, Lee YS, Carthew RW and Sontheimer EJ, 2004. A Dicer‐2‐dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila. Cell, 117, 83–94. [DOI] [PubMed] [Google Scholar]
  71. Pillai RS, Bhattacharyya SN, Artus CG, Zoller T, Cougot N, Basyuk E, Bertrand E and Filipowicz W, 2005. Inhibition of translational initiation by Let‐7 MicroRNA in human cells. Science, 309, 1573–1576. [DOI] [PubMed] [Google Scholar]
  72. Polson AG and Bass BL, 1994. Preferential selection of adenosines for modification by double‐stranded RNA adenosine deaminase. EMBO J, 13, 5701–5711. [DOI] [PMC free article] [PubMed] [Google Scholar]
  73. Provost P, Dishart D, Doucet J, Frendewey D, Samuelsson B and Radmark O, 2002. Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J, 21, 5864–5874. [DOI] [PMC free article] [PubMed] [Google Scholar]
  74. Qin H, Chen F, Huan X, Machida S, Song J and Yuan YA, 2010. Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double‐stranded RNA‐binding fold for protein‐protein interaction. RNA, 16, 474–481. [DOI] [PMC free article] [PubMed] [Google Scholar]
  75. Roignant JY, Carre C, Mugat B, Szymczak D, Lepesant JA and Antoniewski C, 2003. Absence of transitive and systemic pathways allows cell‐specific and isoform‐specific RNAi in Drosophila. RNA, 9, 299–308. [DOI] [PMC free article] [PubMed] [Google Scholar]
  76. Romano N and Macino G, 1992. Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol Microbiol, 6, 3343–3353. [DOI] [PubMed] [Google Scholar]
  77. Rouya C, Siddiqui N, Morita M, Duchaine TF, Fabian MR and Sonenberg N, 2014. Human DDX6 effects miRNA‐mediated gene silencing via direct binding to CNOT1. RNA, 20, 1398–1409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  78. Sadler AJ and Williams BR, 2007. Structure and function of the protein kinase R. Curr Top Microbiol Immunol, 316, 253–292. [DOI] [PubMed] [Google Scholar]
  79. Scadden AD and Smith CW, 2001. RNAi is antagonized by A–>I hyper‐editing. EMBO Rep, 2, 1107–1111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  80. Scadden AD, 2005. The RISC subunit Tudor‐SN binds to hyper‐edited double‐stranded RNA and promotes its cleavage. Nat Struct Mol Biol, 12, 489–496. [DOI] [PubMed] [Google Scholar]
  81. Schmitter D, Filkowski J, Sewer A, Pillai RS, Oakeley EJ, Zavolan M, Svoboda P and Filipowicz W, 2006. Effects of Dicer and Argonaute down‐regulation on mRNA levels in human HEK293 cells. Nucleic Acids Res, 34, 4801–4815. [DOI] [PMC free article] [PubMed] [Google Scholar]
  82. Schwarz DS, Hutvagner G, Haley B and Zamore PD, 2002. Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways. Mol Cell, 10, 537–548. [DOI] [PubMed] [Google Scholar]
  83. Smardon A, Spoerke JM, Stacey SC, Klein ME, Mackin N and Maine EM, 2000. EGO‐1 is related to RNA‐directed RNA polymerase and functions in germ‐line development and RNA interference in C. elegans. Curr Biol, 10, 169–178. [DOI] [PubMed] [Google Scholar]
  84. Song JJ, Liu J, Tolia NH, Schneiderman J, Smith SK, Martienssen RA, Hannon GJ and Joshua‐Tor L, 2003. The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat Struct Biol, 10, 1026–1032. [DOI] [PubMed] [Google Scholar]
  85. Song JJ, Smith SK, Hannon GJ and Joshua‐Tor L, 2004. Crystal structure of Argonaute and its implications for RISC slicer activity. Science, 305, 1434–1437. [DOI] [PubMed] [Google Scholar]
  86. Sontheimer EJ, 2005. Assembly and function of RNA silencing complexes. Nat Rev Mol Cell Biol, 6, 127–138. [DOI] [PubMed] [Google Scholar]
  87. Stein P, Svoboda P, Anger M and Schultz RM, 2003. RNAi: mammalian oocytes do it without RNA‐dependent RNA polymerase. RNA, 9, 187–192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  88. Svoboda P and Cara AD, 2006. Hairpin RNA: a secondary structure of primary importance. Cell Mol Life Sci, 63, 901–908. [DOI] [PMC free article] [PubMed] [Google Scholar]
  89. Tabara H, Grishok A and Mello CC, 1998. RNAi in C. elegans: soaking in the genome sequence. Science, 282, 430–431. [DOI] [PubMed] [Google Scholar]
  90. Timmons L and Fire A, 1998. Specific interference by ingested dsRNA. Nature, 395, 854. [DOI] [PubMed] [Google Scholar]
  91. Tomoyasu Y, Miller SC, Tomita S, Schoppmeier M, Grossmann D and Bucher G, 2008. Exploring systemic RNA interference in insects: a genome‐wide survey for RNAi genes in Tribolium. Genome Biol, 9, R10. [DOI] [PMC free article] [PubMed] [Google Scholar]
  92. Tonkin LA, Saccomanno L, Morse DP, Brodigan T, Krause M and Bass BL, 2002. RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans. EMBO J, 21, 6025–6035. [DOI] [PMC free article] [PubMed] [Google Scholar]
  93. Tonkin LA and Bass BL, 2003. Mutations in RNAi rescue aberrant chemotaxis of ADAR mutants. Science, 302, 1725. [DOI] [PMC free article] [PubMed] [Google Scholar]
  94. van der Krol AR, Mur LA, Beld M, Mol JN and Stuitje AR, 1990. Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell, 2, 291–299. [DOI] [PMC free article] [PubMed] [Google Scholar]
  95. Voinnet O, Pinto YM and Baulcombe DC, 1999. Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants. Proc Natl Acad Sci U S A, 96, 14147–14152. [DOI] [PMC free article] [PubMed] [Google Scholar]
  96. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI and Martienssen RA, 2002. Regulation of heterochromatic silencing and histone H3 lysine‐9 methylation by RNAi. Science, 297, 1833–1837. [DOI] [PubMed] [Google Scholar]
  97. Wang Q, Khillan J, Gadue P and Nishikura K, 2000. Requirement of the RNA editing deaminase ADAR1 gene for embryonic erythropoiesis. Science, 290, 1765–1768. [DOI] [PubMed] [Google Scholar]
  98. Whangbo JS and Hunter CP, 2008. Environmental RNA interference. Trends Genet, 24, 297–305. [DOI] [PubMed] [Google Scholar]
  99. Winter J, Jung S, Keller S, Gregory RI and Diederichs S, 2009. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol, 11, 228–234. [DOI] [PubMed] [Google Scholar]
  100. Xie Q and Guo HS, 2006. Systemic antiviral silencing in plants. Virus Res, 118, 1–6. [DOI] [PubMed] [Google Scholar]
  101. Xu W and Han Z, 2008. Cloning and phylogenetic analysis of sid‐1‐like genes from aphids. J Insect Sci, 8, 1–6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  102. Yan KS, Yan S, Farooq A, Han A, Zeng L and Zhou MM, 2003. Structure and conserved RNA binding of the PAZ domain. Nature, 426, 468–474. [DOI] [PubMed] [Google Scholar]
  103. Yang W, Chendrimada TP, Wang Q, Higuchi M, Seeburg PH, Shiekhattar R and Nishikura K, 2006. Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat Struct Mol Biol, 13, 13–21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  104. Yoneyama M, Kikuchi M, Natsukawa T, Shinobu N, Imaizumi T, Miyagishi M, Taira K, Akira S and Fujita T, 2004. The RNA helicase RIG‐I has an essential function in double‐stranded RNA‐induced innate antiviral responses. Nat Immunol, 5, 730–737. [DOI] [PubMed] [Google Scholar]
  105. Yuan YR, Pei Y, Ma JB, Kuryavyi V, Zhadina M, Meister G, Chen HY, Dauter Z, Tuschl T and Patel DJ, 2005. Crystal structure of A. aeolicus argonaute, a site‐specific DNA‐guided endoribonuclease, provides insights into RISC‐mediated mRNA cleavage. Mol Cell, 19, 405–419. [DOI] [PMC free article] [PubMed] [Google Scholar]
  106. Zamore PD, Tuschl T, Sharp PA and Bartel DP, 2000. RNAi: double‐stranded RNA directs the ATP‐dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell, 101, 25–33. [DOI] [PubMed] [Google Scholar]
  107. Zhang H, Kolb FA, Brondani V, Billy E and Filipowicz W, 2002. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J, 21, 5875–5885. [DOI] [PMC free article] [PubMed] [Google Scholar]
  108. Zhang H, Kolb FA, Jaskiewicz L, Westhof E and Filipowicz W, 2004. Single processing center models for human Dicer and bacterial RNase III. Cell, 118, 57–68. [DOI] [PubMed] [Google Scholar]
  109. Adilakshmi T, Sudol I and Tapinos N, 2012. Combinatorial Action of miRNAs Regulates Transcriptional and Post‐Transcriptional Gene Silencing following in vivo PNS Injury. PLoS ONE, 7, e39674–e39674. [DOI] [PMC free article] [PubMed] [Google Scholar]
  110. Agranat L, Raitskin O, Sperling J and Sperling R, 2008. The editing enzyme ADAR1 and the mRNA surveillance protein hUpf1 interact in the cell nucleus. Proc Natl Acad Sci U S A, 105, 5028–5033. [DOI] [PMC free article] [PubMed] [Google Scholar]
  111. Ahlenstiel CL, Lim HGW, Cooper DA, Ishida T, Kelleher AD and Suzuki K, 2012. Direct evidence of nuclear Argonaute distribution during transcriptional silencing links the actin cytoskeleton to nuclear RNAi machinery in human cells. Nucleic Acids Research, 40, 1579–1595. [DOI] [PMC free article] [PubMed] [Google Scholar]
  112. Aizer A, Kalo A, Kafri P, Shraga A, Ben‐Yishay R, Jacob A, Kinor N and Shav‐Tal Y, 2014. Quantifying mRNA targeting to P‐bodies in living human cells reveals their dual role in mRNA decay and storage. Journal of Cell Science, 127, 4443–4456. [DOI] [PubMed] [Google Scholar]
  113. Alarcon CR, Lee H, Goodarzi H, Halberg N and Tavazoie SF, 2015. N‐6‐methyladenosine marks primary microRNAs for processing. Nature, 519, 482–+. [DOI] [PMC free article] [PubMed] [Google Scholar]
  114. Allo M, Buggiano V, Fededa JP, Petrillo E, Schor I, de la Mata M, Agirre E, Plass M, Eyras E, Elela SA, Klinck R, Chabot B and Kornblihtt AR, 2009. Control of alternative splicing through siRNA‐mediated transcriptional gene silencing. Nature Structural & Molecular Biology, 16, 717–724. [DOI] [PubMed] [Google Scholar]
  115. Allo M, Agirre E, Bessonov S, Bertucci P, Acuna LG, Buggiano V, Bellora N, Singh B, Petrillo E, Blaustein M, Minana B, Dujardin G, Pozzi B, Pelisch F, Bechara E, Agafonov DE, Srebrow A, Luhrmann R, Valcarcel J, Eyras E and Kornblihtt AR, 2014. Argonaute‐1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells. Proc Natl Acad Sci U S A, 111, 15622–15629. [DOI] [PMC free article] [PubMed] [Google Scholar]
  116. Alon S, Mor E, Vigneault F, Church GM, Locatelli F, Galeano F, Gallo A, Shomron N and Eisenberg E, 2012. Systematic identification of edited microRNAs in the human brain. Genome Research, 22, 1533–1540. [DOI] [PMC free article] [PubMed] [Google Scholar]
  117. Amarante MK, Oda JMM, Reiche EMV, Morimoto HK, Aoki MN and Watanabe MAE, 2011. Human endogenous RNAs: Implications for the immunomodulation of Toll‐like receptor 3. Experimental and Therapeutic Medicine, 2, 925–929. [DOI] [PMC free article] [PubMed] [Google Scholar]
  118. Ameres SL, Martinez J and Schroeder R, 2007. Molecular basis for target RNA recognition and cleavage by human RISC. Cell, 130, 101–112. [DOI] [PubMed] [Google Scholar]
  119. Ameyar‐Zazoua M, Rachez C, Souidi M, Robin P, Fritsch L, Young R, Morozova N, Fenouil R, Descostes N, Andrau J‐C, Mathieu J, Hamiche A, Ait‐Si‐Ali S, Muchardt C, Batsche E and Harel‐Bellan A, 2012. Argonaute proteins couple chromatin silencing to alternative splicing. Nature Structural & Molecular Biology, 19, 998–U946. [DOI] [PubMed] [Google Scholar]
  120. Ando Y, Maida Y, Morinaga A, Burroughs AM, Kimura R, Chiba J, Suzuki H, Masutomi K and Hayashizaki Y, 2011a. Two‐step cleavage of hairpin RNA with 5 ‘ overhangs by human DICER. Bmc Molecular Biology, 12, 6–6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  121. Ando Y, Tomaru Y, Morinaga A, Burroughs AM, Kawaji H, Kubosaki A, Kimura R, Tagata M, Ino Y, Hirano H, Chiba J, Suzuki H, Carninci P and Hayashizaki Y, 2011b. Nuclear Pore Complex Protein Mediated Nuclear Localization of Dicer Protein in Human Cells. PLoS ONE, 6, e23385–e23385. [DOI] [PMC free article] [PubMed] [Google Scholar]
  122. Aporntewan C, Phokaew C, Piriyapongsa J, Ngamphiw C, Ittiwut C, Tongsima S and Mutirangura A, 2011. Hypomethylation of Intragenic LINE‐1 Represses Transcription in Cancer Cells through AGO2. PLoS ONE, 6, e17934–e17934. [DOI] [PMC free article] [PubMed] [Google Scholar]
  123. Arroyo JD, Chevillet JR, Kroh EM, Ruf IK, Pritchard CC, Gibson DF, Mitchell PS, Bennett CF, Pogosova‐Agadjanyan EL, Stirewalt DL, Tait JF and Tewari M, 2011. Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc Natl Acad Sci U S A, 108, 5003–5008. [DOI] [PMC free article] [PubMed] [Google Scholar]
  124. Athanasiadis A, Rich A and Maas S, 2004. Widespread A‐to‐I RNA editing of Alu‐containing mRNAs in the human transcriptome. Plos Biology, 2, e391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  125. Azuma‐Mukai A, Oguri H, Mituyama T, Qian ZR, Asai K, Siomi H and Siomi MC, 2008. Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing. Proc Natl Acad Sci U S A, 105, 7964–7969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  126. Babiarz JE, Ruby JG, Wang YM, Bartel DP and Blelloch R, 2008. Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor‐independent, Dicer‐dependent small RNAs. Genes & Development, 22, 2773–2785. [DOI] [PMC free article] [PubMed] [Google Scholar]
  127. Babiarz JE, Hsu R, Melton C, Thomas M, Ullian EM and Blelloch R, 2011. A role for noncanonical microRNAs in the mammalian brain revealed by phenotypic differences in Dgcr8 versus Dicer1 knockouts and small RNA sequencing. Rna, 17, 1489–1501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  128. Baglio SR, Rooijers K, Koppers‐Lalic D, Verweij FJ, Pérez Lanzón M, Zini N, Naaijkens B, Perut F, Niessen HWM, Baldini N and Pegtel DM, 2015. Human bone marrow‐ and adipose‐mesenchymal stem cells secrete exosomes enriched in distinctive miRNA and tRNA species. Stem Cell Research and Therapy, 6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  129. Bahn JH, Ahn J, Lin XZ, Zhang Q, Lee JH, Civelek M and Xiao XS, 2015. Genomic analysis of ADAR1 binding and its involvement in multiple RNA processing pathways. Nature Communications, 6, 6355–6355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  130. Bai BY, Liu H and Laiho M, 2014. Small RNA expression and deep sequencing analyses of the nucleolus reveal the presence of nucleolus‐associated microRNAs. Febs Open Bio, 4, 441–449. [DOI] [PMC free article] [PubMed] [Google Scholar]
  131. Bannwarth S, Talakoub L, Letourneur F, Duarte M, Purcell DF, Hiscott J and Gatignol A, 2001. Organization of the human tarbp2 gene reveals two promoters that are repressed in an astrocytic cell line. Journal of Biological Chemistry, 276, 48803–48813. [DOI] [PubMed] [Google Scholar]
  132. Barad O, Mann M, Chapnik E, Shenoy A, Blelloch R, Barkai N and Hornstein E, 2012. Efficiency and specificity in microRNA biogenesis. Nature Structural & Molecular Biology, 19, 650–+. [DOI] [PMC free article] [PubMed] [Google Scholar]
  133. Barr I and Guo F, 2014. Primary microRNA processing assay reconstituted using recombinant drosha and DGCR8. Methods in Molecular Biology, 1095, 73–86. [DOI] [PMC free article] [PubMed] [Google Scholar]
  134. Barr I, Weitz SH, Atkin T, Hsu PK, Karayiorgou M, Gogos JA, Weiss S and Guo F, 2015. Cobalt(III) Protoporphyrin Activates the DGCR8 Protein and Can Compensate microRNA Processing Deficiency. Chemistry & Biology, 22, 793–802. [DOI] [PMC free article] [PubMed] [Google Scholar]
  135. Bartel DP, 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281–297. [DOI] [PubMed] [Google Scholar]
  136. Beane RL, Ram R, Gabillet S, Arar K, Monia BP and Corey DR, 2007. Inhibiting gene expression with locked nucleic acids (LNAs) that target chromosomal DNA. Biochemistry, 46, 7572–7580. [DOI] [PMC free article] [PubMed] [Google Scholar]
  137. Behm‐Ansmant I, Rehwinkel J, Doerks T, Stark A, Bork P and Izaurralde E, 2006. MRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1: DCP2 decapping complexes. Genes & Development, 20, 1885–1898. [DOI] [PMC free article] [PubMed] [Google Scholar]
  138. Bellemer C, Bortolin‐Cavaille ML, Schmidt U, Jensen SMR, Kjems J, Bertrand E and Cavaille J, 2012. Microprocessor dynamics and interactions at endogenous imprinted C19MC microRNA genes. Journal of Cell Science, 125, 2709–2720. [DOI] [PubMed] [Google Scholar]
  139. Bellingham SA, Coleman BM and Hill AF, 2012. Small RNA deep sequencing reveals a distinct miRNA signature released in exosomes from prion‐infected neuronal cells. Nucleic Acids Research, 40, 10937–10949. [DOI] [PMC free article] [PubMed] [Google Scholar]
  140. Benetti R, Gonzalo S, Jaco I, Munoz P, Gonzalez S, Schoeftner S, Murchison E, Andl T, Chen T, Klatt P, Li E, Serrano M, Millar S, Hannon G and Blasco MA, 2008. A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2‐dependent regulation of DNA methyltransferases. Nature Structural & Molecular Biology, 15, 268–279. [DOI] [PMC free article] [PubMed] [Google Scholar]
  141. Benhamed M, Herbig U, Ye T, Dejean A and Bischof O, 2012. Senescence is an endogenous trigger for microRNA‐directed transcriptional gene silencing in human cells. Nature Cell Biology, 14, 266–+. [DOI] [PMC free article] [PubMed] [Google Scholar]
  142. Bennasser Y, Le SY, Benkirane M and Jeang KT, 2005. Evidence that HIV‐1 encodes an siRNA and a suppressor of RNA silencing. Immunity, 22, 607–619. [DOI] [PubMed] [Google Scholar]
  143. Benoit M and Plevin MJ, 2013. Backbone resonance assignments of the micro‐RNA precursor binding region of human TRBP. Biomolecular Nmr Assignments, 7, 229–233. [DOI] [PubMed] [Google Scholar]
  144. Berezhna SY, Supekova L, Supek F, Schultz PG and Deniz AA, 2006. siRNA in human cells selectively localizes to target RNA sites. Proc Natl Acad Sci U S A, 103, 7682–7687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  145. Berezikov E, Chung WJ, Willis J, Cuppen E and Lai EC, 2007. Mammalian mirtron genes. Molecular Cell, 28, 328–336. [DOI] [PMC free article] [PubMed] [Google Scholar]
  146. Bernard MA, Wang LY and Tachado SD, 2015. DICER‐ARGONAUTE2 Complex in Continuous Fluorogenic Assays of RNA Interference Enzymes. PLoS ONE, 10, e0120614–e0120614. [DOI] [PMC free article] [PubMed] [Google Scholar]
  147. Bernstein E, Caudy AA, Hammond SM and Hannon GJ, 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409, 363–366. [DOI] [PubMed] [Google Scholar]
  148. Betancur JG and Tomari Y, 2012. Dicer is dispensable for asymmetric RISC loading in mammals. Rna, 18, 24–30. [DOI] [PMC free article] [PubMed] [Google Scholar]
  149. Bevilacqua PC, George CX, Samuel CE and Cech TR, 1998. Binding of the protein kinase PKR to RNAs with secondary structure defects: Role of the tandem A‐G mismatch and noncontiguous helixes. Biochemistry, 37, 6303–6316. [DOI] [PubMed] [Google Scholar]
  150. Billy E, Brondani V, Zhang HD, Muller U and Filipowicz W, 2001. Specific interference with gene expression induced by long, double‐stranded RNA in mouse embryonal teratocarcinoma cell lines. Proc Natl Acad Sci U S A, 98, 14428–14433. [DOI] [PMC free article] [PubMed] [Google Scholar]
  151. Bogerd HP, Karnowski HW, Cai XZ, Shin J, Pohlers M and Cullen BR, 2010. A Mammalian Herpesvirus Uses Noncanonical Expression and Processing Mechanisms to Generate Viral MicroRNAs. Molecular Cell, 37, 135–142. [DOI] [PMC free article] [PubMed] [Google Scholar]
  152. Bommer UA, Borovjagin AV, Greagg MA, Jeffrey IW, Russell P, Laing KG, Lee M and Clemens MJ, 2002. The mRNA of the translationally controlled tumor protein P23/TCTP is a highly structured RNA, which activates the dsRNA‐dependent protein kinase PKR. Rna, 8, 478–496. [DOI] [PMC free article] [PubMed] [Google Scholar]
  153. Borchert GM, Lanier W and Davidson BL, 2006. RNA polymerase III transcribes human microRNAs. Nat Struct Mol Biol, 13, 1097–1101. [DOI] [PubMed] [Google Scholar]
  154. Braun JE, Huntzinger E, Fauser M and Izaurralde E, 2011. GW182 Proteins Directly Recruit Cytoplasmic Deadenylase Complexes to miRNA Targets. Molecular Cell, 44, 120–133. [DOI] [PubMed] [Google Scholar]
  155. Bronevetsky Y, Villarino AV, Eisley CJ, Barbeau R, Barczak AJ, Heinz GA, Kremmer E, Heissmeyer V, McManus MT, Erle DJ, Rao A and Ansel KM, 2013. T cell activation induces proteasomal degradation of Argonaute and rapid remodeling of the microRNA repertoire. Journal of Experimental Medicine, 210, 417–432. [DOI] [PMC free article] [PubMed] [Google Scholar]
  156. Brudecki L, Ferguson DA, McCall CE and El Gazzar M, 2013. MicroRNA‐146a and RBM4 form a negative feed‐forward loop that disrupts cytokine mRNA translation following TLR4 responses in human THP‐1 monocytes. Immunology and Cell Biology, 91, 532–540. [DOI] [PMC free article] [PubMed] [Google Scholar]
  157. Buck AH, Coakley G, Simbari F, McSorley HJ, Quintana JF, Le Bihan T, Kumar S, Abreu‐Goodger C, Lear M, Harcus Y, Ceroni A, Babayan SA, Blaxter M, Ivens A and Maizels RM, 2014. Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity. Nature Communications, 5, 5488–5488. [DOI] [PMC free article] [PubMed] [Google Scholar]
  158. Burroughs AM, Ando Y, de Hoon MJL, Tomaru Y, Suzuki H, Hayashizaki Y and Daub CO, 2011. Deep‐sequencing of human argonaute‐associated small RNAs provides insight into miRNA sorting and reveals argonaute association with RNA fragments of diverse origin. RNA Biology, 8, 158–177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  159. Calabrese JM, Seila AC, Yeo GW and Sharp PA, 2007. RNA sequence analysis defines Dicer's role in mouse embryonic stem cells. Proc Natl Acad Sci U S A, 104, 18097–18102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  160. Canella D, Praz V, Reina JH, Cousin P and Hernandez N, 2010. Defining the RNA polymerase III transcriptome: Genome‐wide localization of the RNA polymerase III transcription machinery in human cells. Genome Res, 20, 710–721. [DOI] [PMC free article] [PubMed] [Google Scholar]
  161. Carlile M, Swan D, Jackson K, Preston‐Fayers K, Ballester B, Flicek P and Werner A, 2009. Strand selective generation of endo‐siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues. Nucleic Acids Research, 37, 2274–2282. [DOI] [PMC free article] [PubMed] [Google Scholar]
  162. Carmell MA, Girard A, van de Kant HJG, Bourc'his D, Bestor TH, de Rooij DG and Hannon GJ, 2007. MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Developmental Cell, 12, 503–514. [DOI] [PubMed] [Google Scholar]
  163. Carmi S, Borukhov I and Levanon EY, 2011. Identification of Widespread Ultra‐Edited Human RNAs. Plos Genetics, 7, e1002317–e1002317. [DOI] [PMC free article] [PubMed] [Google Scholar]
  164. Castanotto D, Tommasi S, Li M, Li H, Yanow S, Pfeifer GP and Rossi JJ, 2005. Short hairpin RNA‐directed cytosine (CpG) methylation of the RASSF1A gene promoter in HeLa cells. Molecular Therapy, 12, 179–183. [DOI] [PubMed] [Google Scholar]
  165. Castellano L and Stebbing J, 2013. Deep sequencing of small RNAs identifies canonical and non‐canonical miRNA and endogenous siRNAs in mammalian somatic tissues. Nucleic Acids Research, 41, 3339–3351. [DOI] [PMC free article] [PubMed] [Google Scholar]
  166. Caudy AA, Myers M, Hannon GJ and Hammond SM, 2002. Fragile X‐related protein and VIG associate with the RNA interference machinery. Genes & Development, 16, 2491–2496. [DOI] [PMC free article] [PubMed] [Google Scholar]
  167. Cerutti H and Casas‐Mollano JA, 2006. On the origin and functions of RNA‐mediated silencing: from protists to man. Curr Genet, 50, 81–99. [DOI] [PMC free article] [PubMed] [Google Scholar]
  168. Chahar HS, Chen SP and Manjunath N, 2013. P‐body components LSM1, GW182, DDX3, DDX6 and XRN1 are recruited to WNV replication sites and positively regulate viral replication. Virology, 436, 1–7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  169. Chakravarthy S, Sternberg SH, Kellenberger CA and Doudna JA, 2010. Substrate‐Specific Kinetics of Dicer‐Catalyzed RNA Processing. Journal of Molecular Biology, 404, 392–402. [DOI] [PMC free article] [PubMed] [Google Scholar]
  170. Chandradoss SD, Schirle NT, Szczepaniak M, MacRae IJ and Joo C, 2015. A Dynamic Search Process Underlies MicroRNA Targeting. Cell, 162, 96–107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  171. Chekulaeva M, Mathys H, Zipprich JT, Attig J, Colic M, Parker R and Filipowicz W, 2011. miRNA repression involves GW182‐mediated recruitment of CCR4‐NOT through conserved W‐containing motifs. Nature Structural & Molecular Biology, 18, 1218–U1262. [DOI] [PMC free article] [PubMed] [Google Scholar]
  172. Cheloufi S, Dos Santos CO, Chong MMW and Hannon GJ, 2010. A Dicer‐independent miRNA biogenesis pathway that requires Ago catalysis. Nature, 465, 584–U576. [DOI] [PMC free article] [PubMed] [Google Scholar]
  173. Chen T, Xiang JF, Zhu SS, Chen SY, Yin QF, Zhang XO, Zhang J, Feng H, Dong R, Li XJ, Yang L and Chen LL, 2015. ADAR1 is required for differentiation and neural induction by regulating microRNA processing in a catalytically independent manner. Cell Research, 25, 459–476. [DOI] [PMC free article] [PubMed] [Google Scholar]
  174. Chendrimada TP, Gregory RI, Kumaraswamy E, Norman J, Cooch N, Nishikura K and Shiekhattar R, 2005. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature, 436, 740–744. [DOI] [PMC free article] [PubMed] [Google Scholar]
  175. Cheng TL, Wang ZZ, Liao QM, Zhu Y, Zhou WH, Xu WQ and Qiu ZL, 2014. MeCP2 Suppresses Nuclear MicroRNA Processing and Dendritic Growth by Regulating the DGCR8/Drosha Complex. Developmental Cell, 28, 547–560. [DOI] [PubMed] [Google Scholar]
  176. Chevillet JR, Kang Q, Ruf IK, Briggs HA, Vojtech LN, Hughes SM, Cheng HH, Arroyo JD, Meredith EK, Gallichotte EN, Pogosova‐Agadjanyan EL, Morrissey C, Stirewalt DL, Hladik F, Yu EY, Higano CS and Tewari M, 2014. Quantitative and stoichiometric analysis of the microRNA content of exosomes. Proc Natl Acad Sci U S A, 111, 14888–14893. [DOI] [PMC free article] [PubMed] [Google Scholar]
  177. Chim SS, Shing TK, Hung EC, Leung TY, Lau TK, Chiu RW and Lo YM, 2008. Detection and characterization of placental microRNAs in maternal plasma. Clin Chem, 54, 482–490. [DOI] [PubMed] [Google Scholar]
  178. Cho S, Park JS and Kang YK, 2014. AGO2 and SETDB1 cooperate in promoter‐targeted transcriptional silencing of the androgen receptor gene. Nucleic Acids Research, 42, 13545–13556. [DOI] [PMC free article] [PubMed] [Google Scholar]
  179. Chong MMW, Zhang GA, Cheloufi S, Neubert TA, Hannon GJ and Littman DR, 2010. Canonical and alternate functions of the microRNA biogenesis machinery. Genes & Development, 24, 1951–1960. [DOI] [PMC free article] [PubMed] [Google Scholar]
  180. Christie M, Boland A, Huntzinger E, Weichenrieder O and Izaurralde E, 2013. Structure of the PAN3 Pseudokinase Reveals the Basis for Interactions with the PAN2 Deadenylase and the GW182 Proteins. Molecular Cell, 51, 360–373. [DOI] [PubMed] [Google Scholar]
  181. Chu CY and Rana TM, 2006. Translation repression in human cells by microRNA‐induced gene silencing requires RCK/p54. Plos Biology, 4, 1122–1136. [DOI] [PMC free article] [PubMed] [Google Scholar]
  182. Cikaluk DE, Tahbaz N, Hendricks LC, DiMattia GE, Hansen D, Pilgrim D and Hobman TC, 1999. GERp95, a membrane‐associated protein that belongs to a family of proteins involved in stem cell differentiation. Molecular Biology of the Cell, 10, 3357–3372. [DOI] [PMC free article] [PubMed] [Google Scholar]
  183. Clerzius G, Gelinas JF, Daher A, Bonnet M, Meurs EF and Gatignol A, 2009. ADAR1 Interacts with PKR during Human Immunodeficiency Virus Infection of Lymphocytes and Contributes to Viral Replication. Journal of Virology, 83, 10119–10128. [DOI] [PMC free article] [PubMed] [Google Scholar]
  184. Clop A, Marcq F, Takeda H, Pirottin D, Tordoir X, Bibe B, Bouix J, Caiment F, Elsen JM, Eychenne F, Larzul C, Laville E, Meish F, Milenkovic D, Tobin J, Charlier C and Georges M, 2006. A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nature Genetics, 38, 813–818. [DOI] [PubMed] [Google Scholar]
  185. Cosentino GP, Venkatesan S, Serluca FC, Green SR, Mathews MB and Sonenberg N, 1995. Double‐stranded‐RNA‐dependent protein kinase and TAR RNA‐binding protein form homo‐ and heterodimers in vivo. Proc Natl Acad Sci U S A, 92, 9445–9449. [DOI] [PMC free article] [PubMed] [Google Scholar]
  186. Cullen BR, 2006. Is RNA interference involved in intrinsic antiviral immunity in mammals? Nature Immunology, 7, 563–567. [DOI] [PubMed] [Google Scholar]
  187. Cullen BR, Cherry S and tenOever BR, 2013. Is RNA interference a physiologically relevant innate antiviral immune response in mammals? Cell Host Microbe, 14, 374–378. [DOI] [PubMed] [Google Scholar]
  188. Daher A, Laraki G, Singh M, Melendez‐Pena CE, Bannwarth S, Peters A, Meurs EF, Braun RE, Patel RC and Gatignol A, 2009. TRBP Control of PACT‐Induced Phosphorylation of Protein Kinase R Is Reversed by Stress. Molecular and Cellular Biology, 29, 254–265. [DOI] [PMC free article] [PubMed] [Google Scholar]
  189. Daniels SM, Melendez‐Pena CE, Scarborough RJ, Daher A, Christensen HS, El Far M, Purcell DFJ, Laine S and Gatignol A, 2009. Characterization of the TRBP domain required for Dicer interaction and function in RNA interference. Bmc Molecular Biology, 10, 38–38. [DOI] [PMC free article] [PubMed] [Google Scholar]
  190. Daniels SM and Gatignol A, 2012. The Multiple Functions of TRBP, at the Hub of Cell Responses to Viruses, Stress, and Cancer. Microbiology and Molecular Biology Reviews, 76, 652–+. [DOI] [PMC free article] [PubMed] [Google Scholar]
  191. Dawson TR, Sansam CL and Emeson RB, 2004. Structure and sequence determinants required for the RNA editing of ADAR2 substrates. Journal of Biological Chemistry, 279, 4941–4951. [DOI] [PubMed] [Google Scholar]
  192. de Veer MJ, Sledz CA and Williams BR, 2005. Detection of foreign RNA: implications for RNAi. Immunol Cell Biol, 83, 224–228. [DOI] [PubMed] [Google Scholar]
  193. De Wit T, Grosveld F and Drabek D, 2002. The tomato RNA‐directed RNA polymerase has no effect on gene silencing by RNA interference in transgenic mice. Transgenic Research, 11, 305–310. [DOI] [PubMed] [Google Scholar]
  194. DeCerbo J and Carmichael GG, 2005. Retention and repression: fates of hyperedited RNAs in the nucleus. Current Opinion in Cell Biology, 17, 302–308. [DOI] [PubMed] [Google Scholar]
  195. Deerberg A, Willkomm S and Restle T, 2013. Minimal mechanistic model of siRNA‐dependent target RNA slicing by recombinant human Argonaute 2 protein. Proc Natl Acad Sci U S A, 110, 17850–17855. [DOI] [PMC free article] [PubMed] [Google Scholar]
  196. Deleavey GF, Frank F, Hassler M, Wisnovsky S, Nagar B and Damha MJ, 2013. The 5 ‘ Binding MID Domain of Human Argonaute2 Tolerates Chemically Modified Nucleotide Analogues. Nucleic Acid Therapeutics, 23, 81–87. [DOI] [PubMed] [Google Scholar]
  197. Deveson I, Li JY and Millar AA, 2013. Expression of human ARGONAUTE 2 inhibits endogenous microRNA activity in Arabidopsis . Frontiers in Plant Science, 4, 96–96. [DOI] [PMC free article] [PubMed] [Google Scholar]
  198. Diallo M, Arenz C, Schmitz K, Sandhoff K and Schepers U, 2003. Long endogenous dsRNAs can induce complete gene silencing in mammalian cells and primary cultures. Oligonucleotides, 13, 381–392. [DOI] [PubMed] [Google Scholar]
  199. Didiot MC, Subramanian M, Flatter E, Mandel JL and Moine H, 2009. Cells lacking the fragile X mental retardation protein (FMRP) have normal RISC activity but exhibit altered stress granule assembly. Molecular Biology of the Cell, 20, 428–437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  200. Diederichs S and Haber DA, 2007. Dual role for argonautes in microRNA processing and posttranscriptional regulation of microRNA expression. Cell, 131, 1097–1108. [DOI] [PubMed] [Google Scholar]
  201. Dismuke WM, Challa P, Navarro I, Stamer WD and Liu YT, 2015. Human aqueous humor exosomes. Experimental Eye Research, 132, 73–77. [DOI] [PMC free article] [PubMed] [Google Scholar]
  202. Doench JG, Petersen CP and Sharp PA, 2003. siRNAs can function as miRNAs. Genes & Development, 17, 438–442. [DOI] [PMC free article] [PubMed] [Google Scholar]
  203. Donze O, Abbas‐Terki T and Picard D, 2001. The Hsp90 chaperone complex is both a facilitator and a repressor of the dsRNA‐dependent kinase PKR. EMBO J, 20, 3771–3780. [DOI] [PMC free article] [PubMed] [Google Scholar]
  204. Doyle M, Badertscher L, Jaskiewicz L, Guttinger S, Jurado S, Hugenschmidt T, Kutay U and Filipowicz W, 2013. The double‐stranded RNA binding domain of human Dicer functions as a nuclear localization signal. Rna, 19, 1238–1252. [DOI] [PMC free article] [PubMed] [Google Scholar]
  205. Drake M, Furuta T, Suen KM, Gonzalez G, Liu B, Kalia A, Ladbury JE, Fire AZ, Skeath JB and Arur S, 2014. A requirement for ERK‐dependent Dicer phosphorylation in coordinating oocyte‐to‐embryo transition in C. elegans. Developmental Cell, 31, 614–628. [DOI] [PMC free article] [PubMed] [Google Scholar]
  206. Du Z, Lee JK, Tjhen R, Strould RM and James TL, 2008. Structural and biochemical insights into the dicing mechanism of mouse Dicer: A conserved lysine is critical for dsRNA cleavage. Proc Natl Acad Sci U S A, 105, 2391–2396. [DOI] [PMC free article] [PubMed] [Google Scholar]
  207. Dueck A, Ziegler C, Eichner A, Berezikov E and Meister G, 2012. microRNAs associated with the different human Argonaute proteins. Nucleic Acids Research, 40, 9850–9862. [DOI] [PMC free article] [PubMed] [Google Scholar]
  208. Duursma AM, Kedde M, Schrier M, le Sage C and Agami R, 2008. miR‐148 targets human DNMT3b protein coding region. Rna, 14, 872–877. [DOI] [PMC free article] [PubMed] [Google Scholar]
  209. Duxbury MS, Ashley SW and Whang EE, 2005. RNA interference: a mammalian SID‐1 homolog enhances siRNA uptake and gene silencing efficacy in human cells. Biochem Biophys Res Commun, 331, 459–463. [DOI] [PubMed] [Google Scholar]
  210. El‐Andaloussi S, Lee Y, Lakhal‐Littleton S, Li J, Seow Y, Gardiner C, Alvarez‐Erviti L, Sargent IL and Wood MJA, 2012. Exosome‐mediated delivery of siRNA in vitro and in vivo. Nature Protocols, 7, 2112–2126. [DOI] [PubMed] [Google Scholar]
  211. El‐Shami M, Pontier D, Lahmy S, Braun L, Picart C, Vega D, Hakimi M‐A, Jacobsen SE, Cooke R and Lagrange T, 2007. Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE‐binding platforms in RNAi‐related components. Genes & Development, 21, 2539–2544. [DOI] [PMC free article] [PubMed] [Google Scholar]
  212. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K and Tuschl T, 2001. Duplexes of 21‐nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 411, 494–498. [DOI] [PubMed] [Google Scholar]
  213. Elkayam E, Kuhn CD, Tocilj A, Haase AD, Greene EM, Hannon GJ and Joshua‐Tor L, 2012. The Structure of Human Argonaute‐2 in Complex with miR‐20a. Cell, 150, 100–110. [DOI] [PMC free article] [PubMed] [Google Scholar]
  214. Ender C, Krek A, Friedlander MR, Beitzinger M, Weinmann L, Chen W, Pfeffer S, Rajewsky N and Meister G, 2008. A Human snoRNA with MicroRNA‐Like Functions. Molecular Cell, 32, 519–528. [DOI] [PubMed] [Google Scholar]
  215. Engels B, Jannot G, Remenyi J, Simard MJ and Hutvagner G, 2012. Polypyrimidine Tract Binding Protein (hnRNP I) Is Possibly a Conserved Modulator of miRNA‐Mediated Gene Regulation. PLoS ONE, 7, e33144–e33144. [DOI] [PMC free article] [PubMed] [Google Scholar]
  216. Enright AJ, John B, Gaul U, Tuschl T, Sander C and Marks DS, 2003. MicroRNA targets in Drosophila. Genome Biology, 5, R1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  217. Eulalio A, Behm‐Ansmant I, Schweizer D and Izaurralde E, 2007. P‐body formation is a consequence, not the cause, of RNA‐mediated gene silencing. Molecular and Cellular Biology, 27, 3970–3981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  218. Fabbri M, Garzon R, Cimmino A, Liu Z, Zanesi N, Callegari E, Liu S, Alder H, Costinean S, Fernandez‐Cymering C, Volinia S, Guler G, Morrison CD, Chan KK, Marcucci G, Calin GA, Huebner K and Croce CM, 2007. MicroRNA‐29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B. Proc Natl Acad Sci U S A, 104, 15805–15810. [DOI] [PMC free article] [PubMed] [Google Scholar]
  219. Fabian MR, Mathonnet G, Sundermeier T, Mathys H, Zipprich JT, Svitkin YV, Rivas F, Jinek M, Wohischlegel J, Doudna JA, Chen CYA, Shyu AB, Yates JR, Hannon GJ, Filipowicz W, Duchaine TF and Sonenberg N, 2009. Mammalian miRNA RISC Recruits CAF1 and PABP to Affect PABP‐Dependent Deadenylation. Molecular Cell, 35, 868–880. [DOI] [PMC free article] [PubMed] [Google Scholar]
  220. Fabian MR, Cieplak MK, Frank F, Morita M, Green J, Srikumar T, Nagar B, Yamamoto T, Raught B, Duchaine TF and Sonenberg N, 2011a. miRNA‐mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4‐NOT. Nature Structural & Molecular Biology, 18, 1211–U1252. [DOI] [PubMed] [Google Scholar]
  221. Fabian MR, Svitkin YV and Sonenberg N, 2011b. An Efficient System for Let‐7 MicroRNA and GW182 Protein‐Mediated Deadenylation In Vitro. Argonaute Proteins: Methods and Protocols., 207–217. [DOI] [PubMed] [Google Scholar]
  222. Faehnle CR, Elkayam E, Haase AD, Hannon GJ and Joshua‐Tor L, 2013. The Making of a Slicer: Activation of Human Argonaute‐1. Cell Reports, 3, 1901–1909. [DOI] [PMC free article] [PubMed] [Google Scholar]
  223. Farh KK, Grimson A, Jan C, Lewis BP, Johnston WK, Lim LP, Burge CB and Bartel DP, 2005. The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science, 310, 1817–1821. [DOI] [PubMed] [Google Scholar]
  224. Feng Y, Zhang XX, Graves P and Zeng Y, 2012. A comprehensive analysis of precursor microRNA cleavage by human Dicer. Rna, 18, 2083–2092. [DOI] [PMC free article] [PubMed] [Google Scholar]
  225. Fenner BJ, Thiagarajan R, Chua HK and Kwang J, 2006. Betanodavirus B2 is an RNA interference antagonist that facilitates intracellular viral RNA accumulation. Journal of Virology, 80, 85–94. [DOI] [PMC free article] [PubMed] [Google Scholar]
  226. Filippov V, Solovyev V, Filippova M and Gill SS, 2000. A novel type of RNase III family proteins in eukaryotes. Gene, 245, 213–221. [DOI] [PubMed] [Google Scholar]
  227. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE and Mello CC, 1998. Potent and specific genetic interference by double‐stranded RNA in Caenorhabditis elegans. Nature, 391, 806–811. [DOI] [PubMed] [Google Scholar]
  228. Flemr M, Malik R, Franke V, Nejepinska J, Sedlacek R, Vlahovicek K and Svoboda P, 2013. A Retrotransposon‐Driven Dicer Isoform Directs Endogenous Small Interfering RNA Production in Mouse Oocytes. Cell, 155, 807–816. [DOI] [PubMed] [Google Scholar]
  229. Flores‐Jasso CF, Arenas‐Huertero C, Reyes JL, Contreras‐Cubas C, Covarrubias A and Vaca L, 2009. First step in pre‐miRNAs processing by human Dicer. Acta Pharmacologica Sinica, 30, 1177–1185. [DOI] [PMC free article] [PubMed] [Google Scholar]
  230. Fortin KR, Nicholson RH and Nicholson AW, 2002. Mouse ribonuclease III. cDNA structure, expression analysis, and chromosomal location. BMC Genomics, 3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  231. Francia S, Michelini F, Saxena A, Tang D, deHoon M , Anelli V, Mione M, Carninci P and di Fagagna FD, 2012. Site‐specific DICER and DROSHA RNA products control the DNA‐damage response. Nature, 488, 231–+. [DOI] [PMC free article] [PubMed] [Google Scholar]
  232. Frank F, Sonenberg N and Nagar B, 2010. Structural basis for 5 ‘‐nucleotide base‐specific recognition of guide RNA by human AGO2. Nature, 465, 818–822. [DOI] [PubMed] [Google Scholar]
  233. Frank F, Fabian MR, Stepinski J, Jemielity J, Darzynkiewicz E, Sonenberg N and Nagar B, 2011. Structural analysis of 5 ‘‐mRNA‐cap interactions with the human AGO2 MID domain. EMBO Rep, 12, 415–420. [DOI] [PMC free article] [PubMed] [Google Scholar]
  234. Friend K, Campbell ZT, Cooke A, Kroll‐Conner P, Wickens MP and Kimble J, 2012. A conserved PUF‐Ago‐eEF1A complex attenuates translation elongation. Nature Structural & Molecular Biology, 19, 176–183. [DOI] [PMC free article] [PubMed] [Google Scholar]
  235. Fu QQ and Yuan YA, 2013. Structural insights into RISC assembly facilitated by dsRNA‐binding domains of human RNA helicase A (DHX9). Nucleic Acids Research, 41, 3457–3470. [DOI] [PMC free article] [PubMed] [Google Scholar]
  236. Fukagawa T, Nogami M, Yoshikawa M, Ikeno M, Okazaki T, Takami Y, Nakayama T and Oshimura M, 2004. Dicer is essential for formation of the heterochromatin structure in vertebrate cells. Nature Cell Biology, 6, 784–791. [DOI] [PubMed] [Google Scholar]
  237. Gagnon KT, Li LD, Chu YJ, Janowski BA and Corey DR, 2014a. RNAi Factors Are Present and Active in Human Cell Nuclei. Cell Reports, 6, 211–221. [DOI] [PMC free article] [PubMed] [Google Scholar]
  238. Gagnon KT, Li LD, Janowski BA and Corey DR, 2014b. Analysis of nuclear RNA interference in human cells by subcellular fractionation and Argonaute loading. Nature Protocols, 9, 2045–2060. [DOI] [PMC free article] [PubMed] [Google Scholar]
  239. Gan HH and Gunsalus KC, 2015. Assembly and analysis of eukaryotic Argonaute‐RNA complexes in microRNA‐target recognition. Nucleic Acids Research, 43, 9613–9625. [DOI] [PMC free article] [PubMed] [Google Scholar]
  240. Gan L, Anton KE, Masterson BA, Vincent VA, Ye S and Gonzalez‐Zulueta M, 2002. Specific interference with gene expression and gene function mediated by long dsRNA in neural cells. J Neurosci Methods, 121, 151–157. [DOI] [PubMed] [Google Scholar]
  241. Gandy SZ, Linnstaedt SD, Muralidhar S, Cashman KA, Rosenthal LJ and Casey JL, 2007. RNA editing of the human herpesvirus 8 kaposin transcript eliminates its transforming activity and is induced during lytic replication. Journal of Virology, 81, 13544–13551. [DOI] [PMC free article] [PubMed] [Google Scholar]
  242. Ganesan G and Rao SMR, 2008. A novel noncoding RNA processed by Drosha is restricted to nucleus in mouse. Rna, 14, 1399–1410. [DOI] [PMC free article] [PubMed] [Google Scholar]
  243. Gantier MP and Williams BR, 2007. The response of mammalian cells to double‐stranded RNA. Cytokine Growth Factor Rev, 18, 363–371. [DOI] [PMC free article] [PubMed] [Google Scholar]
  244. Garcia‐Lopez J, Hourcade JD and del Mazo J, 2013. Reprogramming of microRNAs by adenosine‐to‐inosine editing and the selective elimination of edited microRNA precursors in mouse oocytes and preimplantation embryos. Nucleic Acids Research, 41, 5483–5493. [DOI] [PMC free article] [PubMed] [Google Scholar]
  245. Gehrke S, Imai Y, Sokol N and Lu BW, 2010. Pathogenic LRRK2 negatively regulates microRNA‐mediated translational repression. Nature, 466, 637–U639. [DOI] [PMC free article] [PubMed] [Google Scholar]
  246. Geiss G, Jin G, Guo J, Bumgarner R, Katze MG and Sen GC, 2001. A comprehensive view of regulation of gene expression by double‐stranded RNA‐mediated cell signaling. Journal of Biological Chemistry, 276, 30178–30182. [DOI] [PubMed] [Google Scholar]
  247. Glanzer J, Miyashiro KY, Sul JY, Barrett L, Belt B, Haydon P and Eberwine J, 2005. RNA splicing capability of live neuronal dendrites. Proc Natl Acad Sci U S A, 102, 16859–16864. [DOI] [PMC free article] [PubMed] [Google Scholar]
  248. Goodarzi H, Zhang S, Buss CG, Fish L, Tavazoie S and Tavazoie SF, 2014. Metastasis‐suppressor transcript destabilization through TARBP2 binding of mRNA hairpins. Nature, 513, 256–+. [DOI] [PMC free article] [PubMed] [Google Scholar]
  249. Goodier JL, Zhang L, Vetter MR and Kazazian HH, 2007. LINE‐1 ORF1 protein localizes in stress granules with other RNA‐Binding proteins, including components of RNA interference RNA‐induced silencing complex. Molecular and Cellular Biology, 27, 6469–6483. [DOI] [PMC free article] [PubMed] [Google Scholar]
  250. Gredell JA, Dittmer MJ, Wu M, Chan C and Walton SP, 2010. Recognition of siRNA Asymmetry by TAR RNA Binding Protein. Biochemistry, 49, 3148–3155. [DOI] [PMC free article] [PubMed] [Google Scholar]
  251. Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N and Shiekhattar R, 2004. The Microprocessor complex mediates the genesis of microRNAs. Nature, 432, 235–240. [DOI] [PubMed] [Google Scholar]
  252. Gregory RI, Chendrimada TP, Cooch N and Shiekhattar R, 2005. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell, 123, 631–640. [DOI] [PubMed] [Google Scholar]
  253. Gregory RI, Chendrimada TP and Shiekhattar R, 2006. MicroRNA biogenesis ‐ Isolation and characterization of the microprocessor complex. In: Methods in Molecular Biology. 33–47. [DOI] [PubMed] [Google Scholar]
  254. Gu S, Jin L, Huang Y, Zhang FJ and Kay MA, 2012a. Slicing‐Independent RISC Activation Requires the Argonaute PAZ Domain. Current Biology, 22, 1536–1542. [DOI] [PMC free article] [PubMed] [Google Scholar]
  255. Gu S, Jin L, Zhang Y, Huang Y, Zhang FJ, Valdmanis PN and Kay MA, 2012b. The Loop Position of shRNAs and Pre‐miRNAs Is Critical for the Accuracy of Dicer Processing In Vivo. Cell, 151, 900–911. [DOI] [PMC free article] [PubMed] [Google Scholar]
  256. Guang S, Bochner AF, Burkhart KB, Burton N, Pavelec DM and Kennedy S, 2010. Small regulatory RNAs inhibit RNA polymerase II during the elongation phase of transcription. Nature, 465, 1097–1101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  257. Gullerova M and Proudfoot NJ, 2012. Convergent transcription induces transcriptional gene silencing in fission yeast and mammalian cells. Nature Structural & Molecular Biology, 19, 1193–1201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  258. Guo YW, Liu J, Elfenbein SJ, Ma YH, Zhong M, Qiu CH, Ding Y and Lu J, 2015. Characterization of the mammalian miRNA turnover landscape. Nucleic Acids Research, 43, 2326–2341. [DOI] [PMC free article] [PubMed] [Google Scholar]
  259. Gupta V, Huang X and Patel RC, 2003. The carboxy‐terminal, M3 motifs of PACT and TRBP have opposite effects on PKR activity. Virology, 315, 283–291. [DOI] [PubMed] [Google Scholar]
  260. Gurtan AM, Lu V, Bhutkar A and Sharp PA, 2012. In vivo structure‐function analysis of human Dicer reveals directional processing of precursor miRNAs. Rna, 18, 1116–1122. [DOI] [PMC free article] [PubMed] [Google Scholar]
  261. Haase AD, Jaskiewicz L, Zhang HD, Laine S, Sack R, Gatignol A and Filipowicz W, 2005. TRBP, a regulator of cellular PKR and HIV‐1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep, 6, 961–967. [DOI] [PMC free article] [PubMed] [Google Scholar]
  262. Haasnoot J, de Vries W, Geutjes EJ, Prins M, de Haan P and Berkhout B, 2007. The Ebola virus VP35 protein is a suppressor of RNA silencing. Plos Pathogens, 3, e86. [DOI] [PMC free article] [PubMed] [Google Scholar]
  263. Haley B and Zamore PD, 2004. Kinetic analysis of the RNAi enzyme complex. Nature Structural & Molecular Biology, 11, 599–606. [DOI] [PubMed] [Google Scholar]
  264. Hammond SM, Bernstein E, Beach D and Hannon GJ, 2000. An RNA‐directed nuclease mediates post‐transcriptional gene silencing in Drosophila cells. Nature, 404, 293–296. [DOI] [PubMed] [Google Scholar]
  265. Han C, Liu YH, Wan GH, Choi HJ, Zhao LQ, Ivan C, He XM, Sood AK, Zhang XN and Lu XB, 2014. The RNA‐Binding Protein DDX1 Promotes Primary MicroRNA Maturation and Inhibits Ovarian Tumor Progression. Cell Reports, 8, 1447–1460. [DOI] [PMC free article] [PubMed] [Google Scholar]
  266. Han JJ, Lee Y, Yeom KH, Kim YK, Jin H and Kim VN, 2004. The Drosha‐DGCR8 complex in primary microRNA processing. Genes & Development, 18, 3016–3027. [DOI] [PMC free article] [PubMed] [Google Scholar]
  267. Hauptmann J, Schraivogel D, Bruckmann A, Manickavel S, Jakob L, Eichner N, Pfaff J, Urban M, Sprunck S, Hafner M, Tuschl T, Deutzmann R and Meister G, 2015. Biochemical isolation of Argonaute protein complexes by Ago‐APP. Proc Natl Acad Sci U S A, 112, 11841–11845. [DOI] [PMC free article] [PubMed] [Google Scholar]
  268. Haussecker D and Proudfoot NJ, 2005. Dicer‐dependent turnover of intergenic transcripts from the human beta‐globin gene cluster. Molecular and Cellular Biology, 25, 9724–9733. [DOI] [PMC free article] [PubMed] [Google Scholar]
  269. Haussecker D, Huang Y, Lau A, Parameswaran P, Fire AZ and Kay MA, 2010. Human tRNA‐derived small RNAs in the global regulation of RNA silencing. Rna, 16, 673–695. [DOI] [PMC free article] [PubMed] [Google Scholar]
  270. Hausser J, Landthaler M, Jaskiewicz L, Gaidatzis D and Zavolan M, 2009. Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C‐miRNA complexes and the degradation of miRNA targets. Genome Research, 19, 2009–2020. [DOI] [PMC free article] [PubMed] [Google Scholar]
  271. Havens MA, Reich AA, Duelli DM and Hastings ML, 2012. Biogenesis of mammalian microRNAs by a non‐canonical processing pathway. Nucleic Acids Research, 40, 4626–4640. [DOI] [PMC free article] [PubMed] [Google Scholar]
  272. Hawkins PG, Santoso S, Adams C, Anest V and Morris KV, 2009. Promoter targeted small RNAs induce long‐term transcriptional gene silencing in human cells. Nucleic Acids Research, 37, 2984–2995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  273. Heraud‐Farlow JE and Walkley CR, 2016. The role of RNA editing by ADAR1 in prevention of innate immune sensing of self‐RNA. J Mol Med (Berl). [DOI] [PubMed] [Google Scholar]
  274. Herbert KM, Pimienta G, DeGregorio SJ, Alexandrov A and Steitz JA, 2013. Phosphorylation of DGCR8 Increases Its Intracellular Stability and Induces a Progrowth miRNA Profile. Cell Reports, 5, 1070–1081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  275. Herbert KM, Sarkar SK, Mills M, De la Herran HCD, Neuman KC and Steitz JA, 2016. A heterotrimer model of the complete Microprocessor complex revealed by single‐molecule subunit counting. Rna, 22, 175–183. [DOI] [PMC free article] [PubMed] [Google Scholar]
  276. Hock J, Weinmann L, Ender C, Rudel S, Kremmer E, Raabe M, Urlaub H and Meister G, 2007. Proteomic and functional analysis of Argonaute‐containing mRNA‐protein complexes in human cells. EMBO Rep, 8, 1052–1060. [DOI] [PMC free article] [PubMed] [Google Scholar]
  277. Hong J, Qian ZK, Shen SY, Min TS, Tan C, Xu JF, Zhao YC and Huang WD, 2005. High doses of siRNAs induce eri‐1 and adar‐1 gene expression and reduce the efficiency of RNA interference in the mouse. Biochemical Journal, 390, 675–679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  278. Horman SR, Janas MM, Litterst C, Wang B, MacRae IJ, Sever MJ, Morrissey DV, Graves P, Luo B, Umesalma S, Qi HH, Miraglia LJ, Novina CD and Orth AP, 2013. Akt‐mediated phosphorylation of argonaute 2 downregulates cleavage and upregulates translational repression of MicroRNA targets. Molecular Cell, 50, 356–367. [DOI] [PMC free article] [PubMed] [Google Scholar]
  279. Hornung V, Ellegast J, Kim S, Brzozka K, Jung A, Kato H, Poeck H, Akira S, Conzelmann KK, Schlee M, Endres S and Hartmann G, 2006. 5′‐Triphosphate RNA is the ligand for RIG‐I. Science, 314, 994–997. [DOI] [PubMed] [Google Scholar]
  280. Houbaviy HB, Dennis L, Jaenisch R and Sharp PA, 2005. Characterization of a highly variable eutherian rnicroRNA gene. Rna, 11, 1245–1257. [DOI] [PMC free article] [PubMed] [Google Scholar]
  281. Hu J and Corey DR, 2007. Inhibiting gene expression with peptide nucleic acid (PNA)–peptide conjugates that target chromosomal DNA. Biochemistry, 46, 7581–7589. [DOI] [PMC free article] [PubMed] [Google Scholar]
  282. Hu J, Chen Z, Xia D, Wu J, Xu H and Ye ZQ, 2012. Promoter‐associated small double‐stranded RNA interacts with heterogeneous nuclear ribonucleoprotein A2/B1 to induce transcriptional activation. Biochemical Journal, 447, 407–416. [DOI] [PubMed] [Google Scholar]
  283. Huang J, Liang Z, Yang B, Tian H, Ma J and Zhang H, 2007. Derepression of microRNA‐mediated protein translation inhibition by apolipoprotein B mRNA‐editing enzyme catalytic polypeptide‐like 3G (APOBEC3G) and its family members. Journal of Biological Chemistry, 282, 33632–33640. [DOI] [PubMed] [Google Scholar]
  284. Huang V, Zheng JS, Qi ZX, Wang J, Place RF, Yu JW, Li H and Li LC, 2013a. Ago1 Interacts with RNA Polymerase II and Binds to the Promoters of Actively Transcribed Genes in Human Cancer Cells. Plos Genetics, 9, e1003821–e1003821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  285. Huang X, Hutchins B and Patel RC, 2002. The C‐terminal, third conserved motif of the protein activator PACT plays an essential role in the activation of double‐stranded‐RNA‐dependent protein kinase (PKR). Biochemical Journal, 366, 175–186. [DOI] [PMC free article] [PubMed] [Google Scholar]
  286. Huang XY, Yuan TZ, Tschannen M, Sun ZF, Jacob H, Du MJ, Liang MH, Dittmar RL, Liu Y, Liang MY, Kohli M, Thibodeau SN, Boardman L and Wang L, 2013b. Characterization of human plasma‐derived exosomal RNAs by deep sequencing. BMC Genomics, 14, 319–319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  287. Hundley HA, Krauchuk AA and Bass BL, 2008. C‐elegans and H‐sapiens mRNAs with edited 3 ‘ UTRs are present on polysomes. Rna, 14, 2050–2060. [DOI] [PMC free article] [PubMed] [Google Scholar]
  288. Hunter T, Hunt T, Jackson RJ and Robertson HD, 1975. The characteristics of inhibition of protein synthesis by double‐stranded ribonucleic acid in reticulocyte lysates. Journal of Biological Chemistry, 250, 409–417. [PubMed] [Google Scholar]
  289. Huntzinger E, Braun JE, Heimstaedt S, Zekri L and Izaurralde E, 2010. Two PABPC1‐binding sites in GW182 proteins promote miRNA‐mediated gene silencing. EMBO J, 29, 4146–4160. [DOI] [PMC free article] [PubMed] [Google Scholar]
  290. Huntzinger E, Kuzuoglu‐Oeztuerk D, Braun JE, Eulalio A, Wohlbold L and Izaurralde E, 2013. The interactions of GW182 proteins with PABP and deadenylases are required for both translational repression and degradation of miRNA targets. Nucleic Acids Research, 41, 978–994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  291. Iavello A, Frech VSL, Gai C, Deregibus MC, Quesenberry PJ and Camussi G, 2016. Role of Alix in miRNA packaging during extracellular vesicle biogenesis. International Journal of Molecular Medicine, 37, 958–966. [DOI] [PMC free article] [PubMed] [Google Scholar]
  292. Iguchi H, Kosaka N and Ochiya T, 2010. Secretory microRNAs as a versatile communication tool. Communicative & integrative biology, 3, 478–481. [DOI] [PMC free article] [PubMed] [Google Scholar]
  293. Ingle H, Kumar S, Raut AA, Mishra A, Kulkarni DD, Kameyama T, Takaoka A, Akira S and Kumar H, 2015. The microRNA miR‐485 targets host and influenza virus transcripts to regulate antiviral immunity and restrict viral replication. Science Signaling, 8, ra126–ra126. [DOI] [PubMed] [Google Scholar]
  294. Ip J, Canham P, Choo KHA, Inaba Y, Jacobs SA, Kalitsis P, Mattiske DM, Ng J, Saffery R, Wong NC, Wong LH and Mann JR, 2012. Normal DNA Methylation Dynamics in DICER1‐Deficient Mouse Embryonic Stem Cells. Plos Genetics, 8, e1002919–e1002919. [DOI] [PMC free article] [PubMed] [Google Scholar]
  295. Ishizuka A, Siomi MC and Siomi H, 2002. A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins. Genes & Development, 16, 2497–2508. [DOI] [PMC free article] [PubMed] [Google Scholar]
  296. Iwasaki S, Kobayashi M, Yoda M, Sakaguchi Y, Katsuma S, Suzuki T and Tomari Y, 2010. Hsc70/Hsp90 chaperone machinery mediates ATP‐dependent RISC loading of small RNA duplexes. Molecular Cell, 39, 292–299. [DOI] [PubMed] [Google Scholar]
  297. Izumi H, Tsuda M, Sato Y, Kosaka N, Ochiya T, Iwamoto H, Namba K and Takeda Y, 2015. Bovine milk exosomes contain microRNA and mRNA and are taken up by human macrophages. Journal of Dairy Science, 98, 2920–2933. [DOI] [PubMed] [Google Scholar]
  298. Izumi T, Burdick R, Shigemi M, Plisov S, Hu WS and Pathak VK, 2013. Mov10 and APOBEC3G Localization to Processing Bodies Is Not Required for Virion Incorporation and Antiviral Activity. Journal of Virology, 87, 11047–11062. [DOI] [PMC free article] [PubMed] [Google Scholar]
  299. Jain S and Parker R, 2013. The discovery and analysis of P Bodies. Adv Exp Med Biol, 768, 23–43. [DOI] [PubMed] [Google Scholar]
  300. Jakymiw A, Lian SL, Eystathioy T, Li SQ, Satoh M, Hamel JC, Fritzler MJ and Chan EKL, 2005. Disruption of GW bodies impairs mammalian RNA interference. Nature Cell Biology, 7, 1267–1274. [DOI] [PubMed] [Google Scholar]
  301. James V, Zhang Y, Foxler DE, de Moor CH, Kong YW, Webb TM, Self TJ, Feng Y, Lagos D, Chu C‐Y, Rana TM, Morley SJ, Longmore GD, Bushell M and Sharp TV, 2010. LIM‐domain proteins, LIMD1, Ajuba, and WTIP are required for microRNA‐mediated gene silencing. Proc Natl Acad Sci U S A, 107, 12499–12504. [DOI] [PMC free article] [PubMed] [Google Scholar]
  302. Jang JH, Jung JS, Choi JI and Kang SK, 2012. Nuclear Ago2/HSP60 Contributes to Broad Spectrum of hATSCs Function via Oct4 Regulation. Antioxidants & Redox Signaling, 16, 383–399. [DOI] [PMC free article] [PubMed] [Google Scholar] [Retracted]
  303. Jannot G, Bajan S, Giguere NJ, Bouasker S, Banville IH, Piquet S, Hutvagner G and Simard MJ, 2011. The ribosomal protein RACK1 is required for microRNA function in both C. elegans and humans. EMBO Rep, 12, 581–586. [DOI] [PMC free article] [PubMed] [Google Scholar]
  304. Janowski BA, Huffman KE, Schwartz JC, Ram R, Hardy D, Shames DS, Minna JD and Corey DR, 2005a. Inhibiting gene expression at transcription start sites in chromosomal DNA with antigene RNAs. Nat Chem Biol, 1, 216–222. [DOI] [PubMed] [Google Scholar]
  305. Janowski BA, Kaihatsu K, Huffman KE, Schwartz JC, Ram R, Hardy D, Mendelson CR and Corey DR, 2005b. Inhibiting transcription of chromosomal DNA with antigene peptide nucleic acids. Nat Chem Biol, 1, 210–215. [DOI] [PubMed] [Google Scholar]
  306. Janowski BA, Huffman KE, Schwartz JC, Ram R, Nordsell R, Shames DS, Minna JD and Corey DR, 2006. Involvement of AGO1 and AGO2 in mammalian transcriptional silencing. Nature Structural & Molecular Biology, 13, 787–792. [DOI] [PubMed] [Google Scholar]
  307. Janowski BA, Younger ST, Hardy DB, Ram R, Huffman KE and Corey DR, 2007. Activating gene expression in mammalian cells with promoter‐targeted duplex RNAs. Nat Chem Biol, 3, 166–173. [DOI] [PubMed] [Google Scholar]
  308. Jaskiewicz L and Filipowicz W, 2008. Role of Dicer in posttranscriptional RNA silencing. Curr Top Microbiol Immunol, 320, 77–97. [DOI] [PubMed] [Google Scholar]
  309. Ji H, Chen MS, Greening DW, He WF, Rai A, Zhang WW and Simpson RJ, 2014. Deep Sequencing of RNA from Three Different Extracellular Vesicle (EV) Subtypes Released from the Human LIM1863 Colon Cancer Cell Line Uncovers Distinct Mirna‐Enrichment Signatures. PLoS ONE, 9, e110314–e110314. [DOI] [PMC free article] [PubMed] [Google Scholar]
  310. Jiang F, Miller MT and Marcotrigiano J, 2011a. Structural Basis for RNA Recognition and Activation of RIG‐I. Nucleic Acid Database. [DOI] [PMC free article] [PubMed] [Google Scholar]
  311. Jiang FG, Ramanathan A, Miller MT, Tang GQ, Gale M, Patel SS and Marcotrigiano J, 2011b. Structural basis of RNA recognition and activation by innate immune receptor RIG‐I. Nature, 479, 423–U184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  312. Jiang G, Zheng L, Pu J, Mei H, Zhao J, Huang K, Zeng F and Tong Q, 2012. Small RNAs Targeting Transcription Start Site Induce Heparanase Silencing through Interference with Transcription Initiation in Human Cancer Cells. PLoS ONE, 7, e31379–e31379. [DOI] [PMC free article] [PubMed] [Google Scholar]
  313. Jiang HL, Sheong FK, Zhu LZ, Gao X, Bernauer J and Huang XH, 2015. Markov State Models Reveal a Two‐Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re‐arrangement. Plos Computational Biology, 11, e1004404–e1004404. [DOI] [PMC free article] [PubMed] [Google Scholar]
  314. Jin H, Suh MR, Han J, Yeom KH, Lee Y, Heo I, Ha M, Hyun S and Kim VN, 2009. Human UPF1 Participates in Small RNA‐Induced mRNA Downregulation. Molecular and Cellular Biology, 29, 5789–5799. [DOI] [PMC free article] [PubMed] [Google Scholar]
  315. Jinek M, Fabian MR, Coyle SM, Sonenberg N and Doudna JA, 2010. Structural insights into the human GW182‐PABC interaction in microRNA‐mediated deadenylation. Nature Structural & Molecular Biology, 17, 238–240. [DOI] [PMC free article] [PubMed] [Google Scholar]
  316. Jo MH, Shin S, Jung SR, Kim E, Song JJ and Hohng S, 2015a. Human Argonaute 2 Has Diverse Reaction Pathways on Target RNAs. Molecular Cell, 59, 117–124. [DOI] [PubMed] [Google Scholar]
  317. Jo MH, Song J‐J and Hohng S, 2015b. Single‐molecule fluorescence measurements reveal the reaction mechanisms of the core‐RISC, composed of human Argonaute 2 and a guide RNA. Bmb Reports, 48, 643–644. [DOI] [PMC free article] [PubMed] [Google Scholar]
  318. Johanson TM, Lew AM and Chong MM, 2013. MicroRNA‐independent roles of the RNase III enzymes Drosha and Dicer. Open Biol, 3, 130144. [DOI] [PMC free article] [PubMed] [Google Scholar]
  319. John B, Enright AJ, Aravin A, Tuschl T, Sander C and Marks DS, 2004. Human MicroRNA targets. Plos Biology, 2, e363. [DOI] [PMC free article] [PubMed] [Google Scholar]
  320. Johnson KL, Price BD, Eckerle LD and Ball LA, 2004. Nodamura virus nonstructural protein B2 can enhance viral RNA accumulation in both mammalian and insect cells. Journal of Virology, 78, 6698–6704. [DOI] [PMC free article] [PubMed] [Google Scholar]
  321. Johnston M, Geoffroy M‐C, Sobala A, Hay R and Hutvagner G, 2010. HSP90 Protein Stabilizes Unloaded Argonaute Complexes and Microscopic P‐bodies in Human Cells. Molecular Biology of the Cell, 21, 1462–1469. [DOI] [PMC free article] [PubMed] [Google Scholar]
  322. Jopling CL, Yi M, Lancaster AM, Lemon SM and Sarnow P, 2005. Modulation of hepatitis C virus RNA abundance by a liver‐specific MicroRNA. Science, 309, 1577–1581. [DOI] [PubMed] [Google Scholar]
  323. Josa‐Prado F, Henley JM and Wilkinson KA, 2015. SUMOylation of Argonaute‐2 regulates RNA interference activity. Biochem Biophys Res Commun, 464, 1066–1071. [DOI] [PMC free article] [PubMed] [Google Scholar]
  324. Jose AM and Hunter CP, 2007. Transport of sequence‐specific RNA interference information between cells. Annu Rev Genet, 41, 305–330. [DOI] [PMC free article] [PubMed] [Google Scholar]
  325. Juvvuna PK, Khandelia P, Lee LM and Makeyev EV, 2012. Argonaute identity defines the length of mature mammalian microRNAs. Nucleic Acids Research, 40, 6808–6820. [DOI] [PMC free article] [PubMed] [Google Scholar]
  326. Kalia M, Willkomm S, Claussen JC, Restle T and Bonvin AM, 2016. Novel Insights into Guide RNA 5′‐Nucleoside/Tide Binding by Human Argonaute 2. Int J Mol Sci, 17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  327. Kandeel M and Kitade Y, 2013. In silico molecular docking analysis of the human Argonaute 2 PAZ domain reveals insights into RNA interference. Journal of Computer‐Aided Molecular Design, 27, 605–614. [DOI] [PubMed] [Google Scholar]
  328. Kaneda M, Tang FC, O'Carroll D, Lao KQ and Surani MA, 2009. Essential role for Argonaute2 protein in mouse oogenesis. Epigenetics & Chromatin, 2, 9–9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  329. Kanellopoulou C, Muljo SA, Kung AL, Ganesan S, Drapkin R, Jenuwein T, Livingston DM and Rajewsky K, 2005. Dicer‐deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes & Development, 19, 489–501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  330. Kasim V, Wu SR, Taira K and Miyagishi M, 2013. Determination of the Role of DDX3 a Factor Involved in Mammalian RNAi Pathway Using an shRNA‐Expression Library. PLoS ONE, 8, e59445–e59445. [DOI] [PMC free article] [PubMed] [Google Scholar]
  331. Kato H, Takeuchi O, Sato S, Yoneyama M, Yamamoto M, Matsui K, Uematsu S, Jung A, Kawai T, Ishii KJ, Yamaguchi O, Otsu K, Tsujimura T, Koh CS, Sousa CRE, Matsuura Y, Fujita T and Akira S, 2006. Differential roles of MDA5 and RIG‐I helicases in the recognition of RNA viruses. Nature, 441, 101–105. [DOI] [PubMed] [Google Scholar]
  332. Kawahara Y, Zinshteyn B, Chendrimada TP, Shiekhattar R and Nishikura K, 2007a. RNA editing of the microRNA‐151 precursor blocks cleavage by the Dicer‐TRBP complex. EMBO Rep, 8, 763–769. [DOI] [PMC free article] [PubMed] [Google Scholar]
  333. Kawahara Y, Zinshteyn B, Sethupathy P, Iizasa H, Hatzigeorgiou AG and Nishikura K, 2007b. Redirection of silencing targets by adenosine‐to‐inosine editing of miRNAs. Science, 315, 1137–1140. [DOI] [PMC free article] [PubMed] [Google Scholar]
  334. Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, Daub CO, Kai C, Kawai J, Yasuda J, Carninci P and Hayashizaki Y, 2008. Hidden layers of human small RNAs. BMC Genomics, 9, 157. [DOI] [PMC free article] [PubMed] [Google Scholar]
  335. Kawasaki H and Taira K, 2004. Induction of DNA methylation and gene silencing by short interfering RNAs in human cells. Nature, 431, 211–217. [DOI] [PubMed] [Google Scholar]
  336. Kedersha N, Stoecklin G, Ayodele M, Yacono P, Lykke‐Andersen J, Fritzler MJ, Scheuner D, Kaufman RJ, Golan DE and Anderson P, 2005. Stress granules and processing bodies are dynamically linked sites of mRNP remodeling. Journal of Cell Biology, 169, 871–884. [DOI] [PMC free article] [PubMed] [Google Scholar]
  337. Kennedy EM, Whisnant AW, Kornepati AVR, Marshall JB, Bogerd HP and Cullen BR, 2015. Production of functional small interfering RNAs by an amino‐terminal deletion mutant of human Dicer. Proc Natl Acad Sci U S A, 112, E6945–E6954. [DOI] [PMC free article] [PubMed] [Google Scholar]
  338. Ketting RF, Fischer SE, Bernstein E, Sijen T, Hannon GJ and Plasterk RH, 2001. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes & Development, 15, 2654–2659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  339. Khvorova A, Reynolds A and Jayasena SD, 2003. Functional siRNAs and miRNAs exhibit strand bias. Cell, 115, 209–216. [DOI] [PubMed] [Google Scholar]
  340. Kim BS, Jung JS, Jang JH, Kang KS and Kang SK, 2011. Nuclear Argonaute 2 regulates adipose tissue‐derived stem cell survival through direct control of miR10b and selenoprotein N1 expression. Aging Cell, 10, 277–291. [DOI] [PubMed] [Google Scholar]
  341. Kim BS, Im YB, Jung SJ, Park CH and Kang SK, 2012. Argonaute2 Regulation for K+ Channel‐Mediated Human Adipose Tissue‐Derived Stromal Cells Self‐Renewal and Survival in Nucleus. Stem Cells and Development, 21, 1736–1748. [DOI] [PubMed] [Google Scholar]
  342. Kim DH, Behlke MA, Rose SD, Chang MS, Choi S and Rossi JJ, 2005. Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nature Biotechnology, 23, 222–226. [DOI] [PubMed] [Google Scholar]
  343. Kim DH, Villeneuve LM, Morris KV and Rossi JJ, 2006. Argonaute‐1 directs siRNA‐mediated transcriptional gene silencing in human cells. Nature Structural & Molecular Biology, 13, 793–797. [DOI] [PubMed] [Google Scholar]
  344. Kim DH, Saetrom P, Snove O and Rossi JJ, 2008. MicroRNA‐directed transcriptional gene silencing in mammalian cells. Proc Natl Acad Sci U S A, 105, 16230–16235. [DOI] [PMC free article] [PubMed] [Google Scholar]
  345. Kim JW, Zhang YH, Zern MA, Rossi JJ and Wu J, 2007. Short hairpin RNA causes the methylation of transforming growth factor‐beta receptor II promoter and silencing of the target gene in rat hepatic stellate cells. Biochem Biophys Res Commun, 359, 292–297. [DOI] [PMC free article] [PubMed] [Google Scholar]
  346. Kim Y, Yeo J, Lee JH, Cho J, Seo D, Kim JS and Kim VN, 2014. Deletion of Human tarbp2 Reveals Cellular MicroRNA Targets and Cell‐Cycle Function of TRBP. Cell Reports, 9, 1061–1074. [DOI] [PubMed] [Google Scholar]
  347. Kincaid RP, Chen YT, Cox JE, Rethwilm A and Sullivan CS, 2014. Noncanonical MicroRNA (miRNA) Biogenesis Gives Rise to Retroviral Mimics of Lymphoproliferative and Immunosuppressive Host miRNAs. Mbio, 5, e00074–e00074. [DOI] [PMC free article] [PubMed] [Google Scholar]
  348. Kinch LN and Grishin NV, 2009. The human Ago2 MC region does not contain an eIF4E‐like mRNA cap binding motif. Biology Direct, 4, 2–2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  349. Kini HK and Walton SP, 2007. In vitro binding of single‐stranded RNA by human Dicer. Febs Letters, 581, 5611–5616. [DOI] [PMC free article] [PubMed] [Google Scholar]
  350. Knuckles P, Vogt MA, Lugert S, Milo M, Chong MMW, Hautbergue GM, Wilson SA, Littman DR and Taylor V, 2012. Drosha regulates neurogenesis by controlling Neurogenin 2 expression independent of microRNAs. Nature Neuroscience, 15, 962–969. [DOI] [PubMed] [Google Scholar]
  351. Kok KH, Ng MHJ, Ching YP and Jin DY, 2007. Human TRBP and PACT directly interact with each other and associate with dicer to facilitate the production of small interfering RNA. Journal of Biological Chemistry, 282, 17649–17657. [DOI] [PubMed] [Google Scholar]
  352. Koppers‐Lalic D, Hackenberg M, Bijnsdorp IV, van Eijndhoven MAJ, Sadek P, Sie D, Zini N, Middeldorp JM, Ylstra B, de Menezes RX, Wurdinger T, Meijer GA and Pegtel DM, 2014. Nontemplated Nucleotide Additions Distinguish the Small RNA Composition in Cells from Exosomes. Cell Reports, 8, 1649–1658. [DOI] [PubMed] [Google Scholar]
  353. Kowalinski E, Lunardi T, McCarthy AA, Louber J, Brunel J, Grigorov B, Gerlier D and Cusack S, 2011. Structural basis for the activation of innate immune pattern‐recognition receptor RIG‐I by viral RNA. Cell, 147, 423–435. [DOI] [PubMed] [Google Scholar]
  354. Kropp J, Salih SM and Khatib H, 2014. Expression of microRNAs in bovine and human pre‐implantation embryo culture media. Frontiers in Genetics, 5, 91–91. [DOI] [PMC free article] [PubMed] [Google Scholar]
  355. Kumar L, Verma S, Vaidya B and Gupta V, 2015. Exosomes: Natural Carriers for siRNA Delivery. Current Pharmaceutical Design, 21, 4556–4565. [DOI] [PubMed] [Google Scholar]
  356. Kumar P, Anaya J, Mudunuri SB and Dutta A, 2014. Meta‐analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. Bmc Biology, 12, 78–78. [DOI] [PMC free article] [PubMed] [Google Scholar]
  357. Kuosmanen SM, Hartikainen J, Hippelainen M, Kokki H, Levonen AL and Tavi P, 2015. MicroRNA Profiling of Pericardial Fluid Samples from Patients with Heart Failure. PLoS ONE, 10, e0119646–e0119646. [DOI] [PMC free article] [PubMed] [Google Scholar]
  358. Kuzuoglu‐Ozturk D, Bhandari D, Huntzinger E, Fauser M, Helms S and Izaurralde E, 2016. miRISC and the CCR4‐NOT complex silence mRNA targets independently of 43S ribosomal scanning. EMBO J. [DOI] [PMC free article] [PubMed] [Google Scholar]
  359. Kwon SC, Nguyen TA, Choi YG, Jo MH, Hohng S, Kim VN and Woo JS, 2016. Structure of Human DROSHA. Cell, 164, 81–90. [DOI] [PubMed] [Google Scholar]
  360. Ladewig E, Okamura K, Flynt AS, Westholm JO and Lai EC, 2012. Discovery of hundreds of mirtrons in mouse and human small RNA data. Genome Research, 22, 1634–1645. [DOI] [PMC free article] [PubMed] [Google Scholar]
  361. Lamontagne B, Larose S, Boulanger J and Elela SA, 2001. The RNase III family: a conserved structure and expanding functions in eukaryotic dsRNA metabolism. Curr Issues Mol Biol, 3, 71–78. [PubMed] [Google Scholar]
  362. Landthaler M, Yalcin A and Tuschl T, 2004. The human DiGeorge syndrome critical region gene 8 and its D‐melanogaster homolog are required for miRNA biogenesis. Current Biology, 14, 2162–2167. [DOI] [PubMed] [Google Scholar]
  363. Laraki G, Clerzius G, Daher A, Melendez‐Pena C, Daniels S and Gatignol A, 2008. Interactions between the double‐stranded RNA‐binding proteins TRBP and PACT define the Medipal domain that mediates protein‐protein interactions. RNA Biology, 5, 92–103. [DOI] [PubMed] [Google Scholar]
  364. Lasser C, 2012. Exosomal RNA as biomarkers and the therapeutic potential of exosome vectors. Expert Opinion on Biological Therapy, 12, S189–S197. [DOI] [PubMed] [Google Scholar]
  365. Lau PW, Potter CS, Carragher B and MacRae IJ, 2009. Structure of the Human Dicer‐TRBP Complex by Electron Microscopy. Structure, 17, 1326–1332. [DOI] [PMC free article] [PubMed] [Google Scholar]
  366. Lau PW, Guiley KZ, De N, Potter CS, Carragher B and MacRae IJ, 2012. The molecular architecture of human Dicer. Nature Structural & Molecular Biology, 19, 436–440. [DOI] [PMC free article] [PubMed] [Google Scholar]
  367. Lawrie CH, Gal S, Dunlop HM, Pushkaran B, Liggins AP, Pulford K, Banham AH, Pezzella F, Boultwood J, Wainscoat JS, Hatton CS and Harris AL, 2008. Detection of elevated levels of tumour‐associated microRNAs in serum of patients with diffuse large B‐cell lymphoma. Br J Haematol, 141, 672–675. [DOI] [PubMed] [Google Scholar]
  368. Lazzaretti D, Tournier I and Izaurralde E, 2009. The C‐terminal domains of human TNRC6A, TNRC6B, and TNRC6C silence bound transcripts independently of Argonaute proteins. Rna, 15, 1059–1066. [DOI] [PMC free article] [PubMed] [Google Scholar]
  369. Lecellier CH, Dunoyer P, Arar K, Lehmann‐Che J, Eyquem S, Himber C, Saib A and Voinnet O, 2005. A cellular microRNA mediates antiviral defense in human cells. Science, 308, 557–560. [DOI] [PubMed] [Google Scholar]
  370. Lee HY, Zhou K, Smith AM, Noland CL and Doudna JA, 2013. Differential roles of human Dicer‐binding proteins TRBP and PACT in small RNA processing. Nucleic Acids Research, 41, 6568–6576. [DOI] [PMC free article] [PubMed] [Google Scholar]
  371. Lee NS, Dohjima T, Bauer G, Li HT, Li MJ, Ehsani A, Salvaterra P and Rossi J, 2002. Expression of small interfering RNAs targeted against HIV‐1 rev transcripts in human cells. Nature Biotechnology, 20, 500–505. [DOI] [PubMed] [Google Scholar]
  372. Lee Y, Ahn C, Han JJ, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S and Kim VN, 2003. The nuclear RNase III Drosha initiates microRNA processing. Nature, 425, 415–419. [DOI] [PubMed] [Google Scholar]
  373. Lee Y, El Andaloussi S and Wood MJA, 2012. Exosomes and microvesicles: extracellular vesicles for genetic information transfer and gene therapy. Human Molecular Genetics, 21, R125–R134. [DOI] [PubMed] [Google Scholar]
  374. Lehmann KA and Bass BL, 1999. The importance of internal loops within RNA substrates of ADAR1. Journal of Molecular Biology, 291, 1–13. [DOI] [PubMed] [Google Scholar]
  375. Leung AK, Vyas S, Rood JE, Bhutkar A, Sharp PA and Chang P, 2011. Poly(ADP‐ribose) regulates stress responses and microRNA activity in the cytoplasm. Molecular Cell, 42, 489–499. [DOI] [PMC free article] [PubMed] [Google Scholar]
  376. Lewis BP, Shih IH, Jones‐Rhoades MW, Bartel DP and Burge CB, 2003. Prediction of mammalian microRNA targets. Cell, 115, 787–798. [DOI] [PubMed] [Google Scholar]
  377. Li H, Li WX and Ding SW, 2002. Induction and suppression of RNA silencing by an animal virus. Science, 296, 1319–1321. [DOI] [PubMed] [Google Scholar]
  378. Li LC, Okino ST, Zhao H, Pookot D, Place RF, Urakami S, Enokida H and Dahiya R, 2006. Small dsRNAs induce transcriptional activation in human cells. Proc Natl Acad Sci U S A, 103, 17337–17342. [DOI] [PMC free article] [PubMed] [Google Scholar]
  379. Li WX, Li H, Lu R, Li F, Dus M, Atkinson P, Brydon EW, Johnson KL, Garcia‐Sastre A, Ball LA, Palese P and Ding SW, 2004. Interferon antagonist proteins of influenza and vaccinia viruses are suppressors of RNA silencing. Proc Natl Acad Sci U S A, 101, 1350–1355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  380. Li XJ, Lu C, Stewart M, Xu HY, Strong RK, Igumenova T and Li PW, 2009a. Structural basis of double‐stranded RNA recognition by the RIG‐I like receptor MDA5. Archives of Biochemistry and Biophysics, 488, 23–33. [DOI] [PubMed] [Google Scholar]
  381. Li XJ, Ranjith‐Kumar CT, Brooks MT, Dharmaiah S, Herr AB, Kao C and Li PW, 2009b. The RIG‐I‐like Receptor LGP2 Recognizes the Termini of Double‐stranded RNA. Journal of Biological Chemistry, 284, 13881–13891. [DOI] [PMC free article] [PubMed] [Google Scholar]
  382. Li ZH, Kim SW, Lin YF, Moore PS, Chang Y and John B, 2009c. Characterization of Viral and Human RNAs Smaller than Canonical MicroRNAs. Journal of Virology, 83, 12751–12758. [DOI] [PMC free article] [PubMed] [Google Scholar]
  383. Li ZH, Ender C, Meister G, Moore PS, Chang Y and John B, 2012. Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs. Nucleic Acids Research, 40, 6787–6799. [DOI] [PMC free article] [PubMed] [Google Scholar]
  384. Lian SL, Li SQ, Abadal GX, Pauley BA, Fritzler MJ and Chan EKL, 2009. The C‐terminal half of human Ago2 binds to multiple GW‐rich regions of GW182 and requires GW182 to mediate silencing. Rna, 15, 804–813. [DOI] [PMC free article] [PubMed] [Google Scholar]
  385. Liang XH and Crooke ST, 2011. Depletion of key protein components of the RISC pathway impairs pre‐ribosomal RNA processing. Nucleic Acids Research, 39, 4875–4889. [DOI] [PMC free article] [PubMed] [Google Scholar]
  386. Lim LP, Lau NC, Garrett‐Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS and Johnson JM, 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature, 433, 769–773. [DOI] [PubMed] [Google Scholar]
  387. Lima WF, Wu HJ, Nichols JG, Sun H, Murray HM and Crooke ST, 2009. Binding and Cleavage Specificities of Human Argonaute2. Journal of Biological Chemistry, 284, 26017–26028. [DOI] [PMC free article] [PubMed] [Google Scholar]
  388. Lin JC and Tarn WY, 2009. RNA‐binding Motif Protein 4 Translocates to Cytoplasmic Granules and Suppresses Translation via Argonaute2 during Muscle Cell Differentiation. Journal of Biological Chemistry, 284, 34658–34665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  389. Lipardi C and Paterson BM, 2009. Identification of an RNA‐dependent RNA polymerase in Drosophila involved in RNAi and transposon suppression. Proc Natl Acad Sci U S A, 106, 15645–15650. [DOI] [PMC free article] [PubMed] [Google Scholar] [Retracted]
  390. Liu C, Zhang X, Huang F, Yang B, Li J, Liu BF, Luo HH, Zhang P and Zhang H, 2012a. APOBEC3G Inhibits MicroRNA‐mediated Repression of Translation by Interfering with the Interaction between Argonaute‐2 and MOV10. Journal of Biological Chemistry, 287, 29373–29383. [DOI] [PMC free article] [PubMed] [Google Scholar]
  391. Liu J, Rivas FV, Wohlschlegel J, Yates JR, 3rd , Parker R and Hannon GJ, 2005a. A role for the P‐body component GW182 in microRNA function. Nature Cell Biology, 7, 1261–1266. [DOI] [PMC free article] [PubMed] [Google Scholar]
  392. Liu J, Hu JX and Corey DR, 2012b. Expanding the action of duplex RNAs into the nucleus: redirecting alternative splicing. Nucleic Acids Research, 40, 1240–1250. [DOI] [PMC free article] [PubMed] [Google Scholar]
  393. Liu J, Hu JX, Hicks JA, Prakash TP and Corey DR, 2015. Modulation of Splicing by Single‐Stranded Silencing RNAs. Nucleic Acid Therapeutics, 25, 113–120. [DOI] [PMC free article] [PubMed] [Google Scholar]
  394. Liu JD, Carmell MA, Rivas FV, Marsden CG, Thomson JM, Song JJ, Hammond SM, Joshua‐Tor L and Hannon GJ, 2004. Argonaute2 is the catalytic engine of mammalian RNAi. Science, 305, 1437–1441. [DOI] [PubMed] [Google Scholar]
  395. Liu JD, Valencia‐Sanchez MA, Hannon GJ and Parker R, 2005b. MicroRNA‐dependent localization of targeted mRNAs to mammalian P‐bodies. Nature Cell Biology, 7, 719–U118. [DOI] [PMC free article] [PubMed] [Google Scholar]
  396. Liu XH, Jin DY, McManus MT and Mourelatos Z, 2012c. Precursor MicroRNA‐Programmed Silencing Complex Assembly Pathways in Mammals. Molecular Cell, 46, 507–517. [DOI] [PMC free article] [PubMed] [Google Scholar]
  397. Liu Y, Tan HL, Tian H, Liang CY, Chen S and Liu QH, 2011. Autoantigen La Promotes Efficient RNAi, Antiviral Response, and Transposon Silencing by Facilitating Multiple‐Turnover RISC Catalysis. Molecular Cell, 44, 502–508. [DOI] [PMC free article] [PubMed] [Google Scholar]
  398. Livengood AJ, Wu CCN and Carson DA, 2007. Opposing roles of RNA receptors TLR3 and RIG‐I in the inflammatory response to double‐stranded RNA in a Kaposi's sarcoma cell line. Cellular Immunology, 249, 55–62. [DOI] [PMC free article] [PubMed] [Google Scholar]
  399. Lopez‐Orozco J, Pare JM, Holme AL, Chaulk SG, Fahlman RP and Hobman TC, 2015. Functional analyses of phosphorylation events in human Argonaute 2. Rna, 21, 2030–2038. [DOI] [PMC free article] [PubMed] [Google Scholar]
  400. Lu SH and Cullen BR, 2004. Adenovirus VA1 noncoding RNA can inhibit small interfering RNA and microRNA biogenesis. Journal of Virology, 78, 12868–12876. [DOI] [PMC free article] [PubMed] [Google Scholar]
  401. Lugli G, Larson J, Martone ME, Jones Y and Smalheiser NR, 2005. Dicer and eIF2c are enriched at postsynaptic densities in adult mouse brain and are modified by neuronal activity in a calpain‐dependent manner. Journal of Neurochemistry, 94, 896–905. [DOI] [PubMed] [Google Scholar]
  402. Luo D, Ding SC, Vela A, Kohlway A, Lindenbach BD and Pyle AM, 2011. Structural insights into RNA recognition by RIG‐I. Cell, 147, 409–422. [DOI] [PMC free article] [PubMed] [Google Scholar]
  403. Luo SS, Ishibashi O, Ishikawa G, Ishikawa T, Katayama A, Mishima T, Takizawa T, Shigihara T, Goto T, Izumi A, Ohkuchi A, Matsubara S, Takeshita T and Takizawa T, 2009. Human Villous Trophoblasts Express and Secrete Placenta‐Specific MicroRNAs into Maternal Circulation via Exosomes. Biology of Reproduction, 81, 717–729. [DOI] [PubMed] [Google Scholar]
  404. Ma E, MacRae IJ, Kirsch JF and Doudna JA, 2008. Autoinhibition of human dicer by its internal helicase domain. Journal of Molecular Biology, 380, 237–243. [DOI] [PMC free article] [PubMed] [Google Scholar]
  405. Ma EB, Zhou KH, Kidwell MA and Doudna JA, 2012. Coordinated Activities of Human Dicer Domains in Regulatory RNA Processing. Journal of Molecular Biology, 422, 466–476. [DOI] [PMC free article] [PubMed] [Google Scholar]
  406. Ma HM, Wu YG, Choi JG and Wu HQ, 2013. Lower and upper stem‐single‐stranded RNA junctions together determine the Drosha cleavage site. Proc Natl Acad Sci U S A, 110, 20687–20692. [DOI] [PMC free article] [PubMed] [Google Scholar]
  407. Ma J, Flemr M, Stein P, Berninger P, Malik R, Zavolan M, Svoboda P and Schultz RM, 2010. MicroRNA Activity Is Suppressed in Mouse Oocytes. Current Biology, 20, 265–270. [DOI] [PMC free article] [PubMed] [Google Scholar]
  408. Ma JB, Ye K and Patel DJ, 2004. Structural basis for overhang‐specific small interfering RNA recognition by the PAZ domain. Nature, 429, 318–322. [DOI] [PMC free article] [PubMed] [Google Scholar]
  409. Macias S, Plass M, Stajuda A, Michlewski G, Eyras E and Caceres JF, 2012. DGCR8 HITS‐CLIP reveals novel functions for the Microprocessor. Nature Structural & Molecular Biology, 19, 760–766. [DOI] [PMC free article] [PubMed] [Google Scholar]
  410. Macias S, Cordiner RA, Gautier P, Plass M and Caceres JF, 2015. DGCR8 Acts as an Adaptor for the Exosome Complex to Degrade Double‐Stranded Structured RNAs. Molecular Cell, 60, 873–885. [DOI] [PMC free article] [PubMed] [Google Scholar]
  411. MacRae IJ, Li F, Zhou K, Cande WZ and Doudna JA, 2006a. Structure of Dicer and mechanistic implications for RNAi. Cold Spring Harbor Symposia on Quantitative Biology, 71, 73–80. [DOI] [PubMed] [Google Scholar]
  412. MacRae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD and Doudna JA, 2006b. Structural basis for double‐stranded RNA processing by Dicer. Science, 311, 195–198. [DOI] [PubMed] [Google Scholar]
  413. MacRae IJ, Zhou K and Doudna JA, 2007. Structural determinants of RNA recognition and cleavage by Dicer. Nature Structural & Molecular Biology, 14, 934–940. [DOI] [PubMed] [Google Scholar]
  414. MacRae IJ, Ma E, Zhou M, Robinson CV and Doudna JA, 2008. In vitro reconstitution of the human RISC‐loading complex. Proc Natl Acad Sci U S A, 105, 512–517. [DOI] [PMC free article] [PubMed] [Google Scholar]
  415. Madsen C, Gronskov K, Brondum‐Nielsen K and Jensen TG, 2009. Normal RNAi response in human fragile x fibroblasts. BMC Research Notes, 2, 177–177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  416. Maida Y, Yasukawa M, Furuuchi M, Lassmann T, Possemato R, Okamoto N, Kasim V, Hayashizaki Y, Hahn WC and Masutomi K, 2009. An RNA‐dependent RNA polymerase formed by TERT and the RMRP RNA. Nature, 461, 230–U104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  417. Maida Y and Masutomi K, 2011. RNA‐dependent RNA polymerases in RNA silencing. Biological Chemistry, 392, 299–304. [DOI] [PubMed] [Google Scholar]
  418. Maida Y, Kyo S, Lassmann T, Hayashizaki Y and Masutomi K, 2013. Off‐Target Effect of Endogenous siRNA Derived from RMRP in Human Cells. International Journal of Molecular Sciences, 14, 9305–9318. [DOI] [PMC free article] [PubMed] [Google Scholar]
  419. Maida Y, Yasukawa M and Masutomi K, 2016. De Novo RNA Synthesis by RNA‐Dependent RNA Polymerase Activity of Telomerase Reverse Transcriptase. Molecular and Cellular Biology, 36, 1248–1259. [DOI] [PMC free article] [PubMed] [Google Scholar]
  420. Maniataki E and Mourelatos Z, 2005a. Human mitochondrial tRNA(Met) is exported to the cytoplasm and associates with the Argonaute 2 protein. Rna, 11, 849–852. [DOI] [PMC free article] [PubMed] [Google Scholar]
  421. Maniataki E and Mourelatos Z, 2005b. A human, ATP‐independent, RISC assembly machine fueled by pre‐miRNA. Genes & Development, 19, 2979–2990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  422. Marques JT, Devosse T, Wang D, Zamanian‐Daryoush M, Serbinowski P, Hartmann R, Fujita T, Behlke MA and Williams BRG, 2006. A structural basis for discriminating between self and nonself double‐stranded RNAs in mammalian cells. Nature Biotechnology, 24, 559–565. [DOI] [PubMed] [Google Scholar]
  423. Martinez I and Melero JA, 2002. A model for the generation of multiple A to G transitions in the human respiratory syncytial virus genome: predicted RNA secondary structures as substrates for adenosine cleaminases that act on RNA. Journal of General Virology, 83, 1445–1455. [DOI] [PubMed] [Google Scholar]
  424. Martinez J, Patkaniowska A, Urlaub H, Luhrmann R and Tuschl T, 2002. Single‐stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell, 110, 563–574. [DOI] [PubMed] [Google Scholar]
  425. Martinez NJ, Chang HM, Borrajo JD and Gregory RI, 2013. The co‐chaperones Fkbp4/5 control Argonaute2 expression and facilitate RISC assembly. Rna, 19, 1583–1593. [DOI] [PMC free article] [PubMed] [Google Scholar]
  426. Martinez NJ and Gregory RI, 2013. Argonaute2 expression is post‐transcriptionally coupled to microRNA abundance. Rna, 19, 605–612. [DOI] [PMC free article] [PubMed] [Google Scholar]
  427. Mathys H, Basquin J, Ozgur S, Czarnocki‐Cieciura M, Bonneau F, Aartse A, Dziembowski A, Nowotny M, Conti E and Filipowicz W, 2014. Structural and biochemical insights to the role of the CCR4‐NOT complex and DDX6 ATPase in microRNA repression. Molecular Cell, 54, 751–765. [DOI] [PubMed] [Google Scholar]
  428. Matranga C, Tomari Y, Shin C, Bartel DP and Zamore PD, 2005. Passenger‐strand cleavage facilitates assembly of siRNA into Ago2‐containing RNAi enzyme complexes. Cell, 123, 607–620. [DOI] [PubMed] [Google Scholar]
  429. Maurin T, Cazalla D, Yang JS, Bortolamiol‐Becet D and Lai EC, 2012. RNase III‐independent microRNA biogenesis in mammalian cells. Rna, 18, 2166–2173. [DOI] [PMC free article] [PubMed] [Google Scholar]
  430. Maute RL, Schneider C, Sumazin P, Holmes A, Califano A, Basso K and Dalla‐Favera R, 2013. tRNA‐derived microRNA modulates proliferation and the DNA damage response and is down‐regulated in B cell lymphoma. Proc Natl Acad Sci U S A, 110, 1404–1409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  431. Mazumder A, Bose M, Chakraborty A, Chakrabarti S and Bhattacharyya SN, 2013. A transient reversal of miRNA‐mediated repression controls macrophage activation. EMBO Rep, 14, 1008–1016. [DOI] [PMC free article] [PubMed] [Google Scholar]
  432. McCartney S, Vermi W, Gilfillan S, Cella M, Murphy TL, Schreiber RD, Murphy KM and Colonna M, 2009. Distinct and complementary functions of MDA5 and TLR3 in poly(I:C)‐mediated activation of mouse NK cells. Journal of Experimental Medicine, 206, 2967–2976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  433. McCartney SA, Thackray LB, Gitlin L, Gilfillan S, Virgin HW and Colonna M, 2008. MDA‐5 recognition of a murine norovirus. Plos Pathogens, 4, e1000108–e1000108. [DOI] [PMC free article] [PubMed] [Google Scholar]
  434. Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G and Tuschl T, 2004. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Molecular Cell, 15, 185–197. [DOI] [PubMed] [Google Scholar]
  435. Meister G and Tuschl T, 2004. Mechanisms of gene silencing by double‐stranded RNA. Nature, 431, 343–349. [DOI] [PubMed] [Google Scholar]
  436. Meister G, Landthaler M, Peters L, Chen PY, Urlaub H, Luhrmann R and Tuschl T, 2005. Identification of novel argonaute‐associated proteins. Current Biology, 15, 2149–2155. [DOI] [PubMed] [Google Scholar]
  437. Meng B, Lui YW, Meng S, Ca C and Hu Y, 2006. Identification of effective siRNA blocking the expression of SARS viral envelope e and RDRP genes. Molecular Biotechnology, 33, 141–148. [DOI] [PMC free article] [PubMed] [Google Scholar]
  438. Meurs E, Chong K, Galabru J, Thomas NS, Kerr IM, Williams BR and Hovanessian AG, 1990. Molecular cloning and characterization of the human double‐stranded RNA‐activated protein kinase induced by interferon. Cell, 62, 379–390. [DOI] [PubMed] [Google Scholar]
  439. Minones‐Moyano E, Friedländer MR, Pallares J, Kagerbauer B, Porta S, Escaramis G, Ferrer I, Estivill X and Marti E, 2013. Upregulation of a small vault RNA (svtRNA2‐1a) is an early event in parkinson disease and induces neuronal dysfunction. RNA Biology, 10, 1093–1106. [DOI] [PMC free article] [PubMed] [Google Scholar]
  440. Momose F, Seo N, Akahori Y, Sawada S, Harada N, Ogura T, Akiyoshi K and Shiku H, 2016. Guanine‐Rich Sequences Are a Dominant Feature of Exosomal microRNAs across the Mammalian Species and Cell Types. PLoS ONE, 11, e0154134–e0154134. [DOI] [PMC free article] [PubMed] [Google Scholar]
  441. Moon JS, Lee SH, Han SH, Kim EJ, Cho H, Lee W, Kim MK, Kim TE, Park HJ, Rhee JK, Kim SJ, Cho SW, Han SH and Oh JW, 2016. Inhibition of hepatitis C virus in mouse models by lipidoid nanoparticle‐mediated systemic delivery of siRNA against PRK2. Nanomedicine: nanotechnology, biology, and medicine. [DOI] [PubMed] [Google Scholar]
  442. Morris KV, Chan SW, Jacobsen SE and Looney DJ, 2004. Small interfering RNA‐induced transcriptional gene silencing in human cells. Science, 305, 1289–1292. [DOI] [PubMed] [Google Scholar]
  443. Morse DP, Aruscavage PJ and Bass BL, 2002. RNA hairpins in noncoding regions of human brain and Caenorhabditis elegans mRNA are edited by adenosine deaminases that act on RNA. Proc Natl Acad Sci U S A, 99, 7906–7911. [DOI] [PMC free article] [PubMed] [Google Scholar]
  444. Much C, Auchynnikava T, Pavlinic D, Buness A, Rappsilber J, Benes V, Allshire R and O'Carroll D, 2016. Endogenous Mouse Dicer Is an Exclusively Cytoplasmic Protein. Plos Genetics, 12, e1006095. [DOI] [PMC free article] [PubMed] [Google Scholar]
  445. Murchison EP, Partridge JF, Tam OH, Cheloufi S and Hannon GJ, 2005. Characterization of Dicer‐deficient murine embryonic stem cells. Proc Natl Acad Sci U S A, 102, 12135–12140. [DOI] [PMC free article] [PubMed] [Google Scholar]
  446. Murchison EP, Stein P, Xuan Z, Pan H, Zhang MQ, Schultz RM and Hannon GJ, 2007. Critical roles for Dicer in the female germline. Genes & Development, 21, 682–693. [DOI] [PMC free article] [PubMed] [Google Scholar]
  447. Murphy D, Dancis B and Brown JR, 2008. The evolution of core proteins involved in microRNA biogenesis. Bmc Evolutionary Biology, 8, 92–92. [DOI] [PMC free article] [PubMed] [Google Scholar]
  448. Nachmani D, Zimmermann A, Djian E, Weisblum Y, Livneh Y, Le VTK, Galun E, Horejsi V, Isakov O, Shomron N, Wolf DG, Hengel H and Mandelboim O, 2014. MicroRNA Editing Facilitates Immune Elimination of HCMV Infected Cells. Plos Pathogens, 10, e1003963–e1003963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  449. Nagata T, Tsuda K, Kobayashi N, Shirouzu M, Kigawa T, Guntert P, Yokoyama S and Muto Y, 2012. Solution structures of the double‐stranded RNA‐binding domains from RNA helicase A. Proteins‐Structure Function and Bioinformatics, 80, 1699–1706. [DOI] [PubMed] [Google Scholar]
  450. Nakanishi K, Ascano M, Gogakos T, Ishibe‐Murakami S, Serganov AA, Briskin D, Morozov P, Tuschl T and Patel DJ, 2013. Eukaryote‐Specific Insertion Elements Control Human ARGONAUTE Slicer Activity. Cell Reports, 3, 1893–1900. [DOI] [PMC free article] [PubMed] [Google Scholar]
  451. Napoli S, Pastori C, Magistri M, Carbone GM and Catapano CV, 2009. Promoter‐specific transcriptional interference and c‐myc gene silencing by siRNAs in human cells. EMBO J, 28, 1708–1719. [DOI] [PMC free article] [PubMed] [Google Scholar]
  452. Nejepinska J, Flemr M and Svoboda P, 2012a. The Canonical RNA Interference Pathway in Animals In: Mallick B. and Ghosh Z. (eds). Regulatory RNAs. Springer, Berlin, Heidelberg: pp. 111–149. [Google Scholar]
  453. Nejepinska J, Malik R, Filkowski J, Flemr M, Filipowicz W and Svoboda P, 2012b. dsRNA expression in the mouse elicits RNAi in oocytes and low adenosine deamination in somatic cells. Nucleic Acids Research, 40, 399–413. [DOI] [PMC free article] [PubMed] [Google Scholar]
  454. Nejepinska J, Malik R, Wagner S and Svoboda P, 2014. Reporters transiently transfected into mammalian cells are highly sensitive to translational repression induced by dsRNA expression. PLoS ONE, 9, e87517. [DOI] [PMC free article] [PubMed] [Google Scholar]
  455. Neve J, Burger K, Li WC, Hoque M, Patel R, Tian B, Gullerova M and Furger A, 2016. Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation. Genome Research, 26, 24–35. [DOI] [PMC free article] [PubMed] [Google Scholar]
  456. Nguyen J and Szoka FC, 2012. Nucleic Acid Delivery: The Missing Pieces of the Puzzle? Accounts of Chemical Research, 45, 1153–1162. [DOI] [PMC free article] [PubMed] [Google Scholar]
  457. Nguyen TA, Jo MH, Choi YG, Park J, Kwon SC, Hohng S, Kim VN and Woo JS, 2015. Functional Anatomy of the Human Microprocessor. Cell, 161, 1374–1387. [DOI] [PubMed] [Google Scholar]
  458. Nicholson RH and Nicholson AW, 2002. Molecular characterization of a mouse cDNA encoding Dicer, a ribonuclease III ortholog involved in RNA interference. Mammalian Genome, 13, 67–73. [DOI] [PubMed] [Google Scholar]
  459. Nie YZ, Zhao QC, Su YJ and Yang JH, 2004. Subcellular distribution of ADAR1 isoforms is synergistically determined by three nuclear discrimination signals and a regulatory motif. Journal of Biological Chemistry, 279, 13249–13255. [DOI] [PubMed] [Google Scholar]
  460. Nie YZ, Hammond GL and Yang JH, 2007. Double‐stranded RNA deaminase ADAR1 increases host susceptibility to virus infection. Journal of Virology, 81, 917–923. [DOI] [PMC free article] [PubMed] [Google Scholar]
  461. Nishi K, Nishi A, Nagasawa T and Ui‐Tei K, 2013. Human TNRC6A is an Argonaute‐navigator protein for microRNA‐mediated gene silencing in the nucleus. Rna, 19, 17–35. [DOI] [PMC free article] [PubMed] [Google Scholar]
  462. Nishi K, Takahashi T, Suzawa M, Miyakawa T, Nagasawa T, Ming Y, Tanokura M and Ui‐Tei K, 2015. Control of the localization and function of a miRNA silencing component TNRC6A by Argonaute protein. Nucleic Acids Research, 43, 9856–9873. [DOI] [PMC free article] [PubMed] [Google Scholar]
  463. Nishikura K, Yoo C, Kim U, Murray JM, Estes PA, Cash FE and Liebhaber SA, 1991. Substrate specificity of the dsRNA unwinding/modifying activity. EMBO J, 10, 3523–3532. [DOI] [PMC free article] [PubMed] [Google Scholar]
  464. Nishikura K, 2010. Functions and Regulation of RNA Editing by ADAR Deaminases. Annual Review of Biochemistry, 79, 321–349. [DOI] [PMC free article] [PubMed] [Google Scholar]
  465. Nishikura K, 2016. A‐to‐I editing of coding and non‐coding RNAs by ADARs. Nature Reviews Molecular Cell Biology, 17, 83–96. [DOI] [PMC free article] [PubMed] [Google Scholar]
  466. Noland CL and Doudna JA, 2013. Multiple sensors ensure guide strand selection in human RNAi pathways. Rna, 19, 639–648. [DOI] [PMC free article] [PubMed] [Google Scholar]
  467. Novellino L, Rossi RL, Bonino F, Cavallone D, Abrignani S, Pagani M and Brunetto MR, 2012. Circulating Hepatitis B Surface Antigen Particles Carry Hepatocellular microRNAs. PLoS ONE, 7, e31952–e31952. [DOI] [PMC free article] [PubMed] [Google Scholar]
  468. Nygardas M, Vuorinen T, Aalto AP, Bamford DH and Hukkanen V, 2009. Inhibition of coxsackievirus B3 and related enteroviruses by antiviral short interfering RNA pools produced using phi 6 RNA‐dependent RNA polymerase. Journal of General Virology, 90, 2468–2473. [DOI] [PubMed] [Google Scholar]
  469. Nykanen A, Haley B and Zamore PD, 2001. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell, 107, 309–321. [DOI] [PubMed] [Google Scholar]
  470. Ohnishi Y, Totoki Y, Toyoda A, Watanabe T, Yamamoto Y, Tokunaga K, Sakaki Y, Sasaki H and Hohjoh H, 2010. Small RNA class transition from siRNA/piRNA to miRNA during pre‐implantation mouse development. Nucleic Acids Research, 38, 5141–5151. [DOI] [PMC free article] [PubMed] [Google Scholar]
  471. Ohrt T, Merkle D, Birkenfeld K, Echeverri CJ and Schwille P, 2006. In situ fluorescence analysis demonstrates active siRNA exclusion from the nucleus by Exportin 5. Nucleic Acids Research, 34, 1369–1380. [DOI] [PMC free article] [PubMed] [Google Scholar]
  472. Ohrt T, Muetze J, Staroske W, Weinmann L, Hock J, Crell K, Meister G and Schwille P, 2008. Fluorescence correlation spectroscopy and fluorescence cross‐correlation spectroscopy reveal the cytoplasmic origination of loaded nuclear RISC in vivo in human cells. Nucleic Acids Research, 36, 6439–6449. [DOI] [PMC free article] [PubMed] [Google Scholar]
  473. Ohrt T, Muetze J, Svoboda P and Schwille P, 2012. Intracellular Localization and Routing of miRNA and RNAi Pathway Components. Curr Top Med Chem, 12, 79–88. [DOI] [PubMed] [Google Scholar]
  474. Okamura K, Ladewig E, Zhou L and Lai EC, 2013. Functional small RNAs are generated from select miRNA hairpin loops in flies and mammals. Genes & Development, 27, 778–792. [DOI] [PMC free article] [PubMed] [Google Scholar]
  475. Ostermann E, Tuddenham L, Macquin C, Alsaleh G, Schreiber‐Becker J, Tanguy M, Bahram S, Pfeffer S and Georgel P, 2012. Deregulation of Type I IFN‐Dependent Genes Correlates with Increased Susceptibility to Cytomegalovirus Acute Infection of Dicer Mutant Mice. PLoS ONE, 7, e43744–e43744. [DOI] [PMC free article] [PubMed] [Google Scholar]
  476. Otsuka M, Takata A, Yoshikawa T, Kojima K, Kishikawa T, Shibata C, Takekawa M, Yoshida H, Omata M and Koike K, 2011. Receptor for Activated Protein Kinase C: Requirement for Efficient MicroRNA Function and Reduced Expression in Hepatocellular Carcinoma. PLoS ONE, 6, e24359–e24359. [DOI] [PMC free article] [PubMed] [Google Scholar]
  477. Ozgur S and Stoecklin G, 2013. Role of Rck‐Pat1b binding in assembly of processing‐bodies. RNA Biology, 10, 528–539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  478. Parameswaran P, Sklan E, Wilkins C, Burgon T, Samuel MA, Lu R, Ansel KM, Heissmeyer V, Einav S, Jackson W, Doukas T, Paranjape S, Polacek C, dos Santos FB, Jalili R, Babrzadeh F, Gharizadeh B, Grimm D, Kay M, Koike S, Sarnow P, Ronaghi M, Ding SW, Harris E, Chow M, Diamond MS, Kirkegaard K, Glenn JS and Fire AZ, 2010. Six RNA Viruses and Forty‐One Hosts: Viral Small RNAs and Modulation of Small RNA Repertoires in Vertebrate and Invertebrate Systems. Plos Pathogens, 6, e1000764–e1000764. [DOI] [PMC free article] [PubMed] [Google Scholar]
  479. Pare JM, Lopez‐Orozco J and Hobman TC, 2011. MicroRNA‐binding is required for recruitment of human Argonaute 2 to stress granules and P‐bodies. Biochem Biophys Res Commun, 414, 259–264. [DOI] [PubMed] [Google Scholar]
  480. Pare JM, LaPointe P and Hobman TC, 2013. Hsp90 cochaperones p23 and FKBP4 physically interact with hAgo2 and activate RNA interference‐mediated silencing in mammalian cells. Molecular Biology of the Cell, 24, 2303–2310. [DOI] [PMC free article] [PubMed] [Google Scholar]
  481. Park HS, Davies MV, Langland JO, Chang HW, Nam YS, Tartaglia J, Paoletti E, Jacobs BL, Kaufman RJ and Venkatesan S, 1994. TAR RNA‐binding protein is an inhibitor of the interferon‐induced protein kinase PKR. Proc Natl Acad Sci U S A, 91, 4713–4717. [DOI] [PMC free article] [PubMed] [Google Scholar]
  482. Park JE, Heo I, Tian Y, Simanshu DK, Chang H, Jee D, Patel DJ and Kim VN, 2011. Dicer recognizes the 5 ‘ end of RNA for efficient and accurate processing. Nature, 475, 201–U107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  483. Park JH and Shin C, 2015. Slicer‐independent mechanism drives small‐RNA strand separation during human RISC assembly. Nucleic Acids Research, 43, 9418–9433. [DOI] [PMC free article] [PubMed] [Google Scholar]
  484. Patel RC and Sen GC, 1998. PACT, a protein activator of the interferon‐induced protein kinase, PKR. EMBO J, 17, 4379–4390. [DOI] [PMC free article] [PubMed] [Google Scholar]
  485. Patranabis S and Bhattacharyya SN, 2016. Phosphorylation of Ago2 and Subsequent Inactivation of let‐7a RNP‐Specific MicroRNAs Control Differentiation of Mammalian Sympathetic Neurons. Molecular and Cellular Biology, 36, 1260–1271. [DOI] [PMC free article] [PubMed] [Google Scholar]
  486. Pawlicki JM and Steitz JA, 2008. Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production. Journal of Cell Biology, 182, 61–76. [DOI] [PMC free article] [PubMed] [Google Scholar]
  487. Pawlicki JM and Steitz JA, 2009. Subnuclear compartmentalization of transiently expressed polyadenylated pri‐microRNAs Processing at transcription sites or accumulation in SC35 foci. Cell Cycle, 8, 345–356. [DOI] [PMC free article] [PubMed] [Google Scholar]
  488. Pegtel DM, van de Garde MDB and Middeldorp JM, 2011. Viral miRNAs exploiting the endosomal‐exosomal pathway for intercellular cross‐talk and immune evasion. Biochimica Et Biophysica Acta‐Gene Regulatory Mechanisms, 1809, 715–721. [DOI] [PubMed] [Google Scholar]
  489. Peng ZY, Cheng YB, Tan BCM, Kang L, Tian ZJ, Zhu YK, Zhang WW, Liang Y, Hu XD, Tan XM, Guo J, Dong ZR, Liang Y, Bao L and Wang J, 2012. Comprehensive analysis of RNA‐Seq data reveals extensive RNA editing in a human transcriptome. Nature Biotechnology, 30, 253. [DOI] [PubMed] [Google Scholar]
  490. Pepin G, Perron MP and Provost P, 2012. Regulation of human Dicer by the resident ER membrane protein CLIMP‐63. Nucleic Acids Research, 40, 11603–11617. [DOI] [PMC free article] [PubMed] [Google Scholar]
  491. Peters L and Meister G, 2007. Argonaute proteins: Mediators of RNA silencing. Molecular Cell, 26, 611–623. [DOI] [PubMed] [Google Scholar]
  492. Pfeffer S, Zavolan M, Grasser FA, Chien M, Russo JJ, Ju J, John B, Enright AJ, Marks D, Sander C and Tuschl T, 2004. Identification of virus‐encoded microRNAs. Science, 304, 734–736. [DOI] [PubMed] [Google Scholar]
  493. Pfeffer S, Sewer A, Lagos‐Quintana M, Sheridan R, Sander C, Grasser FA, van Dyk LF, Ho CK, Shuman S, Chien M, Russo JJ, Ju J, Randall G, Lindenbach BD, Rice CM, Simon V, Ho DD, Zavolan M and Tuschl T, 2005. Identification of microRNAs of the herpesvirus family. Nature Methods, 2, 269–276. [DOI] [PubMed] [Google Scholar]
  494. Pham JW, Pellino JL, Lee YS, Carthew RW and Sontheimer EJ, 2004. A Dicer‐2‐dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila. Cell, 117, 83–94. [DOI] [PubMed] [Google Scholar]
  495. Phua SLC, Sivakamasundari V, Shao Y, Cai XH, Zhang LF, Lufkin T and Featherstone M, 2011. Nuclear Accumulation of an Uncapped RNA Produced by Drosha Cleavage of a Transcript Encoding miR‐10b and HOXD4. PLoS ONE, 6, e25689–e25689. [DOI] [PMC free article] [PubMed] [Google Scholar]
  496. Pichlmair A, Schulz O, Tan CP, Naslund TI, Liljestrom P, Weber F and Reis e Sousa C, 2006. RIG‐I‐mediated antiviral responses to single‐stranded RNA bearing 5′‐phosphates. Science, 314, 997–1001. [DOI] [PubMed] [Google Scholar]
  497. Pillai RS, Artus CG and Filipowicz W, 2004. Tethering of human Ago proteins to mRNA mimics the miRNA‐mediated repression of protein synthesis. Rna, 10, 1518–1525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  498. Pillai RS, Bhattacharyya SN, Artus CG, Zoller T, Cougot N, Basyuk E, Bertrand E and Filipowicz W, 2005. Inhibition of translational initiation by Let‐7 microRNA in human cells. Science, 309, 1573–1576. [DOI] [PubMed] [Google Scholar]
  499. Place RF, Li LC, Pookot D, Noonan EJ and Dahiya R, 2008. MicroRNA‐373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci U S A, 105, 1608–1613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  500. Plante I, Davidovic L, Ouellet DL, Gobeil LA, Tremblay S, Khandjian EW and Provost P, 2006. Dicer‐derived MicroRNAs are utilized by the fragile X mental retardation protein for assembly on target RNAs. Journal of Biomedicine and Biotechnology, 2006, 64347–64347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  501. Plante I, Ple H, Landry P, Gunaratne PH and Provost P, 2012. Modulation of microRNA activity by semi‐nnicroRNAs. Frontiers in Genetics, 3, 99‐Article No.: 99. [DOI] [PMC free article] [PubMed] [Google Scholar]
  502. Polson AG and Bass BL, 1994. Preferential selection of adenosines for modification by double‐stranded RNA adenosine deaminase. EMBO J, 13, 5701–5711. [DOI] [PMC free article] [PubMed] [Google Scholar]
  503. Poulsen H, Jorgensen R, Heding A, Nielsen FC, Bonven B and Egebjerg J, 2006. Dimerization of ADAR2 is mediated by the double‐stranded RNA binding domain. Rna, 12, 1350–1360. [DOI] [PMC free article] [PubMed] [Google Scholar]
  504. Provost P, Dishart D, Doucet J, Frendewey D, Samuelsson B and Radmark O, 2002. Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J, 21, 5864–5874. [DOI] [PMC free article] [PubMed] [Google Scholar]
  505. Puthenveetil S, Whitby L, Ren J, Kelnar K, Krebs JF and Beal PA, 2006. Controlling activation of the RNA‐dependent protein kinase by siRNAs using site‐specific chemical modification. Nucleic Acids Research, 34, 4900–4911. [DOI] [PMC free article] [PubMed] [Google Scholar]
  506. Qi HH, Ongusaha PP, Myllyharju J, Cheng DM, Pakkanen O, Shi YJ, Lee SW, Peng JM and Shi Y, 2008. Prolyl 4‐hydroxylation regulates Argonaute 2 stability. Nature, 455, 421–U478. [DOI] [PMC free article] [PubMed] [Google Scholar]
  507. Rak J, 2013. Extracellular vesicles ‐ biomarkers and effectors of the cellular interactome in cancer. Frontiers in Pharmacology, 4, 21–21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  508. Rehwinkel J, Behm‐Ansmant I, Gatfield D and Izaurralde E, 2005. A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA‐mediated gene silencing. Rna, 11, 1640–1647. [DOI] [PMC free article] [PubMed] [Google Scholar]
  509. Ren YF, Li GL, Wu JM, Xue YF, Song YJ, Lv L, Zhang XJ and Tang KF, 2012. Dicer‐Dependent Biogenesis of Small RNAs Derived from 7SL RNA. PLoS ONE, 7, e40705–e40705. [DOI] [PMC free article] [PubMed] [Google Scholar]
  510. Reynolds A, Anderson EM, Vermeulen A, Fedorov Y, Robinson K, Leake D, Karpilow J, Marshall WS and Khvorova A, 2006. Induction of the interferon response by siRNA is cell type‐ and duplex length‐dependent. Rna, 12, 988–993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  511. Rice GI, Kasher PR, Forte GMA, Mannion NM, Greenwood SM, Szynkiewicz M, Dickerson JE, Bhaskar SS, Zampini M, Briggs TA, Jenkinson EM, Bacino CA, Battini R, Bertini E, Brogan PA, Brueton LA, Carpanelli M, De Laet C, de Lonlay P, del Toro M, Desguerre I, Fazzi E, Garcia‐Cazorla A, Heiberg A, Kawaguchi M, Kumar R, Lin J, Lourenco CM, Male AM, Marques W, Mignot C, Olivieri I, Orcesi S, Prabhakar P, Rasmussen M, Robinson RA, Rozenberg F, Schmidt JL, Steindl K, Tan TY, van der Merwe WG, Vanderver A, Vassallo G, Wakeling EL, Wassmer E, Whittaker E, Livingston JH, Lebon P, Suzuki T, McLaughlin PJ, Keegan LP, O'Connell MA, Lovell SC and Crow YJ, 2012. Mutations in ADAR1 cause Aicardi‐Goutieres syndrome associated with a type I interferon signature. Nature Genetics, 44, 1243–1248. [DOI] [PMC free article] [PubMed] [Google Scholar]
  512. Rivas FV, Tolia NH, Song JJ, Aragon JP, Liu JD, Hannon GJ and Joshua‐Tor L, 2005. Purified Argonaute2 and an siRNA form recombinant human RISC. Nature Structural & Molecular Biology, 12, 340–349. [DOI] [PubMed] [Google Scholar]
  513. Robb GB, Brown KM, Khurana J and Rana TM, 2005. Specific and potent RNAi in the nucleus of human cells. Nature Structural & Molecular Biology, 12, 133–137. [DOI] [PubMed] [Google Scholar]
  514. Robb GB and Rana TM, 2007. RNA helicase A interacts with RISC in human cells and functions in RISC loading. Molecular Cell, 26, 523–537. [DOI] [PubMed] [Google Scholar]
  515. Rudel S, Flatley A, Weinmann L, Kremmer E and Meister G, 2008. A multifunctional human Argonaute2‐specific monoclonal antibody. Rna, 14, 1244–1253. [DOI] [PMC free article] [PubMed] [Google Scholar]
  516. Rudel S, Wang YL, Lenobel R, Korner R, Hsiao HH, Urlaub H, Patel D and Meister G, 2011. Phosphorylation of human Argonaute proteins affects small RNA binding. Nucleic Acids Research, 39, 2330–2343. [DOI] [PMC free article] [PubMed] [Google Scholar]
  517. Rybak A, Fuchs H, Hadian K, Smirnova L, Wulczyn EA, Michel G, Nitsch R, Krappmann D and Wulczyn FG, 2009. The let‐7 target gene mouse lin‐41 is a stem cell specific E3 ubiquitin ligase for the miRNA pathway protein Ago2. Nature Cell Biology, 11, 1411–U1458. [DOI] [PubMed] [Google Scholar]
  518. Ryu I, Park JH, An S, Kwon OS and Jang SK, 2013. eIF4GI Facilitates the MicroRNA‐Mediated Gene Silencing. PLoS ONE, 8, e55725–e55725. [DOI] [PMC free article] [PubMed] [Google Scholar]
  519. Sadler AJ and Williams BR, 2007. Structure and function of the protein kinase R. Curr Top Microbiol Immunol, 316, 253–292. [DOI] [PubMed] [Google Scholar]
  520. Salameh A, Lee AK, Cardo‐Vila M, Nunes DN, Efstathiou E, Staquicini FI, Dobroff AS, Marchio S, Navone NM, Hosoya H, Lauer RC, Wen SJ, Salmeron CC, Hoang A, Newsham I, Lima LA, Carraro DM, Oliviero S, Kolonin MG, Sidman RL, Do KA, Troncoso P, Logothetis CJ, Brentani RR, Calin GA, Cavenee WK, Dias‐Neto E, Pasqualini R and Arap W, 2015. PRUNE2 is a human prostate cancer suppressor regulated by the intronic long noncoding RNA PCA3. Proc Natl Acad Sci U S A, 112, 8403–8408. [DOI] [PMC free article] [PubMed] [Google Scholar]
  521. Salomon WE, Jolly SM, Moore MJ, Zamore PD and Serebrov V, 2015. Single‐Molecule Imaging Reveals that Argonaute Reshapes the Binding Properties of Its Nucleic Acid Guides. Cell, 162, 84–95. [DOI] [PMC free article] [PubMed] [Google Scholar]
  522. Sam M, Wurst W, Kluppel M, Jin O, Heng H and Bernstein A, 1998. Aquarius, a novel gene isolated by gene trapping with an RNA‐dependent RNA polymerase motif. Developmental Dynamics, 212, 304–317. [DOI] [PubMed] [Google Scholar]
  523. Samuel CE, 2011. Adenosine deaminases acting on RNA (ADARs) are both antiviral and proviral. Virology, 411, 180–193. [DOI] [PMC free article] [PubMed] [Google Scholar]
  524. Sanchez‐Vargas I, Scott JC, Poole‐Smith BK, Franz AW, Barbosa‐Solomieu V, Wilusz J, Olson KE and Blair CD, 2009. Dengue virus type 2 infections of Aedes aegypti are modulated by the mosquito's RNA interference pathway. Plos Pathogens, 5, e1000299. [DOI] [PMC free article] [PubMed] [Google Scholar]
  525. Savas JN, Makusky A, Ottosen S, Baillat D, Then F, Krainc D, Shiekhattar R, Markey SP and Tanese N, 2008. Huntington's disease protein contributes to RNA‐mediated gene silencing through association with Argonaute and P bodies. Proc Natl Acad Sci U S A, 105, 10820–10825. [DOI] [PMC free article] [PubMed] [Google Scholar]
  526. Scadden AD and Smith CW, 2001. RNAi is antagonized by A–>I hyper‐editing. EMBO Rep, 2, 1107–1111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  527. Scadden AD, 2005. The RISC subunit Tudor‐SN binds to hyper‐edited double‐stranded RNA and promotes its cleavage. Nature Structural & Molecular Biology, 12, 489–496. [DOI] [PubMed] [Google Scholar]
  528. Schamberger A, Sarkadi B and Orban TI, 2012. Human mirtrons can express functional microRNAs simultaneously from both arms in a flanking exon‐independent manner. RNA Biology, 9, 1177–1185. [DOI] [PMC free article] [PubMed] [Google Scholar]
  529. Schirle NT and MacRae IJ, 2012. The Crystal Structure of Human Argonaute2. Science, 336, 1037–1040. [DOI] [PMC free article] [PubMed] [Google Scholar]
  530. Schirle NT, Sheu‐Gruttadauria J and MacRae IJ, 2014. Structural basis for microRNA targeting. Science, 346, 608–613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  531. Schirle NT, Sheu‐Gruttadauria J, Chandradoss SD, Joo C and MacRae IJ, 2015. Water‐mediated recognition of t1‐adenosine anchors Argonaute2 to microRNA targets. Elife, 4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  532. Schlee M and Hartmann G, 2010. The Chase for the RIG‐I Ligand‐Recent Advances. Molecular Therapy, 18, 1254–1262. [DOI] [PMC free article] [PubMed] [Google Scholar]
  533. Schoenberg DR and Maquat LE, 2012. Regulation of cytoplasmic mRNA decay. Nature Reviews Genetics, 13, 246–259. [DOI] [PMC free article] [PubMed] [Google Scholar]
  534. Schwamborn JC, Berezikov E and Knoblich JA, 2009. The TRIM‐NHL Protein TRIM32 Activates MicroRNAs and Prevents Self‐Renewal in Mouse Neural Progenitors. Cell, 136, 913–925. [DOI] [PMC free article] [PubMed] [Google Scholar]
  535. Schwartz T, Rould MA, Lowenhaupt K, Herbert A and Rich A, 1999. Crystal structure of the Z alpha domain of the human editing enzyme ADAR1 bound to left‐handed Z‐DNA. Science, 284, 1841–1845. [DOI] [PubMed] [Google Scholar]
  536. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N and Zamore PD, 2003. Asymmetry in the assembly of the RNAi enzyme complex. Cell, 115, 199–208. [DOI] [PubMed] [Google Scholar]
  537. Sen A, Pruijssers AJ, Dermody TS, Garcia‐Sastre A and Greenberg HB, 2011. The Early Interferon Response to Rotavirus Is Regulated by PKR and Depends on MAVS/IPS‐1, RIG‐I, MDA‐5, and IRF3. Journal of Virology, 85, 3717–3732. [DOI] [PMC free article] [PubMed] [Google Scholar]
  538. Seo GJ, Kincaid RP, Phanaksri T, Burke JM, Pare JM, Cox JE, Hsiang TY, Krug RM and Sullivan CS, 2013. Reciprocal Inhibition between Intracellular Antiviral Signaling and the RNAi Machinery in Mammalian Cells. Cell Host & Microbe, 14, 435–445. [DOI] [PMC free article] [PubMed] [Google Scholar]
  539. Seong Y, Lim DH, Kim A, Seo JH, Lee YS, Song H and Kwon YS, 2014. Global identification of target recognition and cleavage by the Microprocessor in human ES cells. Nucleic Acids Research, 42, 12806–12821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  540. Shapiro JS, Schmid S, Aguado LC, Sabin LR, Yasunaga A, Shim JV, Sachs D, Cherry S and Tenoever BR, 2014. Drosha as an interferon‐independent antiviral factor. Proc Natl Acad Sci U S A, 111, 7108–7113. [DOI] [PMC free article] [PubMed] [Google Scholar]
  541. Sharma A, 2015. Transgenerational epigenetic inheritance: resolving uncertainty and evolving biology. Biomolecular concepts, 6, 87–103. [DOI] [PubMed] [Google Scholar]
  542. Sharma NR, Wang XH, Majerciak V, Ajiro M, Kruhlak M, Meyers C and Zheng ZM, 2016. Cell Type‐ and Tissue Context‐dependent Nuclear Distribution of Human Ago2. Journal of Biological Chemistry, 291, 2302–2309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  543. Shen J, Xia WY, Khotskaya YB, Huo LF, Nakanishi K, Lim SO, Du Y, Wang Y, Chang WC, Chen CH, Hsu JL, Wu Y, Lam YC, James BP, Liu XP, Liu CG, Patel DJ and Hung MC, 2013. EGFR modulates microRNA maturation in response to hypoxia through phosphorylation of AGO2. Nature, 497, 383–387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  544. Shi H, Tschudi C and Ullu E, 2006. Functional replacement of Trypanosoma brucei Argonaute by the human slicer Argonaute2. Rna, 12, 943–947. [DOI] [PMC free article] [PubMed] [Google Scholar]
  545. Shih JD, Waks Z, Kedersha N and Silver PA, 2011. Visualization of single mRNAs reveals temporal association of proteins with microRNA‐regulated mRNA. Nucleic Acids Research, 39, 7740–7749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  546. Shinagawa T and Ishii S, 2003. Generation of Ski‐knockdown mice by expressing a long double‐strand RNA from an RNA polymerase II promoter. Genes & Development, 17, 1340–1345. [DOI] [PMC free article] [PubMed] [Google Scholar]
  547. Shtam TA, Kovalev RA, Varfolomeeva EY, Makarov EM, Kil YV and Filatov MV, 2013. Exosomes are natural carriers of exogenous siRNA to human cells in vitro. Cell Communication and Signaling, 11, 88–88. [DOI] [PMC free article] [PubMed] [Google Scholar]
  548. Sibley CR, Seow Y, Saayman S, Dijkstra KK, El Andaloussi S, Weinberg MS and Wood MJA, 2012. The biogenesis and characterization of mammalian microRNAs of mirtron origin. Nucleic Acids Research, 40, 438–448. [DOI] [PMC free article] [PubMed] [Google Scholar]
  549. Sinkkonen L, Hugenschmidt T, Berninger P, Gaidatzis D, Mohn F, Artus‐Revel CG, Zavolan M, Svoboda P and Filipowicz W, 2008. MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nature Structural & Molecular Biology, 15, 259–267. [DOI] [PubMed] [Google Scholar]
  550. Sinkkonen L, Hugenschmidt T, Filipowicz W and Svoboda P, 2010. Dicer Is Associated with Ribosomal DNA Chromatin in Mammalian Cells. PLoS ONE, 5, e12175–e12175. [DOI] [PMC free article] [PubMed] [Google Scholar]
  551. Slater L, Bartlett NW, Haas JJ, Zhu J, Message SD, Walton RP, Sykes A, Dahdaleh S, Clarke DL, Belvisi MG, Kon OM, Fujita T, Jeffery PK, Johnston SL and Edwards MR, 2010. Co‐ordinated Role of TLR3, RIG‐I and MDA5 in the Innate Response to Rhinovirus in Bronchial Epithelium. Plos Pathogens, 6, e1001178–e1001178. [DOI] [PMC free article] [PubMed] [Google Scholar]
  552. Smalheiser NR, Lugli G, Thimmapuram J, Cook EH and Larson J, 2011. Endogenous siRNAs and noncoding RNA‐derived small RNAs are expressed in adult mouse hippocampus and are up‐regulated in olfactory discrimination training. Rna, 17, 166–181. [DOI] [PMC free article] [PubMed] [Google Scholar]
  553. Smibert P, Yang J‐S, Azzam G, Liu J‐L and Lai EC, 2013. Homeostatic control of Argonaute stability by microRNA availability. Nature Structural & Molecular Biology, 20, 789–+. [DOI] [PMC free article] [PubMed] [Google Scholar]
  554. Sohn SY, Bae WJ, Kim JJ, Yeom KH, Kim VN and Cho Y, 2007. Crystal structure of human DGCR8 core. Nature Structural & Molecular Biology, 14, 847–853. [DOI] [PubMed] [Google Scholar]
  555. Soifer HS, Sano M, Sakurai K, Chomchan P, Saetrom P, Sherman MA, Collingwood MA, Behlke MA and Rossi JJ, 2008. A role for the Dicer helicase domain in the processing of thermodynamically unstable hairpin RNAs. Nucleic Acids Research, 36, 6511–6522. [DOI] [PMC free article] [PubMed] [Google Scholar]
  556. Sollier J, Stork CT, Garcia‐Rubio ML, Paulsen RD, Aguilera A and Cimprich KA, 2014. Transcription‐coupled nucleotide excision repair factors promote R‐loop‐induced genome instability. Molecular Cell, 56, 777–785. [DOI] [PMC free article] [PubMed] [Google Scholar]
  557. Song JJ, Smith SK, Hannon GJ and Joshua‐Tor L, 2004. Crystal structure of Argonaute and its implications for RISC slicer activity. Science, 305, 1434–1437. [DOI] [PubMed] [Google Scholar]
  558. Stalder L, Heusermann W, Sokol L, Trojer D, Wirz J, Hean J, Fritzsche A, Aeschimann F, Pfanzagl V, Basselet P, Weiler J, Hintersteiner M, Morrissey DV and Meisner‐Kober NC, 2013. The rough endoplasmatic reticulum is a central nucleation site of siRNA‐mediated RNA silencing. EMBO J, 32, 1115–1127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  559. Stefl R, Oberstrass FC, Hood JL, Jourdan M, Zimmermann M, Skrisovska L, Maris C, Peng L, Hofr C, Emeson RB and Allain FH, 2010. The solution structure of the ADAR2 dsRBM‐RNA complex reveals a sequence‐specific readout of the minor groove. Cell, 143, 225–237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  560. Stein P, Svoboda P, Anger M and Schultz RM, 2003. RNAi: Mammalian oocytes do it without RNA‐dependent RNA polymerase. Rna, 9, 187–192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  561. Stein P, Zeng F, Pan H and Schultz RM, 2005. Absence of non‐specific effects of RNA interference triggered by long double‐stranded RNA in mouse oocytes. Developmental Biology, 286, 464–471. [DOI] [PubMed] [Google Scholar]
  562. Stein P, Rozhkov NV, Li F, Cardenas FL, Davydenk O, Vandivier LE, Gregory BD, Hannon GJ and Schultz RM, 2015. Essential Role for Endogenous siRNAs during Meiosis in Mouse Oocytes. Plos Genetics, 11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  563. Stoica C, Carmichael JB, Parker H, Pare J and Hobman TC, 2006. Interactions between the RNA interference effector protein Ago1 and 14‐3‐3 proteins ‐ Consequences for cell cycle progression. Journal of Biological Chemistry, 281, 37646–37651. [DOI] [PubMed] [Google Scholar]
  564. Su H, Trombly MI, Chen J and Wang XZ, 2009. Essential and overlapping functions for mammalian Argonautes in microRNA silencing. Genes & Development, 23, 304–317. [DOI] [PMC free article] [PubMed] [Google Scholar]
  565. Suh MR, Lee Y, Kim JY, Kim SK, Moon SH, Lee JY, Cha KY, Chung HM, Yoon HS, Moon SY, Kim VN and Kim KS, 2004. Human embryonic stem cells express a unique set of microRNAs. Developmental Biology, 270, 488–498. [DOI] [PubMed] [Google Scholar]
  566. Suh N, Baehner L, Moltzahn F, Melton C, Shenoy A, Chen J and Blelloch R, 2010. MicroRNA Function Is Globally Suppressed in Mouse Oocytes and Early Embryos. Current Biology, 20, 271–277. [DOI] [PMC free article] [PubMed] [Google Scholar]
  567. Suk K, Choi J, Suzuki Y, Ozturk SB, Mellor JC, Wong KH, MacKay JL, Gregory RI and Roth FP, 2011. Reconstitution of human RNA interference in budding yeast. Nucleic Acids Research, 39, E43–U59. [DOI] [PMC free article] [PubMed] [Google Scholar]
  568. Sullivan CS, Grundhoff AT, Tevethia S, Pipas JM and Ganem D, 2005. SV40‐encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells. Nature, 435, 682–686. [DOI] [PubMed] [Google Scholar]
  569. Suzuki HI, Katsura A, Yasuda T, Ueno T, Mano H, Sugimoto K and Miyazono K, 2015. Small‐RNA asymmetry is directly driven by mammalian Argonautes. Nature Structural & Molecular Biology, 22, 512–+. [DOI] [PubMed] [Google Scholar]
  570. Suzuki K, Juelich T, Lim H, Ishida T, Watanebe T, Cooper DA, Rao S and Kelleher AD, 2008. Closed chromatin architecture is induced by an RNA duplex targeting the HIV‐1 promoter region. Journal of Biological Chemistry, 283, 23353–23363. [DOI] [PMC free article] [PubMed] [Google Scholar]
  571. Svoboda P, Stein P, Anger M, Bernstein E, Hannon GJ and Schultz RM, 2004. RNAi and expression of retrotransposons MuERV‐L and IAP in preimplantation mouse embryos. Developmental Biology, 269, 276–285. [DOI] [PubMed] [Google Scholar]
  572. Svoboda P, 2014. Renaissance of mammalian endogenous RNAi. Febs Letters, 588, 2550–2556. [DOI] [PubMed] [Google Scholar]
  573. Swahari V, Nakamura A, Baran‐Gale J, Garcia I, Crowther AJ, Sons R, Gershon TR, Hammond S, Sethupathy P and Deshmukh M, 2016. Essential Function of Dicer in Resolving DNA Damage in the Rapidly Dividing Cells of the Developing and Malignant Cerebellum. Cell Reports, 14, 216–224. [DOI] [PMC free article] [PubMed] [Google Scholar]
  574. Tahbaz N, Carmichael JB and Hobman TC, 2001. GERp95 belongs to a family of signal‐transducing proteins and requires Hsp90 activity for stability and Golgi localization. Journal of Biological Chemistry, 276, 43294–43299. [DOI] [PubMed] [Google Scholar]
  575. Tahbaz N, Kolb FA, Zhang HD, Jaronczyk K, Filipowicz W and Hobman TC, 2004. Characterization of the interactions between mammalian PAZ PIWI domain proteins and Dicer. EMBO Rep, 5, 189–194. [DOI] [PMC free article] [PubMed] [Google Scholar]
  576. Taira K, 2006. Induction of DNA methylation and gene silencing by short interfering RNAs in human cells. Nature, 441, 1176. [DOI] [PubMed] [Google Scholar]
  577. Takahashi T, Zenno S, Ishibashi O, Takizawa T, Saigo K and Ui‐Tei K, 2014. Interactions between the non‐seed region of siRNA and RNA‐binding RLC/RISC proteins, Ago and TRBP, in mammalian cells. Nucleic Acids Research, 42, 5256–5269. [DOI] [PMC free article] [PubMed] [Google Scholar]
  578. Takeshita D, Zenno S, Lee WC, Nagata K, Saigo K and Tanokura M, 2007. Homodimeric structure and double‐stranded RNA cleavage activity of the c‐terminal RNase III domain of human Dicer. Journal of Molecular Biology, 374, 106–120. [DOI] [PubMed] [Google Scholar]
  579. Takimoto K, Wakiyama M and Yokoyama S, 2009. Mammalian GW182 contains multiple Argonaute‐binding sites and functions in microRNA‐mediated translational repression. Rna, 15, 1078–1089. [DOI] [PMC free article] [PubMed] [Google Scholar]
  580. Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, Hodges E, Anger M, Sachidanandam R, Schultz RM and Hannon GJ, 2008. Pseudogene‐derived small interfering RNAs regulate gene expression in mouse oocytes. Nature, 453, 534–U538. [DOI] [PMC free article] [PubMed] [Google Scholar]
  581. Tan GS, Garchow BG, Liu XH, Yeung J, Morris JP, Cuellar TL, McManus MT and Kiriakidou M, 2009a. Expanded RNA‐binding activities of mammalian Argonaute 2. Nucleic Acids Research, 37, 7533–7545. [DOI] [PMC free article] [PubMed] [Google Scholar]
  582. Tan GS, Garchow BG, Liu XH, Metzler D and Kiriakidou M, 2011. Clarifying mammalian RISC assembly in vitro. Bmc Molecular Biology, 12, 19–19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  583. Tan YL, Zhang B, Wu T, Skogerbo G, Zhu XP, Guo XQ, He SM and Chen RS, 2009b. Transcriptional inhibiton of Hoxd4 expression by miRNA‐10a in human breast cancer cells. Bmc Molecular Biology, 10, 12–12. [DOI] [PMC free article] [PubMed] [Google Scholar]
  584. Tang F, Kaneda M, O'Carroll D, Hajkova P, Barton SC, Sun YA, Lee C, Tarakhovsky A, Lao KQ and Surani MA, 2007. Maternal microRNAs are essential for mouse zygotic development. Genes & Development, 21, 644–648. [DOI] [PMC free article] [PubMed] [Google Scholar]
  585. Taylor DW, Ma EB, Shigematsu H, Cianfrocco MA, Noland CL, Nagayama K, Nogales E, Doudna JA and Wang HW, 2013. Substrate‐specific structural rearrangements of human Dicer. Nature Structural & Molecular Biology, 20, 662–+. [DOI] [PMC free article] [PubMed] [Google Scholar]
  586. Thonberg H, Scheele CC, Dahlgren C and Wahlestedt C, 2004. Characterization of RNA interference in rat PC12 cells: requirement of GERp95. Biochem Biophys Res Commun, 318, 927–934. [DOI] [PubMed] [Google Scholar]
  587. Thuringer D, Jego G, Berthenet K, Hammann A, Solary E and Garrido C, 2016. Gap junction‐mediated transfer of miR‐145‐5p from microvascular endothelial cells to colon cancer cells inhibits angiogenesis. Oncotarget. [DOI] [PMC free article] [PubMed] [Google Scholar]
  588. Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN and Patel DJ, 2014. A Phosphate‐Binding Pocket within the Platform‐PAZ‐Connector Helix Cassette of Human Dicer. Molecular Cell, 53, 606–616. [DOI] [PMC free article] [PubMed] [Google Scholar]
  589. Ting AH, Schuebel KE, Herman JG and Baylin SB, 2005. Short double‐stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation. Nature Genetics, 37, 906–910. [DOI] [PMC free article] [PubMed] [Google Scholar]
  590. Ting AH, Suzuki H, Cope L, Schuebel KE, Lee BH, Toyota M, Imai K, Shinomura Y, Tokino T and Baylin SB, 2008. A requirement for DICER to maintain full promoter CpG island hypermethylation in human cancer cells. Cancer Research, 68, 2570–2575. [DOI] [PMC free article] [PubMed] [Google Scholar]
  591. Tomari Y, Du T, Haley B, Schwarz DS, Bennett R, Cook HA, Koppetsch BS, Theurkauf WE and Zamore PD, 2004a. RISC assembly defects in the Drosophila RNAi mutant armitage. Cell, 116, 831–841. [DOI] [PubMed] [Google Scholar]
  592. Tomari Y, Matranga C, Haley B, Martinez N and Zamore PD, 2004b. A protein sensor for siRNA asymmetry. Science, 306, 1377–1380. [DOI] [PubMed] [Google Scholar]
  593. Tomaselli S, Galeano F, Alon S, Raho S, Galardi S, Polito VA, Presutti C, Vincenti S, Eisenberg E, Locatelli F and Gallo A, 2015. Modulation of microRNA editing, expression and processing by ADAR2 deaminase in glioblastoma. Genome Biology, 16, 5–5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  594. Toth KF, Pezic D, Stuwe E and Webster A, 2016. The piRNA Pathway Guards the Germline Genome Against Transposable Elements. In: Non‐Coding Rna and the Reproductive System. 51–77. [DOI] [PMC free article] [PubMed] [Google Scholar]
  595. Tran N, Raponi M, Dawes IW and Arndt GM, 2004. Control of specific gene expression in mammalian cells by co‐expression of long complementary RNAs. Febs Letters, 573, 127–134. [DOI] [PubMed] [Google Scholar]
  596. Tsujimura K, Irie K, Nakashima H, Egashira Y, Fukao Y, Fujiwara M, Itoh M, Uesaka M, Imamura T, Nakahata Y, Yamashita Y, Abe T, Takamori S and Nakashima K, 2015. miR‐199a Links MeCP2 with mTOR Signaling and Its Dysregulation Leads to Rett Syndrome Phenotypes. Cell Reports, 12, 1887–1901. [DOI] [PubMed] [Google Scholar]
  597. Tu CC, Zhong Y, Nguyen L, Tsai A, Sridevi P, Tarn WY and Wang JYJ, 2015. The kinase ABL phosphorylates the microprocessor subunit DGCR8 to stimulate primary microRNA processing in response to DNA damage. Science Signaling, 8, ra64–ra64. [DOI] [PMC free article] [PubMed] [Google Scholar]
  598. Turchinovich A, Weiz L, Langheinz A and Burwinkel B, 2011. Characterization of extracellular circulating microRNA. Nucleic Acids Research, 39, 7223–7233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  599. Valen E, Preker P, Andersen PR, Zhao X, Chen Y, Ender C, Dueck A, Meister G, Sandelin A and Jensen TH, 2011. Biogenic mechanisms and utilization of small RNAs derived from human protein‐coding genes. Nature Structural & Molecular Biology, 18, 1075–1082. [DOI] [PubMed] [Google Scholar]
  600. Vance V and Vaucheret H, 2001. RNA silencing in plants–defense and counterdefense. Science, 292, 2277–2280. [DOI] [PubMed] [Google Scholar]
  601. Venkatesh T, Suresh PS and Tsutsumi R, 2016. tRFs: miRNAs in disguise. Gene, 579, 133–138. [DOI] [PubMed] [Google Scholar]
  602. Vesely C, Tauber S, Sedlazeck FJ, von Haeseler A and Jantsch MF, 2012. Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs. Genome Research, 22, 1468–1476. [DOI] [PMC free article] [PubMed] [Google Scholar]
  603. Vesely C, Tauber S, Sedlazeck FJ, Tajaddod M, von Haeseler A and Jantsch MF, 2014. ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain. Nucleic Acids Research, 42, 12155–12168. [DOI] [PMC free article] [PubMed] [Google Scholar]
  604. Wahlgren J, Karlson TD, Brisslert M, Sani FV, Telemo E, Sunnerhagen P and Valadi H, 2012. Plasma exosomes can deliver exogenous short interfering RNA to monocytes and lymphocytes. Nucleic Acids Research, 40, e130–e130. [DOI] [PMC free article] [PubMed] [Google Scholar]
  605. Wahlgren J, Statello L, Skogberg G, Telemo E and Valadi H, 2016. Delivery of Small Interfering RNAs to Cells via Exosomes. Sirna Delivery Methods: Methods and Protocols., 105–125. [DOI] [PubMed] [Google Scholar]
  606. Wang HW, Noland C, Siridechadilok B, Taylor DW, Ma EB, Felderer K, Doudna JA and Nogales E, 2009. Structural insights into RNA processing by the human RISC‐loading complex. Nature Structural & Molecular Biology, 16, 1148–U1144. [DOI] [PMC free article] [PubMed] [Google Scholar]
  607. Wang J, Huang V, Ye L, Barcena A, Lin G, Lue TF and Li L‐C, 2015a. Identification of Small Activating RNAs that Enhance Endogenous OCT4 Expression in Human Mesenchymal Stem Cells. Stem Cells and Development, 24, 345–353. [DOI] [PMC free article] [PubMed] [Google Scholar]
  608. Wang SQ, Liu DY, Jin R, Zhu YP and Xu AE, 2015b. Differential Responses of Normal Human Melanocytes to Intra‐ and Extracellular dsRNA. DNA and Cell Biology, 34, 391–399. [DOI] [PMC free article] [PubMed] [Google Scholar]
  609. Wang XH, Aliyari R, Li WX, Li HW, Kim K, Carthew R, Atkinson P and Ding SW, 2006. RNA interference directs innate immunity against viruses in adult Drosophila. Science, 312, 452–454. [DOI] [PMC free article] [PubMed] [Google Scholar]
  610. Wang Y, Lacroix G, Haines J, Doukhanine E, Almazan G and Richard S, 2010. The QKI‐6 RNA binding protein localizes with the MBP mRNAs in stress granules of glial cells. PLoS ONE, 5, 1–10. [DOI] [PMC free article] [PubMed] [Google Scholar]
  611. Wang Y, Mercier R, Hobman TC and LaPointe P, 2013a. Regulation of RNA interference by Hsp90 is an evolutionarily conserved process. Biochimica Et Biophysica Acta‐Molecular Cell Research, 1833, 2673–2681. [DOI] [PubMed] [Google Scholar]
  612. Wang Y, Vogel G, Yu Z and Richard S, 2013b. The QKI‐5 and QKI‐6 RNA binding proteins regulate the expression of microRNA 7 in glial cells. Molecular and Cellular Biology, 33, 1233–1243. [DOI] [PMC free article] [PubMed] [Google Scholar]
  613. Wang YM, Medvid R, Melton C, Jaenisch R and Blelloch R, 2007. DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self‐renewal. Nature Genetics, 39, 380–385. [DOI] [PMC free article] [PubMed] [Google Scholar]
  614. Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N and Imai H, 2006. Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon‐derived siRNAs in oocytes and germline small RNAs in testes. Genes & Development, 20, 1732–1743. [DOI] [PMC free article] [PubMed] [Google Scholar]
  615. Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi‐Miyagawa S, Obata Y, Chiba H, Kohara Y, Kono T, Nakano T, Surani MA, Sakaki Y and Sasaki H, 2008. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature, 453, 539–U539. [DOI] [PubMed] [Google Scholar]
  616. Wee LM, Flores‐Jasso CF, Salomon WE and Zamore PD, 2012. Argonaute Divides Its RNA Guide into Domains with Distinct Functions and RNA‐Binding Properties. Cell, 151, 1055–1067. [DOI] [PMC free article] [PubMed] [Google Scholar]
  617. Wei HB, Zhou B, Zhang F, Tu YY, Hu YN, Zhang BG and Zhai QW, 2013. Profiling and Identification of Small rDNA‐Derived RNAs and Their Potential Biological Functions. PLoS ONE, 8, e56842–e56842. [DOI] [PMC free article] [PubMed] [Google Scholar]
  618. Wei JX, Yang J, Sun JF, Jia LT, Zhang Y, Zhang HZ, Li X, Meng YL, Yao LB and Yang AG, 2009. Both Strands of siRNA Have Potential to Guide Posttranscriptional Gene Silencing in Mammalian Cells. PLoS ONE, 4, e5382–e5382. [DOI] [PMC free article] [PubMed] [Google Scholar]
  619. Wei W, Ba ZQ, Gao M, Wu Y, Ma YT, Amiard S, White CI, Danielsen JMR, Yang YG and Qi YJ, 2012. A Role for Small RNAs in DNA Double‐Strand Break Repair. Cell, 149, 101–112. [DOI] [PubMed] [Google Scholar]
  620. Weinberg MS, Villeneuve LM, Ehsani A, Amarzguioui M, Aagaard L, Chen ZX, Riggs AD, Rossi JJ and Morris KV, 2006. The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells. Rna, 12, 256–262. [DOI] [PMC free article] [PubMed] [Google Scholar]
  621. Weinmann L, Hock J, Ivacevic T, Ohrt T, Mutze J, Schwille P, Kremmer E, Benes V, Urlaub H and Meister G, 2009. Importin 8 is a gene silencing factor that targets argonaute proteins to distinct mRNAs. Cell, 136, 496–507. [DOI] [PubMed] [Google Scholar]
  622. Weissbach R and Scadden ADJ, 2012. Tudor‐SN and ADAR1 are components of cytoplasmic stress granules. Rna, 18, 462–471. [DOI] [PMC free article] [PubMed] [Google Scholar]
  623. Weitz SH, Gong M, Barr I, Weiss S and Guo F, 2014. Processing of microRNA primary transcripts requires heme in mammalian cells. Proc Natl Acad Sci U S A, 111, 1861–1866. [DOI] [PMC free article] [PubMed] [Google Scholar]
  624. Wen JY, Ladewig E, Shenker S, Mohammed J and Lai EC, 2015. Analysis of Nearly One Thousand Mammalian Mirtrons Reveals Novel Features of Dicer Substrates. Plos Computational Biology, 11, e1004441–e1004441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  625. Westholm JO, Ladewig E, Okamura K, Robine N and Lai EC, 2012. Common and distinct patterns of terminal modifications to mirtrons and canonical microRNAs. Rna, 18, 177–192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  626. White E, Schlackow M, Kamieniarz‐Gdula K, Proudfoot NJ and Gullerova M, 2014. Human nuclear Dicer restricts the deleterious accumulation of endogenous double‐stranded RNA. Nature Structural & Molecular Biology, 21, 552–559. [DOI] [PMC free article] [PubMed] [Google Scholar]
  627. Wichroski MJ, Robb GB and Rana TM, 2006. Human retroviral host restriction factors APOBEC3G and APOBEC3F localize to mRNA processing bodies. Plos Pathogens, 2, 374–383. [DOI] [PMC free article] [PubMed] [Google Scholar]
  628. Wilkins C, Dishongh R, Moore SC, Whitt MA, Chow M and Machaca K, 2005. RNA interference is an antiviral defence mechanism in Caenorhabditis elegans. Nature, 436, 1044–1047. [DOI] [PubMed] [Google Scholar]
  629. Wilson RC, Tambe A, Kidwell MA, Noland CL, Schneider CP and Doudna JA, 2015. Dicer‐TRBP Complex Formation Ensures Accurate Mammalian MicroRNA Biogenesis. Molecular Cell, 57, 397–407. [DOI] [PMC free article] [PubMed] [Google Scholar]
  630. Winter J, Link S, Witzigmann D, Hildenbrand C, Previti C and Diederichs S, 2013. Loop‐miRs: active microRNAs generated from single‐stranded loop regions. Nucleic Acids Research, 41, 5503–5512. [DOI] [PMC free article] [PubMed] [Google Scholar]
  631. Wolfrum C, Shi S, Jayaprakash KN, Jayaraman M, Wang G, Pandey RK, Rajeev KG, Nakayama T, Charrise K, Ndungo EM, Zimmermann T, Koteliansky V, Manoharan M and Stoffel M, 2007. Mechanisms and optimization of in vivo delivery of lipophilic siRNAs. Nature Biotechnology, 25, 1149–1157. [DOI] [PubMed] [Google Scholar]
  632. Wong SK and Lazinski DW, 2002. Replicating hepatitis delta virus RNA is edited in the nucleus by the small form of ADAR1. Proc Natl Acad Sci U S A, 99, 15118–15123. [DOI] [PMC free article] [PubMed] [Google Scholar]
  633. Wu C, So J, Davis‐Dusenbery BN, Qi HH, Bloch DB, Shi Y, Lagna G and Hata A, 2011. Hypoxia Potentiates MicroRNA‐Mediated Gene Silencing through Posttranslational Modification of Argonaute2. Molecular and Cellular Biology, 31, 4760–4774. [DOI] [PMC free article] [PubMed] [Google Scholar]
  634. Wu GP, Yang GH, Zhang RX, Xu GY, Zhang L, Wen W, Lu JB, Liu JY and Yu Y, 2015a. Altered microRNA Expression Profiles of Extracellular Vesicles in Nasal Mucus From Patients With Allergic Rhinitis. Allergy Asthma & Immunology Research, 7, 449–457. [DOI] [PMC free article] [PubMed] [Google Scholar]
  635. Wu WX, Zhang W, Duggan ES, Booth JL, Zou MH and Metcalf JP, 2015b. RIG‐I and TLR3 are both required for maximum interferon induction by influenza virus in human lung alveolar epithelial cells. Virology, 482, 181–188. [DOI] [PMC free article] [PubMed] [Google Scholar]
  636. Xia J, Joyce CE, Bowcock AM and Zhang WX, 2013. Noncanonical microRNAs and endogenous siRNAs in normal and psoriatic human skin. Human Molecular Genetics, 22, 737–748. [DOI] [PMC free article] [PubMed] [Google Scholar]
  637. Xie MY, Li MF, Vilborg A, Lee N, Shu MD, Yartseva V, Sestan N and Steitz JA, 2013. Mammalian 5 ‘‐Capped MicroRNA Precursors that Generate a SingleMicroRNA. Cell, 155, 1568–1580. [DOI] [PMC free article] [PubMed] [Google Scholar]
  638. Xu N, Gkountela S, Saeed K and Akusjarvi G, 2009. The 5′‐end heterogeneity of adenovirus virus‐associated RNAI contributes to the asymmetric guide strand incorporation into the RNA‐induced silencing complex. Nucleic Acids Research, 37, 6950–6959. [DOI] [PMC free article] [PubMed] [Google Scholar]
  639. Xu S, Xue CY, Li JP, Bi YZ and Cao YC, 2011. Marek's Disease Virus Type 1 MicroRNA miR‐M3 Suppresses Cisplatin‐Induced Apoptosis by Targeting SMAD2 of the Transforming Growth Factor Beta Signal Pathway. Journal of Virology, 85, 276–285. [DOI] [PMC free article] [PubMed] [Google Scholar]
  640. Yang N and Kazazian HH Jr, 2006. L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells. Nature Structural & Molecular Biology, 13, 763–771. [DOI] [PubMed] [Google Scholar]
  641. Yang S, Tutton S, Pierce E and Yoon K, 2001. Specific double‐stranded RNA interference in undifferentiated mouse embryonic stem cells. Molecular and Cellular Biology, 21, 7807–7816. [DOI] [PMC free article] [PubMed] [Google Scholar]
  642. Yang WD, Wang QD, Howell KL, Lee JT, Cho DSC, Murray JM and Nishikura K, 2005. ADAR1 RNA deaminase limits short interfering RNA efficacy in mammalian cells. Journal of Biological Chemistry, 280, 3946–3953. [DOI] [PMC free article] [PubMed] [Google Scholar]
  643. Yang WD, Chendrimada TP, Wang QD, Higuchi M, Seeburg PH, Shiekhattar R and Nishikura K, 2006a. Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nature Structural & Molecular Biology, 13, 13–21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  644. Yang X, Murthy V, Schultz K, Tatro JB, Fitzgerald KA and Beasley D, 2006b. Toll‐like receptor 3 signaling evokes a proinflammatory and proliferative phenotype in human vascular smooth muscle cells. American Journal of Physiology‐Heart and Circulatory Physiology, 291, H2334–H2343. [DOI] [PubMed] [Google Scholar]
  645. Yao B, Li SQ, Lian SL, Fritzler MJ and Chan EKL, 2011. Mapping of Ago2‐GW182 Functional Interactions. Argonaute Proteins: Methods and Protocols., 45–62. [DOI] [PubMed] [Google Scholar]
  646. Ye XC, Huang NA, Liu Y, Paroo Z, Huerta C, Li P, Chen S, Liu QH and Zhang H, 2011. Structure of C3PO and mechanism of human RISC activation. Nature Structural & Molecular Biology, 18, 650–U643. [DOI] [PMC free article] [PubMed] [Google Scholar]
  647. Yi CE, Bekker JM, Miller G, Hill KL and Crosbie RH, 2003. Specific and potent RNA interference in terminally differentiated myotubes. Journal of Biological Chemistry, 278, 934–939. [DOI] [PubMed] [Google Scholar]
  648. Yoda M, Kawamata T, Paroo Z, Ye XC, Iwasaki S, Liu QH and Tomari Y, 2010. ATP‐dependent human RISC assembly pathways. Nature Structural & Molecular Biology, 17, 17–U29. [DOI] [PMC free article] [PubMed] [Google Scholar]
  649. Yoneyama M, Kikuchi M, Natsukawa T, Shinobu N, Imaizumi T, Miyagishi M, Taira K, Akira S and Fujita T, 2004. The RNA helicase RIG‐I has an essential function in double‐stranded RNA‐induced innate antiviral responses. Nature Immunology, 5, 730–737. [DOI] [PubMed] [Google Scholar]
  650. Yoon YJ, Kim OY and Gho YS, 2014. Extracellular vesicles as emerging intercellular communicasomes. Bmb Reports, 47, 531–539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  651. Younger ST and Corey DR, 2011. Transcriptional gene silencing in mammalian cells by miRNA mimics that target gene promoters. Nucleic Acids Research, 39, 5682–5691. [DOI] [PMC free article] [PubMed] [Google Scholar]
  652. Yu JH, Yang WH, Gulick T, Bloch KD and Bloch DB, 2005. Ge‐1 is a central component of the mammalian cytoplasmic mRNA processing body. Rna, 11, 1795–1802. [DOI] [PMC free article] [PubMed] [Google Scholar]
  653. Yuan YR, Pei Y, Ma JB, Kuryavyi V, Zhadina M, Meister G, Chen HY, Dauter Z, Tuschl T and Patel DJ, 2005. Crystal structure of A‐aeolicus Argonaute, a site‐specific DNA‐guided endoribonuclease, provides insights into RISC‐mediated mRNA cleavage. Molecular Cell, 19, 405–419. [DOI] [PMC free article] [PubMed] [Google Scholar]
  654. Zamore PD, Tuschl T, Sharp PA and Bartel DP, 2000. RNAi: double‐stranded RNA directs the ATP‐dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell, 101, 25–33. [DOI] [PubMed] [Google Scholar]
  655. Zekri L, Huntzinger E, Heimstadt S and Izaurralde E, 2009. The silencing domain of GW182 interacts with PABPC1 to promote translational repression and degradation of microRNA targets and is required for target release. Molecular and Cellular Biology, 29, 6220–6231. [DOI] [PMC free article] [PubMed] [Google Scholar]
  656. Zekri L, Kuzuoglu‐Ozturk D and Izaurralde E, 2013. GW182 proteins cause PABP dissociation from silenced miRNA targets in the absence of deadenylation. EMBO J, 32, 1052–1065. [DOI] [PMC free article] [PubMed] [Google Scholar]
  657. Zeng Y, Wagner EJ and Cullen BR, 2002. Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Molecular Cell, 9, 1327–1333. [DOI] [PubMed] [Google Scholar]
  658. Zeng Y, Sankala H, Zhang XX and Graves PR, 2008. Phosphorylation of Argonaute 2 at serine‐387 facilitates its localization to processing bodies. Biochemical Journal, 413, 429–436. [DOI] [PubMed] [Google Scholar]
  659. Zhang HD, Kolb FA, Brondani V, Billy E and Filipowicz W, 2002. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J, 21, 5875–5885. [DOI] [PMC free article] [PubMed] [Google Scholar]
  660. Zhang HD, Kolb FA, Jaskiewicz L, Westhof E and Filipowicz W, 2004. Single processing center models for human dicer and bacterial RNase III. Cell, 118, 57–68. [DOI] [PubMed] [Google Scholar]
  661. Zhang L, Hou D, Chen X, Li D, Zhu L, Zhang Y, Li J, Bian Z, Liang X, Cai X, Yin Y, Wang C, Zhang T, Zhu D, Zhang D, Xu J, Chen Q, Ba Y, Liu J, Wang Q, Chen J, Wang J, Wang M, Zhang Q, Zhang J, Zen K and Zhang CY, 2012. Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross‐kingdom regulation by microRNA. Cell Research, 22, 107–126. [DOI] [PMC free article] [PubMed] [Google Scholar]
  662. Zhang MX, Zhang C, Shen YH, Wang J, Li XN, Chen L, Zhang Y, Coselli JS and Wang XL, 2008a. Effect of 27nt small RNA on endothelial nitric‐oxide synthase expression. Molecular Biology of the Cell, 19, 3997–4005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  663. Zhang MX, Zhang C, Shen YH, Wang J, Li XN, Zhang Y, Coselli J and Wang XL, 2008b. Biogenesis of short intronic repeat 27nt small RNA from endothelial nitric oxide synthase gene. Journal of Biological Chemistry. [DOI] [PMC free article] [PubMed] [Google Scholar]
  664. Zhang XZ, Li HT, Burnett JC and Rossi JJ, 2014. The role of antisense long noncoding RNA in small RNA‐triggered gene activation. Rna, 20, 1916–1928. [DOI] [PMC free article] [PubMed] [Google Scholar]
  665. Zheng XF and Bevilacqua PC, 2004. Activation of the protein kinase PKR by short double‐stranded RNAs with single‐stranded tails. Rna, 10, 1934–1945. [DOI] [PMC free article] [PubMed] [Google Scholar]
  666. Zheng ZM, Tang SA and Tao MF, 2005. Development of resistance to RNAi in mammalian cells. In: Strategies for Silencing Gene Expression. 105–118. [DOI] [PMC free article] [PubMed] [Google Scholar]
  667. Zhou HM, Yang L, Li HJ, Li LJ and Chen JM, 2009. Residues that affect human Argonaute2 concentration in cytoplasmic processing bodies. Biochem Biophys Res Commun, 378, 620–624. [DOI] [PubMed] [Google Scholar]
  668. Zipprich JT, Bhattacharyya S, Mathys H and Filipowicz W, 2009. Importance of the C‐terminal domain of the human GW182 protein TNRC6C for translational repression. Rna, 15, 781–793. [DOI] [PMC free article] [PubMed] [Google Scholar]
  669. Zou J, Chang M, Nie P and Secombes CJ, 2009. Origin and evolution of the RIG‐I like RNA helicase gene family. Bmc Evolutionary Biology, 9, 85. [DOI] [PMC free article] [PubMed] [Google Scholar]
  670. Andermatt I, Wilson N and Stoeckli ET, 2014. In ovo electroporation of miRNA‐based‐plasmids to investigate gene function in the developing neural tube. Methods in Molecular Biology, 1101, 353–368. [DOI] [PubMed] [Google Scholar]
  671. Baeriswyl T, Mauti O and Stoeckli ET, 2008. Temporal control of gene silencing by in ovo electroporation. Methods in Molecular Biology, 442, 231–244. [DOI] [PubMed] [Google Scholar]
  672. Chen CH, Zhou YL, Wu YF, Cao Y, Gao JS and Tang JB, 2009a. Effectiveness of MicroRNA in Down‐Regulation of TGF‐beta Gene Expression in Digital Flexor Tendons of Chickens. In Vitro and In Vivo Study. Journal of Hand Surgery‐American, 34A, 1777–1784. [DOI] [PubMed] [Google Scholar]
  673. Chen M, Payne WS, Hunt H, Zhang HM, Holmen SL and Dodgson JB, 2008. Inhibition of Marek's disease virus replication by retroviral vector‐based RNA interference. Virology, 377, 265–272. [DOI] [PubMed] [Google Scholar]
  674. Chen M, Payne WS, Dunn JR, Chang S, Zhang HM, Hunt HD and Dodgson JB, 2009b. Retroviral delivery of RNA interference against Marek's disease virus in vivo. Poultry Science, 88, 1373–1380. [DOI] [PubMed] [Google Scholar]
  675. Chen SCY, Stern P, Guo ZY and Chen JZ, 2011. Expression of Multiple Artificial MicroRNAs from a Chicken miRNA126‐Based Lentiviral Vector. Plos One, 6, e22437–e22437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  676. Chen Y, Huang ZY, Wang B, Yu QM, Liu R, Xu Q, Chang GB, Ding JT and Chen GH, 2015. Duck RIG‐I CARD Domain Induces the Chicken IFN‐beta by Activating NF‐kappa B. Biomed Research International, 2015, 348792–348792. [DOI] [PMC free article] [PubMed] [Google Scholar]
  677. Coupeau D, Dambrine G and Rasschaert D, 2012. Kinetic expression analysis of the cluster mdv1‐mir‐M9‐M4, genes meq and vIL‐8 differs between the lytic and latent phases of Marek's disease virus infection. Journal of General Virology, 93, 1519–1529. [DOI] [PubMed] [Google Scholar]
  678. Dai FP, Yusuf F, Farjah GH and Brand‐Saberi B, 2005. RNAi‐induced targeted silencing of developmental control genes during chicken embryogenesis. Developmental Biology, 285, 80–90. [DOI] [PubMed] [Google Scholar]
  679. Das RM, Van Hateren NJ, Howell GR, Farrell ER, Bangs FK, Porteous VC, Manning EM, McGrew MJ, Ohyama K, Sacco MA, Halley PA, Sang HM, Storey KG, Placzek M, Tickle C, Nair VK and Wilson SA, 2006. A robust system for RNA interference in the chicken using a modified microRNA operon. Developmental Biology, 294, 554–563. [DOI] [PubMed] [Google Scholar]
  680. Deng JH, Deng P, Lin SL and Ying SY, 2015. Gene Silencing In Vitro and In Vivo Using Intronic MicroRNAs. RNA Interference: Challenges and Therapeutic Opportunities., 321–340. [DOI] [PubMed] [Google Scholar]
  681. Dinh H, Hong YH and Lillehoj HS, 2014. Modulation of microRNAs in two genetically disparate chicken lines showing different necrotic enteritis disease susceptibility. Veterinary Immunology and Immunopathology, 159, 74–82. [DOI] [PubMed] [Google Scholar]
  682. Flemr M, Malik R, Franke V, Nejepinska J, Sedlacek R, Vlahovicek K and Svoboda P, 2013. A retrotransposon‐driven dicer isoform directs endogenous small interfering RNA production in mouse oocytes. Cell, 155, 807–816. [DOI] [PubMed] [Google Scholar]
  683. Fukagawa T, Nogami M, Yoshikawa M, Ikeno M, Okazaki T, Takami Y, Nakayama T and Oshimura M, 2004. Dicer is essential for formation of the heterochromatin structure in vertebrate cells. Nature Cell Biology, 6, 784–791. [DOI] [PubMed] [Google Scholar]
  684. Giles KE, Ghirlando R and Felsenfeld G, 2010. Maintenance of a constitutive heterochromatin domain in vertebrates by a Dicer‐dependent mechanism. Nature Cell Biology, 12, 94–U246. [DOI] [PMC free article] [PubMed] [Google Scholar]
  685. Godnic I, Zorc M, Skok DJ, Calin GA, Horvat S, Dovc P, Kovac M and Kunej T, 2013. Genome‐Wide and Species‐Wide In Silico Screening for Intragenic MicroRNAs in Human, Mouse and Chicken. Plos One, 8, e65165–e65165. [DOI] [PMC free article] [PubMed] [Google Scholar]
  686. Gonzalez‐Lopez C, Martinez‐Costas J, Esteban M and Benavente J, 2003. Evidence that avian reovirus sigma A protein is an inhibitor of the double‐stranded RNA‐dependent protein kinase. Journal of General Virology, 84, 1629–1639. [DOI] [PubMed] [Google Scholar]
  687. Gunaratne PH, Lin YC, Benham AL, Drnevich J, Coarfa C, Tennakoon JB, Creighton CJ, Kim JH, Milosavljevic A, Watson M, Griffiths‐Jones S and Clayton DF, 2011. Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain. Bmc Genomics, 12, 277–277. [DOI] [PMC free article] [PubMed] [Google Scholar]
  688. Haesler S, Rochefort C, Georgi B, Licznerski P, Osten P and Scharff C, 2007. Incomplete and inaccurate vocal imitation after knockdown of FoxP2 in songbird basal ganglia nucleus area X. Plos Biology, 5, 2885–2897. [DOI] [PMC free article] [PubMed] [Google Scholar]
  689. Han B, Lian L, Li X, Zhao C, Qu L, Liu C, Song J and Yang N, 2016. Chicken gga‐miR‐103‐3p Targets CCNE1 and TFDP2 and Inhibits MDCC‐MSB1 Cell Migration. G3‐Genes Genomes Genetics. [DOI] [PMC free article] [PubMed] [Google Scholar]
  690. Hayashi T, Watanabe C, Suzuki Y, Tanikawa T, Uchida Y and Saito T, 2014. Chicken MDA5 Senses Short Double‐Stranded RNA with Implications for Antiviral Response against Avian Influenza Viruses in Chicken. Journal of Innate Immunity, 6, 58–71. [DOI] [PMC free article] [PubMed] [Google Scholar]
  691. Herbert A, Lowenhaupt K, Spitzner J and Rich A, 1995. Double‐stranded RNA adenosine deaminase binds Z‐DNA in vitro. Nucleic Acids Symp Ser, 16–19. [PubMed] [Google Scholar]
  692. Hu SQ, Cao W, Yang MJ, Liu HH, Li L and Wang JW, 2014. Molecular characterization, tissue distribution, and expression of two ovarian Dicer isoforms during follicle development in goose (Anser cygnoides). Biology, 170, 33–41. [DOI] [PubMed] [Google Scholar]
  693. Hutcheson JM, Susta L, Stice SL, Afonso CL and West FD, 2015. Delayed Newcastle disease virus replication using RNA interference to target the nucleoprotein. Biologicals, 43, 274–280. [DOI] [PMC free article] [PubMed] [Google Scholar]
  694. International Chicken Genome Sequencing C , 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432, 695–716. [DOI] [PubMed] [Google Scholar]
  695. Karpala AJ, Lowenthal JW and Bean AG, 2008. Activation of the TLR3 pathway regulates IFN beta production in chickens. Developmental and Comparative Immunology, 32, 435–444. [DOI] [PubMed] [Google Scholar]
  696. Karpala AJ, Stewart C, McKay J, Lowenthal JW and Bean AG, 2011. Characterization of chicken Mda5 activity: regulation of IFN‐beta in the absence of RIG‐I functionality. J Immunol, 186, 5397–5405. [DOI] [PubMed] [Google Scholar]
  697. Kim TH, Yun TW, Rengaraj D, Lee SI, Lim SM, Seo HW, Park TS and Han JY, 2012. Conserved functional characteristics of the PIWI family members in chicken germ cell lineage. Theriogenology, 78, 1948–1959. [DOI] [PubMed] [Google Scholar]
  698. Kint J, Fernandez‐Gutierrez M, Maier HJ, Britton P, Langereis MA, Koumans J, Wiegertjes GF and Forlenza M, 2015. Activation of the chicken type I interferon response by infectious bronchitis coronavirus. Journal of Virology, 89, 1156–1167. [DOI] [PMC free article] [PubMed] [Google Scholar]
  699. Lambeth LS, Yao YX, Smith LP, Zhao YG and Nair V, 2009a. MicroRNAs 221 and 222 target p27(Kip1) in Marek's disease virus‐transformed tumour cell line MSB‐1. Journal of General Virology, 90, 1164–1171. [DOI] [PubMed] [Google Scholar]
  700. Lambeth LS, Zhao YG, Smith LP, Kgosana L and Nair V, 2009b. Targeting Marek's disease virus by RNA interference delivered from a herpesvirus vaccine. Vaccine, 27, 298–306. [DOI] [PubMed] [Google Scholar]
  701. Lee CC, Wu CC and Lin TL, 2012. Characterization of chicken melanoma differentiation‐associated gene 5 (MDA5) from alternative translation initiation. Comparative Immunology Microbiology and Infectious Diseases, 35, 335–343. [DOI] [PubMed] [Google Scholar]
  702. Lee CC, Wu CC and Lin TL, 2014. Chicken melanoma differentiation‐associated gene 5 (MDA5) recognizes infectious bursal disease virus infection and triggers MDA5‐related innate immunity. Archives of Virology, 159, 1671–1686. [DOI] [PMC free article] [PubMed] [Google Scholar]
  703. Lee SH, Eldi P, Cho SY and Rangasamy D, 2009. Control of chicken CR1 retrotransposons is independent of Dicer‐mediated RNA interference pathway. Bmc Biology, 7, 53–53. [DOI] [PMC free article] [PubMed] [Google Scholar]
  704. Lee SI, Lee BR, Hwang YS, Lee HC, Rengaraj D, Song G, Park TS and Han JY, 2011. MicroRNA‐mediated posttranscriptional regulation is required for maintaining undifferentiated properties of blastoderm and primordial germ cells in chickens. Proc Natl Acad Sci U S A, 108, 10426–10431. [DOI] [PMC free article] [PubMed] [Google Scholar]
  705. Lee SI, Ji MR, Jang YJ, Jeon MH, Kim JS, Park JK, Jeon IS and Byun SJ, 2015. Characterization and miRNA‐mediated posttranscriptional regulation of vitelline membrane outer layer protein I in the adult chicken oviduct. In Vitro Cellular & Developmental Biology‐Animal, 51, 222–229. [DOI] [PubMed] [Google Scholar]
  706. Li H, Sun GR, Tian YD, Han RL, Li GX and Kang XT, 2013. MicroRNAs‐1614‐3p gene seed region polymorphisms and association analysis with chicken production traits. Journal of Applied Genetics, 54, 209–213. [DOI] [PubMed] [Google Scholar]
  707. Li WZ, Chen HJ, Sutton T, Obadan A and Perez DR, 2014a. Interactions between the Influenza A Virus RNA Polymerase Components and Retinoic Acid‐Inducible Gene I. Journal of Virology, 88, 10432–10447. [DOI] [PMC free article] [PubMed] [Google Scholar]
  708. Li X, Lian L, Zhang DX, Qu LJ and Yang N, 2014b. gga‐miR‐26a targets NEK6 and suppresses Marek's disease lymphoma cell proliferation. Poultry Science, 93, 1097–1105. [DOI] [PubMed] [Google Scholar]
  709. Li ZJ, Zhang YP, Li Y, Zheng HW, Zheng YS and Liu CJ, 2014c. Distinct expression pattern of miRNAs in Marek's disease virus infected‐chicken splenic tumors and non‐tumorous spleen tissues. Research in Veterinary Science, 97, 156–161. [DOI] [PubMed] [Google Scholar]
  710. Lian L, Li X, Zhao CF, Han B, Qu LJ, Song JZ, Liu CJ and Yang N, 2015a. Chicken gga‐miR‐181a targets MYBL1 and shows an inhibitory effect on proliferation of Marek's disease virus‐transformed lymphoid cell line. Poultry Science, 94, 2616–2621. [DOI] [PubMed] [Google Scholar]
  711. Lian L, Zhang DX, Wang Q, Yang N and Qu LJ, 2015b. The inhibitory effects of gga‐miR‐199‐3p, gga‐miR‐140‐3p, and gga‐miR‐221‐5p in Marek's disease tumorigenesis. Poultry Science, 94, 2131–2135. [DOI] [PubMed] [Google Scholar]
  712. Lim SL, Tsend‐Ayush E, Kortschak RD, Jacob R, Ricciardelli C, Oehler MK and Grutzner F, 2013. Conservation and Expression of PIWI‐Interacting RNA Pathway Genes in Male and Female Adult Gonad of Amniotes. Biology of Reproduction, 89, 136–136. [DOI] [PubMed] [Google Scholar]
  713. Lin S‐L, Chang DC and Ying S‐Y, 2006a. Isolation and identification of gene‐specific microRNAs. In: Methods in Molecular Biology. 313–320. [DOI] [PubMed] [Google Scholar]
  714. Lin S‐L, Chang S‐JE and Ying S‐Y, 2006b. Transgene‐like animal models using intronic microRNAs. In: Methods in Molecular Biology. 321–334. [DOI] [PubMed] [Google Scholar]
  715. Lin S‐L and Ying S‐Y, 2006. Gene silencing in vitro and in vivo using intronic microRNAs. In: Methods in Molecular Biology. 295–312. [DOI] [PubMed] [Google Scholar]
  716. Lin SL, Chang DC and Ying SY, 2013a. Isolation and identification of gene‐specific microRNAs. Methods in Molecular Biology, 936, 271–278. [DOI] [PubMed] [Google Scholar]
  717. Lin SL, Chang SJ and Ying SY, 2013b. Transgene‐like animal models using intronic microRNAs. Methods in Molecular Biology, 936, 279–294. [DOI] [PubMed] [Google Scholar]
  718. Lin SL and Ying SY, 2013. Gene silencing in vitro and in vivo using intronic microRNAs. Methods in Molecular Biology, 936, 209–229. [DOI] [PubMed] [Google Scholar]
  719. Lostale‐Seijo I, Martinez‐Costas J and Benavente J, 2016. Interferon induction by avian reovirus. Virology, 487, 104–111. [DOI] [PubMed] [Google Scholar]
  720. Luo GZ, Hafner M, Shi Z, Brown M, Feng GH, Tuschl T, Wang XJ and Li X, 2012. Genome‐wide annotation and analysis of zebra finch microRNA repertoire reveal sex‐biased expression. Bmc Genomics, 13, 727. [DOI] [PMC free article] [PubMed] [Google Scholar]
  721. Luo J, Sun AJ, Teng M, Zhou H, Cui ZZ, Qu LH and Zhang GP, 2011. Expression profiles of microRNAs encoded by the oncogenic Marek's disease virus reveal two distinct expression patterns in vivo during different phases of disease. Journal of General Virology, 92, 608–620. [DOI] [PubMed] [Google Scholar]
  722. Mauti O, Baeriswyl T and Stoeckli ET, 2008. Gene Silencing by Injection and Electroporation of dsRNA in Avian Embryos. Cold Spring Harbor Protocols, 2008, pdb.prot5094‐pdb.prot5094. [DOI] [PubMed] [Google Scholar]
  723. Morgan R, Anderson A, Bernberg E, Kamboj S, Huang E, Lagasse G, Isaacs G, Parcells M, Meyers BC, Green PJ and Burnside J, 2008. Sequence Conservation and Differential Expression of Marek's Disease Virus MicroRNAs. Journal of Virology, 82, 12213–12220. [DOI] [PMC free article] [PubMed] [Google Scholar]
  724. Muylkens B, Coupeau D, Dambrine G, Trapp S and Rasschaert D, 2010. Marek's disease virus microRNA designated Mdv1‐pre‐miR‐M4 targets both cellular and viral genes. Archives of Virology, 155, 1823–1837. [DOI] [PubMed] [Google Scholar]
  725. O'Neill G, 2007. Australia tackles bird flu using RNAi. Nature Biotechnology, 25, 605–606. [DOI] [PubMed] [Google Scholar]
  726. Pekarik V, Bourikas D, Miglino N, Joset P, Preiswerk S and Stoeckli ET, 2003. Screening for gene function in chicken embryo using RNAi and electroporation. Nature Biotechnology, 21, 93–96. [DOI] [PubMed] [Google Scholar]
  727. Sahare AA, Bedekar MK, Jain SK, Singh A, Singh S and Sarkhel BC, 2015. Inhibition of Infectious Bursal Disease Virus by Vector Delivered SiRNA in Cell Culture. Animal Biotechnology, 26, 58–64. [DOI] [PubMed] [Google Scholar]
  728. Sato F, Nakagawa T, Ito M, Kitagawa Y and Hattori MA, 2004. Application of RNA interference to chicken embryos using small interferfing RNA. Journal of Experimental Zoology Part a‐Comparative Experimental Biology, 301A, 820–827. [DOI] [PubMed] [Google Scholar]
  729. Sato H, Oshiumi H, Takaki H, Hikono H and Seya T, 2015. Evolution of the DEAD box helicase family in chicken: Chickens have no DHX9 ortholog. Microbiology and Immunology, 59, 633–640. [DOI] [PubMed] [Google Scholar]
  730. Stewart CR, Karpala AJ, Lowther S, Lowenthal JW and Bean AG, 2011. Immunostimulatory Motifs Enhance Antiviral siRNAs Targeting Highly Pathogenic Avian Influenza H5N1. Plos One, 6, e21552–e21552. [DOI] [PMC free article] [PubMed] [Google Scholar]
  731. Stik G, Dambrine G, Pfeffer S and Rasschaert D, 2013. The Oncogenic MicroRNA OncomiR‐21 Overexpressed during Marek's Disease Lymphomagenesis Is Transactivated by the Viral Oncoprotein Meq. Journal of Virology, 87, 80–93. [DOI] [PMC free article] [PubMed] [Google Scholar]
  732. Strassheim S, Stik G, Rasschaert D and Laurent S, 2012. mdv1‐miR‐M7‐5p, located in the newly identified first intron of the latency‐associated transcript of Marek's disease virus, targets the immediate‐early genes ICP4 and ICP27. Journal of General Virology, 93, 1731–1742. [DOI] [PubMed] [Google Scholar]
  733. Taft RJ, Glazov EA, Lassmann T, Hayashizaki Y, Carninci P and Mattick JS, 2009. Small RNAs derived from snoRNAs. RNA, 15, 1233–1240. [DOI] [PMC free article] [PubMed] [Google Scholar]
  734. Tian F, Luo J, Zhang HM, Chang S and Song JZ, 2012. MiRNA expression signatures induced by Marek's disease virus infection in chickens. Genomics, 99, 152–159. [DOI] [PubMed] [Google Scholar]
  735. Tian Y, Lu LZ, Fu Y, Zhao J, Zhang C, Yuan QY and Shen JD, 2007. Assignment of Dicer gene to chicken chromosome 5 by radiation hybrid panel mapping. Biochemical Genetics, 45, 239–243. [DOI] [PubMed] [Google Scholar]
  736. Villanueva AI, Kulkarni RR and Sharif S, 2011. Synthetic double‐stranded RNA oligonucleotides are immunostimulatory for chicken spleen cells. Developmental and Comparative Immunology, 35, 28–34. [DOI] [PMC free article] [PubMed] [Google Scholar]
  737. Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez‐Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER and Wilson RK, 2010. The genome of a songbird. Nature, 464, 757–762. [DOI] [PMC free article] [PubMed] [Google Scholar]
  738. Wei RR, Ma XQ, Wang GH, Guo HJ, Liu JZ, Fan LX and Cheng ZQ, 2015. Synergistic inhibition of avian leukosis virus subgroup J replication by miRNA‐embedded siRNA interference of double‐target. Virology Journal, 12, 45–45. [DOI] [PMC free article] [PubMed] [Google Scholar]
  739. Wilson NH and Stoeckli ET, 2011. Cell type specific, traceable gene silencing for functional gene analysis during vertebrate neural development. Nucleic Acids Research, 39, e133–e133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  740. Wilson NH and Stoeckli ET, 2012. In ovo Electroporation of miRNA‐based Plasmids in the Developing Neural Tube and Assessment of Phenotypes by DiI Injection in Open‐book Preparations. Jove‐Journal of Visualized Experiments. [DOI] [PMC free article] [PubMed] [Google Scholar]
  741. Xu HT, Yao YX, Smith LP and Nair V, 2010. MicroRNA‐26a‐mediated regulation of interleukin‐2 expression in transformed avian lymphocyte lines. Cancer Cell International, 10, 15–15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  742. Xu S, Xue CY, Li JP, Bi YZ and Cao YC, 2011. Marek's Disease Virus Type 1 MicroRNA miR‐M3 Suppresses Cisplatin‐Induced Apoptosis by Targeting SMAD2 of the Transforming Growth Factor Beta Signal Pathway. Journal of Virology, 85, 276–285. [DOI] [PMC free article] [PubMed] [Google Scholar]
  743. Xu WP, Shao Q, Zang YL, Guo Q, Zhang YC and Li ZD, 2015. Pigeon RIG‐I Function in Innate Immunity against H9N2 IAV and IBDV. Viruses‐Basel, 7, 4131–4151. [DOI] [PMC free article] [PubMed] [Google Scholar]
  744. Yao YX, Zhao YG, Xu HT, Smith LP, Lawrie CH, Watson M and Nair V, 2008. MicroRNA profile of Marek's disease virus‐transformed T‐cell line MSB‐1: Predominance of virus‐encoded microRNAs. Journal of Virology, 82, 4007–4015. [DOI] [PMC free article] [PubMed] [Google Scholar]
  745. Yin RF, Ding ZA, Liu XX, Mu LZ, Cong YL and Stoeger T, 2010. Inhibition of Newcastle disease virus replication by RNA interference targeting the matrix protein gene in chicken embryo fibroblasts. Journal of Virological Methods, 167, 107–111. [DOI] [PubMed] [Google Scholar]
  746. Ying S‐Y and Lin S‐L, 2009. Intron‐Mediated RNA Interference and microRNA Biogenesis. In: Methods in Molecular Biology. 387–413. [DOI] [PubMed] [Google Scholar]
  747. Ying SY, Chang CP and Lin SL, 2010. Intron‐Mediated RNA Interference, Intronic MicroRNAs, and Applications. In: RNA Therapeutics: Function, Design, and Delivery. 203–235. [DOI] [PubMed] [Google Scholar]
  748. Zhang SL, Sun YJ, Chen HJ, Dai YB, Zhan Y, Yu SQ, Qiu XS, Tan L, Song CP and Ding C, 2014. Activation of the PKR/eIF2 alpha signaling cascade inhibits replication of Newcastle disease virus. Virology Journal, 11, 62–62. [DOI] [PMC free article] [PubMed] [Google Scholar]
  749. Zhao YG, Yao YX, Xu HT, Lambeth L, Smith LP, Kgosana L, Wang XW and Nair V, 2009. A Functional MicroRNA‐155 Ortholog Encoded by the Oncogenic Marek's Disease Virus. Journal of Virology, 83, 489–492. [DOI] [PMC free article] [PubMed] [Google Scholar]
  750. Zhao YG, Xu HT, Yao YX, Smith LP, Kgosana L, Green J, Petherbridge L, Baigent SJ and Nair V, 2011. Critical Role of the Virus‐Encoded MicroRNA‐155 Ortholog in the Induction of Marek's Disease Lymphomas. Plos Pathogens, 7, e1001305–e1001305. [DOI] [PMC free article] [PubMed] [Google Scholar]
  751. Zhou X, Guo H, Chen K, Cheng HH and Zhou RJ, 2010. Identification, chromosomal mapping and conserved synteny of porcine Argonaute family of genes. Genetica, 138, 805–812. [DOI] [PubMed] [Google Scholar]
  752. Andrews OE, Cha DJ, Wei CY and Patton JG, 2014. RNAi‐Mediated Gene silencing in Zebrafish Triggered by Convergent Transcription. Scientific Reports, 4, 5222–5222. [DOI] [PMC free article] [PubMed] [Google Scholar]
  753. Bazzini AA, Lee MT and Giraldez AJ, 2012. Ribosome Profiling Shows That miR‐430 Reduces Translation Before Causing mRNA Decay in Zebrafish. Science, 336, 233–237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  754. Blum M, De Robertis EM, Wallingford JB and Niehrs C, 2015. Morpholinos: Antisense and Sensibility. Developmental Cell, 35, 145–149. [DOI] [PubMed] [Google Scholar]
  755. Choi WY, Giraldez AJ and Schier AF, 2007. Target protectors reveal dampening and balancing of nodal agonist and antagonist by miR‐430. Science, 318, 271–274. [DOI] [PubMed] [Google Scholar]
  756. Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson ND, Wolfe SA and Giraldez AJ, 2010. A novel miRNA processing pathway independent of dicer requires argonaute2 catalytic activity. Science, 328, 1694–1698. [DOI] [PMC free article] [PubMed] [Google Scholar]
  757. De Rienzo G, Gutzman JH and Sive H, 2012. Efficient shRNA‐Mediated Inhibition of Gene Expression in Zebrafish. Zebrafish, 9, 97–107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  758. Dong Z, Peng J and Guo S, 2013. Stable gene silencing in zebrafish with spatiotemporally targetable RNA interference. Genetics, 193, 1065–1071. [DOI] [PMC free article] [PubMed] [Google Scholar]
  759. Eisen JS and Smith JC, 2008. Controlling morpholino experiments: don't stop making antisense. Development, 135, 1735–1743. [DOI] [PubMed] [Google Scholar]
  760. Francia S, Michelini F, Saxena A, Tang D, de Hoon M, Anelli V, Mione M, Carninci P and d'Adda di Fagagna F, 2012. Site‐specific DICER and DROSHA RNA products control the DNA‐damage response. Nature, 488, 231–235. [DOI] [PMC free article] [PubMed] [Google Scholar]
  761. Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, Inoue K, Enright AJ and Schier AF, 2006. Zebrafish MiR‐430 promotes deadenylation and clearance of maternal mRNAs. Science, 312, 75–79. [DOI] [PubMed] [Google Scholar]
  762. Gotesman M, Soliman H, Besch R and El‐Matbouli M, 2014. In vitro inhibition of Cyprinid herpesvirus‐3 replication by RNAi. J Virol Methods, 206, 63–66. [DOI] [PMC free article] [PubMed] [Google Scholar]
  763. Guo S, Xu D, Xu H‐x, Wang T, Li J‐l and Lu L‐q, 2012. Suppression of RNA interference pathway in vitro by Grass carp reovirus. Virologica Sinica, 27, 109–119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  764. Heath G, Childs D, Docker MF, McCauley DW and Whyard S, 2014. RNA Interference Technology to Control Pest Sea Lampreys ‐ A Proof‐of‐Concept. Plos One, 9, e88387–e88387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  765. Houwing S, Kamminga LM, Berezikov E, Cronembold D, Girard A, van den Elst H, Filippov DV, Blaser H, Raz E, Moens CB, Plasterk RHA, Hannon GJ, Draper BW and Ketting RF, 2007. A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in zebrafish. Cell, 129, 69–82. [DOI] [PubMed] [Google Scholar]
  766. Huang HY, Houwing S, Kaaij LJT, Meppelink A, Redl S, Gauci S, Vos H, Draper BW, Moens CB, Burgering BM, Ladurner P, Krijgsveld J, Berezikov E and Ketting RF, 2011. Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. EMBO J, 30, 3298–3308. [DOI] [PMC free article] [PubMed] [Google Scholar]
  767. Kamminga LM, Luteijn MJ, den Broeder MJ, Redl S, Kaaij LJT, Roovers EF, Ladurner P, Berezikov E and Ketting RF, 2010. Hen1 is required for oocyte development and piRNA stability in zebrafish. EMBO J, 29, 3688–3700. [DOI] [PMC free article] [PubMed] [Google Scholar]
  768. Kedde M, Strasser MJ, Boldajipour B, Vrielink J, Le Sage C, Nagel R, Voorhoeve PM, Van Duijse J, Orom UA, Lund AH, Perrakis A, Raz E, Agami R and Slanchev K, 2007. RNA‐binding protein Dnd1 inhibits microRNA access to target mRNA. Cell, 131, 1273–1286. [DOI] [PubMed] [Google Scholar]
  769. Li YX, Farrell MJ, Liu RP, Mohanty N and Kirby ML, 2000. Double‐stranded RNA injection produces null phenotypes in zebrafish. Developmental Biology, 217, 394–405. [DOI] [PubMed] [Google Scholar]
  770. Mangos S, Vanderbeld B, Krawetz R, Sudol K and Kelly GM, 2001. Ran binding protein RanBP1 in zebrafish embryonic development. Molecular Reproduction and Development, 59, 235–248. [DOI] [PubMed] [Google Scholar]
  771. McFarlane L, Svingen T, Braasch I, Koopman P, Schartl M and Wilhelm D, 2011. Expansion of the Ago gene family in the teleost clade. Development Genes and Evolution, 221, 95–104. [DOI] [PubMed] [Google Scholar]
  772. Mishima Y, Giraldez AJ, Takeda Y, Fujiwara T, Sakamoto H, Schier AF and Inoue K, 2006. Differential regulation of germline mRNAs in soma and germ cells by zebrafish miR‐430. Current Biology, 16, 2135–2142. [DOI] [PMC free article] [PubMed] [Google Scholar]
  773. Mishima Y, Fukao A, Kishimoto T, Sakamoto H, Fujiwara T and Inoue K, 2012. Translational inhibition by deadenylation‐independent mechanisms is central to microRNA‐mediated silencing in zebrafish. Proc Natl Acad Sci U S A, 109, 1104–1109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  774. Murphy D, Dancis B and Brown JR, 2008. The evolution of core proteins involved in microRNA biogenesis. Bmc Evolutionary Biology, 8, 92–92. [DOI] [PMC free article] [PubMed] [Google Scholar]
  775. Oates AC, Bruce AEE and Ho RK, 2000. Too much interference: Injection of double‐stranded RNA has nonspecific effects in the zebrafish embryo. Developmental Biology, 224, 20–28. [DOI] [PubMed] [Google Scholar]
  776. Rothenburg S, Deigendesch N, Dey M, Dever TE and Tazi L, 2008. Double‐stranded RNA‐activated protein kinase PKR of fishes and amphibians: Varying the number of double‐stranded RNA binding domains and lineage‐specific duplications. Bmc Biology, 6, 12–12. [DOI] [PMC free article] [PubMed] [Google Scholar]
  777. Shen XB, Xu D, Li JL and Lu LQ, 2013. Molecular cloning and immune responsive expression of a ribonuclease III ortholog involved in RNA interference, dicer, in grass carp Ctenopharyngodon idella. Journal of Fish Biology, 83, 1234–1248. [DOI] [PubMed] [Google Scholar]
  778. Svoboda P, Stein P, Hayashi H and Schultz RM, 2000. Selective reduction of dormant maternal mRNAs in mouse oocytes by RNA interference. Development, 127, 4147–4156. [DOI] [PubMed] [Google Scholar]
  779. Svoboda P and Flemr M, 2010. The role of miRNAs and endogenous siRNAs in maternal‐to‐zygotic reprogramming and the establishment of pluripotency. EMBO Rep, 11, 590–597. [DOI] [PMC free article] [PubMed] [Google Scholar]
  780. Thornton JE, Du P, Jing LL, Sjekloca L, Lin SB, Grossi E, Sliz P, Zon LI and Gregory RI, 2014. Selective microRNA uridylation by Zcchc6 (TUT7) and Zcchc11 (TUT4). Nucleic Acids Research, 42, 11777–11791. [DOI] [PMC free article] [PubMed] [Google Scholar]
  781. Wang L, Zhou JY, Yao JH, Lu DR, Qiao XJ and Jia W, 2010. U6 promoter‐driven siRNA injection has nonspecific effects in zebrafish. Biochem Biophys Res Commun, 391, 1363–1368. [DOI] [PubMed] [Google Scholar]
  782. Wianny F and Zernicka‐Goetz M, 2000. Specific interference with gene function by double‐stranded RNA in early mouse development. Nature Cell Biology, 2, 70–75. [DOI] [PubMed] [Google Scholar]
  783. Wienholds E, Koudijs MJ, van Eeden FJM, Cuppen E and Plasterk RHA, 2003. The microRNA‐producing enzyme Dicer1 is essential for zebrafish development. Nature Genetics, 35, 217–218. [DOI] [PubMed] [Google Scholar]
  784. Yi TF, Arthanari H, Akabayov B, Song HD, Papadopoulos E, Qi HH, Jedrychowski M, Guttler T, Guo CC, Luna RE, Gygi SP, Huang SA and Wagner G, 2015. eIF1A augments Ago2‐mediated Dicer‐independent miRNA biogenesis and RNA interference. Nature Communications, 6, 7194–7194. [DOI] [PMC free article] [PubMed] [Google Scholar]
  785. Ying SY, Chang CP and Lin SL, 2010. Intron‐mediated RNA interference, intronic microRNAs, and applications. Methods Mol Biol, 629, 205–237. [DOI] [PubMed] [Google Scholar]
  786. Zhao XF, Fjose A, Larsen N, Helvik JV and Drivenes O, 2008. Treatment with small interfering RNA affects the microRNA pathway and causes unspecific defects in zebrafish embryos. Febs Journal, 275, 2177–2184. [DOI] [PubMed] [Google Scholar]
  787. Zhao ZX, Cao Y, Li M and Meng AM, 2001. Double‐stranded RNA injection produces nonspecific defects in zebrafish. Developmental Biology, 229, 215–223. [DOI] [PubMed] [Google Scholar]
  788. Abe M, Naqvi A, Hendriks GJ, Feltzin V, Zhu YQ, Grigoriev A and Bonini NM, 2014. Impact of age‐associated increase in 2 ‘‐O‐methylation of miRNAs on aging and neurodegeneration in Drosophila. Genes & Development, 28, 44–57. [DOI] [PMC free article] [PubMed] [Google Scholar]
  789. Adelman ZN, Anderson MAE, Liu M, Zhang L and Myles KM, 2012. Sindbis virus induces the production of a novel class of endogenous siRNAs in Aedes aegypti mosquitoes. Insect Molecular Biology, 21, 357–368. [DOI] [PMC free article] [PubMed] [Google Scholar]
  790. Ameres SL, Horwich MD, Hung JH, Xu J, Ghildiyal M, Weng ZP and Zamore PD, 2010. Target RNA‐Directed Trimming and Tailing of Small Silencing RNAs. Science, 328, 1534–1539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  791. Antic S, Wolfinger MT, Skucha A, Hosiner S and Dorner S, 2015. General and MicroRNA‐Mediated mRNA Degradation Occurs on Ribosome Complexes in Drosophila Cells. Molecular and Cellular Biology, 35, 2309–2320. [DOI] [PMC free article] [PubMed] [Google Scholar]
  792. Azzam G, Smibert P, Lai EC and Liu JL, 2012. Drosophila Argonaute 1 and its miRNA biogenesis partners are required for oocyte formation and germline cell division. Developmental Biology, 365, 384–394. [DOI] [PMC free article] [PubMed] [Google Scholar]
  793. Bansal R and Michel AP, 2013. Core RNAi Machinery and Sid1, a Component for Systemic RNAi, in the Hemipteran Insect, Aphis glycines. International Journal of Molecular Sciences, 14, 3786–3801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  794. Barraud P, Heale BSE, O'Connell MA and Allain FHT, 2012. Solution structure of the N‐terminal dsRBD of Drosophila ADAR and interaction studies with RNA. Biochimie, 94, 1499–1509. [DOI] [PMC free article] [PubMed] [Google Scholar]
  795. Behm‐Ansmant I, Rehwinkel J, Doerks T, Stark A, Bork P and Izaurralde E, 2006. MRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1: DCP2 decapping complexes. Genes & Development, 20, 1885–1898. [DOI] [PMC free article] [PubMed] [Google Scholar]
  796. Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, Hung JH, Okamura K, Dai Q, Bortolamiol‐Becet D, Martin R, Zhao YJ, Zamore PD, Hannon GJ, Marra MA, Weng ZP, Perrimon N and Lai EC, 2011. Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Research, 21, 203–215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  797. Bernhardt SA, Simmons MP, Olson KE, Beaty BJ, Blair CD and Black WC, 2012. Rapid Intraspecific Evolution of miRNA and siRNA Genes in the Mosquito Aedes aegypti. Plos One, 7, e44198–e44198. [DOI] [PMC free article] [PubMed] [Google Scholar]
  798. Bernstein E, Caudy AA, Hammond SM and Hannon GJ, 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409, 363–366. [DOI] [PubMed] [Google Scholar]
  799. Blandin S, Moita LF, Kocher T, Wilm M, Kafatos FC and Levashina EA, 2002. Reverse genetics in the mosquito Anopheles gambiae: targeted disruption of the Defensin gene. EMBO Rep, 3, 852–856. [DOI] [PMC free article] [PubMed] [Google Scholar]
  800. Bozzetti MP, Specchia V, Cattenoz PB, Laneve P, Geusa A, Sahin HB, Di Tommaso S, Friscini A, Massari S, Diebold C and Giangrande A, 2015. The Drosophila fragile X mental retardation protein participates in the piRNA pathway. Journal of Cell Science, 128, 2070–2084. [DOI] [PubMed] [Google Scholar]
  801. Bucher G, Scholten J and Klingler M, 2002. Parental RNAi in Tribolium (Coleoptera). Curr Biol, 12, R85–86. [DOI] [PubMed] [Google Scholar]
  802. Burroughs AM, Ando Y, de Hoon MJL, Tomaru Y, Nishibu T, Ukekawa R, Funakoshi T, Kurokawa T, Suzuki H, Hayashizaki Y and Daub CO, 2010. A comprehensive survey of 3 ‘ animal miRNA modification events and a possible role for 3 ‘ adenylation in modulating miRNA targeting effectiveness. Genome Research, 20, 1398–1410. [DOI] [PMC free article] [PubMed] [Google Scholar]
  803. Campbell CL, Keene KM, Brackney DE, Olson KE, Blair CD, Wilusz J and Foy BD, 2008. Aedes aegypti uses RNA interference in defense against Sindbis virus infection. Bmc Microbiology, 8, 47–47. [DOI] [PMC free article] [PubMed] [Google Scholar]
  804. Cappelle K, de Oliveira CF, Van Eynde B, Christiaens O and Smagghe G, 2016. The involvement of clathrin‐mediated endocytosis and two Sid‐1‐like transmembrane proteins in double‐stranded RNA uptake in the Colorado potato beetle midgut. Insect Molecular Biology. [DOI] [PubMed] [Google Scholar]
  805. Caudy AA, Myers M, Hannon GJ and Hammond SM, 2002. Fragile X‐related protein and VIG associate with the RNA interference machinery. Genes & Development, 16, 2491–2496. [DOI] [PMC free article] [PubMed] [Google Scholar]
  806. Caudy AA, Ketting RF, Hammond SM, Denli AM, Bathoorn AMP, Tops BBJ, Silva JM, Myers MM, Hannon GJ and Plasterk RHA, 2003. A micrococcal nuclease homolog in RNAi effector complexes. Nature, 425, 411–414. [DOI] [PubMed] [Google Scholar]
  807. Cenik ES, Fukunaga R, Lu G, Dutcher R, Wang YM, Hall TMT and Zamore PD, 2011. Phosphate and R2D2 Restrict the Substrate Specificity of Dicer‐2, an ATP‐Driven Ribonuclease. Molecular Cell, 42, 172–184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  808. Cernilogar FM, Burroughs AM, Lanzuolo C, Breiling A, Imhof A and Orlando V, 2013. RNA‐Interference Components Are Dispensable for Transcriptional Silencing of the Drosophila Bithorax‐Complex. Plos One, 8, e65740–e65740. [DOI] [PMC free article] [PubMed] [Google Scholar]
  809. Cerutti H and Casas‐Mollano JA, 2006. On the origin and functions of RNA‐mediated silencing: from protists to man. Curr Genet, 50, 81–99. [DOI] [PMC free article] [PubMed] [Google Scholar]
  810. Chak LL, Mohammed J, Lai EC, Tucker‐Kellogg G and Okamura K, 2015. A deeply conserved, noncanonical miRNA hosted by ribosomal DNA. Rna, 21, 375–384. [DOI] [PMC free article] [PubMed] [Google Scholar]
  811. Chawla G and Sokol NS, 2014. ADAR mediates differential expression of polycistronic microRNAs. Nucleic Acids Research, 42, 5245–5255. [DOI] [PMC free article] [PubMed] [Google Scholar]
  812. Chekulaeva M, Filipowicz W and Parker R, 2009. Multiple independent domains of dGW182 function in miRNA‐mediated repression in Drosophila. Rna, 15, 794–803. [DOI] [PMC free article] [PubMed] [Google Scholar]
  813. Chekulaeva M, Parker R and Filipowicz W, 2010. The GW/WG repeats of Drosophila GW182 function as effector motifs for miRNA‐mediated repression. Nucleic Acids Research, 38, 6673–6683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  814. Chekulaeva M, Mathys H, Zipprich JT, Attig J, Colic M, Parker R and Filipowicz W, 2011. miRNA repression involves GW182‐mediated recruitment of CCR4‐NOT through conserved W‐containing motifs. Nature Structural & Molecular Biology, 18, 1218–U1262. [DOI] [PMC free article] [PubMed] [Google Scholar]
  815. Chen YH, Jia XT, Zhao L, Li CZ, Zhang SA, Chen YG, Weng SP and He JG, 2011. Identification and functional characterization of Dicer2 and five single VWC domain proteins of Litopenaeus vannamei. Developmental and Comparative Immunology, 35, 661–671. [DOI] [PubMed] [Google Scholar]
  816. Chen YH, Zhao L, Jia XT, Li XY, Li CZ, Yan H, Weng SP and He JG, 2012. Isolation and characterization of cDNAs encoding Ars2 and Pasha homologs, two components of the RNA interference pathway in Litopenaeus vannamei. Fish & Shellfish Immunology, 32, 373–380. [DOI] [PubMed] [Google Scholar]
  817. Chung WJ, Okamura K, Martin R and Lai EC, 2008. Endogenous RNA interference provides a somatic Defense against Drosophila transposons. Current Biology, 18, 795–802. [DOI] [PMC free article] [PubMed] [Google Scholar]
  818. Cui YL, Huang TZ and Zhang XB, 2015. RNA editing of microRNA prevents RNA‐induced silencing complex recognition of target mRNA. Open Biology, 5, 150126–150126. [DOI] [PMC free article] [PubMed] [Google Scholar] [Retracted]
  819. Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C, Dus M, Perrimon N, Kellis M, Wohlschlegel JA, Sachidanandam R, Hannon GJ and Brennecke J, 2008. An endogenous small interfering RNA pathway in Drosophila. Nature, 453, 798–U797. [DOI] [PMC free article] [PubMed] [Google Scholar]
  820. Czech B, Zhou R, Erlich Y, Brennecke J, Binari R, Villalta C, Gordon A, Perrimon N and Hannon GJ, 2009. Hierarchical Rules for Argonaute Loading in Drosophila. Molecular Cell, 36, 445–456. [DOI] [PMC free article] [PubMed] [Google Scholar]
  821. Dechklar M, Udomkit A and Panyim S, 2008. Characterization of Argonaute cDNA from Penaeus monodon and implication of its role in RNA interference. Biochem Biophys Res Commun, 367, 768–774. [DOI] [PubMed] [Google Scholar]
  822. Dekanty A, Romero NM, Bertolin AP, Thomas MG, Leishman CC, Perez‐Perri JI, Boccaccio GL and Wappner P, 2010. Drosophila Genome‐Wide RNAi Screen Identifies Multiple Regulators of HIF‐Dependent Transcription in Hypoxia. Plos Genetics, 6, e1000994–e1000994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  823. Denli AM, Tops BBJ, Plasterk RHA, Ketting RF and Hannon GJ, 2004. Processing of primary microRNAs by the Microprocessor complex. Nature, 432, 231–235. [DOI] [PubMed] [Google Scholar]
  824. Deshpande G, Calhoun G and Schedl P, 2005. Drosophila argonaute‐2 is required early in embryogenesis for the assembly of centric/centromeric heterochromatin, nuclear division, nuclear migration, and germ‐cell formation. Genes & Development, 19, 1680–1685. [DOI] [PMC free article] [PubMed] [Google Scholar]
  825. Dong Y and Friedrich M, 2005. Nymphal RNAi: systemic RNAi mediated gene knockdown in juvenile grasshopper. Bmc Biotechnology, 5, 25–25. [DOI] [PMC free article] [PubMed] [Google Scholar]
  826. Dzitoyeva S, Dimitrijevic N and Manev H, 2003. Gamma‐aminobutyric acid B receptor 1 mediates behavior‐impairing actions of alcohol in Drosophila: adult RNA interference and pharmacological evidence. Proc Natl Acad Sci U S A, 100, 5485–5490. [DOI] [PMC free article] [PubMed] [Google Scholar]
  827. Eulalio A, Huntzinger E and Izaurralde E, 2008. GW182 interaction with Argonaute is essential for miRNA‐mediated translational repression and mRNA decay. Nature Structural & Molecular Biology, 15, 346–353. [DOI] [PubMed] [Google Scholar]
  828. Eulalio A, Tritschler F, Buettner R, Weichenrieder O, Izaurralde E and Truffault V, 2009. The RRM domain in GW182 proteins contributes to miRNA‐mediated gene silencing. Nucleic Acids Research, 37, 2974–2983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  829. Fagegaltier D, Bouge AL, Berry B, Poisot E, Sismeiro O, Coppee JY, Theodore L, Voinnet O and Antoniewski C, 2009. The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila. Proc Natl Acad Sci U S A, 106, 21258–21263. [DOI] [PMC free article] [PubMed] [Google Scholar]
  830. Feinberg EH and Hunter CP, 2003. Transport of dsRNA into cells by the transmembrane protein SID‐1. Science, 301, 1545–1547. [DOI] [PubMed] [Google Scholar]
  831. Feltzin VL, Khaladkar M, Abe M, Parisi M, Hendriks GJ, Kim J and Bonini NM, 2015. The exonuclease Nibbler regulates age‐associated traits and modulates piRNA length in Drosophila. Aging Cell, 14, 443–452. [DOI] [PMC free article] [PubMed] [Google Scholar]
  832. Filippov V, Solovyev V, Filippova M and Gill SS, 2000. A novel type of RNase III family proteins in eukaryotes. Gene, 245, 213–221. [DOI] [PubMed] [Google Scholar]
  833. Flynt AS, Greimann JC, Chung WJ, Lima CD and Lai EC, 2010. MicroRNA Biogenesis via Splicing and Exosome‐Mediated Trimming in Drosophila. Molecular Cell, 38, 900–907. [DOI] [PMC free article] [PubMed] [Google Scholar]
  834. Forstemann K, Tomari Y, Du TT, Vagin VV, Denli AM, Bratu DP, Klattenhoff C, Theurkauf WE and Zamore PD, 2005. Normal microRNA maturation and germ‐line stem cell maintenance requires loquacious, a double‐stranded RNA‐binding domain protein. Plos Biology, 3, 1187–1201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  835. Forstemann K, Horwich MD, Wee L, Tomari Y and Zamore PD, 2007. Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by Dicer‐1. Cell, 130, 287–297. [DOI] [PMC free article] [PubMed] [Google Scholar]
  836. Fu Q and Wang PJ, 2014. Mammalian piRNAs: Biogenesis, function, and mysteries. Spermatogenesis, 4, e27889–e27889. [DOI] [PMC free article] [PubMed] [Google Scholar]
  837. Fukaya T and Tomari Y, 2011. PABP is not essential for microRNA‐mediated translational repression and deadenylation in vitro. EMBO J, 30, 4998–5009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  838. Fukaya T, Iwakawa H‐o and Tomari Y, 2014. MicroRNAs Block Assembly of eIF4F Translation Initiation Complex in Drosophila. Molecular Cell, 56, 67–78. [DOI] [PubMed] [Google Scholar]
  839. Fukunaga R, Han BW, Hung JH, Xu J, Weng ZP and Zamore PD, 2012. Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals. Cell, 151, 533–546. [DOI] [PMC free article] [PubMed] [Google Scholar]
  840. Fukunaga R, Colpan C, Han BW and Zamore PD, 2014. Inorganic phosphate blocks binding of pre‐miRNA to Dicer‐2 via its PAZ domain. EMBO J, 33, 371–384. [DOI] [PMC free article] [PubMed] [Google Scholar]
  841. Galiana‐Arnoux D, Dostert C, Schneemann A, Hoffmann JA and Imler JL, 2006. Essential function in vivo for Dicer‐2 in host defense against RNA viruses in drosophila. Nature Immunology, 7, 590–597. [DOI] [PubMed] [Google Scholar]
  842. Gandhi SG, Bag I, Sengupta S, Pal‐Bhadra M and Bhadra U, 2015. Drosophila oncogene Gas41 is an RNA interference modulator that intersects heterochromatin and the small interfering RNA pathway. Febs Journal, 282, 153–173. [DOI] [PubMed] [Google Scholar]
  843. Gerbasi VR, Preall JB, Golden DE, Powell DW, Cummins TD and Sontheimer EJ, 2011. Blanks, a nuclear siRNA/dsRNA‐binding complex component, is required for Drosophila spermiogenesis. Proc Natl Acad Sci U S A, 108, 3204–3209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  844. Ghildiyal M, Seitz H, Horwich MD, Li CJ, Du TT, Lee S, Xu J, Kittler ELW, Zapp ML, Weng ZP and Zamore PD, 2008. Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science, 320, 1077–1081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  845. Ghildiyal M, Xu J, Seitz H, Weng ZP and Zamore PD, 2010. Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. Rna, 16, 43–56. [DOI] [PMC free article] [PubMed] [Google Scholar]
  846. Ghosh S, Kakumani PK, Kumar A, Malhotra P, Mukherjee SK and Bhatnagar RK, 2014. Genome wide screening of RNAi factors of Sf21 cells reveal several novel pathway associated proteins. Bmc Genomics, 15, 775–775. [DOI] [PMC free article] [PubMed] [Google Scholar]
  847. Gomez‐Orte E and Belles X, 2009. MicroRNA‐dependent metamorphosis in hemimetabolan insects. Proc Natl Acad Sci U S A, 106, 21678–21682. [DOI] [PMC free article] [PubMed] [Google Scholar]
  848. Gong L, Wang Z, Wang H, Qi J, Hu M and Hu Q, 2015. Core RNAi machinery and three Sid‐1 related genes in Spodoptera litura (Fabricius). International Journal of Agriculture and Biology, 17, 937–944. [Google Scholar]
  849. Gracheva E, Dus M and Elgin SCR, 2009. Drosophila RISC Component VIG and Its Homolog Vig2 Impact Heterochromatin Formation. Plos One, 4, e6182–e6182. [DOI] [PMC free article] [PubMed] [Google Scholar]
  850. Haac ME, Anderson MAE, Eggleston H, Myles KM and Adelman ZN, 2015. The hub protein loquacious connects the microRNA and short interfering RNA pathways in mosquitoes. Nucleic Acids Research, 43, 3688–3700. [DOI] [PMC free article] [PubMed] [Google Scholar]
  851. Haase AD, 2016. A Small RNA‐Based Immune System Defends Germ Cells against Mobile Genetic Elements. Stem Cells International, 2016, 7595791–7595791. [DOI] [PMC free article] [PubMed] [Google Scholar]
  852. Han BW, Hung JH, Weng ZP, Zamore PD and Ameres SL, 2011. The 3 ‘‐to‐5 ‘ Exoribonuclease Nibbler Shapes the 3 ‘ Ends of MicroRNAs Bound to Drosophila Argonaute1. Current Biology, 21, 1878–1887. [DOI] [PMC free article] [PubMed] [Google Scholar]
  853. Han BW and Zamore PD, 2014. PiRNAs. Current Biology, 24, R730–R733. [DOI] [PubMed] [Google Scholar]
  854. Hartig JV, Esslinger S, Bottcher R, Saito K and Forstemann K, 2009. Endo‐siRNAs depend on a new isoform of loquacious and target artificially introduced, high‐copy sequences. EMBO J, 28, 2932–2944. [DOI] [PMC free article] [PubMed] [Google Scholar]
  855. Hartig JV and Forstemann K, 2011. Loqs‐PD and R2D2 define independent pathways for RISC generation in Drosophila. Nucleic Acids Research, 39, 3836–3851. [DOI] [PMC free article] [PubMed] [Google Scholar]
  856. He YD and Zhang XB, 2012. Comprehensive characterization of viral miRNAs involved in white spot syndrome virus (WSSV) infection. RNA biology, 9, 1019–1029. [DOI] [PubMed] [Google Scholar]
  857. Herbert KM, Pimienta G, DeGregorio SJ, Alexandrov A and Steitz JA, 2013. Phosphorylation of DGCR8 Increases Its Intracellular Stability and Induces a Progrowth miRNA Profile. Cell Reports, 5, 1070–1081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  858. Honeybee Genome Sequencing C, 2006. Insights into social insects from the genome of the honeybee Apis mellifera. Nature, 443, 931–949. [DOI] [PMC free article] [PubMed] [Google Scholar]
  859. Horwich MD, Li CJ, Matranga C, Vagin V, Farley G, Wang P and Zamore PD, 2007. The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single‐stranded siRNAs in RISC. Current Biology, 17, 1265–1272. [DOI] [PubMed] [Google Scholar]
  860. Hoy MA, Waterhouse RM, Wu K, Estep AS, Ioannidis P, Palmer WJ, Pomerantz AF, Simao FA, Thomas J, Jiggins FM, Murphy TD, Pritham EJ, Robertson HM, Zdobnov EM, Gibbs RA and Richards S, 2016. Genome sequencing of the phytoseiid predatory mite Metaseiulus occidentalis reveals completely atomised Hox genes and super‐dynamic intron evolution. Genome biology and evolution. [DOI] [PMC free article] [PubMed] [Google Scholar]
  861. Huang HD, Li YJ, Szulwach KE, Zhang GQ, Jin P and Chen DH, 2014. AGO3 Slicer activity regulates mitochondria‐nuage localization of Armitage and piRNA amplification. Journal of Cell Biology, 206, 217–230. [DOI] [PMC free article] [PubMed] [Google Scholar]
  862. Huang TZ, Xu DD and Zhang XB, 2012. Characterization of shrimp Drosha in virus infection. Fish & Shellfish Immunology, 33, 575–581. [DOI] [PubMed] [Google Scholar]
  863. Huang TZ and Zhang XB, 2013. Host defense against DNA virus infection in shrimp is mediated by the siRNA pathway. European Journal of Immunology, 43, 137–146. [DOI] [PubMed] [Google Scholar]
  864. Huntzinger E, Braun JE, Heimstaedt S, Zekri L and Izaurralde E, 2010. Two PABPC1‐binding sites in GW182 proteins promote miRNA‐mediated gene silencing. EMBO J, 29, 4146–4160. [DOI] [PMC free article] [PubMed] [Google Scholar]
  865. Huntzinger E, Kuzuoglu‐Oeztuerk D, Braun JE, Eulalio A, Wohlbold L and Izaurralde E, 2013. The interactions of GW182 proteins with PABP and deadenylases are required for both translational repression and degradation of miRNA targets. Nucleic Acids Research, 41, 978–994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  866. Ishizuka A, Siomi MC and Siomi H, 2002. A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins. Genes & Development, 16, 2497–2508. [DOI] [PMC free article] [PubMed] [Google Scholar]
  867. Iwasaki S, Kawamata T and Tomari Y, 2009. Drosophila Argonaute1 and Argonaute2 Employ Distinct Mechanisms for Translational Repression. Molecular Cell, 34, 58–67. [DOI] [PubMed] [Google Scholar]
  868. Iwasaki S, Sasaki HM, Sakaguchi Y, Suzuki T, Tadakuma H and Tomari Y, 2015. Defining fundamental steps in the assembly of the Drosophila RNAi enzyme complex. Nature, 521, 533–U274. [DOI] [PubMed] [Google Scholar]
  869. Jariyapong P, Weerachatyanukul W, Direkbusarakom S, Hirono I, Wuthisuthimethavee S and Chotwiwatthanakun C, 2015. Enhancement of shrimp immunity against white spot syndrome virus by Macrobrachium rosenbergii nodavirus‐like particle encapsulated VP28 double‐stranded RNA. Aquaculture, 446, 325–332. [Google Scholar]
  870. Jaskiewicz L and Filipowicz W, 2008. Role of Dicer in posttranscriptional RNA silencing. Curr Top Microbiol Immunol, 320, 77–97. [DOI] [PubMed] [Google Scholar]
  871. Jaubert‐Possamai S, Rispe C, Tanguy S, Gordon K, Walsh T, Edwards O and Tagu D, 2010. Expansion of the miRNA Pathway in the Hemipteran Insect Acyrthosiphon pisum. Molecular Biology and Evolution, 27, 979–987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  872. Jiang F, Ye XC, Liu X, Fincher L, McKearin D and Liu QH, 2005. Dicer‐1 and R3D1‐L catalyze microRNA maturation in Drosophila. Genes & Development, 19, 1674–1679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  873. Jiang FF, Lu FL, Li PX, Liu W, Zhao L, Wang QF, Cao XF, Zhang L and Zhang YQ, 2016. Drosophila Homolog of FMRP Maintains Genome Integrity by Interacting with Piwi. Journal of Genetics and Genomics, 43, 11–24. [DOI] [PubMed] [Google Scholar]
  874. Jin ZG and Xie T, 2007. Dcr‐1 maintains Drosophila ovarian stem cells. Current Biology, 17, 539–544. [DOI] [PubMed] [Google Scholar]
  875. Kadener S, Rodriguez J, Abruzzi KC, Khodor YL, Sugino K, Marr MT, Nelson S and Rosbash M, 2009. Genome‐wide identification of targets of the drosha‐pasha/DGCR8 complex. Rna, 15, 537–545. [DOI] [PMC free article] [PubMed] [Google Scholar]
  876. Kavi HH and Birchler JA, 2009. Interaction of RNA polymerase II and the small RNA machinery affects heterochromatic silencing in Drosophila. Epigenetics & Chromatin, 2, 15–15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  877. Kawamata T, Seitz H and Tomari Y, 2009. Structural determinants of miRNAs for RISC loading and slicer‐independent unwinding. Nature Structural & Molecular Biology, 16, 953–U977. [DOI] [PubMed] [Google Scholar]
  878. Kawamura Y, Saito K, Kin T, Ono Y, Asai K, Sunohara T, Okada TN, Siomi MC and Siomi H, 2008. Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells. Nature, 453, 793–U795. [DOI] [PubMed] [Google Scholar]
  879. Keene KM, Foy BD, Sanchez‐Vargas I, Beaty BJ, Blair CD and Olson KE, 2004. RNA interference acts as a natural antiviral response to O'nyong‐nyong virus (Alphavirus; Togaviridae) infection of Anopheles gambiae. Proc Natl Acad Sci U S A, 101, 17240–17245. [DOI] [PMC free article] [PubMed] [Google Scholar]
  880. Kim K, Lee YS, Harris D, Nakahara K and Carthew RW, 2006. The RNAi pathway initiated by Dicer‐2 in Drosophila. Cold Spring Harbor Symposia on Quantitative Biology, 71, 39–44. [DOI] [PubMed] [Google Scholar]
  881. Kim K, Lee YS and Carthew RW, 2007. Conversion of pre‐RISC to holo‐RISC by Ago2 during assembly of RNAi complexes. Rna, 13, 22–29. [DOI] [PMC free article] [PubMed] [Google Scholar]
  882. Kolliopoulou A and Swevers L, 2013. Functional analysis of the RNAi response in ovary‐derived silkmoth Bm5 cells. Insect Biochemistry and Molecular Biology, 43, 654–663. [DOI] [PubMed] [Google Scholar]
  883. Ku HY, Gangaraju VK, Qi HY, Liu N and Lin HF, 2016. Tudor‐SN Interacts with Piwi Antagonistically in Regulating Spermatogenesis but Synergistically in Silencing Transposons in Drosophila. Plos Genetics, 12, e1005813–e1005813. [DOI] [PMC free article] [PubMed] [Google Scholar]
  884. Kurscheid S, Lew‐Tabor AE, Valle MR, Bruyeres AG, Doogan VJ, Munderloh UG, Guerrero FD, Barrero RA and Bellgard MI, 2009. Evidence of a tick RNAi pathway by comparative genomics and reverse genetics screen of targets with known loss‐of‐function phenotypes in Drosophila. Bmc Molecular Biology, 10, 26–26. [DOI] [PMC free article] [PubMed] [Google Scholar]
  885. Kuzuoglu‐Ozturk D, Bhandari D, Huntzinger E, Fauser M, Helms S and Izaurralde E, 2016. miRISC and the CCR4‐NOT complex silence mRNA targets independently of 43S ribosomal scanning. EMBO J. [DOI] [PMC free article] [PubMed] [Google Scholar]
  886. Labreuche Y, Veloso A, de la Vega E, Gross PS, Chapman RW, Browdy CL and Warr GW, 2010. Non‐specific activation of antiviral immunity and induction of RNA interference may engage the same pathway in the Pacific white leg shrimp Litopenaeus vannamei. Developmental and Comparative Immunology, 34, 1209–1218. [DOI] [PubMed] [Google Scholar]
  887. Landthaler M, Yalcin A and Tuschl T, 2004. The human DiGeorge syndrome critical region gene 8 and its D‐melanogaster homolog are required for miRNA biogenesis. Current Biology, 14, 2162–2167. [DOI] [PubMed] [Google Scholar]
  888. Lau PW, Guiley KZ, De N, Potter CS, Carragher B and MacRae IJ, 2012. The molecular architecture of human Dicer. Nature Structural & Molecular Biology, 19, 436–440. [DOI] [PMC free article] [PubMed] [Google Scholar]
  889. Lee M, Choi Y, Kim K, Jin H, Lim J, Nguyen TA, Yang J, Jeong M, Giraldez AJ, Yang H, Patel DJ and Kim VN, 2014. Adenylation of maternally inherited microRNAs by Wispy. Molecular Cell, 56, 696–707. [DOI] [PMC free article] [PubMed] [Google Scholar]
  890. Lee YS, Nakahara K, Pham JW, Kim K, He ZY, Sontheimer EJ and Carthew RW, 2004. Distinct roles for Drosophila Dicer‐1 and Dicer‐2 in the siRNA/miRNA silencing pathways. Cell, 117, 69–81. [DOI] [PubMed] [Google Scholar]
  891. Leebonoi W, Sukthaworn S, Panyim S and Udomkit A, 2015. A novel gonad‐specific Argonaute 4 serves as a defense against transposons in the black tiger shrimp Penaeus monodon. Fish & Shellfish Immunology, 42, 280–288. [DOI] [PubMed] [Google Scholar]
  892. Leger P, Lara E, Jagla B, Sismeiro O, Mansuroglu Z, Coppee JY, Bonnefoy E and Bouloy M, 2013. Dicer‐2‐and Piwi‐Mediated RNA Interference in Rift Valley Fever Virus‐Infected Mosquito Cells. Journal of Virology, 87, 1631–1648. [DOI] [PMC free article] [PubMed] [Google Scholar]
  893. Lewis SH, Salmela H and Obbard DJ, 2016. Duplication and Diversification of Dipteran Argonaute Genes, and the Evolutionary Divergence of Piwi and Aubergine. Genome biology and evolution, 8, 507–518. [DOI] [PMC free article] [PubMed] [Google Scholar]
  894. Li H, Li WX and Ding SW, 2002. Induction and suppression of RNA silencing by an animal virus. Science, 296, 1319–1321. [DOI] [PubMed] [Google Scholar]
  895. Li WH, Prazak L, Chatterjee N, Gruninger S, Krug L, Theodorou D and Dubnau J, 2013. Activation of transposable elements during aging and neuronal decline in Drosophila. Nature Neuroscience, 16, 529–+. [DOI] [PMC free article] [PubMed] [Google Scholar]
  896. Lim SJ, Scott A, Xiong XP, Vahidpour S, Karijolich J, Guo DD, Pei SS, Yu YT, Zhou R and Li WX, 2014. Requirement for CRIF1 in RNA interference and Dicer‐2 stability. RNA biology, 11, 1171–1179. [DOI] [PMC free article] [PubMed] [Google Scholar]
  897. Lipardi C, Wei Q and Paterson BM, 2001. RNAi as random degradative PCR: siRNA primers convert mRNA into dsRNAs that are degraded to generate new siRNAs. Cell, 107, 297–307. [DOI] [PubMed] [Google Scholar]
  898. Lipardi C and Paterson BM, 2009. Identification of an RNA‐dependent RNA polymerase in Drosophila involved in RNAi and transposon suppression (Retracted article. See vol. 108, pg. 15010, 2011). Proc Natl Acad Sci U S A, 106, 15645–15650. [DOI] [PMC free article] [PubMed] [Google Scholar] [Retracted]
  899. Lipardi C and Paterson BM, 2011. Retraction for Lipardi and Paterson, “Identification of an RNA‐dependent RNA polymerase in Drosophila involved in RNAi and transposon suppression”. Proc Natl Acad Sci U S A, 108, 15010. [DOI] [PMC free article] [PubMed] [Google Scholar]
  900. Liu N, Abe M, Sabin LR, Hendriks GJ, Naqvi AS, Yu ZM, Cherry S and Bonini NM, 2011. The Exoribonuclease Nibbler Controls 3 ‘ End Processing of MicroRNAs in Drosophila. Current Biology, 21, 1888–1893. [DOI] [PMC free article] [PubMed] [Google Scholar]
  901. Liu QH, Rand TA, Kalidas S, Du FH, Kim HE, Smith DP and Wang XD, 2003. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science, 301, 1921–1925. [DOI] [PubMed] [Google Scholar]
  902. Liu W, Liu JB, Lu YH, Gong YC, Zhu M, Chen F, Liang Z, Zhu LY, Kuang SL, Hu XL, Cao GL, Xue RY and Gong CL, 2015. Immune signaling pathways activated in response to different pathogenic micro‐organisms in Bombyx mori. Molecular Immunology, 65, 391–397. [DOI] [PubMed] [Google Scholar]
  903. Liu Y, Ye XC, Jiang F, Liang CY, Chen DM, Peng JM, Kinch LN, Grishin NV and Liu QH, 2009. C3PO, an Endoribonuclease That Promotes RNAi by Facilitating RISC Activation. Science, 325, 750–753. [DOI] [PMC free article] [PubMed] [Google Scholar]
  904. Lozano J, Gomez‐Orte E, Lee HJ and Belles X, 2012. Super‐induction of Dicer‐2 expression by alien double‐stranded RNAs: an evolutionary ancient response to viral infection? Development Genes and Evolution, 222, 229–235. [DOI] [PubMed] [Google Scholar]
  905. Lucchetta EM, Carthew RW and Ismagilov RF, 2009. The Endo‐siRNA Pathway Is Essential for Robust Development of the Drosophila Embryo. Plos One, 4, e7576–e7576. [DOI] [PMC free article] [PubMed] [Google Scholar]
  906. Luhur A, Chawla G, Wu YC, Li J and Sokol NS, 2014. Drosha‐independent DGCR8/Pasha pathway regulates neuronal morphogenesis. Proc Natl Acad Sci U S A, 111, 1421–1426. [DOI] [PMC free article] [PubMed] [Google Scholar]
  907. Luo Y, Wang XH, Yu D and Kang L, 2012. The SID‐1 double‐stranded RNA transporter is not required for systemic RNAi in the migratory locust. RNA biology, 9, 663–671. [DOI] [PubMed] [Google Scholar]
  908. MacRae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD and Doudna JA, 2006. Structural basis for double‐stranded RNA processing by Dicer. Science, 311, 195–198. [DOI] [PubMed] [Google Scholar]
  909. MacRae IJ, Zhou K and Doudna JA, 2007. Structural determinants of RNA recognition and cleavage by Dicer. Nature Structural and Molecular Biology, 14, 934–940. [DOI] [PubMed] [Google Scholar]
  910. Maralit BA, Komatsu M, Hipolito SG, Hirono I and Kondo H, 2015. Microarray Analysis of Immunity Against WSSV in Response to Injection of Non‐specific Long dsRNA in Kuruma Shrimp, Marsupenaeus japonicus. Marine Biotechnology, 17, 493–501. [DOI] [PubMed] [Google Scholar]
  911. Marques JT, Kim K, Wu PH, Alleyne TM, Jafari N and Carthew RW, 2010. Loqs and R2D2 act sequentially in the siRNA pathway in Drosophila. Nature Structural & Molecular Biology, 17, 24–U37. [DOI] [PMC free article] [PubMed] [Google Scholar]
  912. Martin R, Smibert P, Yalcin A, Tyler DM, Schafer U, Tuschl T and Lai EC, 2009. A Drosophila pasha Mutant Distinguishes the Canonical MicroRNA and Mirtron Pathways. Molecular and Cellular Biology, 29, 861–870. [DOI] [PMC free article] [PubMed] [Google Scholar]
  913. Matranga C, Tomari Y, Shin C, Bartel DP and Zamore PD, 2005. Passenger‐strand cleavage facilitates assembly of siRNA into Ago2‐containing RNAi enzyme complexes. Cell, 123, 607–620. [DOI] [PubMed] [Google Scholar]
  914. Miyoshi K, Tsukumo H, Nagami T, Siomi H and Siomi MC, 2005. Slicer function of Drosophila Argonautes and its involvement in RISC formation. Genes & Development, 19, 2837–2848. [DOI] [PMC free article] [PubMed] [Google Scholar]
  915. Miyoshi K, Okada TN, Siomi H and Siomi MC, 2009. Characterization of the miRNA‐RISC loading complex and miRNA‐RISC formed in the Drosophila miRNA pathway. Rna, 15, 1282–1291. [DOI] [PMC free article] [PubMed] [Google Scholar]
  916. Miyoshi K, Miyoshi T, Hartig JV, Siomi H and Siomi MC, 2010a. Molecular mechanisms that funnel RNA precursors into endogenous small‐interfering RNA and microRNA biogenesis pathways in Drosophila. Rna, 16, 506–515. [DOI] [PMC free article] [PubMed] [Google Scholar]
  917. Miyoshi T, Takeuchi A, Siomi H and Siomi MC, 2010b. A direct role for Hsp90 in pre‐RISC formation in Drosophila. Nature Structural & Molecular Biology, 17, 1024–1026. [DOI] [PubMed] [Google Scholar]
  918. Mon H, Li Z, Kobayashi I, Tomita S, Lee J, Sezutsu H, Tamura T and Kusakabe T, 2013. Soaking RNAi in Bombyx mori BmN4‐SID1 cells arrests cell cycle progression. Journal of Insect Science, 13, 155–155. [DOI] [PMC free article] [PubMed] [Google Scholar]
  919. Morazzani EM, Wiley MR, Murreddu MG, Adelman ZN and Myles KM, 2012. Production of Virus‐Derived Ping‐Pong‐Dependent piRNA‐like Small RNAs in the Mosquito Soma. Plos Pathogens, 8, e1002470–e1002470. [DOI] [PMC free article] [PubMed] [Google Scholar]
  920. Moretti F, Kaiser C, Zdanowicz‐Specht A and Hentze MW, 2012. PABP and the poly(A) tail augment microRNA repression by facilitated miRISC binding. Nature Structural & Molecular Biology, 19, 603–+. [DOI] [PubMed] [Google Scholar]
  921. Moshkovich N, Nisha P, Boyle PJ, Thompson BA, Dale RK and Lei EP, 2011. RNAi‐independent role for Argonaute2 in CTCF/CP190 chromatin insulator function. Genes & Development, 25, 1686–1701. [DOI] [PMC free article] [PubMed] [Google Scholar]
  922. Mugat B, Akkouche A, Serrano V, Armenise C, Li B, Brun C, Fulga TA, Van Vactor D, Pelisson A and Chambeyron S, 2015. MicroRNA‐Dependent Transcriptional Silencing of Transposable Elements in Drosophila Follicle Cells. Plos Genetics, 11, e1005194–e1005194. [DOI] [PMC free article] [PubMed] [Google Scholar]
  923. Murota Y, Ishizu H, Nakagawa S, Iwasaki YW, Shibata S, Kamatani MK, Saito K, Okano H, Siomi H and Siomi MC, 2014. Yb Integrates piRNA Intermediates and Processing Factors into Perinuclear Bodies to Enhance piRISC Assembly. Cell Reports, 8, 103–113. [DOI] [PubMed] [Google Scholar]
  924. Murphy D, Dancis B and Brown JR, 2008. The evolution of core proteins involved in microRNA biogenesis. Bmc Evolutionary Biology, 8, 92–92. [DOI] [PMC free article] [PubMed] [Google Scholar]
  925. Nagao A, Mituyama T, Huang HD, Chen DH, Siomi MC and Siomi H, 2010. Biogenesis pathways of piRNAs loaded onto AGO3 in the Drosophila testis. Rna, 16, 2503–2515. [DOI] [PMC free article] [PubMed] [Google Scholar]
  926. Nayak A, Berry B, Tassetto M, Kunitomi M, Acevedo A, Deng CH, Krutchinsky A, Gross J, Antoniewski C and Andino R, 2010. Cricket paralysis virus antagonizes Argonaute 2 to modulate antiviral defense in Drosophila. Nature Structural & Molecular Biology, 17, 547–U541. [DOI] [PMC free article] [PubMed] [Google Scholar]
  927. Nishida KM, Miyoshi K, Ogino A, Miyoshi T, Siomi H and Siomi MC, 2013. Roles of R2D2, a Cytoplasmic D2 Body Component, in the Endogenous siRNA Pathway in Drosophila. Molecular Cell, 49, 680–691. [DOI] [PubMed] [Google Scholar]
  928. Niu JZ, Smagghe G, De Coninck DIM, Van Nieuwerburgh F, Deforce D and Meeus I, 2016. In vivo study of Dicer‐2‐mediated immune response of the small interfering RNA pathway upon systemic infections of virulent and avirulent viruses in Bombus terrestris. Insect Biochemistry and Molecular Biology, 70, 127–137. [DOI] [PubMed] [Google Scholar]
  929. Nykanen A, Haley B and Zamore PD, 2001. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell, 107, 309–321. [DOI] [PubMed] [Google Scholar]
  930. Okamura K, Hagen JW, Duan H, Tyler DM and Lai EC, 2007. The mirtron pathway generates microRNA‐class regulatory RNAs in Drosophila. Cell, 130, 89–100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  931. Okamura K, Balla S, Martin R, Liu N and Lai EC, 2008a. Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster. Nature Structural & Molecular Biology, 15, 581–590. [DOI] [PMC free article] [PubMed] [Google Scholar]
  932. Okamura K, Chung WJ and Lai EC, 2008b. The long and short of inverted repeat genes in animals ‐ microRNAs, mirtrons and hairpin RNAs. Cell Cycle, 7, 2840–2845. [DOI] [PMC free article] [PubMed] [Google Scholar]
  933. Okamura K, Chung WJ, Ruby JG, Guo HL, Bartel DP and Lai EC, 2008c. The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature, 453, 803–U808. [DOI] [PMC free article] [PubMed] [Google Scholar]
  934. Okamura K, Liu N and Lai EC, 2009. Distinct Mechanisms for MicroRNA Strand Selection by Drosophila Argonautes. Molecular Cell, 36, 431–444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  935. Okamura K, Robine N, Liu Y, Liu QH and Lai EC, 2011. R2D2 Organizes Small Regulatory RNA Pathways in Drosophila. Molecular and Cellular Biology, 31, 884–896. [DOI] [PMC free article] [PubMed] [Google Scholar]
  936. Okamura K, Ladewig E, Zhou L and Lai EC, 2013. Functional small RNAs are generated from select miRNA hairpin loops in flies and mammals. Genes & Development, 27, 778–792. [DOI] [PMC free article] [PubMed] [Google Scholar]
  937. Ortiz‐Rivas B, Jaubert‐Possamai S, Tanguy S, Gauthier JP, Tagu D and Claude R, 2012. Evolutionary study of duplications of the miRNA machinery in aphids associated with striking rate acceleration and changes in expression profiles. Bmc Evolutionary Biology, 12, 216–216. [DOI] [PMC free article] [PubMed] [Google Scholar]
  938. Palladino MJ, Keegan LP, O'Connell MA and Reenan RA, 2000. dADAR, a Drosophila double‐stranded RNA‐specific adenosine deaminase is highly developmentally regulated and is itself a target for RNA editing. Rna, 6, 1004–1018. [DOI] [PMC free article] [PubMed] [Google Scholar]
  939. Palmer WJ and Jiggins FM, 2015. Comparative Genomics Reveals the Origins and Diversity of Arthropod Immune Systems. Molecular Biology and Evolution, 32, 2111–2129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  940. Paradkar PN, Trinidad L, Voysey R, Duchemin JB and Walker PJ, 2012. Secreted Vago restricts West Nile virus infection in Culex mosquito cells by activating the Jak‐STAT pathway. Proc Natl Acad Sci U S A, 109, 18915–18920. [DOI] [PMC free article] [PubMed] [Google Scholar]
  941. Paro S, Li XH, O'Connell MA and Keegan LP, 2012. Regulation and Functions of ADAR in Drosophila. In: Adenosine Deaminases Acting on Rna. 221–236. [DOI] [PubMed] [Google Scholar]
  942. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Muller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E and Ruvkun G, 2000. Conservation of the sequence and temporal expression of let‐7 heterochronic regulatory RNA. Nature, 408, 86–89. [DOI] [PubMed] [Google Scholar]
  943. Peters L and Meister G, 2007. Argonaute proteins: mediators of RNA silencing. Molecular Cell, 26, 611–623. [DOI] [PubMed] [Google Scholar]
  944. Peters NT, Rohrbach JA, Zalewski BA, Byrkett CM and Vaughn JC, 2003. RNA editing and regulation of Drosophila 4f‐rnp expression by sas‐10 antisense readthrough mRNA transcripts. Rna, 9, 698–710. [DOI] [PMC free article] [PubMed] [Google Scholar]
  945. Pham JW, Pellino JL, Lee YS, Carthew RW and Sontheimer EJ, 2004. A Dicer‐2‐dependent 80S complex cleaves targeted mRNAs during RNAi in Drosophila. Cell, 117, 83–94. [DOI] [PubMed] [Google Scholar]
  946. Phetrungnapha A, Ho T, Udomkit A, Panyim S and Ongvarrasopone C, 2013. Molecular cloning and functional characterization of Argonaute‐3 gene from Penaeus monodon. Fish & Shellfish Immunology, 35, 874–882. [DOI] [PubMed] [Google Scholar]
  947. Pinder BD and Smibert CA, 2013. microRNA‐independent recruitment of Argonaute 1 to nanos mRNA through the Smaug RNA‐binding protein. EMBO Rep, 14, 80–86. [DOI] [PMC free article] [PubMed] [Google Scholar]
  948. Pressman S, Reinke CA, Wang XH and Carthew RW, 2012. A Systematic Genetic Screen to Dissect the MicroRNA Pathway in Drosophila. G3‐Genes Genomes. Genetics, 2, 437–448. [DOI] [PMC free article] [PubMed] [Google Scholar]
  949. Provost P, Dishart D, Doucet J, Frendewey D, Samuelsson B and Radmark O, 2002. Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J, 21, 5864–5874. [DOI] [PMC free article] [PubMed] [Google Scholar]
  950. Pushpavalli S, Bag I, Pal‐Bhadra M and Bhadra U, 2012. Drosophila Argonaute‐1 is critical for transcriptional cosuppression and heterochromatin formation. Chromosome Research, 20, 333–351. [DOI] [PMC free article] [PubMed] [Google Scholar]
  951. Qi H, Watanabe T, Ku H‐Y, Liu N, Zhong M and Lin H, 2011. The Yb Body, a Major Site for Piwi‐associated RNA Biogenesis and a Gateway for Piwi Expression and Transport to the Nucleus in Somatic Cells. Journal of Biological Chemistry, 286, 3789–3797. [DOI] [PMC free article] [PubMed] [Google Scholar]
  952. Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, Wetzer R, Martin JW and Cunningham CW, 2010. Arthropod relationships revealed by phylogenomic analysis of nuclear protein‐coding sequences. Nature, 463, 1079–1083. [DOI] [PubMed] [Google Scholar]
  953. Rehwinkel J, Behm‐Ansmant I, Gatfield D and Izaurralde E, 2005. A crucial role for GW182 and the DCP1: DCP2 decapping complex in miRNA‐mediated gene silencing. Rna, 11, 1640–1647. [DOI] [PMC free article] [PubMed] [Google Scholar]
  954. Reimao‐Pinto MM, Ignatova V, Burkard TR, Hung JH, Manzenreither RA, Sowemimo I, Herzog VA, Reichholf B, Farina‐Lopez S and Ameres SL, 2015. Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila. Molecular Cell, 59, 203–216. [DOI] [PMC free article] [PubMed] [Google Scholar]
  955. Roignant JY, Carre C, Mugat B, Szymczak D, Lepesant JA and Antoniewski C, 2003. Absence of transitive and systemic pathways allows cell‐specific and isoform‐specific RNAi in Drosophila. Rna, 9, 299–308. [DOI] [PMC free article] [PubMed] [Google Scholar]
  956. Ruby JG, Jan CH and Bartel DP, 2007. Intronic microRNA precursors that bypass Drosha processing. Nature, 448, 83–86. [DOI] [PMC free article] [PubMed] [Google Scholar]
  957. Sabin LR and Cherry S, 2013. Small creatures use small RNAs to direct antiviral defenses. European Journal of Immunology, 43, 27–33. [DOI] [PMC free article] [PubMed] [Google Scholar]
  958. Saito K, Ishizuka A, Siomi H and Siomi MC, 2005. Processing of pre‐microRNAs by the Dicer‐1‐Loquacious complex in Drosophila cells. Plos Biology, 3, 1202–1212. [DOI] [PMC free article] [PubMed] [Google Scholar]
  959. Saito K, Sakaguchi Y, Suzuki T, Suzuki T, Siomi H and Siomi MC, 2007. Pimet, the Drosophila homolog of HEN1, mediates 2 ‘‐O‐methylation of PIWI‐interacting RNAs at their 3 ‘ ends. Genes & Development, 21, 1603–1608. [DOI] [PMC free article] [PubMed] [Google Scholar]
  960. Saito K, Ishizu H, Komai M, Kotani H, Kawamura Y, Nishida KM, Siomi H and Siomi MC, 2010. Roles for the Yb body components Armitage and Yb in primary piRNA biogenesis in Drosophila. Genes & Development, 24, 2493–2498. [DOI] [PMC free article] [PubMed] [Google Scholar]
  961. Saleh MC, Tassetto M, van Rij RP, Goic B, Gausson V, Berry B, Jacquier C, Antoniewski C and Andino R, 2009. Antiviral immunity in Drosophila requires systemic RNA interference spread. Nature, 458, 346–350. [DOI] [PMC free article] [PubMed] [Google Scholar]
  962. Sanchez‐Vargas I, Scott JC, Poole‐Smith BK, Franz AWE, Barbosa‐Solomieu V, Wilusz J, Olson KE and Blair CD, 2009. Dengue Virus Type 2 Infections of Aedes aegypti Are Modulated by the Mosquito's RNA Interference Pathway. Plos Pathogens, 5, e1000299–e1000299. [DOI] [PMC free article] [PubMed] [Google Scholar]
  963. Sato K and Siomi MC, 2013. Piwi‐interacting RNAs: biological functions and biogenesis. Essays in biochemistry, 54, 39–52. [DOI] [PubMed] [Google Scholar]
  964. Schnettler E, Donald CL, Human S, Watson M, Siu RWC, McFarlane M, Fazakerley JK, Kohl A and Fragkoudis R, 2013a. Knockdown of piRNA pathway proteins results in enhanced Semliki Forest virus production in mosquito cells. Journal of General Virology, 94, 1680–1689. [DOI] [PMC free article] [PubMed] [Google Scholar]
  965. Schnettler E, Ratinier M, Watson M, Shaw AE, McFarlane M, Varela M, Elliott RM, Palmarini M and Kohl A, 2013b. RNA Interference Targets Arbovirus Replication in Culicoides Cells. Journal of Virology, 87, 2441–2454. [DOI] [PMC free article] [PubMed] [Google Scholar]
  966. Schnettler E, Tykalova H, Watson M, Sharma M, Sterken MG, Obbard DJ, Lewis SH, McFarlane M, Bell‐Sakyi L, Barry G, Weisheit S, Best SM, Kuhn RJ, Pijlman GP, Chase‐Topping ME, Gould EA, Grubhoffer L, Fazakerley JK and Kohl A, 2014. Induction and suppression of tick cell antiviral RNAi responses by tick‐borne flaviviruses. Nucleic Acids Research, 42, 9436–9446. [DOI] [PMC free article] [PubMed] [Google Scholar]
  967. Schuster S, Zirkel F, Kurth A, van Cleef KWR, Drosten C, van Rij RP and Junglen S, 2014. A Unique Nodavirus with Novel Features: Mosinovirus Expresses Two Subgenomic RNAs, a Capsid Gene of Unknown Origin, and a Suppressor of the Antiviral RNA Interference Pathway. Journal of Virology, 88, 13447–13459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  968. Schwarz DS, Hutvagner G, Haley B and Zamore PD, 2002. Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways. Molecular Cell, 10, 537–548. [DOI] [PubMed] [Google Scholar]
  969. Schwarz DS, Tomari Y and Zamore PD, 2004. The RNA‐induced silencing complex is a Mg2+‐dependent endonuclease. Current Biology, 14, 787–791. [DOI] [PubMed] [Google Scholar]
  970. Shih JD and Hunter CP, 2011. SID‐1 is a dsRNA‐selective dsRNA‐gated channel. Rna, 17, 1057–1065. [DOI] [PMC free article] [PubMed] [Google Scholar]
  971. Shreve JT, Shukle RH, Subramanyam S, Johnson AJ, Schemerhorn BJ, Williams CE and Stuart JJ, 2013. A genome‐wide survey of small interfering RNA and microRNA pathway genes in a galling insect. Journal of Insect Physiology, 59, 367–376. [DOI] [PubMed] [Google Scholar]
  972. Sinha NK, Trettin KD, Aruscavage PJ and Bass BL, 2015. Drosophila Dicer‐2 Cleavage Is Mediated by Helicase‐ and dsRNA Termini‐Dependent States that Are Modulated by Loquacious‐PD. Molecular Cell, 58, 406–417. [DOI] [PMC free article] [PubMed] [Google Scholar]
  973. Smibert P, Bejarano F, Wang D, Garaulet DL, Yang JS, Martin R, Bortolamiol‐Becet D, Robine N, Hiesinger PR and Lai EC, 2011. A Drosophila genetic screen yields allelic series of core microRNA biogenesis factors and reveals post‐developmental roles for microRNAs. Rna, 17, 1997–2010. [DOI] [PMC free article] [PubMed] [Google Scholar]
  974. Song JS, Guo W, Jiang F, Kang L and Zhou ST, 2013. Argonaute 1 is indispensable for juvenile hormone mediated oogenesis in the migratory locust, Locusta migratoria. Insect Biochemistry and Molecular Biology, 43, 879–887. [DOI] [PubMed] [Google Scholar]
  975. Su JS, Oanh DTH, Lyons RE, Leeton L, van Hulten MCW, Tan SH, Song L, Rajendran KV and Walker PJ, 2008. A key gene of the RNA interference pathway in the black tiger shrimp, Penaeus monodon: Identification and functional characterisation of Dicer‐1. Fish & Shellfish Immunology, 24, 223–233. [DOI] [PubMed] [Google Scholar]
  976. Taliaferro JM, Aspden JL, Bradley T, Marwha D, Blanchette M and Rio DC, 2013. Two new and distinct roles for Drosophila Argonaute‐2 in the nucleus: alternative pre‐mRNA splicing and transcriptional repression. Genes & Development, 27, 378–389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  977. Tomari Y, Du TT, Haley B, Schwarz DS, Bennett R, Cook HA, Koppetsch BS, Theurkauf WE and Zamore PD, 2004a. RISC assembly defects in the Drosophila RNAi mutant armitage. Cell, 116, 831–841. [DOI] [PubMed] [Google Scholar]
  978. Tomari Y, Matranga C, Haley B, Martinez N and Zamore PD, 2004b. A protein sensor for siRNA asymmetry. Science, 306, 1377–1380. [DOI] [PubMed] [Google Scholar]
  979. Tomari Y and Zamore PD, 2005. Perspective: machines for RNAi. Genes Dev, 19, 517–529. [DOI] [PubMed] [Google Scholar]
  980. Tomari Y, Du T and Zamore PD, 2007. Sorting of Drosophila small silencing RNAs. Cell, 130, 299–308. [DOI] [PMC free article] [PubMed] [Google Scholar]
  981. Tomoyasu Y, Miller SC, Tomita S, Schoppmeier M, Grossmann D and Bucher G, 2008. Exploring systemic RNA interference in insects: a genome‐wide survey for RNAi genes in Tribolium. Genome Biology, 9, R10–R10. [DOI] [PMC free article] [PubMed] [Google Scholar]
  982. Tsutsumi A, Kawamata T, Izumi N, Seitz H and Tomari Y, 2011. Recognition of the pre‐miRNA structure by Drosophila Dicer‐1. Nature Structural & Molecular Biology, 18, 1153–U1189. [DOI] [PubMed] [Google Scholar]
  983. van Cleef KWR, van Mierlo JT, Miesen P, Overheul GJ, Fros JJ, Schuster S, Marklewitz M, Pijlman GP, Junglen S and van Rij RP, 2014. Mosquito and Drosophila entomobirnaviruses suppress dsRNA‐ and siRNA‐induced RNAi. Nucleic Acids Research, 42, 8732–8744. [DOI] [PMC free article] [PubMed] [Google Scholar]
  984. van Rij RP, Saleh MC, Berry B, Foo C, Houk A, Antoniewski C and Andino R, 2006. The RNA silencing endonuclease Argonaute 2 mediates specific antiviral immunity in Drosophila melanogaster. Genes & Development, 20, 2985–2995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  985. Vodovar N, Bronkhorst AW, van Cleef KWR, Miesen P, Blanc H, van Rij RP and Saleh MC, 2012. Arbovirus‐Derived piRNAs Exhibit a Ping‐Pong Signature in Mosquito Cells. Plos One, 7, e30861–e30861. [DOI] [PMC free article] [PubMed] [Google Scholar]
  986. Wang H, Ma ZJ, Niu KY, Xiao Y, Wu XF, Pan CY, Zhao Y, Wang K, Zhang YY and Liu N, 2016. Antagonistic roles of Nibbler and Hen1 in modulating piRNA 3 ‘ ends in Drosophila. Development, 143, 530–539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  987. Wang HD, Gong L, Qi JW, Hu MY, Zhong GH and Gong L, 2014. Molecular cloning and characterization of a SID‐1‐like gene in Plutella xylostella. Archives of Insect Biochemistry and Physiology, 87, 164–176. [DOI] [PubMed] [Google Scholar]
  988. Wang PH, Yang LS, Gu ZH, Weng SP, Yu XQ and He JG, 2013. Nucleic acid‐induced antiviral immunity in shrimp. Antiviral Research, 99, 270–280. [DOI] [PubMed] [Google Scholar]
  989. Wang PH, Weng SP and He JG, 2015a. Nucleic acid‐induced antiviral immunity in invertebrates: An evolutionary perspective. Developmental and Comparative Immunology, 48, 291–296. [DOI] [PubMed] [Google Scholar]
  990. Wang XH, Aliyari R, Li WX, Li HW, Kim K, Carthew R, Atkinson P and Ding SW, 2006. RNA interference directs innate immunity against viruses in adult Drosophila. Science, 312, 452–454. [DOI] [PMC free article] [PubMed] [Google Scholar]
  991. Wang Z, Wu D, Liu Y, Xia X, Gong W, Qiu Y, Yang J, Zheng Y, Li J, Wang YF, Xiang Y, Hu Y and Zhou X, 2015b. Drosophila Dicer‐2 has an RNA interference‐independent function that modulates Toll immune signaling. Science advances, 1, e1500228–e1500228. [DOI] [PMC free article] [PubMed] [Google Scholar]
  992. Welker NC, Maity TS, Ye XC, Aruscavage PJ, Krauchuk AA, Liu QH and Bass BL, 2011. Dicer's Helicase Domain Discriminates dsRNA Termini to Promote an Altered Reaction Mode. Molecular Cell, 41, 589–599. [DOI] [PMC free article] [PubMed] [Google Scholar]
  993. Wen JY, Duan H, Bejarano F, Okamura K, Fabian L, Brill JA, Bortolamiol‐Becet D, Martin R, Ruby JG and Lai EC, 2015. Adaptive Regulation of Testis Gene Expression and Control of Male Fertility by the Drosophila Harpin RNA Pathway. Molecular Cell, 57, 165–178. [DOI] [PMC free article] [PubMed] [Google Scholar]
  994. Westholm JO, Ladewig E, Okamura K, Robine N and Lai EC, 2012. Common and distinct patterns of terminal modifications to mirtrons and canonical microRNAs. Rna, 18, 177–192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  995. Winter F, Edaye S, Huttenhofer A and Brunel C, 2007. Anopheles gambiae miRNAs as actors of defence reaction against Plasmodium invasion. Nucleic Acids Research, 35, 6953–6962. [DOI] [PMC free article] [PubMed] [Google Scholar]
  996. Wynant N, Santos D, Subramanyam SH, Verlinden H and Broeck JV, 2015. Drosha, Dicer‐1 and Argonaute‐1 in the desert locust: Phylogenetic analyses, transcript profiling and regulation during phase transition and feeding. Journal of Insect Physiology, 75, 20–29. [DOI] [PubMed] [Google Scholar]
  997. Xiong XP, Vogler G, Kurthkoti K, Samsonova A and Zhou R, 2015. SmD1 Modulates the miRNA Pathway Independently of Its Pre‐mRNA Splicing Function. Plos Genetics, 11, e1005475–e1005475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  998. Xu HJ, Chen T, Ma XF, Xue J, Pan PL, Zhang XC, Cheng JA and Zhang CX, 2013. Genome‐wide screening for components of small interfering RNA (siRNA) and micro‐RNA (miRNA) pathways in the brown planthopper, Nilaparvata lugens (Hemiptera: Delphacidae). Insect Molecular Biology, 22, 635–647. [DOI] [PubMed] [Google Scholar]
  999. Xu KY, Bogert BA, Li WJ, Su K, Lee A and Gao FB, 2004. The fragile X‐related gene affects the crawling behavior of Drosophila larvae by regulating the mRNA level of the DEG/ENaC protein pickpocket1. Current Biology, 14, 1025–1034. [DOI] [PubMed] [Google Scholar]
  1000. Xu W and Han Z, 2008. Cloning and phylogenetic analysis of sid‐1‐like genes from aphids. Journal of insect science (Online), 8, 1–6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1001. Yang JS, Smibert P, Westholm JO, Jee D, Maurin T and Lai EC, 2014a. Intertwined pathways for Argonaute‐mediated microRNA biogenesis in Drosophila. Nucleic Acids Research, 42, 1987–2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1002. Yang LL, Chen DS, Duan RH, Xia LX, Wang J, Qurashi A, Jin P and Chen DH, 2007. Argonaute 1 regulates the fate of germline stem cells in Drosophila. Development, 134, 4265–4272. [DOI] [PubMed] [Google Scholar]
  1003. Yang LS, Li XL, Jiang S, Qiu LH, Zhou FL, Liu WJ and Jiang SG, 2014b. Characterization of Argonaute2 gene from black tiger shrimp (Penaeus monodon) and its responses to immune challenges. Fish & Shellfish Immunology, 36, 261–269. [DOI] [PubMed] [Google Scholar]
  1004. Ye XC, Paroo Z and Liu QH, 2007. Functional anatomy of the Drosophila MicroRNA‐ generating enzyme. Journal of Biological Chemistry, 282, 28373–28378. [DOI] [PubMed] [Google Scholar]
  1005. Yoda M, Kawamata T, Paroo Z, Ye XC, Iwasaki S, Liu QH and Tomari Y, 2010. ATP‐dependent human RISC assembly pathways. Nature Structural & Molecular Biology, 17, 17–U29. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1006. Zambon RA, Vakharia VN and Wu LP, 2006. RNAi is an antiviral immune response against a dsRNA virus in Drosophila melanogaster. Cellular Microbiology, 8, 880–889. [DOI] [PubMed] [Google Scholar]
  1007. Zhang H, Kolb FA, Brondani V, Billy E and Filipowicz W, 2002. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J, 21, 5875–5885. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1008. Zhang XY, Lu K, Zhou JL and Zhou Q, 2013. Molecular characterization and gene functional analysis of Dicer‐2 gene from Nilaparvata lugens (Hemiptera: Geometroidea). Insect Science, 20, 61–68. [DOI] [PubMed] [Google Scholar]
  1009. Zhao CY, Gonzales MAA, Poland TM and Mittapalli O, 2015. Core RNAi machinery and gene knockdown in the emerald ash borer (Agrilus planipennis). Journal of Insect Physiology, 72, 70–78. [DOI] [PubMed] [Google Scholar]
  1010. Zhou R, Czech B, Brennecke J, Sachidanandam R, Wohlschlegel JA, Perrimon N and Hannon GJ, 2009. Processing of Drosophila endo‐siRNAs depends on a specific Loquacious isoform. Rna, 15, 1886–1895. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1011. Zhu L, Tatsuke T, Li ZQ, Mon H, Xu J, Lee JM and Kusakabe T, 2012. Molecular cloning of BmTUDOR‐SN and analysis of its role in the RNAi pathway in the silkworm, Bombyx mori (Lepidoptera: Bombycidae). Applied Entomology and Zoology, 47, 207–215. [Google Scholar]
  1012. Zografidis A, Van Nieuwerburgh F, Kolliopoulou A, Apostolou‐Karampelis K, Head SR, Deforce D, Smagghe G and Swevers L, 2015. Viral Small‐RNA Analysis of Bombyx mori Larval Midgut during Persistent and Pathogenic Cytoplasmic Polyhedrosis Virus Infection. Journal of Virology, 89, 11473–11486. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1013. Athanasiadis A, Rich A and Maas S, 2004. Widespread A‐to‐I RNA editing of Alu‐containing mRNAs in the human transcriptome. PLoS Biol, 2, e391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1014. Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, Eachus R and Pasquinelli AE, 2005. Regulation by let‐7 and lin‐4 miRNAs results in target mRNA degradation. Cell, 122, 553–563. [DOI] [PubMed] [Google Scholar]
  1015. Bartel DP, 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281–297. [DOI] [PubMed] [Google Scholar]
  1016. Bernstein E, Caudy AA, Hammond SM and Hannon GJ, 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409, 363–366. [DOI] [PubMed] [Google Scholar]
  1017. Brennecke J, Stark A, Russell RB and Cohen SM, 2005. Principles of microRNA‐target recognition. PLoS Biol, 3, e85. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1018. Carmell MA, Xuan Z, Zhang MQ and Hannon GJ, 2002. The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev, 16, 2733–2742. [DOI] [PubMed] [Google Scholar]
  1019. Cerutti H and Casas‐Mollano JA, 2006. On the origin and functions of RNA‐mediated silencing: from protists to man. Curr Genet, 50, 81–99. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1020. Chen Y, Boland A, Kuzuoglu‐Ozturk D, Bawankar P, Loh B, Chang CT, Weichenrieder O and Izaurralde E, 2014. A DDX6‐CNOT1 complex and W‐binding pockets in CNOT9 reveal direct links between miRNA target recognition and silencing. Mol Cell, 54, 737–750. [DOI] [PubMed] [Google Scholar]
  1021. Chera S, de Rosa R, Miljkovic‐Licina M, Dobretz K, Ghila L, Kaloulis K and Galliot B, 2006. Silencing of the hydra serine protease inhibitor Kazal1 gene mimics the human SPINK1 pancreatic phenotype. J Cell Sci, 119, 846–857. [DOI] [PubMed] [Google Scholar]
  1022. Cogoni C and Macino G, 1999. Gene silencing in Neurospora crassa requires a protein homologous to RNA‐dependent RNA polymerase. Nature, 399, 166–169. [DOI] [PubMed] [Google Scholar]
  1023. Dalmay T, Horsefield R, Braunstein TH and Baulcombe DC, 2001. SDE3 encodes an RNA helicase required for post‐transcriptional gene silencing in Arabidopsis . EMBO J, 20, 2069–2078. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1024. Decker CJ and Parker R, 2012. P‐bodies and stress granules: possible roles in the control of translation and mRNA degradation. Cold Spring Harb Perspect Biol, 4, a012286. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1025. Djuranovic S, Nahvi A and Green R, 2012. miRNA‐mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science, 336, 237–240. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1026. Dlakic M, 2006. DUF283 domain of Dicer proteins has a double‐stranded RNA‐binding fold. Bioinformatics, 22, 2711–2714. [DOI] [PubMed] [Google Scholar]
  1027. Doench JG, Petersen CP and Sharp PA, 2003. siRNAs can function as miRNAs. Genes Dev, 17, 438–442. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1028. Du T and Zamore PD, 2005. microPrimer: the biogenesis and function of microRNA. Development, 132, 4645–4652. [DOI] [PubMed] [Google Scholar]
  1029. Eichhorn SW, Guo H, McGeary SE, Rodriguez‐Mias RA, Shin C, Baek D, Hsu SH, Ghoshal K, Villen J and Bartel DP, 2014. mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Mol Cell, 56, 104–115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1030. Faehnle CR and Joshua‐Tor L, 2007. Argonautes confront new small RNAs. Curr Opin Chem Biol, 11, 569–577. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1031. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE and Mello CC, 1998. Potent and specific genetic interference by double‐stranded RNA in Caenorhabditis elegans. Nature, 391, 806–811. [DOI] [PubMed] [Google Scholar]
  1032. Friedman RC, Farh KK, Burge CB and Bartel DP, 2009. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res, 19, 92–105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1033. Gantier MP and Williams BR, 2007. The response of mammalian cells to double‐stranded RNA. Cytokine Growth Factor Rev, 18, 363–371. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1034. Geiss G, Jin G, Guo J, Bumgarner R, Katze MG and Sen GC, 2001. A comprehensive view of regulation of gene expression by double‐stranded RNA‐mediated cell signaling. J Biol Chem, 276, 30178–30182. [DOI] [PubMed] [Google Scholar]
  1035. Geldhof P, Visser A, Clark D, Saunders G, Britton C, Gilleard J, Berriman M and Knox D, 2007. RNA interference in parasitic helminths: current situation, potential pitfalls and future prospects. Parasitology, 134, 609–619. [DOI] [PubMed] [Google Scholar]
  1036. Grice LF and Degnan BM, 2015. The origin of the ADAR gene family and animal RNA editing. BMC Evol Biol, 15, 4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1037. Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A, Ruvkun G and Mello CC, 2001. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell, 106, 23–34. [DOI] [PubMed] [Google Scholar]
  1038. Hall IM, Shankaranarayana GD, Noma K, Ayoub N, Cohen A and Grewal SI, 2002. Establishment and maintenance of a heterochromatin domain. Science, 297, 2232–2237. [DOI] [PubMed] [Google Scholar]
  1039. Hamilton AJ and Baulcombe DC, 1999. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science, 286, 950–952. [DOI] [PubMed] [Google Scholar]
  1040. Higuchi M, Maas S, Single FN, Hartner J, Rozov A, Burnashev N, Feldmeyer D, Sprengel R and Seeburg PH, 2000. Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA‐editing enzyme ADAR2. Nature, 406, 78–81. [DOI] [PubMed] [Google Scholar]
  1041. Himber C, Dunoyer P, Moissiard G, Ritzenthaler C and Voinnet O, 2003. Transitivity‐dependent and ‐independent cell‐to‐cell movement of RNA silencing. EMBO J, 22, 4523–4533. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1042. Hunter T, Hunt T, Jackson RJ and Robertson HD, 1975. The characteristics of inhibition of protein synthesis by double‐stranded ribonucleic acid in reticulocyte lysates. J Biol Chem, 250, 409–417. [PubMed] [Google Scholar]
  1043. Hutvagner G and Zamore PD, 2002. A microRNA in a multiple‐turnover RNAi enzyme complex. Science, 297, 2056–2060. [DOI] [PubMed] [Google Scholar]
  1044. Huvenne H and Smagghe G, 2010. Mechanisms of dsRNA uptake in insects and potential of RNAi for pest control: a review. J Insect Physiol, 56, 227–235. [DOI] [PubMed] [Google Scholar]
  1045. Jaskiewicz L and Filipowicz W, 2008. Role of Dicer in posttranscriptional RNA silencing. Curr Top Microbiol Immunol, 320, 77–97. [DOI] [PubMed] [Google Scholar]
  1046. Jinek M and Doudna JA, 2009. A three‐dimensional view of the molecular machinery of RNA interference. Nature, 457, 405–412. [DOI] [PubMed] [Google Scholar]
  1047. Kawahara Y, Zinshteyn B, Chendrimada TP, Shiekhattar R and Nishikura K, 2007a. RNA editing of the microRNA‐151 precursor blocks cleavage by the Dicer‐TRBP complex. EMBO Rep, 8, 763–769. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1048. Kawahara Y, Zinshteyn B, Sethupathy P, Iizasa H, Hatzigeorgiou AG and Nishikura K, 2007b. Redirection of silencing targets by adenosine‐to‐inosine editing of miRNAs. Science, 315, 1137–1140. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1049. Ketting RF, 2011. The many faces of RNAi. Dev Cell, 20, 148–161. [DOI] [PubMed] [Google Scholar]
  1050. Kim VN, Han J and Siomi MC, 2009. Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol, 10, 126–139. [DOI] [PubMed] [Google Scholar]
  1051. Kozomara A and Griffiths‐Jones S, 2014. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res, 42, D68–73. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1052. Lee RC, Feinbaum RL and Ambros V, 1993. The C. elegans heterochronic gene lin‐4 encodes small RNAs with antisense complementarity to lin‐14. Cell, 75, 843–854. [DOI] [PubMed] [Google Scholar]
  1053. Lehmann KA and Bass BL, 1999. The importance of internal loops within RNA substrates of ADAR1. J Mol Biol, 291, 1–13. [DOI] [PubMed] [Google Scholar]
  1054. Lim LP, Lau NC, Garrett‐Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS and Johnson JM, 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature, 433, 769–773. [DOI] [PubMed] [Google Scholar]
  1055. Lingel A, Simon B, Izaurralde E and Sattler M, 2003. Structure and nucleic‐acid binding of the Drosophila Argonaute 2 PAZ domain. Nature, 426, 465–469. [DOI] [PubMed] [Google Scholar]
  1056. Lingel A, Simon B, Izaurralde E and Sattler M, 2004. Nucleic acid 3′‐end recognition by the Argonaute2 PAZ domain. Nat Struct Mol Biol, 11, 576–577. [DOI] [PubMed] [Google Scholar]
  1057. Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, Song JJ, Hammond SM, Joshua‐Tor L and Hannon GJ, 2004. Argonaute2 is the catalytic engine of mammalian RNAi. Science, 305, 1437–1441. [DOI] [PubMed] [Google Scholar]
  1058. Liu J, Valencia‐Sanchez MA, Hannon GJ and Parker R, 2005. MicroRNA‐dependent localization of targeted mRNAs to mammalian P‐bodies. Nat Cell Biol, 7, 719–723. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1059. Ma JB, Ye K and Patel DJ, 2004. Structural basis for overhang‐specific small interfering RNA recognition by the PAZ domain. Nature, 429, 318–322. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1060. Ma JB, Yuan YR, Meister G, Pei Y, Tuschl T and Patel DJ, 2005. Structural basis for 5′‐end‐specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature, 434, 666–670. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1061. MacRae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD and Doudna JA, 2006. Structural basis for double‐stranded RNA processing by Dicer. Science, 311, 195–198. [DOI] [PubMed] [Google Scholar]
  1062. MacRae IJ, Zhou K and Doudna JA, 2007. Structural determinants of RNA recognition and cleavage by Dicer. Nat Struct Mol Biol, 14, 934–940. [DOI] [PubMed] [Google Scholar]
  1063. Marques JT and Carthew RW, 2007. A call to arms: coevolution of animal viruses and host innate immune responses. Trends Genet, 23, 359–364. [DOI] [PubMed] [Google Scholar]
  1064. Martinez J, Patkaniowska A, Urlaub H, Luhrmann R and Tuschl T, 2002. Single‐stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell, 110, 563–574. [DOI] [PubMed] [Google Scholar]
  1065. Meins F, Jr , Si‐Ammour A and Blevins T, 2005. RNA silencing systems and their relevance to plant development. Annu Rev Cell Dev Biol, 21, 297–318. [DOI] [PubMed] [Google Scholar]
  1066. Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G and Tuschl T, 2004. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol Cell, 15, 185–197. [DOI] [PubMed] [Google Scholar]
  1067. Meister G and Tuschl T, 2004. Mechanisms of gene silencing by double‐stranded RNA. Nature, 431, 343–349. [DOI] [PubMed] [Google Scholar]
  1068. Meurs E, Chong K, Galabru J, Thomas NS, Kerr IM, Williams BR and Hovanessian AG, 1990. Molecular cloning and characterization of the human double‐stranded RNA‐activated protein kinase induced by interferon. Cell, 62, 379–390. [DOI] [PubMed] [Google Scholar]
  1069. Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L, Rappsilber J, Mann M and Dreyfuss G, 2002. miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev, 16, 720–728. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1070. Mourrain P, Beclin C, Elmayan T, Feuerbach F, Godon C, Morel JB, Jouette D, Lacombe AM, Nikic S, Picault N, Remoue K, Sanial M, Vo TA and Vaucheret H, 2000. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell, 101, 533–542. [DOI] [PubMed] [Google Scholar]
  1071. Murphy D, Dancis B and Brown JR, 2008. The evolution of core proteins involved in microRNA biogenesis. BMC Evol Biol, 8, 92. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1072. Napoli C, Lemieux C and Jorgensen R, 1990. Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co‐Suppression of Homologous Genes in trans. Plant Cell, 2, 279–289. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1073. Newmark PA, Reddien PW, Cebria F and Sanchez Alvarado A, 2003. Ingestion of bacterially expressed double‐stranded RNA inhibits gene expression in planarians. Proc Natl Acad Sci U S A, 100 Suppl 1, 11861–11865. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1074. Nishihara T, Zekri L, Braun JE and Izaurralde E, 2013. miRISC recruits decapping factors to miRNA targets to enhance their degradation. Nucleic Acids Res, 41, 8692–8705. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1075. Nishikura K, Yoo C, Kim U, Murray JM, Estes PA, Cash FE and Liebhaber SA, 1991. Substrate specificity of the dsRNA unwinding/modifying activity. EMBO J, 10, 3523–3532. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1076. Nishikura K, 2010. Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem, 79, 321–349. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1077. Nykanen A, Haley B and Zamore PD, 2001. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell, 107, 309–321. [DOI] [PubMed] [Google Scholar]
  1078. Orii H, Mochii M and Watanabe K, 2003. A simple “soaking method” for RNA interference in the planarian Dugesia japonica. Dev Genes Evol, 213, 138–141. [DOI] [PubMed] [Google Scholar]
  1079. Palladino MJ, Keegan LP, O'Connell MA and Reenan RA, 2000. A‐to‐I pre‐mRNA editing in Drosophila is primarily involved in adult nervous system function and integrity. Cell, 102, 437–449. [DOI] [PubMed] [Google Scholar]
  1080. Parker JS, Roe SM and Barford D, 2004. Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J, 23, 4727–4737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1081. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Muller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E and Ruvkun G, 2000. Conservation of the sequence and temporal expression of let‐7 heterochronic regulatory RNA. Nature, 408, 86–89. [DOI] [PubMed] [Google Scholar]
  1082. Pham JW, Pellino JL, Lee YS, Carthew RW and Sontheimer EJ, 2004. A Dicer‐2‐dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila. Cell, 117, 83–94. [DOI] [PubMed] [Google Scholar]
  1083. Pillai RS, Bhattacharyya SN, Artus CG, Zoller T, Cougot N, Basyuk E, Bertrand E and Filipowicz W, 2005. Inhibition of translational initiation by Let‐7 MicroRNA in human cells. Science, 309, 1573–1576. [DOI] [PubMed] [Google Scholar]
  1084. Polson AG and Bass BL, 1994. Preferential selection of adenosines for modification by double‐stranded RNA adenosine deaminase. EMBO J, 13, 5701–5711. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1085. Provost P, Dishart D, Doucet J, Frendewey D, Samuelsson B and Radmark O, 2002. Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J, 21, 5864–5874. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1086. Qin H, Chen F, Huan X, Machida S, Song J and Yuan YA, 2010. Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double‐stranded RNA‐binding fold for protein‐protein interaction. RNA, 16, 474–481. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1087. Roignant JY, Carre C, Mugat B, Szymczak D, Lepesant JA and Antoniewski C, 2003. Absence of transitive and systemic pathways allows cell‐specific and isoform‐specific RNAi in Drosophila. RNA, 9, 299–308. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1088. Romano N and Macino G, 1992. Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol Microbiol, 6, 3343–3353. [DOI] [PubMed] [Google Scholar]
  1089. Rouya C, Siddiqui N, Morita M, Duchaine TF, Fabian MR and Sonenberg N, 2014. Human DDX6 effects miRNA‐mediated gene silencing via direct binding to CNOT1. RNA, 20, 1398–1409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1090. Sadler AJ and Williams BR, 2007. Structure and function of the protein kinase R. Curr Top Microbiol Immunol, 316, 253–292. [DOI] [PubMed] [Google Scholar]
  1091. Scadden AD and Smith CW, 2001. RNAi is antagonized by A–>I hyper‐editing. EMBO Rep, 2, 1107–1111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1092. Scadden AD, 2005. The RISC subunit Tudor‐SN binds to hyper‐edited double‐stranded RNA and promotes its cleavage. Nat Struct Mol Biol, 12, 489–496. [DOI] [PubMed] [Google Scholar]
  1093. Schmitter D, Filkowski J, Sewer A, Pillai RS, Oakeley EJ, Zavolan M, Svoboda P and Filipowicz W, 2006. Effects of Dicer and Argonaute down‐regulation on mRNA levels in human HEK293 cells. Nucleic Acids Res, 34, 4801–4815. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1094. Schwarz DS, Hutvagner G, Haley B and Zamore PD, 2002. Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways. Mol Cell, 10, 537–548. [DOI] [PubMed] [Google Scholar]
  1095. Smardon A, Spoerke JM, Stacey SC, Klein ME, Mackin N and Maine EM, 2000. EGO‐1 is related to RNA‐directed RNA polymerase and functions in germ‐line development and RNA interference in C. elegans. Curr Biol, 10, 169–178. [DOI] [PubMed] [Google Scholar]
  1096. Song JJ, Liu J, Tolia NH, Schneiderman J, Smith SK, Martienssen RA, Hannon GJ and Joshua‐Tor L, 2003. The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat Struct Biol, 10, 1026–1032. [DOI] [PubMed] [Google Scholar]
  1097. Song JJ, Smith SK, Hannon GJ and Joshua‐Tor L, 2004. Crystal structure of Argonaute and its implications for RISC slicer activity. Science, 305, 1434–1437. [DOI] [PubMed] [Google Scholar]
  1098. Sontheimer EJ, 2005. Assembly and function of RNA silencing complexes. Nat Rev Mol Cell Biol, 6, 127–138. [DOI] [PubMed] [Google Scholar]
  1099. Stein P, Svoboda P, Anger M and Schultz RM, 2003. RNAi: mammalian oocytes do it without RNA‐dependent RNA polymerase. RNA, 9, 187–192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1100. Svoboda P and Cara AD, 2006. Hairpin RNA: a secondary structure of primary importance. Cell Mol Life Sci, 63, 901–908. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1101. Tabara H, Grishok A and Mello CC, 1998. RNAi in C. elegans: soaking in the genome sequence. Science, 282, 430–431. [DOI] [PubMed] [Google Scholar]
  1102. Timmons L and Fire A, 1998. Specific interference by ingested dsRNA. Nature, 395, 854. [DOI] [PubMed] [Google Scholar]
  1103. Tomoyasu Y, Miller SC, Tomita S, Schoppmeier M, Grossmann D and Bucher G, 2008. Exploring systemic RNA interference in insects: a genome‐wide survey for RNAi genes in Tribolium. Genome Biol, 9, R10. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1104. Tonkin LA, Saccomanno L, Morse DP, Brodigan T, Krause M and Bass BL, 2002. RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans. EMBO J, 21, 6025–6035. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1105. Tonkin LA and Bass BL, 2003. Mutations in RNAi rescue aberrant chemotaxis of ADAR mutants. Science, 302, 1725. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1106. van der Krol AR, Mur LA, Beld M, Mol JN and Stuitje AR, 1990. Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell, 2, 291–299. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1107. Voinnet O, Pinto YM and Baulcombe DC, 1999. Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants. Proc Natl Acad Sci U S A, 96, 14147–14152. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1108. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI and Martienssen RA, 2002. Regulation of heterochromatic silencing and histone H3 lysine‐9 methylation by RNAi. Science, 297, 1833–1837. [DOI] [PubMed] [Google Scholar]
  1109. Wang Q, Khillan J, Gadue P and Nishikura K, 2000. Requirement of the RNA editing deaminase ADAR1 gene for embryonic erythropoiesis. Science, 290, 1765–1768. [DOI] [PubMed] [Google Scholar]
  1110. Whangbo JS and Hunter CP, 2008. Environmental RNA interference. Trends Genet, 24, 297–305. [DOI] [PubMed] [Google Scholar]
  1111. Winter J, Jung S, Keller S, Gregory RI and Diederichs S, 2009. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol, 11, 228–234. [DOI] [PubMed] [Google Scholar]
  1112. Xie Q and Guo HS, 2006. Systemic antiviral silencing in plants. Virus Res, 118, 1–6. [DOI] [PubMed] [Google Scholar]
  1113. Xu W and Han Z, 2008. Cloning and phylogenetic analysis of sid‐1‐like genes from aphids. J Insect Sci, 8, 1–6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1114. Yan KS, Yan S, Farooq A, Han A, Zeng L and Zhou MM, 2003. Structure and conserved RNA binding of the PAZ domain. Nature, 426, 468–474. [DOI] [PubMed] [Google Scholar]
  1115. Yang W, Chendrimada TP, Wang Q, Higuchi M, Seeburg PH, Shiekhattar R and Nishikura K, 2006. Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat Struct Mol Biol, 13, 13–21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1116. Yoneyama M, Kikuchi M, Natsukawa T, Shinobu N, Imaizumi T, Miyagishi M, Taira K, Akira S and Fujita T, 2004. The RNA helicase RIG‐I has an essential function in double‐stranded RNA‐induced innate antiviral responses. Nat Immunol, 5, 730–737. [DOI] [PubMed] [Google Scholar]
  1117. Yuan YR, Pei Y, Ma JB, Kuryavyi V, Zhadina M, Meister G, Chen HY, Dauter Z, Tuschl T and Patel DJ, 2005. Crystal structure of A. aeolicus argonaute, a site‐specific DNA‐guided endoribonuclease, provides insights into RISC‐mediated mRNA cleavage. Mol Cell, 19, 405–419. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1118. Zamore PD, Tuschl T, Sharp PA and Bartel DP, 2000. RNAi: double‐stranded RNA directs the ATP‐dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell, 101, 25–33. [DOI] [PubMed] [Google Scholar]
  1119. Zhang H, Kolb FA, Brondani V, Billy E and Filipowicz W, 2002. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J, 21, 5875–5885. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1120. Zhang H, Kolb FA, Jaskiewicz L, Westhof E and Filipowicz W, 2004. Single processing center models for human Dicer and bacterial RNase III. Cell, 118, 57–68. [DOI] [PubMed] [Google Scholar]
  1121. Adilakshmi T, Sudol I and Tapinos N, 2012. Combinatorial Action of miRNAs Regulates Transcriptional and Post‐Transcriptional Gene Silencing following in vivo PNS Injury. PLoS ONE, 7, e39674–e39674. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1122. Agranat L, Raitskin O, Sperling J and Sperling R, 2008. The editing enzyme ADAR1 and the mRNA surveillance protein hUpf1 interact in the cell nucleus. Proc Natl Acad Sci U S A, 105, 5028–5033. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1123. Ahlenstiel CL, Lim HGW, Cooper DA, Ishida T, Kelleher AD and Suzuki K, 2012. Direct evidence of nuclear Argonaute distribution during transcriptional silencing links the actin cytoskeleton to nuclear RNAi machinery in human cells. Nucleic Acids Research, 40, 1579–1595. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1124. Aizer A, Kalo A, Kafri P, Shraga A, Ben‐Yishay R, Jacob A, Kinor N and Shav‐Tal Y, 2014. Quantifying mRNA targeting to P‐bodies in living human cells reveals their dual role in mRNA decay and storage. Journal of Cell Science, 127, 4443–4456. [DOI] [PubMed] [Google Scholar]
  1125. Alarcon CR, Lee H, Goodarzi H, Halberg N and Tavazoie SF, 2015. N‐6‐methyladenosine marks primary microRNAs for processing. Nature, 519, 482–+. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1126. Allo M, Buggiano V, Fededa JP, Petrillo E, Schor I, de la Mata M, Agirre E, Plass M, Eyras E, Elela SA, Klinck R, Chabot B and Kornblihtt AR, 2009. Control of alternative splicing through siRNA‐mediated transcriptional gene silencing. Nature Structural & Molecular Biology, 16, 717–724. [DOI] [PubMed] [Google Scholar]
  1127. Allo M, Agirre E, Bessonov S, Bertucci P, Acuna LG, Buggiano V, Bellora N, Singh B, Petrillo E, Blaustein M, Minana B, Dujardin G, Pozzi B, Pelisch F, Bechara E, Agafonov DE, Srebrow A, Luhrmann R, Valcarcel J, Eyras E and Kornblihtt AR, 2014. Argonaute‐1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells. Proc Natl Acad Sci U S A, 111, 15622–15629. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1128. Alon S, Mor E, Vigneault F, Church GM, Locatelli F, Galeano F, Gallo A, Shomron N and Eisenberg E, 2012. Systematic identification of edited microRNAs in the human brain. Genome Research, 22, 1533–1540. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1129. Amarante MK, Oda JMM, Reiche EMV, Morimoto HK, Aoki MN and Watanabe MAE, 2011. Human endogenous RNAs: Implications for the immunomodulation of Toll‐like receptor 3. Experimental and Therapeutic Medicine, 2, 925–929. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1130. Ameres SL, Martinez J and Schroeder R, 2007. Molecular basis for target RNA recognition and cleavage by human RISC. Cell, 130, 101–112. [DOI] [PubMed] [Google Scholar]
  1131. Ameyar‐Zazoua M, Rachez C, Souidi M, Robin P, Fritsch L, Young R, Morozova N, Fenouil R, Descostes N, Andrau J‐C, Mathieu J, Hamiche A, Ait‐Si‐Ali S, Muchardt C, Batsche E and Harel‐Bellan A, 2012. Argonaute proteins couple chromatin silencing to alternative splicing. Nature Structural & Molecular Biology, 19, 998–U946. [DOI] [PubMed] [Google Scholar]
  1132. Ando Y, Maida Y, Morinaga A, Burroughs AM, Kimura R, Chiba J, Suzuki H, Masutomi K and Hayashizaki Y, 2011a. Two‐step cleavage of hairpin RNA with 5 ‘ overhangs by human DICER. Bmc Molecular Biology, 12, 6–6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1133. Ando Y, Tomaru Y, Morinaga A, Burroughs AM, Kawaji H, Kubosaki A, Kimura R, Tagata M, Ino Y, Hirano H, Chiba J, Suzuki H, Carninci P and Hayashizaki Y, 2011b. Nuclear Pore Complex Protein Mediated Nuclear Localization of Dicer Protein in Human Cells. PLoS ONE, 6, e23385–e23385. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1134. Aporntewan C, Phokaew C, Piriyapongsa J, Ngamphiw C, Ittiwut C, Tongsima S and Mutirangura A, 2011. Hypomethylation of Intragenic LINE‐1 Represses Transcription in Cancer Cells through AGO2. PLoS ONE, 6, e17934–e17934. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1135. Arroyo JD, Chevillet JR, Kroh EM, Ruf IK, Pritchard CC, Gibson DF, Mitchell PS, Bennett CF, Pogosova‐Agadjanyan EL, Stirewalt DL, Tait JF and Tewari M, 2011. Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc Natl Acad Sci U S A, 108, 5003–5008. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1136. Athanasiadis A, Rich A and Maas S, 2004. Widespread A‐to‐I RNA editing of Alu‐containing mRNAs in the human transcriptome. Plos Biology, 2, e391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1137. Azuma‐Mukai A, Oguri H, Mituyama T, Qian ZR, Asai K, Siomi H and Siomi MC, 2008. Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing. Proc Natl Acad Sci U S A, 105, 7964–7969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1138. Babiarz JE, Ruby JG, Wang YM, Bartel DP and Blelloch R, 2008. Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor‐independent, Dicer‐dependent small RNAs. Genes & Development, 22, 2773–2785. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1139. Babiarz JE, Hsu R, Melton C, Thomas M, Ullian EM and Blelloch R, 2011. A role for noncanonical microRNAs in the mammalian brain revealed by phenotypic differences in Dgcr8 versus Dicer1 knockouts and small RNA sequencing. Rna, 17, 1489–1501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1140. Baglio SR, Rooijers K, Koppers‐Lalic D, Verweij FJ, Pérez Lanzón M, Zini N, Naaijkens B, Perut F, Niessen HWM, Baldini N and Pegtel DM, 2015. Human bone marrow‐ and adipose‐mesenchymal stem cells secrete exosomes enriched in distinctive miRNA and tRNA species. Stem Cell Research and Therapy, 6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1141. Bahn JH, Ahn J, Lin XZ, Zhang Q, Lee JH, Civelek M and Xiao XS, 2015. Genomic analysis of ADAR1 binding and its involvement in multiple RNA processing pathways. Nature Communications, 6, 6355–6355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1142. Bai BY, Liu H and Laiho M, 2014. Small RNA expression and deep sequencing analyses of the nucleolus reveal the presence of nucleolus‐associated microRNAs. Febs Open Bio, 4, 441–449. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1143. Bannwarth S, Talakoub L, Letourneur F, Duarte M, Purcell DF, Hiscott J and Gatignol A, 2001. Organization of the human tarbp2 gene reveals two promoters that are repressed in an astrocytic cell line. Journal of Biological Chemistry, 276, 48803–48813. [DOI] [PubMed] [Google Scholar]
  1144. Barad O, Mann M, Chapnik E, Shenoy A, Blelloch R, Barkai N and Hornstein E, 2012. Efficiency and specificity in microRNA biogenesis. Nature Structural & Molecular Biology, 19, 650–+. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1145. Barr I and Guo F, 2014. Primary microRNA processing assay reconstituted using recombinant drosha and DGCR8. Methods in Molecular Biology, 1095, 73–86. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1146. Barr I, Weitz SH, Atkin T, Hsu PK, Karayiorgou M, Gogos JA, Weiss S and Guo F, 2015. Cobalt(III) Protoporphyrin Activates the DGCR8 Protein and Can Compensate microRNA Processing Deficiency. Chemistry & Biology, 22, 793–802. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1147. Bartel DP, 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281–297. [DOI] [PubMed] [Google Scholar]
  1148. Beane RL, Ram R, Gabillet S, Arar K, Monia BP and Corey DR, 2007. Inhibiting gene expression with locked nucleic acids (LNAs) that target chromosomal DNA. Biochemistry, 46, 7572–7580. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1149. Behm‐Ansmant I, Rehwinkel J, Doerks T, Stark A, Bork P and Izaurralde E, 2006. MRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1: DCP2 decapping complexes. Genes & Development, 20, 1885–1898. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1150. Bellemer C, Bortolin‐Cavaille ML, Schmidt U, Jensen SMR, Kjems J, Bertrand E and Cavaille J, 2012. Microprocessor dynamics and interactions at endogenous imprinted C19MC microRNA genes. Journal of Cell Science, 125, 2709–2720. [DOI] [PubMed] [Google Scholar]
  1151. Bellingham SA, Coleman BM and Hill AF, 2012. Small RNA deep sequencing reveals a distinct miRNA signature released in exosomes from prion‐infected neuronal cells. Nucleic Acids Research, 40, 10937–10949. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1152. Benetti R, Gonzalo S, Jaco I, Munoz P, Gonzalez S, Schoeftner S, Murchison E, Andl T, Chen T, Klatt P, Li E, Serrano M, Millar S, Hannon G and Blasco MA, 2008. A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2‐dependent regulation of DNA methyltransferases. Nature Structural & Molecular Biology, 15, 268–279. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1153. Benhamed M, Herbig U, Ye T, Dejean A and Bischof O, 2012. Senescence is an endogenous trigger for microRNA‐directed transcriptional gene silencing in human cells. Nature Cell Biology, 14, 266–+. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1154. Bennasser Y, Le SY, Benkirane M and Jeang KT, 2005. Evidence that HIV‐1 encodes an siRNA and a suppressor of RNA silencing. Immunity, 22, 607–619. [DOI] [PubMed] [Google Scholar]
  1155. Benoit M and Plevin MJ, 2013. Backbone resonance assignments of the micro‐RNA precursor binding region of human TRBP. Biomolecular Nmr Assignments, 7, 229–233. [DOI] [PubMed] [Google Scholar]
  1156. Berezhna SY, Supekova L, Supek F, Schultz PG and Deniz AA, 2006. siRNA in human cells selectively localizes to target RNA sites. Proc Natl Acad Sci U S A, 103, 7682–7687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1157. Berezikov E, Chung WJ, Willis J, Cuppen E and Lai EC, 2007. Mammalian mirtron genes. Molecular Cell, 28, 328–336. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1158. Bernard MA, Wang LY and Tachado SD, 2015. DICER‐ARGONAUTE2 Complex in Continuous Fluorogenic Assays of RNA Interference Enzymes. PLoS ONE, 10, e0120614–e0120614. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1159. Bernstein E, Caudy AA, Hammond SM and Hannon GJ, 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409, 363–366. [DOI] [PubMed] [Google Scholar]
  1160. Betancur JG and Tomari Y, 2012. Dicer is dispensable for asymmetric RISC loading in mammals. Rna, 18, 24–30. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1161. Bevilacqua PC, George CX, Samuel CE and Cech TR, 1998. Binding of the protein kinase PKR to RNAs with secondary structure defects: Role of the tandem A‐G mismatch and noncontiguous helixes. Biochemistry, 37, 6303–6316. [DOI] [PubMed] [Google Scholar]
  1162. Billy E, Brondani V, Zhang HD, Muller U and Filipowicz W, 2001. Specific interference with gene expression induced by long, double‐stranded RNA in mouse embryonal teratocarcinoma cell lines. Proc Natl Acad Sci U S A, 98, 14428–14433. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1163. Bogerd HP, Karnowski HW, Cai XZ, Shin J, Pohlers M and Cullen BR, 2010. A Mammalian Herpesvirus Uses Noncanonical Expression and Processing Mechanisms to Generate Viral MicroRNAs. Molecular Cell, 37, 135–142. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1164. Bommer UA, Borovjagin AV, Greagg MA, Jeffrey IW, Russell P, Laing KG, Lee M and Clemens MJ, 2002. The mRNA of the translationally controlled tumor protein P23/TCTP is a highly structured RNA, which activates the dsRNA‐dependent protein kinase PKR. Rna, 8, 478–496. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1165. Borchert GM, Lanier W and Davidson BL, 2006. RNA polymerase III transcribes human microRNAs. Nat Struct Mol Biol, 13, 1097–1101. [DOI] [PubMed] [Google Scholar]
  1166. Braun JE, Huntzinger E, Fauser M and Izaurralde E, 2011. GW182 Proteins Directly Recruit Cytoplasmic Deadenylase Complexes to miRNA Targets. Molecular Cell, 44, 120–133. [DOI] [PubMed] [Google Scholar]
  1167. Bronevetsky Y, Villarino AV, Eisley CJ, Barbeau R, Barczak AJ, Heinz GA, Kremmer E, Heissmeyer V, McManus MT, Erle DJ, Rao A and Ansel KM, 2013. T cell activation induces proteasomal degradation of Argonaute and rapid remodeling of the microRNA repertoire. Journal of Experimental Medicine, 210, 417–432. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1168. Brudecki L, Ferguson DA, McCall CE and El Gazzar M, 2013. MicroRNA‐146a and RBM4 form a negative feed‐forward loop that disrupts cytokine mRNA translation following TLR4 responses in human THP‐1 monocytes. Immunology and Cell Biology, 91, 532–540. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1169. Buck AH, Coakley G, Simbari F, McSorley HJ, Quintana JF, Le Bihan T, Kumar S, Abreu‐Goodger C, Lear M, Harcus Y, Ceroni A, Babayan SA, Blaxter M, Ivens A and Maizels RM, 2014. Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity. Nature Communications, 5, 5488–5488. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1170. Burroughs AM, Ando Y, de Hoon MJL, Tomaru Y, Suzuki H, Hayashizaki Y and Daub CO, 2011. Deep‐sequencing of human argonaute‐associated small RNAs provides insight into miRNA sorting and reveals argonaute association with RNA fragments of diverse origin. RNA Biology, 8, 158–177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1171. Calabrese JM, Seila AC, Yeo GW and Sharp PA, 2007. RNA sequence analysis defines Dicer's role in mouse embryonic stem cells. Proc Natl Acad Sci U S A, 104, 18097–18102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1172. Canella D, Praz V, Reina JH, Cousin P and Hernandez N, 2010. Defining the RNA polymerase III transcriptome: Genome‐wide localization of the RNA polymerase III transcription machinery in human cells. Genome Res, 20, 710–721. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1173. Carlile M, Swan D, Jackson K, Preston‐Fayers K, Ballester B, Flicek P and Werner A, 2009. Strand selective generation of endo‐siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues. Nucleic Acids Research, 37, 2274–2282. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1174. Carmell MA, Girard A, van de Kant HJG, Bourc'his D, Bestor TH, de Rooij DG and Hannon GJ, 2007. MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Developmental Cell, 12, 503–514. [DOI] [PubMed] [Google Scholar]
  1175. Carmi S, Borukhov I and Levanon EY, 2011. Identification of Widespread Ultra‐Edited Human RNAs. Plos Genetics, 7, e1002317–e1002317. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1176. Castanotto D, Tommasi S, Li M, Li H, Yanow S, Pfeifer GP and Rossi JJ, 2005. Short hairpin RNA‐directed cytosine (CpG) methylation of the RASSF1A gene promoter in HeLa cells. Molecular Therapy, 12, 179–183. [DOI] [PubMed] [Google Scholar]
  1177. Castellano L and Stebbing J, 2013. Deep sequencing of small RNAs identifies canonical and non‐canonical miRNA and endogenous siRNAs in mammalian somatic tissues. Nucleic Acids Research, 41, 3339–3351. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1178. Caudy AA, Myers M, Hannon GJ and Hammond SM, 2002. Fragile X‐related protein and VIG associate with the RNA interference machinery. Genes & Development, 16, 2491–2496. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1179. Cerutti H and Casas‐Mollano JA, 2006. On the origin and functions of RNA‐mediated silencing: from protists to man. Curr Genet, 50, 81–99. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1180. Chahar HS, Chen SP and Manjunath N, 2013. P‐body components LSM1, GW182, DDX3, DDX6 and XRN1 are recruited to WNV replication sites and positively regulate viral replication. Virology, 436, 1–7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1181. Chakravarthy S, Sternberg SH, Kellenberger CA and Doudna JA, 2010. Substrate‐Specific Kinetics of Dicer‐Catalyzed RNA Processing. Journal of Molecular Biology, 404, 392–402. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1182. Chandradoss SD, Schirle NT, Szczepaniak M, MacRae IJ and Joo C, 2015. A Dynamic Search Process Underlies MicroRNA Targeting. Cell, 162, 96–107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1183. Chekulaeva M, Mathys H, Zipprich JT, Attig J, Colic M, Parker R and Filipowicz W, 2011. miRNA repression involves GW182‐mediated recruitment of CCR4‐NOT through conserved W‐containing motifs. Nature Structural & Molecular Biology, 18, 1218–U1262. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1184. Cheloufi S, Dos Santos CO, Chong MMW and Hannon GJ, 2010. A Dicer‐independent miRNA biogenesis pathway that requires Ago catalysis. Nature, 465, 584–U576. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1185. Chen T, Xiang JF, Zhu SS, Chen SY, Yin QF, Zhang XO, Zhang J, Feng H, Dong R, Li XJ, Yang L and Chen LL, 2015. ADAR1 is required for differentiation and neural induction by regulating microRNA processing in a catalytically independent manner. Cell Research, 25, 459–476. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1186. Chendrimada TP, Gregory RI, Kumaraswamy E, Norman J, Cooch N, Nishikura K and Shiekhattar R, 2005. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature, 436, 740–744. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1187. Cheng TL, Wang ZZ, Liao QM, Zhu Y, Zhou WH, Xu WQ and Qiu ZL, 2014. MeCP2 Suppresses Nuclear MicroRNA Processing and Dendritic Growth by Regulating the DGCR8/Drosha Complex. Developmental Cell, 28, 547–560. [DOI] [PubMed] [Google Scholar]
  1188. Chevillet JR, Kang Q, Ruf IK, Briggs HA, Vojtech LN, Hughes SM, Cheng HH, Arroyo JD, Meredith EK, Gallichotte EN, Pogosova‐Agadjanyan EL, Morrissey C, Stirewalt DL, Hladik F, Yu EY, Higano CS and Tewari M, 2014. Quantitative and stoichiometric analysis of the microRNA content of exosomes. Proc Natl Acad Sci U S A, 111, 14888–14893. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1189. Chim SS, Shing TK, Hung EC, Leung TY, Lau TK, Chiu RW and Lo YM, 2008. Detection and characterization of placental microRNAs in maternal plasma. Clin Chem, 54, 482–490. [DOI] [PubMed] [Google Scholar]
  1190. Cho S, Park JS and Kang YK, 2014. AGO2 and SETDB1 cooperate in promoter‐targeted transcriptional silencing of the androgen receptor gene. Nucleic Acids Research, 42, 13545–13556. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1191. Chong MMW, Zhang GA, Cheloufi S, Neubert TA, Hannon GJ and Littman DR, 2010. Canonical and alternate functions of the microRNA biogenesis machinery. Genes & Development, 24, 1951–1960. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1192. Christie M, Boland A, Huntzinger E, Weichenrieder O and Izaurralde E, 2013. Structure of the PAN3 Pseudokinase Reveals the Basis for Interactions with the PAN2 Deadenylase and the GW182 Proteins. Molecular Cell, 51, 360–373. [DOI] [PubMed] [Google Scholar]
  1193. Chu CY and Rana TM, 2006. Translation repression in human cells by microRNA‐induced gene silencing requires RCK/p54. Plos Biology, 4, 1122–1136. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1194. Cikaluk DE, Tahbaz N, Hendricks LC, DiMattia GE, Hansen D, Pilgrim D and Hobman TC, 1999. GERp95, a membrane‐associated protein that belongs to a family of proteins involved in stem cell differentiation. Molecular Biology of the Cell, 10, 3357–3372. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1195. Clerzius G, Gelinas JF, Daher A, Bonnet M, Meurs EF and Gatignol A, 2009. ADAR1 Interacts with PKR during Human Immunodeficiency Virus Infection of Lymphocytes and Contributes to Viral Replication. Journal of Virology, 83, 10119–10128. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1196. Clop A, Marcq F, Takeda H, Pirottin D, Tordoir X, Bibe B, Bouix J, Caiment F, Elsen JM, Eychenne F, Larzul C, Laville E, Meish F, Milenkovic D, Tobin J, Charlier C and Georges M, 2006. A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nature Genetics, 38, 813–818. [DOI] [PubMed] [Google Scholar]
  1197. Cosentino GP, Venkatesan S, Serluca FC, Green SR, Mathews MB and Sonenberg N, 1995. Double‐stranded‐RNA‐dependent protein kinase and TAR RNA‐binding protein form homo‐ and heterodimers in vivo. Proc Natl Acad Sci U S A, 92, 9445–9449. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1198. Cullen BR, 2006. Is RNA interference involved in intrinsic antiviral immunity in mammals? Nature Immunology, 7, 563–567. [DOI] [PubMed] [Google Scholar]
  1199. Cullen BR, Cherry S and tenOever BR, 2013. Is RNA interference a physiologically relevant innate antiviral immune response in mammals? Cell Host Microbe, 14, 374–378. [DOI] [PubMed] [Google Scholar]
  1200. Daher A, Laraki G, Singh M, Melendez‐Pena CE, Bannwarth S, Peters A, Meurs EF, Braun RE, Patel RC and Gatignol A, 2009. TRBP Control of PACT‐Induced Phosphorylation of Protein Kinase R Is Reversed by Stress. Molecular and Cellular Biology, 29, 254–265. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1201. Daniels SM, Melendez‐Pena CE, Scarborough RJ, Daher A, Christensen HS, El Far M, Purcell DFJ, Laine S and Gatignol A, 2009. Characterization of the TRBP domain required for Dicer interaction and function in RNA interference. Bmc Molecular Biology, 10, 38–38. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1202. Daniels SM and Gatignol A, 2012. The Multiple Functions of TRBP, at the Hub of Cell Responses to Viruses, Stress, and Cancer. Microbiology and Molecular Biology Reviews, 76, 652–+. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1203. Dawson TR, Sansam CL and Emeson RB, 2004. Structure and sequence determinants required for the RNA editing of ADAR2 substrates. Journal of Biological Chemistry, 279, 4941–4951. [DOI] [PubMed] [Google Scholar]
  1204. de Veer MJ, Sledz CA and Williams BR, 2005. Detection of foreign RNA: implications for RNAi. Immunol Cell Biol, 83, 224–228. [DOI] [PubMed] [Google Scholar]
  1205. De Wit T, Grosveld F and Drabek D, 2002. The tomato RNA‐directed RNA polymerase has no effect on gene silencing by RNA interference in transgenic mice. Transgenic Research, 11, 305–310. [DOI] [PubMed] [Google Scholar]
  1206. DeCerbo J and Carmichael GG, 2005. Retention and repression: fates of hyperedited RNAs in the nucleus. Current Opinion in Cell Biology, 17, 302–308. [DOI] [PubMed] [Google Scholar]
  1207. Deerberg A, Willkomm S and Restle T, 2013. Minimal mechanistic model of siRNA‐dependent target RNA slicing by recombinant human Argonaute 2 protein. Proc Natl Acad Sci U S A, 110, 17850–17855. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1208. Deleavey GF, Frank F, Hassler M, Wisnovsky S, Nagar B and Damha MJ, 2013. The 5 ‘ Binding MID Domain of Human Argonaute2 Tolerates Chemically Modified Nucleotide Analogues. Nucleic Acid Therapeutics, 23, 81–87. [DOI] [PubMed] [Google Scholar]
  1209. Deveson I, Li JY and Millar AA, 2013. Expression of human ARGONAUTE 2 inhibits endogenous microRNA activity in Arabidopsis . Frontiers in Plant Science, 4, 96–96. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1210. Diallo M, Arenz C, Schmitz K, Sandhoff K and Schepers U, 2003. Long endogenous dsRNAs can induce complete gene silencing in mammalian cells and primary cultures. Oligonucleotides, 13, 381–392. [DOI] [PubMed] [Google Scholar]
  1211. Didiot MC, Subramanian M, Flatter E, Mandel JL and Moine H, 2009. Cells lacking the fragile X mental retardation protein (FMRP) have normal RISC activity but exhibit altered stress granule assembly. Molecular Biology of the Cell, 20, 428–437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1212. Diederichs S and Haber DA, 2007. Dual role for argonautes in microRNA processing and posttranscriptional regulation of microRNA expression. Cell, 131, 1097–1108. [DOI] [PubMed] [Google Scholar]
  1213. Dismuke WM, Challa P, Navarro I, Stamer WD and Liu YT, 2015. Human aqueous humor exosomes. Experimental Eye Research, 132, 73–77. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1214. Doench JG, Petersen CP and Sharp PA, 2003. siRNAs can function as miRNAs. Genes & Development, 17, 438–442. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1215. Donze O, Abbas‐Terki T and Picard D, 2001. The Hsp90 chaperone complex is both a facilitator and a repressor of the dsRNA‐dependent kinase PKR. EMBO J, 20, 3771–3780. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1216. Doyle M, Badertscher L, Jaskiewicz L, Guttinger S, Jurado S, Hugenschmidt T, Kutay U and Filipowicz W, 2013. The double‐stranded RNA binding domain of human Dicer functions as a nuclear localization signal. Rna, 19, 1238–1252. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1217. Drake M, Furuta T, Suen KM, Gonzalez G, Liu B, Kalia A, Ladbury JE, Fire AZ, Skeath JB and Arur S, 2014. A requirement for ERK‐dependent Dicer phosphorylation in coordinating oocyte‐to‐embryo transition in C. elegans. Developmental Cell, 31, 614–628. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1218. Du Z, Lee JK, Tjhen R, Strould RM and James TL, 2008. Structural and biochemical insights into the dicing mechanism of mouse Dicer: A conserved lysine is critical for dsRNA cleavage. Proc Natl Acad Sci U S A, 105, 2391–2396. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1219. Dueck A, Ziegler C, Eichner A, Berezikov E and Meister G, 2012. microRNAs associated with the different human Argonaute proteins. Nucleic Acids Research, 40, 9850–9862. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1220. Duursma AM, Kedde M, Schrier M, le Sage C and Agami R, 2008. miR‐148 targets human DNMT3b protein coding region. Rna, 14, 872–877. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1221. Duxbury MS, Ashley SW and Whang EE, 2005. RNA interference: a mammalian SID‐1 homolog enhances siRNA uptake and gene silencing efficacy in human cells. Biochem Biophys Res Commun, 331, 459–463. [DOI] [PubMed] [Google Scholar]
  1222. El‐Andaloussi S, Lee Y, Lakhal‐Littleton S, Li J, Seow Y, Gardiner C, Alvarez‐Erviti L, Sargent IL and Wood MJA, 2012. Exosome‐mediated delivery of siRNA in vitro and in vivo. Nature Protocols, 7, 2112–2126. [DOI] [PubMed] [Google Scholar]
  1223. El‐Shami M, Pontier D, Lahmy S, Braun L, Picart C, Vega D, Hakimi M‐A, Jacobsen SE, Cooke R and Lagrange T, 2007. Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE‐binding platforms in RNAi‐related components. Genes & Development, 21, 2539–2544. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1224. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K and Tuschl T, 2001. Duplexes of 21‐nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 411, 494–498. [DOI] [PubMed] [Google Scholar]
  1225. Elkayam E, Kuhn CD, Tocilj A, Haase AD, Greene EM, Hannon GJ and Joshua‐Tor L, 2012. The Structure of Human Argonaute‐2 in Complex with miR‐20a. Cell, 150, 100–110. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1226. Ender C, Krek A, Friedlander MR, Beitzinger M, Weinmann L, Chen W, Pfeffer S, Rajewsky N and Meister G, 2008. A Human snoRNA with MicroRNA‐Like Functions. Molecular Cell, 32, 519–528. [DOI] [PubMed] [Google Scholar]
  1227. Engels B, Jannot G, Remenyi J, Simard MJ and Hutvagner G, 2012. Polypyrimidine Tract Binding Protein (hnRNP I) Is Possibly a Conserved Modulator of miRNA‐Mediated Gene Regulation. PLoS ONE, 7, e33144–e33144. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1228. Enright AJ, John B, Gaul U, Tuschl T, Sander C and Marks DS, 2003. MicroRNA targets in Drosophila. Genome Biology, 5, R1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1229. Eulalio A, Behm‐Ansmant I, Schweizer D and Izaurralde E, 2007. P‐body formation is a consequence, not the cause, of RNA‐mediated gene silencing. Molecular and Cellular Biology, 27, 3970–3981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1230. Fabbri M, Garzon R, Cimmino A, Liu Z, Zanesi N, Callegari E, Liu S, Alder H, Costinean S, Fernandez‐Cymering C, Volinia S, Guler G, Morrison CD, Chan KK, Marcucci G, Calin GA, Huebner K and Croce CM, 2007. MicroRNA‐29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B. Proc Natl Acad Sci U S A, 104, 15805–15810. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1231. Fabian MR, Mathonnet G, Sundermeier T, Mathys H, Zipprich JT, Svitkin YV, Rivas F, Jinek M, Wohischlegel J, Doudna JA, Chen CYA, Shyu AB, Yates JR, Hannon GJ, Filipowicz W, Duchaine TF and Sonenberg N, 2009. Mammalian miRNA RISC Recruits CAF1 and PABP to Affect PABP‐Dependent Deadenylation. Molecular Cell, 35, 868–880. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1232. Fabian MR, Cieplak MK, Frank F, Morita M, Green J, Srikumar T, Nagar B, Yamamoto T, Raught B, Duchaine TF and Sonenberg N, 2011a. miRNA‐mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4‐NOT. Nature Structural & Molecular Biology, 18, 1211–U1252. [DOI] [PubMed] [Google Scholar]
  1233. Fabian MR, Svitkin YV and Sonenberg N, 2011b. An Efficient System for Let‐7 MicroRNA and GW182 Protein‐Mediated Deadenylation In Vitro. Argonaute Proteins: Methods and Protocols., 207–217. [DOI] [PubMed] [Google Scholar]
  1234. Faehnle CR, Elkayam E, Haase AD, Hannon GJ and Joshua‐Tor L, 2013. The Making of a Slicer: Activation of Human Argonaute‐1. Cell Reports, 3, 1901–1909. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1235. Farh KK, Grimson A, Jan C, Lewis BP, Johnston WK, Lim LP, Burge CB and Bartel DP, 2005. The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science, 310, 1817–1821. [DOI] [PubMed] [Google Scholar]
  1236. Feng Y, Zhang XX, Graves P and Zeng Y, 2012. A comprehensive analysis of precursor microRNA cleavage by human Dicer. Rna, 18, 2083–2092. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1237. Fenner BJ, Thiagarajan R, Chua HK and Kwang J, 2006. Betanodavirus B2 is an RNA interference antagonist that facilitates intracellular viral RNA accumulation. Journal of Virology, 80, 85–94. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1238. Filippov V, Solovyev V, Filippova M and Gill SS, 2000. A novel type of RNase III family proteins in eukaryotes. Gene, 245, 213–221. [DOI] [PubMed] [Google Scholar]
  1239. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE and Mello CC, 1998. Potent and specific genetic interference by double‐stranded RNA in Caenorhabditis elegans. Nature, 391, 806–811. [DOI] [PubMed] [Google Scholar]
  1240. Flemr M, Malik R, Franke V, Nejepinska J, Sedlacek R, Vlahovicek K and Svoboda P, 2013. A Retrotransposon‐Driven Dicer Isoform Directs Endogenous Small Interfering RNA Production in Mouse Oocytes. Cell, 155, 807–816. [DOI] [PubMed] [Google Scholar]
  1241. Flores‐Jasso CF, Arenas‐Huertero C, Reyes JL, Contreras‐Cubas C, Covarrubias A and Vaca L, 2009. First step in pre‐miRNAs processing by human Dicer. Acta Pharmacologica Sinica, 30, 1177–1185. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1242. Fortin KR, Nicholson RH and Nicholson AW, 2002. Mouse ribonuclease III. cDNA structure, expression analysis, and chromosomal location. BMC Genomics, 3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1243. Francia S, Michelini F, Saxena A, Tang D, deHoon M , Anelli V, Mione M, Carninci P and di Fagagna FD, 2012. Site‐specific DICER and DROSHA RNA products control the DNA‐damage response. Nature, 488, 231‐+. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1244. Frank F, Sonenberg N and Nagar B, 2010. Structural basis for 5 ‘‐nucleotide base‐specific recognition of guide RNA by human AGO2. Nature, 465, 818–822. [DOI] [PubMed] [Google Scholar]
  1245. Frank F, Fabian MR, Stepinski J, Jemielity J, Darzynkiewicz E, Sonenberg N and Nagar B, 2011. Structural analysis of 5 ‘‐mRNA‐cap interactions with the human AGO2 MID domain. EMBO Rep, 12, 415–420. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1246. Friend K, Campbell ZT, Cooke A, Kroll‐Conner P, Wickens MP and Kimble J, 2012. A conserved PUF‐Ago‐eEF1A complex attenuates translation elongation. Nature Structural & Molecular Biology, 19, 176–183. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1247. Fu QQ and Yuan YA, 2013. Structural insights into RISC assembly facilitated by dsRNA‐binding domains of human RNA helicase A (DHX9). Nucleic Acids Research, 41, 3457–3470. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1248. Fukagawa T, Nogami M, Yoshikawa M, Ikeno M, Okazaki T, Takami Y, Nakayama T and Oshimura M, 2004. Dicer is essential for formation of the heterochromatin structure in vertebrate cells. Nature Cell Biology, 6, 784–791. [DOI] [PubMed] [Google Scholar]
  1249. Gagnon KT, Li LD, Chu YJ, Janowski BA and Corey DR, 2014a. RNAi Factors Are Present and Active in Human Cell Nuclei. Cell Reports, 6, 211–221. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1250. Gagnon KT, Li LD, Janowski BA and Corey DR, 2014b. Analysis of nuclear RNA interference in human cells by subcellular fractionation and Argonaute loading. Nature Protocols, 9, 2045–2060. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1251. Gan HH and Gunsalus KC, 2015. Assembly and analysis of eukaryotic Argonaute‐RNA complexes in microRNA‐target recognition. Nucleic Acids Research, 43, 9613–9625. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1252. Gan L, Anton KE, Masterson BA, Vincent VA, Ye S and Gonzalez‐Zulueta M, 2002. Specific interference with gene expression and gene function mediated by long dsRNA in neural cells. J Neurosci Methods, 121, 151–157. [DOI] [PubMed] [Google Scholar]
  1253. Gandy SZ, Linnstaedt SD, Muralidhar S, Cashman KA, Rosenthal LJ and Casey JL, 2007. RNA editing of the human herpesvirus 8 kaposin transcript eliminates its transforming activity and is induced during lytic replication. Journal of Virology, 81, 13544–13551. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1254. Ganesan G and Rao SMR, 2008. A novel noncoding RNA processed by Drosha is restricted to nucleus in mouse. Rna, 14, 1399–1410. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1255. Gantier MP and Williams BR, 2007. The response of mammalian cells to double‐stranded RNA. Cytokine Growth Factor Rev, 18, 363–371. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1256. Garcia‐Lopez J, Hourcade JD and del Mazo J, 2013. Reprogramming of microRNAs by adenosine‐to‐inosine editing and the selective elimination of edited microRNA precursors in mouse oocytes and preimplantation embryos. Nucleic Acids Research, 41, 5483–5493. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1257. Gehrke S, Imai Y, Sokol N and Lu BW, 2010. Pathogenic LRRK2 negatively regulates microRNA‐mediated translational repression. Nature, 466, 637–U639. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1258. Geiss G, Jin G, Guo J, Bumgarner R, Katze MG and Sen GC, 2001. A comprehensive view of regulation of gene expression by double‐stranded RNA‐mediated cell signaling. Journal of Biological Chemistry, 276, 30178–30182. [DOI] [PubMed] [Google Scholar]
  1259. Glanzer J, Miyashiro KY, Sul JY, Barrett L, Belt B, Haydon P and Eberwine J, 2005. RNA splicing capability of live neuronal dendrites. Proc Natl Acad Sci U S A, 102, 16859–16864. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1260. Goodarzi H, Zhang S, Buss CG, Fish L, Tavazoie S and Tavazoie SF, 2014. Metastasis‐suppressor transcript destabilization through TARBP2 binding of mRNA hairpins. Nature, 513, 256–+. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1261. Goodier JL, Zhang L, Vetter MR and Kazazian HH, 2007. LINE‐1 ORF1 protein localizes in stress granules with other RNA‐Binding proteins, including components of RNA interference RNA‐induced silencing complex. Molecular and Cellular Biology, 27, 6469–6483. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1262. Gredell JA, Dittmer MJ, Wu M, Chan C and Walton SP, 2010. Recognition of siRNA Asymmetry by TAR RNA Binding Protein. Biochemistry, 49, 3148–3155. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1263. Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N and Shiekhattar R, 2004. The Microprocessor complex mediates the genesis of microRNAs. Nature, 432, 235–240. [DOI] [PubMed] [Google Scholar]
  1264. Gregory RI, Chendrimada TP, Cooch N and Shiekhattar R, 2005. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell, 123, 631–640. [DOI] [PubMed] [Google Scholar]
  1265. Gregory RI, Chendrimada TP and Shiekhattar R, 2006. MicroRNA biogenesis ‐ Isolation and characterization of the microprocessor complex. In: Methods in Molecular Biology. 33–47. [DOI] [PubMed] [Google Scholar]
  1266. Gu S, Jin L, Huang Y, Zhang FJ and Kay MA, 2012a. Slicing‐Independent RISC Activation Requires the Argonaute PAZ Domain. Current Biology, 22, 1536–1542. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1267. Gu S, Jin L, Zhang Y, Huang Y, Zhang FJ, Valdmanis PN and Kay MA, 2012b. The Loop Position of shRNAs and Pre‐miRNAs Is Critical for the Accuracy of Dicer Processing In Vivo. Cell, 151, 900–911. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1268. Guang S, Bochner AF, Burkhart KB, Burton N, Pavelec DM and Kennedy S, 2010. Small regulatory RNAs inhibit RNA polymerase II during the elongation phase of transcription. Nature, 465, 1097–1101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1269. Gullerova M and Proudfoot NJ, 2012. Convergent transcription induces transcriptional gene silencing in fission yeast and mammalian cells. Nature Structural & Molecular Biology, 19, 1193–1201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1270. Guo YW, Liu J, Elfenbein SJ, Ma YH, Zhong M, Qiu CH, Ding Y and Lu J, 2015. Characterization of the mammalian miRNA turnover landscape. Nucleic Acids Research, 43, 2326–2341. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1271. Gupta V, Huang X and Patel RC, 2003. The carboxy‐terminal, M3 motifs of PACT and TRBP have opposite effects on PKR activity. Virology, 315, 283–291. [DOI] [PubMed] [Google Scholar]
  1272. Gurtan AM, Lu V, Bhutkar A and Sharp PA, 2012. In vivo structure‐function analysis of human Dicer reveals directional processing of precursor miRNAs. Rna, 18, 1116–1122. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1273. Haase AD, Jaskiewicz L, Zhang HD, Laine S, Sack R, Gatignol A and Filipowicz W, 2005. TRBP, a regulator of cellular PKR and HIV‐1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep, 6, 961–967. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1274. Haasnoot J, de Vries W, Geutjes EJ, Prins M, de Haan P and Berkhout B, 2007. The Ebola virus VP35 protein is a suppressor of RNA silencing. Plos Pathogens, 3, e86. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1275. Haley B and Zamore PD, 2004. Kinetic analysis of the RNAi enzyme complex. Nature Structural & Molecular Biology, 11, 599–606. [DOI] [PubMed] [Google Scholar]
  1276. Hammond SM, Bernstein E, Beach D and Hannon GJ, 2000. An RNA‐directed nuclease mediates post‐transcriptional gene silencing in Drosophila cells. Nature, 404, 293–296. [DOI] [PubMed] [Google Scholar]
  1277. Han C, Liu YH, Wan GH, Choi HJ, Zhao LQ, Ivan C, He XM, Sood AK, Zhang XN and Lu XB, 2014. The RNA‐Binding Protein DDX1 Promotes Primary MicroRNA Maturation and Inhibits Ovarian Tumor Progression. Cell Reports, 8, 1447–1460. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1278. Han JJ, Lee Y, Yeom KH, Kim YK, Jin H and Kim VN, 2004. The Drosha‐DGCR8 complex in primary microRNA processing. Genes & Development, 18, 3016–3027. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1279. Hauptmann J, Schraivogel D, Bruckmann A, Manickavel S, Jakob L, Eichner N, Pfaff J, Urban M, Sprunck S, Hafner M, Tuschl T, Deutzmann R and Meister G, 2015. Biochemical isolation of Argonaute protein complexes by Ago‐APP. Proc Natl Acad Sci U S A, 112, 11841–11845. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1280. Haussecker D and Proudfoot NJ, 2005. Dicer‐dependent turnover of intergenic transcripts from the human beta‐globin gene cluster. Molecular and Cellular Biology, 25, 9724–9733. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1281. Haussecker D, Huang Y, Lau A, Parameswaran P, Fire AZ and Kay MA, 2010. Human tRNA‐derived small RNAs in the global regulation of RNA silencing. Rna, 16, 673–695. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1282. Hausser J, Landthaler M, Jaskiewicz L, Gaidatzis D and Zavolan M, 2009. Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C‐miRNA complexes and the degradation of miRNA targets. Genome Research, 19, 2009–2020. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1283. Havens MA, Reich AA, Duelli DM and Hastings ML, 2012. Biogenesis of mammalian microRNAs by a non‐canonical processing pathway. Nucleic Acids Research, 40, 4626–4640. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1284. Hawkins PG, Santoso S, Adams C, Anest V and Morris KV, 2009. Promoter targeted small RNAs induce long‐term transcriptional gene silencing in human cells. Nucleic Acids Research, 37, 2984–2995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1285. Heraud‐Farlow JE and Walkley CR, 2016. The role of RNA editing by ADAR1 in prevention of innate immune sensing of self‐RNA. J Mol Med (Berl). [DOI] [PubMed] [Google Scholar]
  1286. Herbert KM, Pimienta G, DeGregorio SJ, Alexandrov A and Steitz JA, 2013. Phosphorylation of DGCR8 Increases Its Intracellular Stability and Induces a Progrowth miRNA Profile. Cell Reports, 5, 1070–1081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1287. Herbert KM, Sarkar SK, Mills M, De la Herran HCD, Neuman KC and Steitz JA, 2016. A heterotrimer model of the complete Microprocessor complex revealed by single‐molecule subunit counting. Rna, 22, 175–183. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1288. Hock J, Weinmann L, Ender C, Rudel S, Kremmer E, Raabe M, Urlaub H and Meister G, 2007. Proteomic and functional analysis of Argonaute‐containing mRNA‐protein complexes in human cells. EMBO Rep, 8, 1052–1060. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1289. Hong J, Qian ZK, Shen SY, Min TS, Tan C, Xu JF, Zhao YC and Huang WD, 2005. High doses of siRNAs induce eri‐1 and adar‐1 gene expression and reduce the efficiency of RNA interference in the mouse. Biochemical Journal, 390, 675–679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1290. Horman SR, Janas MM, Litterst C, Wang B, MacRae IJ, Sever MJ, Morrissey DV, Graves P, Luo B, Umesalma S, Qi HH, Miraglia LJ, Novina CD and Orth AP, 2013. Akt‐mediated phosphorylation of argonaute 2 downregulates cleavage and upregulates translational repression of MicroRNA targets. Molecular Cell, 50, 356–367. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1291. Hornung V, Ellegast J, Kim S, Brzozka K, Jung A, Kato H, Poeck H, Akira S, Conzelmann KK, Schlee M, Endres S and Hartmann G, 2006. 5′‐Triphosphate RNA is the ligand for RIG‐I. Science, 314, 994–997. [DOI] [PubMed] [Google Scholar]
  1292. Houbaviy HB, Dennis L, Jaenisch R and Sharp PA, 2005. Characterization of a highly variable eutherian rnicroRNA gene. Rna, 11, 1245–1257. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1293. Hu J and Corey DR, 2007. Inhibiting gene expression with peptide nucleic acid (PNA)–peptide conjugates that target chromosomal DNA. Biochemistry, 46, 7581–7589. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1294. Hu J, Chen Z, Xia D, Wu J, Xu H and Ye ZQ, 2012. Promoter‐associated small double‐stranded RNA interacts with heterogeneous nuclear ribonucleoprotein A2/B1 to induce transcriptional activation. Biochemical Journal, 447, 407–416. [DOI] [PubMed] [Google Scholar]
  1295. Huang J, Liang Z, Yang B, Tian H, Ma J and Zhang H, 2007. Derepression of microRNA‐mediated protein translation inhibition by apolipoprotein B mRNA‐editing enzyme catalytic polypeptide‐like 3G (APOBEC3G) and its family members. Journal of Biological Chemistry, 282, 33632–33640. [DOI] [PubMed] [Google Scholar]
  1296. Huang V, Zheng JS, Qi ZX, Wang J, Place RF, Yu JW, Li H and Li LC, 2013a. Ago1 Interacts with RNA Polymerase II and Binds to the Promoters of Actively Transcribed Genes in Human Cancer Cells. Plos Genetics, 9, e1003821–e1003821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1297. Huang X, Hutchins B and Patel RC, 2002. The C‐terminal, third conserved motif of the protein activator PACT plays an essential role in the activation of double‐stranded‐RNA‐dependent protein kinase (PKR). Biochemical Journal, 366, 175–186. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1298. Huang XY, Yuan TZ, Tschannen M, Sun ZF, Jacob H, Du MJ, Liang MH, Dittmar RL, Liu Y, Liang MY, Kohli M, Thibodeau SN, Boardman L and Wang L, 2013b. Characterization of human plasma‐derived exosomal RNAs by deep sequencing. BMC Genomics, 14, 319–319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1299. Hundley HA, Krauchuk AA and Bass BL, 2008. C‐elegans and H‐sapiens mRNAs with edited 3 ‘ UTRs are present on polysomes. Rna, 14, 2050–2060. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1300. Hunter T, Hunt T, Jackson RJ and Robertson HD, 1975. The characteristics of inhibition of protein synthesis by double‐stranded ribonucleic acid in reticulocyte lysates. Journal of Biological Chemistry, 250, 409–417. [PubMed] [Google Scholar]
  1301. Huntzinger E, Braun JE, Heimstaedt S, Zekri L and Izaurralde E, 2010. Two PABPC1‐binding sites in GW182 proteins promote miRNA‐mediated gene silencing. EMBO J, 29, 4146–4160. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1302. Huntzinger E, Kuzuoglu‐Oeztuerk D, Braun JE, Eulalio A, Wohlbold L and Izaurralde E, 2013. The interactions of GW182 proteins with PABP and deadenylases are required for both translational repression and degradation of miRNA targets. Nucleic Acids Research, 41, 978–994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1303. Iavello A, Frech VSL, Gai C, Deregibus MC, Quesenberry PJ and Camussi G, 2016. Role of Alix in miRNA packaging during extracellular vesicle biogenesis. International Journal of Molecular Medicine, 37, 958–966. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1304. Iguchi H, Kosaka N and Ochiya T, 2010. Secretory microRNAs as a versatile communication tool. Communicative & integrative biology, 3, 478–481. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1305. Ingle H, Kumar S, Raut AA, Mishra A, Kulkarni DD, Kameyama T, Takaoka A, Akira S and Kumar H, 2015. The microRNA miR‐485 targets host and influenza virus transcripts to regulate antiviral immunity and restrict viral replication. Science Signaling, 8, ra126–ra126. [DOI] [PubMed] [Google Scholar]
  1306. Ip J, Canham P, Choo KHA, Inaba Y, Jacobs SA, Kalitsis P, Mattiske DM, Ng J, Saffery R, Wong NC, Wong LH and Mann JR, 2012. Normal DNA Methylation Dynamics in DICER1‐Deficient Mouse Embryonic Stem Cells. Plos Genetics, 8, e1002919–e1002919. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1307. Ishizuka A, Siomi MC and Siomi H, 2002. A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins. Genes & Development, 16, 2497–2508. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1308. Iwasaki S, Kobayashi M, Yoda M, Sakaguchi Y, Katsuma S, Suzuki T and Tomari Y, 2010. Hsc70/Hsp90 chaperone machinery mediates ATP‐dependent RISC loading of small RNA duplexes. Molecular Cell, 39, 292–299. [DOI] [PubMed] [Google Scholar]
  1309. Izumi H, Tsuda M, Sato Y, Kosaka N, Ochiya T, Iwamoto H, Namba K and Takeda Y, 2015. Bovine milk exosomes contain microRNA and mRNA and are taken up by human macrophages. Journal of Dairy Science, 98, 2920–2933. [DOI] [PubMed] [Google Scholar]
  1310. Izumi T, Burdick R, Shigemi M, Plisov S, Hu WS and Pathak VK, 2013. Mov10 and APOBEC3G Localization to Processing Bodies Is Not Required for Virion Incorporation and Antiviral Activity. Journal of Virology, 87, 11047–11062. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1311. Jain S and Parker R, 2013. The discovery and analysis of P Bodies. Adv Exp Med Biol, 768, 23–43. [DOI] [PubMed] [Google Scholar]
  1312. Jakymiw A, Lian SL, Eystathioy T, Li SQ, Satoh M, Hamel JC, Fritzler MJ and Chan EKL, 2005. Disruption of GW bodies impairs mammalian RNA interference. Nature Cell Biology, 7, 1267–1274. [DOI] [PubMed] [Google Scholar]
  1313. James V, Zhang Y, Foxler DE, de Moor CH, Kong YW, Webb TM, Self TJ, Feng Y, Lagos D, Chu C‐Y, Rana TM, Morley SJ, Longmore GD, Bushell M and Sharp TV, 2010. LIM‐domain proteins, LIMD1, Ajuba, and WTIP are required for microRNA‐mediated gene silencing. Proc Natl Acad Sci U S A, 107, 12499–12504. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1314. Jang JH, Jung JS, Choi JI and Kang SK, 2012. Nuclear Ago2/HSP60 Contributes to Broad Spectrum of hATSCs Function via Oct4 Regulation. Antioxidants & Redox Signaling, 16, 383–399. [DOI] [PMC free article] [PubMed] [Google Scholar] [Retracted]
  1315. Jannot G, Bajan S, Giguere NJ, Bouasker S, Banville IH, Piquet S, Hutvagner G and Simard MJ, 2011. The ribosomal protein RACK1 is required for microRNA function in both C. elegans and humans. EMBO Rep, 12, 581–586. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1316. Janowski BA, Huffman KE, Schwartz JC, Ram R, Hardy D, Shames DS, Minna JD and Corey DR, 2005a. Inhibiting gene expression at transcription start sites in chromosomal DNA with antigene RNAs. Nat Chem Biol, 1, 216–222. [DOI] [PubMed] [Google Scholar]
  1317. Janowski BA, Kaihatsu K, Huffman KE, Schwartz JC, Ram R, Hardy D, Mendelson CR and Corey DR, 2005b. Inhibiting transcription of chromosomal DNA with antigene peptide nucleic acids. Nat Chem Biol, 1, 210–215. [DOI] [PubMed] [Google Scholar]
  1318. Janowski BA, Huffman KE, Schwartz JC, Ram R, Nordsell R, Shames DS, Minna JD and Corey DR, 2006. Involvement of AGO1 and AGO2 in mammalian transcriptional silencing. Nature Structural & Molecular Biology, 13, 787–792. [DOI] [PubMed] [Google Scholar]
  1319. Janowski BA, Younger ST, Hardy DB, Ram R, Huffman KE and Corey DR, 2007. Activating gene expression in mammalian cells with promoter‐targeted duplex RNAs. Nat Chem Biol, 3, 166–173. [DOI] [PubMed] [Google Scholar]
  1320. Jaskiewicz L and Filipowicz W, 2008. Role of Dicer in posttranscriptional RNA silencing. Curr Top Microbiol Immunol, 320, 77–97. [DOI] [PubMed] [Google Scholar]
  1321. Ji H, Chen MS, Greening DW, He WF, Rai A, Zhang WW and Simpson RJ, 2014. Deep Sequencing of RNA from Three Different Extracellular Vesicle (EV) Subtypes Released from the Human LIM1863 Colon Cancer Cell Line Uncovers Distinct Mirna‐Enrichment Signatures. PLoS ONE, 9, e110314–e110314. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1322. Jiang F, Miller MT and Marcotrigiano J, 2011a. Structural Basis for RNA Recognition and Activation of RIG‐I. Nucleic Acid Database. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1323. Jiang FG, Ramanathan A, Miller MT, Tang GQ, Gale M, Patel SS and Marcotrigiano J, 2011b. Structural basis of RNA recognition and activation by innate immune receptor RIG‐I. Nature, 479, 423–U184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1324. Jiang G, Zheng L, Pu J, Mei H, Zhao J, Huang K, Zeng F and Tong Q, 2012. Small RNAs Targeting Transcription Start Site Induce Heparanase Silencing through Interference with Transcription Initiation in Human Cancer Cells. PLoS ONE, 7, e31379–e31379. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1325. Jiang HL, Sheong FK, Zhu LZ, Gao X, Bernauer J and Huang XH, 2015. Markov State Models Reveal a Two‐Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re‐arrangement. Plos Computational Biology, 11, e1004404–e1004404. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1326. Jin H, Suh MR, Han J, Yeom KH, Lee Y, Heo I, Ha M, Hyun S and Kim VN, 2009. Human UPF1 Participates in Small RNA‐Induced mRNA Downregulation. Molecular and Cellular Biology, 29, 5789–5799. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1327. Jinek M, Fabian MR, Coyle SM, Sonenberg N and Doudna JA, 2010. Structural insights into the human GW182‐PABC interaction in microRNA‐mediated deadenylation. Nature Structural & Molecular Biology, 17, 238–240. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1328. Jo MH, Shin S, Jung SR, Kim E, Song JJ and Hohng S, 2015a. Human Argonaute 2 Has Diverse Reaction Pathways on Target RNAs. Molecular Cell, 59, 117–124. [DOI] [PubMed] [Google Scholar]
  1329. Jo MH, Song J‐J and Hohng S, 2015b. Single‐molecule fluorescence measurements reveal the reaction mechanisms of the core‐RISC, composed of human Argonaute 2 and a guide RNA. Bmb Reports, 48, 643–644. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1330. Johanson TM, Lew AM and Chong MM, 2013. MicroRNA‐independent roles of the RNase III enzymes Drosha and Dicer. Open Biol, 3, 130144. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1331. John B, Enright AJ, Aravin A, Tuschl T, Sander C and Marks DS, 2004. Human MicroRNA targets. Plos Biology, 2, e363. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1332. Johnson KL, Price BD, Eckerle LD and Ball LA, 2004. Nodamura virus nonstructural protein B2 can enhance viral RNA accumulation in both mammalian and insect cells. Journal of Virology, 78, 6698–6704. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1333. Johnston M, Geoffroy M‐C, Sobala A, Hay R and Hutvagner G, 2010. HSP90 Protein Stabilizes Unloaded Argonaute Complexes and Microscopic P‐bodies in Human Cells. Molecular Biology of the Cell, 21, 1462–1469. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1334. Jopling CL, Yi M, Lancaster AM, Lemon SM and Sarnow P, 2005. Modulation of hepatitis C virus RNA abundance by a liver‐specific MicroRNA. Science, 309, 1577–1581. [DOI] [PubMed] [Google Scholar]
  1335. Josa‐Prado F, Henley JM and Wilkinson KA, 2015. SUMOylation of Argonaute‐2 regulates RNA interference activity. Biochem Biophys Res Commun, 464, 1066–1071. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1336. Jose AM and Hunter CP, 2007. Transport of sequence‐specific RNA interference information between cells. Annu Rev Genet, 41, 305–330. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1337. Juvvuna PK, Khandelia P, Lee LM and Makeyev EV, 2012. Argonaute identity defines the length of mature mammalian microRNAs. Nucleic Acids Research, 40, 6808–6820. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1338. Kalia M, Willkomm S, Claussen JC, Restle T and Bonvin AM, 2016. Novel Insights into Guide RNA 5′‐Nucleoside/Tide Binding by Human Argonaute 2. Int J Mol Sci, 17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1339. Kandeel M and Kitade Y, 2013. In silico molecular docking analysis of the human Argonaute 2 PAZ domain reveals insights into RNA interference. Journal of Computer‐Aided Molecular Design, 27, 605–614. [DOI] [PubMed] [Google Scholar]
  1340. Kaneda M, Tang FC, O'Carroll D, Lao KQ and Surani MA, 2009. Essential role for Argonaute2 protein in mouse oogenesis. Epigenetics & Chromatin, 2, 9–9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1341. Kanellopoulou C, Muljo SA, Kung AL, Ganesan S, Drapkin R, Jenuwein T, Livingston DM and Rajewsky K, 2005. Dicer‐deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes & Development, 19, 489–501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1342. Kasim V, Wu SR, Taira K and Miyagishi M, 2013. Determination of the Role of DDX3 a Factor Involved in Mammalian RNAi Pathway Using an shRNA‐Expression Library. PLoS ONE, 8, e59445–e59445. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1343. Kato H, Takeuchi O, Sato S, Yoneyama M, Yamamoto M, Matsui K, Uematsu S, Jung A, Kawai T, Ishii KJ, Yamaguchi O, Otsu K, Tsujimura T, Koh CS, Sousa CRE, Matsuura Y, Fujita T and Akira S, 2006. Differential roles of MDA5 and RIG‐I helicases in the recognition of RNA viruses. Nature, 441, 101–105. [DOI] [PubMed] [Google Scholar]
  1344. Kawahara Y, Zinshteyn B, Chendrimada TP, Shiekhattar R and Nishikura K, 2007a. RNA editing of the microRNA‐151 precursor blocks cleavage by the Dicer‐TRBP complex. EMBO Rep, 8, 763–769. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1345. Kawahara Y, Zinshteyn B, Sethupathy P, Iizasa H, Hatzigeorgiou AG and Nishikura K, 2007b. Redirection of silencing targets by adenosine‐to‐inosine editing of miRNAs. Science, 315, 1137–1140. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1346. Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, Daub CO, Kai C, Kawai J, Yasuda J, Carninci P and Hayashizaki Y, 2008. Hidden layers of human small RNAs. BMC Genomics, 9, 157. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1347. Kawasaki H and Taira K, 2004. Induction of DNA methylation and gene silencing by short interfering RNAs in human cells. Nature, 431, 211–217. [DOI] [PubMed] [Google Scholar]
  1348. Kedersha N, Stoecklin G, Ayodele M, Yacono P, Lykke‐Andersen J, Fritzler MJ, Scheuner D, Kaufman RJ, Golan DE and Anderson P, 2005. Stress granules and processing bodies are dynamically linked sites of mRNP remodeling. Journal of Cell Biology, 169, 871–884. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1349. Kennedy EM, Whisnant AW, Kornepati AVR, Marshall JB, Bogerd HP and Cullen BR, 2015. Production of functional small interfering RNAs by an amino‐terminal deletion mutant of human Dicer. Proc Natl Acad Sci U S A, 112, E6945–E6954. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1350. Ketting RF, Fischer SE, Bernstein E, Sijen T, Hannon GJ and Plasterk RH, 2001. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes & Development, 15, 2654–2659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1351. Khvorova A, Reynolds A and Jayasena SD, 2003. Functional siRNAs and miRNAs exhibit strand bias. Cell, 115, 209–216. [DOI] [PubMed] [Google Scholar]
  1352. Kim BS, Jung JS, Jang JH, Kang KS and Kang SK, 2011. Nuclear Argonaute 2 regulates adipose tissue‐derived stem cell survival through direct control of miR10b and selenoprotein N1 expression. Aging Cell, 10, 277–291. [DOI] [PubMed] [Google Scholar]
  1353. Kim BS, Im YB, Jung SJ, Park CH and Kang SK, 2012. Argonaute2 Regulation for K+ Channel‐Mediated Human Adipose Tissue‐Derived Stromal Cells Self‐Renewal and Survival in Nucleus. Stem Cells and Development, 21, 1736–1748. [DOI] [PubMed] [Google Scholar]
  1354. Kim DH, Behlke MA, Rose SD, Chang MS, Choi S and Rossi JJ, 2005. Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nature Biotechnology, 23, 222–226. [DOI] [PubMed] [Google Scholar]
  1355. Kim DH, Villeneuve LM, Morris KV and Rossi JJ, 2006. Argonaute‐1 directs siRNA‐mediated transcriptional gene silencing in human cells. Nature Structural & Molecular Biology, 13, 793–797. [DOI] [PubMed] [Google Scholar]
  1356. Kim DH, Saetrom P, Snove O and Rossi JJ, 2008. MicroRNA‐directed transcriptional gene silencing in mammalian cells. Proc Natl Acad Sci U S A, 105, 16230–16235. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1357. Kim JW, Zhang YH, Zern MA, Rossi JJ and Wu J, 2007. Short hairpin RNA causes the methylation of transforming growth factor‐beta receptor II promoter and silencing of the target gene in rat hepatic stellate cells. Biochem Biophys Res Commun, 359, 292–297. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1358. Kim Y, Yeo J, Lee JH, Cho J, Seo D, Kim JS and Kim VN, 2014. Deletion of Human tarbp2 Reveals Cellular MicroRNA Targets and Cell‐Cycle Function of TRBP. Cell Reports, 9, 1061–1074. [DOI] [PubMed] [Google Scholar]
  1359. Kincaid RP, Chen YT, Cox JE, Rethwilm A and Sullivan CS, 2014. Noncanonical MicroRNA (miRNA) Biogenesis Gives Rise to Retroviral Mimics of Lymphoproliferative and Immunosuppressive Host miRNAs. Mbio, 5, e00074–e00074. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1360. Kinch LN and Grishin NV, 2009. The human Ago2 MC region does not contain an eIF4E‐like mRNA cap binding motif. Biology Direct, 4, 2–2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1361. Kini HK and Walton SP, 2007. In vitro binding of single‐stranded RNA by human Dicer. Febs Letters, 581, 5611–5616. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1362. Knuckles P, Vogt MA, Lugert S, Milo M, Chong MMW, Hautbergue GM, Wilson SA, Littman DR and Taylor V, 2012. Drosha regulates neurogenesis by controlling Neurogenin 2 expression independent of microRNAs. Nature Neuroscience, 15, 962–969. [DOI] [PubMed] [Google Scholar]
  1363. Kok KH, Ng MHJ, Ching YP and Jin DY, 2007. Human TRBP and PACT directly interact with each other and associate with dicer to facilitate the production of small interfering RNA. Journal of Biological Chemistry, 282, 17649–17657. [DOI] [PubMed] [Google Scholar]
  1364. Koppers‐Lalic D, Hackenberg M, Bijnsdorp IV, van Eijndhoven MAJ, Sadek P, Sie D, Zini N, Middeldorp JM, Ylstra B, de Menezes RX, Wurdinger T, Meijer GA and Pegtel DM, 2014. Nontemplated Nucleotide Additions Distinguish the Small RNA Composition in Cells from Exosomes. Cell Reports, 8, 1649–1658. [DOI] [PubMed] [Google Scholar]
  1365. Kowalinski E, Lunardi T, McCarthy AA, Louber J, Brunel J, Grigorov B, Gerlier D and Cusack S, 2011. Structural basis for the activation of innate immune pattern‐recognition receptor RIG‐I by viral RNA. Cell, 147, 423–435. [DOI] [PubMed] [Google Scholar]
  1366. Kropp J, Salih SM and Khatib H, 2014. Expression of microRNAs in bovine and human pre‐implantation embryo culture media. Frontiers in Genetics, 5, 91–91. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1367. Kumar L, Verma S, Vaidya B and Gupta V, 2015. Exosomes: Natural Carriers for siRNA Delivery. Current Pharmaceutical Design, 21, 4556–4565. [DOI] [PubMed] [Google Scholar]
  1368. Kumar P, Anaya J, Mudunuri SB and Dutta A, 2014. Meta‐analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. Bmc Biology, 12, 78–78. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1369. Kuosmanen SM, Hartikainen J, Hippelainen M, Kokki H, Levonen AL and Tavi P, 2015. MicroRNA Profiling of Pericardial Fluid Samples from Patients with Heart Failure. PLoS ONE, 10, e0119646–e0119646. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1370. Kuzuoglu‐Ozturk D, Bhandari D, Huntzinger E, Fauser M, Helms S and Izaurralde E, 2016. miRISC and the CCR4‐NOT complex silence mRNA targets independently of 43S ribosomal scanning. EMBO J. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1371. Kwon SC, Nguyen TA, Choi YG, Jo MH, Hohng S, Kim VN and Woo JS, 2016. Structure of Human DROSHA. Cell, 164, 81–90. [DOI] [PubMed] [Google Scholar]
  1372. Ladewig E, Okamura K, Flynt AS, Westholm JO and Lai EC, 2012. Discovery of hundreds of mirtrons in mouse and human small RNA data. Genome Research, 22, 1634–1645. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1373. Lamontagne B, Larose S, Boulanger J and Elela SA, 2001. The RNase III family: a conserved structure and expanding functions in eukaryotic dsRNA metabolism. Curr Issues Mol Biol, 3, 71–78. [PubMed] [Google Scholar]
  1374. Landthaler M, Yalcin A and Tuschl T, 2004. The human DiGeorge syndrome critical region gene 8 and its D‐melanogaster homolog are required for miRNA biogenesis. Current Biology, 14, 2162–2167. [DOI] [PubMed] [Google Scholar]
  1375. Laraki G, Clerzius G, Daher A, Melendez‐Pena C, Daniels S and Gatignol A, 2008. Interactions between the double‐stranded RNA‐binding proteins TRBP and PACT define the Medipal domain that mediates protein‐protein interactions. RNA Biology, 5, 92–103. [DOI] [PubMed] [Google Scholar]
  1376. Lasser C, 2012. Exosomal RNA as biomarkers and the therapeutic potential of exosome vectors. Expert Opinion on Biological Therapy, 12, S189–S197. [DOI] [PubMed] [Google Scholar]
  1377. Lau PW, Potter CS, Carragher B and MacRae IJ, 2009. Structure of the Human Dicer‐TRBP Complex by Electron Microscopy. Structure, 17, 1326–1332. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1378. Lau PW, Guiley KZ, De N, Potter CS, Carragher B and MacRae IJ, 2012. The molecular architecture of human Dicer. Nature Structural & Molecular Biology, 19, 436–440. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1379. Lawrie CH, Gal S, Dunlop HM, Pushkaran B, Liggins AP, Pulford K, Banham AH, Pezzella F, Boultwood J, Wainscoat JS, Hatton CS and Harris AL, 2008. Detection of elevated levels of tumour‐associated microRNAs in serum of patients with diffuse large B‐cell lymphoma. Br J Haematol, 141, 672–675. [DOI] [PubMed] [Google Scholar]
  1380. Lazzaretti D, Tournier I and Izaurralde E, 2009. The C‐terminal domains of human TNRC6A, TNRC6B, and TNRC6C silence bound transcripts independently of Argonaute proteins. Rna, 15, 1059–1066. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1381. Lecellier CH, Dunoyer P, Arar K, Lehmann‐Che J, Eyquem S, Himber C, Saib A and Voinnet O, 2005. A cellular microRNA mediates antiviral defense in human cells. Science, 308, 557–560. [DOI] [PubMed] [Google Scholar]
  1382. Lee HY, Zhou K, Smith AM, Noland CL and Doudna JA, 2013. Differential roles of human Dicer‐binding proteins TRBP and PACT in small RNA processing. Nucleic Acids Research, 41, 6568–6576. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1383. Lee NS, Dohjima T, Bauer G, Li HT, Li MJ, Ehsani A, Salvaterra P and Rossi J, 2002. Expression of small interfering RNAs targeted against HIV‐1 rev transcripts in human cells. Nature Biotechnology, 20, 500–505. [DOI] [PubMed] [Google Scholar]
  1384. Lee Y, Ahn C, Han JJ, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S and Kim VN, 2003. The nuclear RNase III Drosha initiates microRNA processing. Nature, 425, 415–419. [DOI] [PubMed] [Google Scholar]
  1385. Lee Y, El Andaloussi S and Wood MJA, 2012. Exosomes and microvesicles: extracellular vesicles for genetic information transfer and gene therapy. Human Molecular Genetics, 21, R125–R134. [DOI] [PubMed] [Google Scholar]
  1386. Lehmann KA and Bass BL, 1999. The importance of internal loops within RNA substrates of ADAR1. Journal of Molecular Biology, 291, 1–13. [DOI] [PubMed] [Google Scholar]
  1387. Leung AK, Vyas S, Rood JE, Bhutkar A, Sharp PA and Chang P, 2011. Poly(ADP‐ribose) regulates stress responses and microRNA activity in the cytoplasm. Molecular Cell, 42, 489–499. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1388. Lewis BP, Shih IH, Jones‐Rhoades MW, Bartel DP and Burge CB, 2003. Prediction of mammalian microRNA targets. Cell, 115, 787–798. [DOI] [PubMed] [Google Scholar]
  1389. Li H, Li WX and Ding SW, 2002. Induction and suppression of RNA silencing by an animal virus. Science, 296, 1319–1321. [DOI] [PubMed] [Google Scholar]
  1390. Li LC, Okino ST, Zhao H, Pookot D, Place RF, Urakami S, Enokida H and Dahiya R, 2006. Small dsRNAs induce transcriptional activation in human cells. Proc Natl Acad Sci U S A, 103, 17337–17342. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1391. Li WX, Li H, Lu R, Li F, Dus M, Atkinson P, Brydon EW, Johnson KL, Garcia‐Sastre A, Ball LA, Palese P and Ding SW, 2004. Interferon antagonist proteins of influenza and vaccinia viruses are suppressors of RNA silencing. Proc Natl Acad Sci U S A, 101, 1350–1355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1392. Li XJ, Lu C, Stewart M, Xu HY, Strong RK, Igumenova T and Li PW, 2009a. Structural basis of double‐stranded RNA recognition by the RIG‐I like receptor MDA5. Archives of Biochemistry and Biophysics, 488, 23–33. [DOI] [PubMed] [Google Scholar]
  1393. Li XJ, Ranjith‐Kumar CT, Brooks MT, Dharmaiah S, Herr AB, Kao C and Li PW, 2009b. The RIG‐I‐like Receptor LGP2 Recognizes the Termini of Double‐stranded RNA. Journal of Biological Chemistry, 284, 13881–13891. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1394. Li ZH, Kim SW, Lin YF, Moore PS, Chang Y and John B, 2009c. Characterization of Viral and Human RNAs Smaller than Canonical MicroRNAs. Journal of Virology, 83, 12751–12758. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1395. Li ZH, Ender C, Meister G, Moore PS, Chang Y and John B, 2012. Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs. Nucleic Acids Research, 40, 6787–6799. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1396. Lian SL, Li SQ, Abadal GX, Pauley BA, Fritzler MJ and Chan EKL, 2009. The C‐terminal half of human Ago2 binds to multiple GW‐rich regions of GW182 and requires GW182 to mediate silencing. Rna, 15, 804–813. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1397. Liang XH and Crooke ST, 2011. Depletion of key protein components of the RISC pathway impairs pre‐ribosomal RNA processing. Nucleic Acids Research, 39, 4875–4889. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1398. Lim LP, Lau NC, Garrett‐Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS and Johnson JM, 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature, 433, 769–773. [DOI] [PubMed] [Google Scholar]
  1399. Lima WF, Wu HJ, Nichols JG, Sun H, Murray HM and Crooke ST, 2009. Binding and Cleavage Specificities of Human Argonaute2. Journal of Biological Chemistry, 284, 26017–26028. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1400. Lin JC and Tarn WY, 2009. RNA‐binding Motif Protein 4 Translocates to Cytoplasmic Granules and Suppresses Translation via Argonaute2 during Muscle Cell Differentiation. Journal of Biological Chemistry, 284, 34658–34665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1401. Lipardi C and Paterson BM, 2009. Identification of an RNA‐dependent RNA polymerase in Drosophila involved in RNAi and transposon suppression. Proc Natl Acad Sci U S A, 106, 15645–15650. [DOI] [PMC free article] [PubMed] [Google Scholar] [Retracted]
  1402. Liu C, Zhang X, Huang F, Yang B, Li J, Liu BF, Luo HH, Zhang P and Zhang H, 2012a. APOBEC3G Inhibits MicroRNA‐mediated Repression of Translation by Interfering with the Interaction between Argonaute‐2 and MOV10. Journal of Biological Chemistry, 287, 29373–29383. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1403. Liu J, Rivas FV, Wohlschlegel J, Yates JR, 3rd , Parker R and Hannon GJ, 2005a. A role for the P‐body component GW182 in microRNA function. Nature Cell Biology, 7, 1261–1266. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1404. Liu J, Hu JX and Corey DR, 2012b. Expanding the action of duplex RNAs into the nucleus: redirecting alternative splicing. Nucleic Acids Research, 40, 1240–1250. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1405. Liu J, Hu JX, Hicks JA, Prakash TP and Corey DR, 2015. Modulation of Splicing by Single‐Stranded Silencing RNAs. Nucleic Acid Therapeutics, 25, 113–120. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1406. Liu JD, Carmell MA, Rivas FV, Marsden CG, Thomson JM, Song JJ, Hammond SM, Joshua‐Tor L and Hannon GJ, 2004. Argonaute2 is the catalytic engine of mammalian RNAi. Science, 305, 1437–1441. [DOI] [PubMed] [Google Scholar]
  1407. Liu JD, Valencia‐Sanchez MA, Hannon GJ and Parker R, 2005b. MicroRNA‐dependent localization of targeted mRNAs to mammalian P‐bodies. Nature Cell Biology, 7, 719–U118. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1408. Liu XH, Jin DY, McManus MT and Mourelatos Z, 2012c. Precursor MicroRNA‐Programmed Silencing Complex Assembly Pathways in Mammals. Molecular Cell, 46, 507–517. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1409. Liu Y, Tan HL, Tian H, Liang CY, Chen S and Liu QH, 2011. Autoantigen La Promotes Efficient RNAi, Antiviral Response, and Transposon Silencing by Facilitating Multiple‐Turnover RISC Catalysis. Molecular Cell, 44, 502–508. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1410. Livengood AJ, Wu CCN and Carson DA, 2007. Opposing roles of RNA receptors TLR3 and RIG‐I in the inflammatory response to double‐stranded RNA in a Kaposi's sarcoma cell line. Cellular Immunology, 249, 55–62. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1411. Lopez‐Orozco J, Pare JM, Holme AL, Chaulk SG, Fahlman RP and Hobman TC, 2015. Functional analyses of phosphorylation events in human Argonaute 2. Rna, 21, 2030–2038. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1412. Lu SH and Cullen BR, 2004. Adenovirus VA1 noncoding RNA can inhibit small interfering RNA and microRNA biogenesis. Journal of Virology, 78, 12868–12876. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1413. Lugli G, Larson J, Martone ME, Jones Y and Smalheiser NR, 2005. Dicer and eIF2c are enriched at postsynaptic densities in adult mouse brain and are modified by neuronal activity in a calpain‐dependent manner. Journal of Neurochemistry, 94, 896–905. [DOI] [PubMed] [Google Scholar]
  1414. Luo D, Ding SC, Vela A, Kohlway A, Lindenbach BD and Pyle AM, 2011. Structural insights into RNA recognition by RIG‐I. Cell, 147, 409–422. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1415. Luo SS, Ishibashi O, Ishikawa G, Ishikawa T, Katayama A, Mishima T, Takizawa T, Shigihara T, Goto T, Izumi A, Ohkuchi A, Matsubara S, Takeshita T and Takizawa T, 2009. Human Villous Trophoblasts Express and Secrete Placenta‐Specific MicroRNAs into Maternal Circulation via Exosomes. Biology of Reproduction, 81, 717–729. [DOI] [PubMed] [Google Scholar]
  1416. Ma E, MacRae IJ, Kirsch JF and Doudna JA, 2008. Autoinhibition of human dicer by its internal helicase domain. Journal of Molecular Biology, 380, 237–243. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1417. Ma EB, Zhou KH, Kidwell MA and Doudna JA, 2012. Coordinated Activities of Human Dicer Domains in Regulatory RNA Processing. Journal of Molecular Biology, 422, 466–476. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1418. Ma HM, Wu YG, Choi JG and Wu HQ, 2013. Lower and upper stem‐single‐stranded RNA junctions together determine the Drosha cleavage site. Proc Natl Acad Sci U S A, 110, 20687–20692. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1419. Ma J, Flemr M, Stein P, Berninger P, Malik R, Zavolan M, Svoboda P and Schultz RM, 2010. MicroRNA Activity Is Suppressed in Mouse Oocytes. Current Biology, 20, 265–270. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1420. Ma JB, Ye K and Patel DJ, 2004. Structural basis for overhang‐specific small interfering RNA recognition by the PAZ domain. Nature, 429, 318–322. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1421. Macias S, Plass M, Stajuda A, Michlewski G, Eyras E and Caceres JF, 2012. DGCR8 HITS‐CLIP reveals novel functions for the Microprocessor. Nature Structural & Molecular Biology, 19, 760–766. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1422. Macias S, Cordiner RA, Gautier P, Plass M and Caceres JF, 2015. DGCR8 Acts as an Adaptor for the Exosome Complex to Degrade Double‐Stranded Structured RNAs. Molecular Cell, 60, 873–885. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1423. MacRae IJ, Li F, Zhou K, Cande WZ and Doudna JA, 2006a. Structure of Dicer and mechanistic implications for RNAi. Cold Spring Harbor Symposia on Quantitative Biology, 71, 73–80. [DOI] [PubMed] [Google Scholar]
  1424. MacRae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD and Doudna JA, 2006b. Structural basis for double‐stranded RNA processing by Dicer. Science, 311, 195–198. [DOI] [PubMed] [Google Scholar]
  1425. MacRae IJ, Zhou K and Doudna JA, 2007. Structural determinants of RNA recognition and cleavage by Dicer. Nature Structural & Molecular Biology, 14, 934–940. [DOI] [PubMed] [Google Scholar]
  1426. MacRae IJ, Ma E, Zhou M, Robinson CV and Doudna JA, 2008. In vitro reconstitution of the human RISC‐loading complex. Proc Natl Acad Sci U S A, 105, 512–517. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1427. Madsen C, Gronskov K, Brondum‐Nielsen K and Jensen TG, 2009. Normal RNAi response in human fragile x fibroblasts. BMC Research Notes, 2, 177–177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1428. Maida Y, Yasukawa M, Furuuchi M, Lassmann T, Possemato R, Okamoto N, Kasim V, Hayashizaki Y, Hahn WC and Masutomi K, 2009. An RNA‐dependent RNA polymerase formed by TERT and the RMRP RNA. Nature, 461, 230–U104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1429. Maida Y and Masutomi K, 2011. RNA‐dependent RNA polymerases in RNA silencing. Biological Chemistry, 392, 299–304. [DOI] [PubMed] [Google Scholar]
  1430. Maida Y, Kyo S, Lassmann T, Hayashizaki Y and Masutomi K, 2013. Off‐Target Effect of Endogenous siRNA Derived from RMRP in Human Cells. International Journal of Molecular Sciences, 14, 9305–9318. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1431. Maida Y, Yasukawa M and Masutomi K, 2016. De Novo RNA Synthesis by RNA‐Dependent RNA Polymerase Activity of Telomerase Reverse Transcriptase. Molecular and Cellular Biology, 36, 1248–1259. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1432. Maniataki E and Mourelatos Z, 2005a. Human mitochondrial tRNA(Met) is exported to the cytoplasm and associates with the Argonaute 2 protein. Rna, 11, 849–852. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1433. Maniataki E and Mourelatos Z, 2005b. A human, ATP‐independent, RISC assembly machine fueled by pre‐miRNA. Genes & Development, 19, 2979–2990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1434. Marques JT, Devosse T, Wang D, Zamanian‐Daryoush M, Serbinowski P, Hartmann R, Fujita T, Behlke MA and Williams BRG, 2006. A structural basis for discriminating between self and nonself double‐stranded RNAs in mammalian cells. Nature Biotechnology, 24, 559–565. [DOI] [PubMed] [Google Scholar]
  1435. Martinez I and Melero JA, 2002. A model for the generation of multiple A to G transitions in the human respiratory syncytial virus genome: predicted RNA secondary structures as substrates for adenosine cleaminases that act on RNA. Journal of General Virology, 83, 1445–1455. [DOI] [PubMed] [Google Scholar]
  1436. Martinez J, Patkaniowska A, Urlaub H, Luhrmann R and Tuschl T, 2002. Single‐stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell, 110, 563–574. [DOI] [PubMed] [Google Scholar]
  1437. Martinez NJ, Chang HM, Borrajo JD and Gregory RI, 2013. The co‐chaperones Fkbp4/5 control Argonaute2 expression and facilitate RISC assembly. Rna, 19, 1583–1593. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1438. Martinez NJ and Gregory RI, 2013. Argonaute2 expression is post‐transcriptionally coupled to microRNA abundance. Rna, 19, 605–612. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1439. Mathys H, Basquin J, Ozgur S, Czarnocki‐Cieciura M, Bonneau F, Aartse A, Dziembowski A, Nowotny M, Conti E and Filipowicz W, 2014. Structural and biochemical insights to the role of the CCR4‐NOT complex and DDX6 ATPase in microRNA repression. Molecular Cell, 54, 751–765. [DOI] [PubMed] [Google Scholar]
  1440. Matranga C, Tomari Y, Shin C, Bartel DP and Zamore PD, 2005. Passenger‐strand cleavage facilitates assembly of siRNA into Ago2‐containing RNAi enzyme complexes. Cell, 123, 607–620. [DOI] [PubMed] [Google Scholar]
  1441. Maurin T, Cazalla D, Yang JS, Bortolamiol‐Becet D and Lai EC, 2012. RNase III‐independent microRNA biogenesis in mammalian cells. Rna, 18, 2166–2173. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1442. Maute RL, Schneider C, Sumazin P, Holmes A, Califano A, Basso K and Dalla‐Favera R, 2013. tRNA‐derived microRNA modulates proliferation and the DNA damage response and is down‐regulated in B cell lymphoma. Proc Natl Acad Sci U S A, 110, 1404–1409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1443. Mazumder A, Bose M, Chakraborty A, Chakrabarti S and Bhattacharyya SN, 2013. A transient reversal of miRNA‐mediated repression controls macrophage activation. EMBO Rep, 14, 1008–1016. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1444. McCartney S, Vermi W, Gilfillan S, Cella M, Murphy TL, Schreiber RD, Murphy KM and Colonna M, 2009. Distinct and complementary functions of MDA5 and TLR3 in poly(I:C)‐mediated activation of mouse NK cells. Journal of Experimental Medicine, 206, 2967–2976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1445. McCartney SA, Thackray LB, Gitlin L, Gilfillan S, Virgin HW and Colonna M, 2008. MDA‐5 recognition of a murine norovirus. Plos Pathogens, 4, e1000108–e1000108. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1446. Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G and Tuschl T, 2004. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Molecular Cell, 15, 185–197. [DOI] [PubMed] [Google Scholar]
  1447. Meister G and Tuschl T, 2004. Mechanisms of gene silencing by double‐stranded RNA. Nature, 431, 343–349. [DOI] [PubMed] [Google Scholar]
  1448. Meister G, Landthaler M, Peters L, Chen PY, Urlaub H, Luhrmann R and Tuschl T, 2005. Identification of novel argonaute‐associated proteins. Current Biology, 15, 2149–2155. [DOI] [PubMed] [Google Scholar]
  1449. Meng B, Lui YW, Meng S, Ca C and Hu Y, 2006. Identification of effective siRNA blocking the expression of SARS viral envelope e and RDRP genes. Molecular Biotechnology, 33, 141–148. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1450. Meurs E, Chong K, Galabru J, Thomas NS, Kerr IM, Williams BR and Hovanessian AG, 1990. Molecular cloning and characterization of the human double‐stranded RNA‐activated protein kinase induced by interferon. Cell, 62, 379–390. [DOI] [PubMed] [Google Scholar]
  1451. Minones‐Moyano E, Friedländer MR, Pallares J, Kagerbauer B, Porta S, Escaramis G, Ferrer I, Estivill X and Marti E, 2013. Upregulation of a small vault RNA (svtRNA2‐1a) is an early event in parkinson disease and induces neuronal dysfunction. RNA Biology, 10, 1093–1106. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1452. Momose F, Seo N, Akahori Y, Sawada S, Harada N, Ogura T, Akiyoshi K and Shiku H, 2016. Guanine‐Rich Sequences Are a Dominant Feature of Exosomal microRNAs across the Mammalian Species and Cell Types. PLoS ONE, 11, e0154134–e0154134. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1453. Moon JS, Lee SH, Han SH, Kim EJ, Cho H, Lee W, Kim MK, Kim TE, Park HJ, Rhee JK, Kim SJ, Cho SW, Han SH and Oh JW, 2016. Inhibition of hepatitis C virus in mouse models by lipidoid nanoparticle‐mediated systemic delivery of siRNA against PRK2. Nanomedicine: nanotechnology, biology, and medicine. [DOI] [PubMed] [Google Scholar]
  1454. Morris KV, Chan SW, Jacobsen SE and Looney DJ, 2004. Small interfering RNA‐induced transcriptional gene silencing in human cells. Science, 305, 1289–1292. [DOI] [PubMed] [Google Scholar]
  1455. Morse DP, Aruscavage PJ and Bass BL, 2002. RNA hairpins in noncoding regions of human brain and Caenorhabditis elegans mRNA are edited by adenosine deaminases that act on RNA. Proc Natl Acad Sci U S A, 99, 7906–7911. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1456. Much C, Auchynnikava T, Pavlinic D, Buness A, Rappsilber J, Benes V, Allshire R and O'Carroll D, 2016. Endogenous Mouse Dicer Is an Exclusively Cytoplasmic Protein. Plos Genetics, 12, e1006095. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1457. Murchison EP, Partridge JF, Tam OH, Cheloufi S and Hannon GJ, 2005. Characterization of Dicer‐deficient murine embryonic stem cells. Proc Natl Acad Sci U S A, 102, 12135–12140. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1458. Murchison EP, Stein P, Xuan Z, Pan H, Zhang MQ, Schultz RM and Hannon GJ, 2007. Critical roles for Dicer in the female germline. Genes & Development, 21, 682–693. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1459. Murphy D, Dancis B and Brown JR, 2008. The evolution of core proteins involved in microRNA biogenesis. Bmc Evolutionary Biology, 8, 92–92. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1460. Nachmani D, Zimmermann A, Djian E, Weisblum Y, Livneh Y, Le VTK, Galun E, Horejsi V, Isakov O, Shomron N, Wolf DG, Hengel H and Mandelboim O, 2014. MicroRNA Editing Facilitates Immune Elimination of HCMV Infected Cells. Plos Pathogens, 10, e1003963–e1003963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1461. Nagata T, Tsuda K, Kobayashi N, Shirouzu M, Kigawa T, Guntert P, Yokoyama S and Muto Y, 2012. Solution structures of the double‐stranded RNA‐binding domains from RNA helicase A. Proteins‐Structure Function and Bioinformatics, 80, 1699–1706. [DOI] [PubMed] [Google Scholar]
  1462. Nakanishi K, Ascano M, Gogakos T, Ishibe‐Murakami S, Serganov AA, Briskin D, Morozov P, Tuschl T and Patel DJ, 2013. Eukaryote‐Specific Insertion Elements Control Human ARGONAUTE Slicer Activity. Cell Reports, 3, 1893–1900. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1463. Napoli S, Pastori C, Magistri M, Carbone GM and Catapano CV, 2009. Promoter‐specific transcriptional interference and c‐myc gene silencing by siRNAs in human cells. EMBO J, 28, 1708–1719. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1464. Nejepinska J, Flemr M and Svoboda P, 2012a. The Canonical RNA Interference Pathway in Animals In: Mallick B. and Ghosh Z. (eds). Regulatory RNAs. Springer, Berlin, Heidelberg: pp. 111–149. [Google Scholar]
  1465. Nejepinska J, Malik R, Filkowski J, Flemr M, Filipowicz W and Svoboda P, 2012b. dsRNA expression in the mouse elicits RNAi in oocytes and low adenosine deamination in somatic cells. Nucleic Acids Research, 40, 399–413. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1466. Nejepinska J, Malik R, Wagner S and Svoboda P, 2014. Reporters transiently transfected into mammalian cells are highly sensitive to translational repression induced by dsRNA expression. PLoS ONE, 9, e87517. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1467. Neve J, Burger K, Li WC, Hoque M, Patel R, Tian B, Gullerova M and Furger A, 2016. Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation. Genome Research, 26, 24–35. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1468. Nguyen J and Szoka FC, 2012. Nucleic Acid Delivery: The Missing Pieces of the Puzzle? Accounts of Chemical Research, 45, 1153–1162. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1469. Nguyen TA, Jo MH, Choi YG, Park J, Kwon SC, Hohng S, Kim VN and Woo JS, 2015. Functional Anatomy of the Human Microprocessor. Cell, 161, 1374–1387. [DOI] [PubMed] [Google Scholar]
  1470. Nicholson RH and Nicholson AW, 2002. Molecular characterization of a mouse cDNA encoding Dicer, a ribonuclease III ortholog involved in RNA interference. Mammalian Genome, 13, 67–73. [DOI] [PubMed] [Google Scholar]
  1471. Nie YZ, Zhao QC, Su YJ and Yang JH, 2004. Subcellular distribution of ADAR1 isoforms is synergistically determined by three nuclear discrimination signals and a regulatory motif. Journal of Biological Chemistry, 279, 13249–13255. [DOI] [PubMed] [Google Scholar]
  1472. Nie YZ, Hammond GL and Yang JH, 2007. Double‐stranded RNA deaminase ADAR1 increases host susceptibility to virus infection. Journal of Virology, 81, 917–923. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1473. Nishi K, Nishi A, Nagasawa T and Ui‐Tei K, 2013. Human TNRC6A is an Argonaute‐navigator protein for microRNA‐mediated gene silencing in the nucleus. Rna, 19, 17–35. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1474. Nishi K, Takahashi T, Suzawa M, Miyakawa T, Nagasawa T, Ming Y, Tanokura M and Ui‐Tei K, 2015. Control of the localization and function of a miRNA silencing component TNRC6A by Argonaute protein. Nucleic Acids Research, 43, 9856–9873. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1475. Nishikura K, Yoo C, Kim U, Murray JM, Estes PA, Cash FE and Liebhaber SA, 1991. Substrate specificity of the dsRNA unwinding/modifying activity. EMBO J, 10, 3523–3532. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1476. Nishikura K, 2010. Functions and Regulation of RNA Editing by ADAR Deaminases. Annual Review of Biochemistry, 79, 321–349. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1477. Nishikura K, 2016. A‐to‐I editing of coding and non‐coding RNAs by ADARs. Nature Reviews Molecular Cell Biology, 17, 83–96. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1478. Noland CL and Doudna JA, 2013. Multiple sensors ensure guide strand selection in human RNAi pathways. Rna, 19, 639–648. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1479. Novellino L, Rossi RL, Bonino F, Cavallone D, Abrignani S, Pagani M and Brunetto MR, 2012. Circulating Hepatitis B Surface Antigen Particles Carry Hepatocellular microRNAs. PLoS ONE, 7, e31952–e31952. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1480. Nygardas M, Vuorinen T, Aalto AP, Bamford DH and Hukkanen V, 2009. Inhibition of coxsackievirus B3 and related enteroviruses by antiviral short interfering RNA pools produced using phi 6 RNA‐dependent RNA polymerase. Journal of General Virology, 90, 2468–2473. [DOI] [PubMed] [Google Scholar]
  1481. Nykanen A, Haley B and Zamore PD, 2001. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell, 107, 309–321. [DOI] [PubMed] [Google Scholar]
  1482. Ohnishi Y, Totoki Y, Toyoda A, Watanabe T, Yamamoto Y, Tokunaga K, Sakaki Y, Sasaki H and Hohjoh H, 2010. Small RNA class transition from siRNA/piRNA to miRNA during pre‐implantation mouse development. Nucleic Acids Research, 38, 5141–5151. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1483. Ohrt T, Merkle D, Birkenfeld K, Echeverri CJ and Schwille P, 2006. In situ fluorescence analysis demonstrates active siRNA exclusion from the nucleus by Exportin 5. Nucleic Acids Research, 34, 1369–1380. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1484. Ohrt T, Muetze J, Staroske W, Weinmann L, Hock J, Crell K, Meister G and Schwille P, 2008. Fluorescence correlation spectroscopy and fluorescence cross‐correlation spectroscopy reveal the cytoplasmic origination of loaded nuclear RISC in vivo in human cells. Nucleic Acids Research, 36, 6439–6449. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1485. Ohrt T, Muetze J, Svoboda P and Schwille P, 2012. Intracellular Localization and Routing of miRNA and RNAi Pathway Components. Curr Top Med Chem, 12, 79–88. [DOI] [PubMed] [Google Scholar]
  1486. Okamura K, Ladewig E, Zhou L and Lai EC, 2013. Functional small RNAs are generated from select miRNA hairpin loops in flies and mammals. Genes & Development, 27, 778–792. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1487. Ostermann E, Tuddenham L, Macquin C, Alsaleh G, Schreiber‐Becker J, Tanguy M, Bahram S, Pfeffer S and Georgel P, 2012. Deregulation of Type I IFN‐Dependent Genes Correlates with Increased Susceptibility to Cytomegalovirus Acute Infection of Dicer Mutant Mice. PLoS ONE, 7, e43744–e43744. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1488. Otsuka M, Takata A, Yoshikawa T, Kojima K, Kishikawa T, Shibata C, Takekawa M, Yoshida H, Omata M and Koike K, 2011. Receptor for Activated Protein Kinase C: Requirement for Efficient MicroRNA Function and Reduced Expression in Hepatocellular Carcinoma. PLoS ONE, 6, e24359–e24359. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1489. Ozgur S and Stoecklin G, 2013. Role of Rck‐Pat1b binding in assembly of processing‐bodies. RNA Biology, 10, 528–539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1490. Parameswaran P, Sklan E, Wilkins C, Burgon T, Samuel MA, Lu R, Ansel KM, Heissmeyer V, Einav S, Jackson W, Doukas T, Paranjape S, Polacek C, dos Santos FB, Jalili R, Babrzadeh F, Gharizadeh B, Grimm D, Kay M, Koike S, Sarnow P, Ronaghi M, Ding SW, Harris E, Chow M, Diamond MS, Kirkegaard K, Glenn JS and Fire AZ, 2010. Six RNA Viruses and Forty‐One Hosts: Viral Small RNAs and Modulation of Small RNA Repertoires in Vertebrate and Invertebrate Systems. Plos Pathogens, 6, e1000764–e1000764. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1491. Pare JM, Lopez‐Orozco J and Hobman TC, 2011. MicroRNA‐binding is required for recruitment of human Argonaute 2 to stress granules and P‐bodies. Biochem Biophys Res Commun, 414, 259–264. [DOI] [PubMed] [Google Scholar]
  1492. Pare JM, LaPointe P and Hobman TC, 2013. Hsp90 cochaperones p23 and FKBP4 physically interact with hAgo2 and activate RNA interference‐mediated silencing in mammalian cells. Molecular Biology of the Cell, 24, 2303–2310. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1493. Park HS, Davies MV, Langland JO, Chang HW, Nam YS, Tartaglia J, Paoletti E, Jacobs BL, Kaufman RJ and Venkatesan S, 1994. TAR RNA‐binding protein is an inhibitor of the interferon‐induced protein kinase PKR. Proc Natl Acad Sci U S A, 91, 4713–4717. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1494. Park JE, Heo I, Tian Y, Simanshu DK, Chang H, Jee D, Patel DJ and Kim VN, 2011. Dicer recognizes the 5 ‘ end of RNA for efficient and accurate processing. Nature, 475, 201–U107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1495. Park JH and Shin C, 2015. Slicer‐independent mechanism drives small‐RNA strand separation during human RISC assembly. Nucleic Acids Research, 43, 9418–9433. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1496. Patel RC and Sen GC, 1998. PACT, a protein activator of the interferon‐induced protein kinase, PKR. EMBO J, 17, 4379–4390. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1497. Patranabis S and Bhattacharyya SN, 2016. Phosphorylation of Ago2 and Subsequent Inactivation of let‐7a RNP‐Specific MicroRNAs Control Differentiation of Mammalian Sympathetic Neurons. Molecular and Cellular Biology, 36, 1260–1271. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1498. Pawlicki JM and Steitz JA, 2008. Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production. Journal of Cell Biology, 182, 61–76. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1499. Pawlicki JM and Steitz JA, 2009. Subnuclear compartmentalization of transiently expressed polyadenylated pri‐microRNAs Processing at transcription sites or accumulation in SC35 foci. Cell Cycle, 8, 345–356. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1500. Pegtel DM, van de Garde MDB and Middeldorp JM, 2011. Viral miRNAs exploiting the endosomal‐exosomal pathway for intercellular cross‐talk and immune evasion. Biochimica Et Biophysica Acta‐Gene Regulatory Mechanisms, 1809, 715–721. [DOI] [PubMed] [Google Scholar]
  1501. Peng ZY, Cheng YB, Tan BCM, Kang L, Tian ZJ, Zhu YK, Zhang WW, Liang Y, Hu XD, Tan XM, Guo J, Dong ZR, Liang Y, Bao L and Wang J, 2012. Comprehensive analysis of RNA‐Seq data reveals extensive RNA editing in a human transcriptome. Nature Biotechnology, 30, 253. [DOI] [PubMed] [Google Scholar]
  1502. Pepin G, Perron MP and Provost P, 2012. Regulation of human Dicer by the resident ER membrane protein CLIMP‐63. Nucleic Acids Research, 40, 11603–11617. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1503. Peters L and Meister G, 2007. Argonaute proteins: Mediators of RNA silencing. Molecular Cell, 26, 611–623. [DOI] [PubMed] [Google Scholar]
  1504. Pfeffer S, Zavolan M, Grasser FA, Chien M, Russo JJ, Ju J, John B, Enright AJ, Marks D, Sander C and Tuschl T, 2004. Identification of virus‐encoded microRNAs. Science, 304, 734–736. [DOI] [PubMed] [Google Scholar]
  1505. Pfeffer S, Sewer A, Lagos‐Quintana M, Sheridan R, Sander C, Grasser FA, van Dyk LF, Ho CK, Shuman S, Chien M, Russo JJ, Ju J, Randall G, Lindenbach BD, Rice CM, Simon V, Ho DD, Zavolan M and Tuschl T, 2005. Identification of microRNAs of the herpesvirus family. Nature Methods, 2, 269–276. [DOI] [PubMed] [Google Scholar]
  1506. Pham JW, Pellino JL, Lee YS, Carthew RW and Sontheimer EJ, 2004. A Dicer‐2‐dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila. Cell, 117, 83–94. [DOI] [PubMed] [Google Scholar]
  1507. Phua SLC, Sivakamasundari V, Shao Y, Cai XH, Zhang LF, Lufkin T and Featherstone M, 2011. Nuclear Accumulation of an Uncapped RNA Produced by Drosha Cleavage of a Transcript Encoding miR‐10b and HOXD4. PLoS ONE, 6, e25689–e25689. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1508. Pichlmair A, Schulz O, Tan CP, Naslund TI, Liljestrom P, Weber F and Reis e Sousa C, 2006. RIG‐I‐mediated antiviral responses to single‐stranded RNA bearing 5′‐phosphates. Science, 314, 997–1001. [DOI] [PubMed] [Google Scholar]
  1509. Pillai RS, Artus CG and Filipowicz W, 2004. Tethering of human Ago proteins to mRNA mimics the miRNA‐mediated repression of protein synthesis. Rna, 10, 1518–1525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1510. Pillai RS, Bhattacharyya SN, Artus CG, Zoller T, Cougot N, Basyuk E, Bertrand E and Filipowicz W, 2005. Inhibition of translational initiation by Let‐7 microRNA in human cells. Science, 309, 1573–1576. [DOI] [PubMed] [Google Scholar]
  1511. Place RF, Li LC, Pookot D, Noonan EJ and Dahiya R, 2008. MicroRNA‐373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci U S A, 105, 1608–1613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1512. Plante I, Davidovic L, Ouellet DL, Gobeil LA, Tremblay S, Khandjian EW and Provost P, 2006. Dicer‐derived MicroRNAs are utilized by the fragile X mental retardation protein for assembly on target RNAs. Journal of Biomedicine and Biotechnology, 2006, 64347–64347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1513. Plante I, Ple H, Landry P, Gunaratne PH and Provost P, 2012. Modulation of microRNA activity by semi‐nnicroRNAs. Frontiers in Genetics, 3, 99‐Article No.: 99. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1514. Polson AG and Bass BL, 1994. Preferential selection of adenosines for modification by double‐stranded RNA adenosine deaminase. EMBO J, 13, 5701–5711. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1515. Poulsen H, Jorgensen R, Heding A, Nielsen FC, Bonven B and Egebjerg J, 2006. Dimerization of ADAR2 is mediated by the double‐stranded RNA binding domain. Rna, 12, 1350–1360. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1516. Provost P, Dishart D, Doucet J, Frendewey D, Samuelsson B and Radmark O, 2002. Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J, 21, 5864–5874. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1517. Puthenveetil S, Whitby L, Ren J, Kelnar K, Krebs JF and Beal PA, 2006. Controlling activation of the RNA‐dependent protein kinase by siRNAs using site‐specific chemical modification. Nucleic Acids Research, 34, 4900–4911. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1518. Qi HH, Ongusaha PP, Myllyharju J, Cheng DM, Pakkanen O, Shi YJ, Lee SW, Peng JM and Shi Y, 2008. Prolyl 4‐hydroxylation regulates Argonaute 2 stability. Nature, 455, 421–U478. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1519. Rak J, 2013. Extracellular vesicles ‐ biomarkers and effectors of the cellular interactome in cancer. Frontiers in Pharmacology, 4, 21–21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1520. Rehwinkel J, Behm‐Ansmant I, Gatfield D and Izaurralde E, 2005. A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA‐mediated gene silencing. Rna, 11, 1640–1647. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1521. Ren YF, Li GL, Wu JM, Xue YF, Song YJ, Lv L, Zhang XJ and Tang KF, 2012. Dicer‐Dependent Biogenesis of Small RNAs Derived from 7SL RNA. PLoS ONE, 7, e40705–e40705. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1522. Reynolds A, Anderson EM, Vermeulen A, Fedorov Y, Robinson K, Leake D, Karpilow J, Marshall WS and Khvorova A, 2006. Induction of the interferon response by siRNA is cell type‐ and duplex length‐dependent. Rna, 12, 988–993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1523. Rice GI, Kasher PR, Forte GMA, Mannion NM, Greenwood SM, Szynkiewicz M, Dickerson JE, Bhaskar SS, Zampini M, Briggs TA, Jenkinson EM, Bacino CA, Battini R, Bertini E, Brogan PA, Brueton LA, Carpanelli M, De Laet C, de Lonlay P, del Toro M, Desguerre I, Fazzi E, Garcia‐Cazorla A, Heiberg A, Kawaguchi M, Kumar R, Lin J, Lourenco CM, Male AM, Marques W, Mignot C, Olivieri I, Orcesi S, Prabhakar P, Rasmussen M, Robinson RA, Rozenberg F, Schmidt JL, Steindl K, Tan TY, van der Merwe WG, Vanderver A, Vassallo G, Wakeling EL, Wassmer E, Whittaker E, Livingston JH, Lebon P, Suzuki T, McLaughlin PJ, Keegan LP, O'Connell MA, Lovell SC and Crow YJ, 2012. Mutations in ADAR1 cause Aicardi‐Goutieres syndrome associated with a type I interferon signature. Nature Genetics, 44, 1243–1248. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1524. Rivas FV, Tolia NH, Song JJ, Aragon JP, Liu JD, Hannon GJ and Joshua‐Tor L, 2005. Purified Argonaute2 and an siRNA form recombinant human RISC. Nature Structural & Molecular Biology, 12, 340–349. [DOI] [PubMed] [Google Scholar]
  1525. Robb GB, Brown KM, Khurana J and Rana TM, 2005. Specific and potent RNAi in the nucleus of human cells. Nature Structural & Molecular Biology, 12, 133–137. [DOI] [PubMed] [Google Scholar]
  1526. Robb GB and Rana TM, 2007. RNA helicase A interacts with RISC in human cells and functions in RISC loading. Molecular Cell, 26, 523–537. [DOI] [PubMed] [Google Scholar]
  1527. Rudel S, Flatley A, Weinmann L, Kremmer E and Meister G, 2008. A multifunctional human Argonaute2‐specific monoclonal antibody. Rna, 14, 1244–1253. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1528. Rudel S, Wang YL, Lenobel R, Korner R, Hsiao HH, Urlaub H, Patel D and Meister G, 2011. Phosphorylation of human Argonaute proteins affects small RNA binding. Nucleic Acids Research, 39, 2330–2343. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1529. Rybak A, Fuchs H, Hadian K, Smirnova L, Wulczyn EA, Michel G, Nitsch R, Krappmann D and Wulczyn FG, 2009. The let‐7 target gene mouse lin‐41 is a stem cell specific E3 ubiquitin ligase for the miRNA pathway protein Ago2. Nature Cell Biology, 11, 1411–U1458. [DOI] [PubMed] [Google Scholar]
  1530. Ryu I, Park JH, An S, Kwon OS and Jang SK, 2013. eIF4GI Facilitates the MicroRNA‐Mediated Gene Silencing. PLoS ONE, 8, e55725–e55725. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1531. Sadler AJ and Williams BR, 2007. Structure and function of the protein kinase R. Curr Top Microbiol Immunol, 316, 253–292. [DOI] [PubMed] [Google Scholar]
  1532. Salameh A, Lee AK, Cardo‐Vila M, Nunes DN, Efstathiou E, Staquicini FI, Dobroff AS, Marchio S, Navone NM, Hosoya H, Lauer RC, Wen SJ, Salmeron CC, Hoang A, Newsham I, Lima LA, Carraro DM, Oliviero S, Kolonin MG, Sidman RL, Do KA, Troncoso P, Logothetis CJ, Brentani RR, Calin GA, Cavenee WK, Dias‐Neto E, Pasqualini R and Arap W, 2015. PRUNE2 is a human prostate cancer suppressor regulated by the intronic long noncoding RNA PCA3. Proc Natl Acad Sci U S A, 112, 8403–8408. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1533. Salomon WE, Jolly SM, Moore MJ, Zamore PD and Serebrov V, 2015. Single‐Molecule Imaging Reveals that Argonaute Reshapes the Binding Properties of Its Nucleic Acid Guides. Cell, 162, 84–95. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1534. Sam M, Wurst W, Kluppel M, Jin O, Heng H and Bernstein A, 1998. Aquarius, a novel gene isolated by gene trapping with an RNA‐dependent RNA polymerase motif. Developmental Dynamics, 212, 304–317. [DOI] [PubMed] [Google Scholar]
  1535. Samuel CE, 2011. Adenosine deaminases acting on RNA (ADARs) are both antiviral and proviral. Virology, 411, 180–193. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1536. Sanchez‐Vargas I, Scott JC, Poole‐Smith BK, Franz AW, Barbosa‐Solomieu V, Wilusz J, Olson KE and Blair CD, 2009. Dengue virus type 2 infections of Aedes aegypti are modulated by the mosquito's RNA interference pathway. Plos Pathogens, 5, e1000299. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1537. Savas JN, Makusky A, Ottosen S, Baillat D, Then F, Krainc D, Shiekhattar R, Markey SP and Tanese N, 2008. Huntington's disease protein contributes to RNA‐mediated gene silencing through association with Argonaute and P bodies. Proc Natl Acad Sci U S A, 105, 10820–10825. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1538. Scadden AD and Smith CW, 2001. RNAi is antagonized by A–>I hyper‐editing. EMBO Rep, 2, 1107–1111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1539. Scadden AD, 2005. The RISC subunit Tudor‐SN binds to hyper‐edited double‐stranded RNA and promotes its cleavage. Nature Structural & Molecular Biology, 12, 489–496. [DOI] [PubMed] [Google Scholar]
  1540. Schamberger A, Sarkadi B and Orban TI, 2012. Human mirtrons can express functional microRNAs simultaneously from both arms in a flanking exon‐independent manner. RNA Biology, 9, 1177–1185. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1541. Schirle NT and MacRae IJ, 2012. The Crystal Structure of Human Argonaute2. Science, 336, 1037–1040. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1542. Schirle NT, Sheu‐Gruttadauria J and MacRae IJ, 2014. Structural basis for microRNA targeting. Science, 346, 608–613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1543. Schirle NT, Sheu‐Gruttadauria J, Chandradoss SD, Joo C and MacRae IJ, 2015. Water‐mediated recognition of t1‐adenosine anchors Argonaute2 to microRNA targets. Elife, 4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1544. Schlee M and Hartmann G, 2010. The Chase for the RIG‐I Ligand‐Recent Advances. Molecular Therapy, 18, 1254–1262. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1545. Schoenberg DR and Maquat LE, 2012. Regulation of cytoplasmic mRNA decay. Nature Reviews Genetics, 13, 246–259. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1546. Schwamborn JC, Berezikov E and Knoblich JA, 2009. The TRIM‐NHL Protein TRIM32 Activates MicroRNAs and Prevents Self‐Renewal in Mouse Neural Progenitors. Cell, 136, 913–925. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1547. Schwartz T, Rould MA, Lowenhaupt K, Herbert A and Rich A, 1999. Crystal structure of the Z alpha domain of the human editing enzyme ADAR1 bound to left‐handed Z‐DNA. Science, 284, 1841–1845. [DOI] [PubMed] [Google Scholar]
  1548. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N and Zamore PD, 2003. Asymmetry in the assembly of the RNAi enzyme complex. Cell, 115, 199–208. [DOI] [PubMed] [Google Scholar]
  1549. Sen A, Pruijssers AJ, Dermody TS, Garcia‐Sastre A and Greenberg HB, 2011. The Early Interferon Response to Rotavirus Is Regulated by PKR and Depends on MAVS/IPS‐1, RIG‐I, MDA‐5, and IRF3. Journal of Virology, 85, 3717–3732. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1550. Seo GJ, Kincaid RP, Phanaksri T, Burke JM, Pare JM, Cox JE, Hsiang TY, Krug RM and Sullivan CS, 2013. Reciprocal Inhibition between Intracellular Antiviral Signaling and the RNAi Machinery in Mammalian Cells. Cell Host & Microbe, 14, 435–445. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1551. Seong Y, Lim DH, Kim A, Seo JH, Lee YS, Song H and Kwon YS, 2014. Global identification of target recognition and cleavage by the Microprocessor in human ES cells. Nucleic Acids Research, 42, 12806–12821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1552. Shapiro JS, Schmid S, Aguado LC, Sabin LR, Yasunaga A, Shim JV, Sachs D, Cherry S and Tenoever BR, 2014. Drosha as an interferon‐independent antiviral factor. Proc Natl Acad Sci U S A, 111, 7108–7113. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1553. Sharma A, 2015. Transgenerational epigenetic inheritance: resolving uncertainty and evolving biology. Biomolecular concepts, 6, 87–103. [DOI] [PubMed] [Google Scholar]
  1554. Sharma NR, Wang XH, Majerciak V, Ajiro M, Kruhlak M, Meyers C and Zheng ZM, 2016. Cell Type‐ and Tissue Context‐dependent Nuclear Distribution of Human Ago2. Journal of Biological Chemistry, 291, 2302–2309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1555. Shen J, Xia WY, Khotskaya YB, Huo LF, Nakanishi K, Lim SO, Du Y, Wang Y, Chang WC, Chen CH, Hsu JL, Wu Y, Lam YC, James BP, Liu XP, Liu CG, Patel DJ and Hung MC, 2013. EGFR modulates microRNA maturation in response to hypoxia through phosphorylation of AGO2. Nature, 497, 383–387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1556. Shi H, Tschudi C and Ullu E, 2006. Functional replacement of Trypanosoma brucei Argonaute by the human slicer Argonaute2. Rna, 12, 943–947. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1557. Shih JD, Waks Z, Kedersha N and Silver PA, 2011. Visualization of single mRNAs reveals temporal association of proteins with microRNA‐regulated mRNA. Nucleic Acids Research, 39, 7740–7749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1558. Shinagawa T and Ishii S, 2003. Generation of Ski‐knockdown mice by expressing a long double‐strand RNA from an RNA polymerase II promoter. Genes & Development, 17, 1340–1345. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1559. Shtam TA, Kovalev RA, Varfolomeeva EY, Makarov EM, Kil YV and Filatov MV, 2013. Exosomes are natural carriers of exogenous siRNA to human cells in vitro. Cell Communication and Signaling, 11, 88–88. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1560. Sibley CR, Seow Y, Saayman S, Dijkstra KK, El Andaloussi S, Weinberg MS and Wood MJA, 2012. The biogenesis and characterization of mammalian microRNAs of mirtron origin. Nucleic Acids Research, 40, 438–448. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1561. Sinkkonen L, Hugenschmidt T, Berninger P, Gaidatzis D, Mohn F, Artus‐Revel CG, Zavolan M, Svoboda P and Filipowicz W, 2008. MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nature Structural & Molecular Biology, 15, 259–267. [DOI] [PubMed] [Google Scholar]
  1562. Sinkkonen L, Hugenschmidt T, Filipowicz W and Svoboda P, 2010. Dicer Is Associated with Ribosomal DNA Chromatin in Mammalian Cells. PLoS ONE, 5, e12175–e12175. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1563. Slater L, Bartlett NW, Haas JJ, Zhu J, Message SD, Walton RP, Sykes A, Dahdaleh S, Clarke DL, Belvisi MG, Kon OM, Fujita T, Jeffery PK, Johnston SL and Edwards MR, 2010. Co‐ordinated Role of TLR3, RIG‐I and MDA5 in the Innate Response to Rhinovirus in Bronchial Epithelium. Plos Pathogens, 6, e1001178–e1001178. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1564. Smalheiser NR, Lugli G, Thimmapuram J, Cook EH and Larson J, 2011. Endogenous siRNAs and noncoding RNA‐derived small RNAs are expressed in adult mouse hippocampus and are up‐regulated in olfactory discrimination training. Rna, 17, 166–181. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1565. Smibert P, Yang J‐S, Azzam G, Liu J‐L and Lai EC, 2013. Homeostatic control of Argonaute stability by microRNA availability. Nature Structural & Molecular Biology, 20, 789–+. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1566. Sohn SY, Bae WJ, Kim JJ, Yeom KH, Kim VN and Cho Y, 2007. Crystal structure of human DGCR8 core. Nature Structural & Molecular Biology, 14, 847–853. [DOI] [PubMed] [Google Scholar]
  1567. Soifer HS, Sano M, Sakurai K, Chomchan P, Saetrom P, Sherman MA, Collingwood MA, Behlke MA and Rossi JJ, 2008. A role for the Dicer helicase domain in the processing of thermodynamically unstable hairpin RNAs. Nucleic Acids Research, 36, 6511–6522. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1568. Sollier J, Stork CT, Garcia‐Rubio ML, Paulsen RD, Aguilera A and Cimprich KA, 2014. Transcription‐coupled nucleotide excision repair factors promote R‐loop‐induced genome instability. Molecular Cell, 56, 777–785. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1569. Song JJ, Smith SK, Hannon GJ and Joshua‐Tor L, 2004. Crystal structure of Argonaute and its implications for RISC slicer activity. Science, 305, 1434–1437. [DOI] [PubMed] [Google Scholar]
  1570. Stalder L, Heusermann W, Sokol L, Trojer D, Wirz J, Hean J, Fritzsche A, Aeschimann F, Pfanzagl V, Basselet P, Weiler J, Hintersteiner M, Morrissey DV and Meisner‐Kober NC, 2013. The rough endoplasmatic reticulum is a central nucleation site of siRNA‐mediated RNA silencing. EMBO J, 32, 1115–1127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1571. Stefl R, Oberstrass FC, Hood JL, Jourdan M, Zimmermann M, Skrisovska L, Maris C, Peng L, Hofr C, Emeson RB and Allain FH, 2010. The solution structure of the ADAR2 dsRBM‐RNA complex reveals a sequence‐specific readout of the minor groove. Cell, 143, 225–237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1572. Stein P, Svoboda P, Anger M and Schultz RM, 2003. RNAi: Mammalian oocytes do it without RNA‐dependent RNA polymerase. Rna, 9, 187–192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1573. Stein P, Zeng F, Pan H and Schultz RM, 2005. Absence of non‐specific effects of RNA interference triggered by long double‐stranded RNA in mouse oocytes. Developmental Biology, 286, 464–471. [DOI] [PubMed] [Google Scholar]
  1574. Stein P, Rozhkov NV, Li F, Cardenas FL, Davydenk O, Vandivier LE, Gregory BD, Hannon GJ and Schultz RM, 2015. Essential Role for Endogenous siRNAs during Meiosis in Mouse Oocytes. Plos Genetics, 11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1575. Stoica C, Carmichael JB, Parker H, Pare J and Hobman TC, 2006. Interactions between the RNA interference effector protein Ago1 and 14‐3‐3 proteins ‐ Consequences for cell cycle progression. Journal of Biological Chemistry, 281, 37646–37651. [DOI] [PubMed] [Google Scholar]
  1576. Su H, Trombly MI, Chen J and Wang XZ, 2009. Essential and overlapping functions for mammalian Argonautes in microRNA silencing. Genes & Development, 23, 304–317. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1577. Suh MR, Lee Y, Kim JY, Kim SK, Moon SH, Lee JY, Cha KY, Chung HM, Yoon HS, Moon SY, Kim VN and Kim KS, 2004. Human embryonic stem cells express a unique set of microRNAs. Developmental Biology, 270, 488–498. [DOI] [PubMed] [Google Scholar]
  1578. Suh N, Baehner L, Moltzahn F, Melton C, Shenoy A, Chen J and Blelloch R, 2010. MicroRNA Function Is Globally Suppressed in Mouse Oocytes and Early Embryos. Current Biology, 20, 271–277. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1579. Suk K, Choi J, Suzuki Y, Ozturk SB, Mellor JC, Wong KH, MacKay JL, Gregory RI and Roth FP, 2011. Reconstitution of human RNA interference in budding yeast. Nucleic Acids Research, 39, E43–U59. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1580. Sullivan CS, Grundhoff AT, Tevethia S, Pipas JM and Ganem D, 2005. SV40‐encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells. Nature, 435, 682–686. [DOI] [PubMed] [Google Scholar]
  1581. Suzuki HI, Katsura A, Yasuda T, Ueno T, Mano H, Sugimoto K and Miyazono K, 2015. Small‐RNA asymmetry is directly driven by mammalian Argonautes. Nature Structural & Molecular Biology, 22, 512–+. [DOI] [PubMed] [Google Scholar]
  1582. Suzuki K, Juelich T, Lim H, Ishida T, Watanebe T, Cooper DA, Rao S and Kelleher AD, 2008. Closed chromatin architecture is induced by an RNA duplex targeting the HIV‐1 promoter region. Journal of Biological Chemistry, 283, 23353–23363. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1583. Svoboda P, Stein P, Anger M, Bernstein E, Hannon GJ and Schultz RM, 2004. RNAi and expression of retrotransposons MuERV‐L and IAP in preimplantation mouse embryos. Developmental Biology, 269, 276–285. [DOI] [PubMed] [Google Scholar]
  1584. Svoboda P, 2014. Renaissance of mammalian endogenous RNAi. Febs Letters, 588, 2550–2556. [DOI] [PubMed] [Google Scholar]
  1585. Swahari V, Nakamura A, Baran‐Gale J, Garcia I, Crowther AJ, Sons R, Gershon TR, Hammond S, Sethupathy P and Deshmukh M, 2016. Essential Function of Dicer in Resolving DNA Damage in the Rapidly Dividing Cells of the Developing and Malignant Cerebellum. Cell Reports, 14, 216–224. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1586. Tahbaz N, Carmichael JB and Hobman TC, 2001. GERp95 belongs to a family of signal‐transducing proteins and requires Hsp90 activity for stability and Golgi localization. Journal of Biological Chemistry, 276, 43294–43299. [DOI] [PubMed] [Google Scholar]
  1587. Tahbaz N, Kolb FA, Zhang HD, Jaronczyk K, Filipowicz W and Hobman TC, 2004. Characterization of the interactions between mammalian PAZ PIWI domain proteins and Dicer. EMBO Rep, 5, 189–194. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1588. Taira K, 2006. Induction of DNA methylation and gene silencing by short interfering RNAs in human cells. Nature, 441, 1176. [DOI] [PubMed] [Google Scholar]
  1589. Takahashi T, Zenno S, Ishibashi O, Takizawa T, Saigo K and Ui‐Tei K, 2014. Interactions between the non‐seed region of siRNA and RNA‐binding RLC/RISC proteins, Ago and TRBP, in mammalian cells. Nucleic Acids Research, 42, 5256–5269. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1590. Takeshita D, Zenno S, Lee WC, Nagata K, Saigo K and Tanokura M, 2007. Homodimeric structure and double‐stranded RNA cleavage activity of the c‐terminal RNase III domain of human Dicer. Journal of Molecular Biology, 374, 106–120. [DOI] [PubMed] [Google Scholar]
  1591. Takimoto K, Wakiyama M and Yokoyama S, 2009. Mammalian GW182 contains multiple Argonaute‐binding sites and functions in microRNA‐mediated translational repression. Rna, 15, 1078–1089. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1592. Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, Hodges E, Anger M, Sachidanandam R, Schultz RM and Hannon GJ, 2008. Pseudogene‐derived small interfering RNAs regulate gene expression in mouse oocytes. Nature, 453, 534–U538. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1593. Tan GS, Garchow BG, Liu XH, Yeung J, Morris JP, Cuellar TL, McManus MT and Kiriakidou M, 2009a. Expanded RNA‐binding activities of mammalian Argonaute 2. Nucleic Acids Research, 37, 7533–7545. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1594. Tan GS, Garchow BG, Liu XH, Metzler D and Kiriakidou M, 2011. Clarifying mammalian RISC assembly in vitro. Bmc Molecular Biology, 12, 19–19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1595. Tan YL, Zhang B, Wu T, Skogerbo G, Zhu XP, Guo XQ, He SM and Chen RS, 2009b. Transcriptional inhibiton of Hoxd4 expression by miRNA‐10a in human breast cancer cells. Bmc Molecular Biology, 10, 12–12. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1596. Tang F, Kaneda M, O'Carroll D, Hajkova P, Barton SC, Sun YA, Lee C, Tarakhovsky A, Lao KQ and Surani MA, 2007. Maternal microRNAs are essential for mouse zygotic development. Genes & Development, 21, 644–648. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1597. Taylor DW, Ma EB, Shigematsu H, Cianfrocco MA, Noland CL, Nagayama K, Nogales E, Doudna JA and Wang HW, 2013. Substrate‐specific structural rearrangements of human Dicer. Nature Structural & Molecular Biology, 20, 662–+. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1598. Thonberg H, Scheele CC, Dahlgren C and Wahlestedt C, 2004. Characterization of RNA interference in rat PC12 cells: requirement of GERp95. Biochem Biophys Res Commun, 318, 927–934. [DOI] [PubMed] [Google Scholar]
  1599. Thuringer D, Jego G, Berthenet K, Hammann A, Solary E and Garrido C, 2016. Gap junction‐mediated transfer of miR‐145‐5p from microvascular endothelial cells to colon cancer cells inhibits angiogenesis. Oncotarget. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1600. Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN and Patel DJ, 2014. A Phosphate‐Binding Pocket within the Platform‐PAZ‐Connector Helix Cassette of Human Dicer. Molecular Cell, 53, 606–616. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1601. Ting AH, Schuebel KE, Herman JG and Baylin SB, 2005. Short double‐stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation. Nature Genetics, 37, 906–910. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1602. Ting AH, Suzuki H, Cope L, Schuebel KE, Lee BH, Toyota M, Imai K, Shinomura Y, Tokino T and Baylin SB, 2008. A requirement for DICER to maintain full promoter CpG island hypermethylation in human cancer cells. Cancer Research, 68, 2570–2575. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1603. Tomari Y, Du T, Haley B, Schwarz DS, Bennett R, Cook HA, Koppetsch BS, Theurkauf WE and Zamore PD, 2004a. RISC assembly defects in the Drosophila RNAi mutant armitage. Cell, 116, 831–841. [DOI] [PubMed] [Google Scholar]
  1604. Tomari Y, Matranga C, Haley B, Martinez N and Zamore PD, 2004b. A protein sensor for siRNA asymmetry. Science, 306, 1377–1380. [DOI] [PubMed] [Google Scholar]
  1605. Tomaselli S, Galeano F, Alon S, Raho S, Galardi S, Polito VA, Presutti C, Vincenti S, Eisenberg E, Locatelli F and Gallo A, 2015. Modulation of microRNA editing, expression and processing by ADAR2 deaminase in glioblastoma. Genome Biology, 16, 5–5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1606. Toth KF, Pezic D, Stuwe E and Webster A, 2016. The piRNA Pathway Guards the Germline Genome Against Transposable Elements. In: Non‐Coding Rna and the Reproductive System. 51–77. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1607. Tran N, Raponi M, Dawes IW and Arndt GM, 2004. Control of specific gene expression in mammalian cells by co‐expression of long complementary RNAs. Febs Letters, 573, 127–134. [DOI] [PubMed] [Google Scholar]
  1608. Tsujimura K, Irie K, Nakashima H, Egashira Y, Fukao Y, Fujiwara M, Itoh M, Uesaka M, Imamura T, Nakahata Y, Yamashita Y, Abe T, Takamori S and Nakashima K, 2015. miR‐199a Links MeCP2 with mTOR Signaling and Its Dysregulation Leads to Rett Syndrome Phenotypes. Cell Reports, 12, 1887–1901. [DOI] [PubMed] [Google Scholar]
  1609. Tu CC, Zhong Y, Nguyen L, Tsai A, Sridevi P, Tarn WY and Wang JYJ, 2015. The kinase ABL phosphorylates the microprocessor subunit DGCR8 to stimulate primary microRNA processing in response to DNA damage. Science Signaling, 8, ra64–ra64. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1610. Turchinovich A, Weiz L, Langheinz A and Burwinkel B, 2011. Characterization of extracellular circulating microRNA. Nucleic Acids Research, 39, 7223–7233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1611. Valen E, Preker P, Andersen PR, Zhao X, Chen Y, Ender C, Dueck A, Meister G, Sandelin A and Jensen TH, 2011. Biogenic mechanisms and utilization of small RNAs derived from human protein‐coding genes. Nature Structural & Molecular Biology, 18, 1075–1082. [DOI] [PubMed] [Google Scholar]
  1612. Vance V and Vaucheret H, 2001. RNA silencing in plants–defense and counterdefense. Science, 292, 2277–2280. [DOI] [PubMed] [Google Scholar]
  1613. Venkatesh T, Suresh PS and Tsutsumi R, 2016. tRFs: miRNAs in disguise. Gene, 579, 133–138. [DOI] [PubMed] [Google Scholar]
  1614. Vesely C, Tauber S, Sedlazeck FJ, von Haeseler A and Jantsch MF, 2012. Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs. Genome Research, 22, 1468–1476. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1615. Vesely C, Tauber S, Sedlazeck FJ, Tajaddod M, von Haeseler A and Jantsch MF, 2014. ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain. Nucleic Acids Research, 42, 12155–12168. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1616. Wahlgren J, Karlson TD, Brisslert M, Sani FV, Telemo E, Sunnerhagen P and Valadi H, 2012. Plasma exosomes can deliver exogenous short interfering RNA to monocytes and lymphocytes. Nucleic Acids Research, 40, e130–e130. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1617. Wahlgren J, Statello L, Skogberg G, Telemo E and Valadi H, 2016. Delivery of Small Interfering RNAs to Cells via Exosomes. Sirna Delivery Methods: Methods and Protocols., 105–125. [DOI] [PubMed] [Google Scholar]
  1618. Wang HW, Noland C, Siridechadilok B, Taylor DW, Ma EB, Felderer K, Doudna JA and Nogales E, 2009. Structural insights into RNA processing by the human RISC‐loading complex. Nature Structural & Molecular Biology, 16, 1148–U1144. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1619. Wang J, Huang V, Ye L, Barcena A, Lin G, Lue TF and Li L‐C, 2015a. Identification of Small Activating RNAs that Enhance Endogenous OCT4 Expression in Human Mesenchymal Stem Cells. Stem Cells and Development, 24, 345–353. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1620. Wang SQ, Liu DY, Jin R, Zhu YP and Xu AE, 2015b. Differential Responses of Normal Human Melanocytes to Intra‐ and Extracellular dsRNA. DNA and Cell Biology, 34, 391–399. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1621. Wang XH, Aliyari R, Li WX, Li HW, Kim K, Carthew R, Atkinson P and Ding SW, 2006. RNA interference directs innate immunity against viruses in adult Drosophila. Science, 312, 452–454. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1622. Wang Y, Lacroix G, Haines J, Doukhanine E, Almazan G and Richard S, 2010. The QKI‐6 RNA binding protein localizes with the MBP mRNAs in stress granules of glial cells. PLoS ONE, 5, 1–10. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1623. Wang Y, Mercier R, Hobman TC and LaPointe P, 2013a. Regulation of RNA interference by Hsp90 is an evolutionarily conserved process. Biochimica Et Biophysica Acta‐Molecular Cell Research, 1833, 2673–2681. [DOI] [PubMed] [Google Scholar]
  1624. Wang Y, Vogel G, Yu Z and Richard S, 2013b. The QKI‐5 and QKI‐6 RNA binding proteins regulate the expression of microRNA 7 in glial cells. Molecular and Cellular Biology, 33, 1233–1243. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1625. Wang YM, Medvid R, Melton C, Jaenisch R and Blelloch R, 2007. DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self‐renewal. Nature Genetics, 39, 380–385. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1626. Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N and Imai H, 2006. Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon‐derived siRNAs in oocytes and germline small RNAs in testes. Genes & Development, 20, 1732–1743. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1627. Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi‐Miyagawa S, Obata Y, Chiba H, Kohara Y, Kono T, Nakano T, Surani MA, Sakaki Y and Sasaki H, 2008. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature, 453, 539–U539. [DOI] [PubMed] [Google Scholar]
  1628. Wee LM, Flores‐Jasso CF, Salomon WE and Zamore PD, 2012. Argonaute Divides Its RNA Guide into Domains with Distinct Functions and RNA‐Binding Properties. Cell, 151, 1055–1067. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1629. Wei HB, Zhou B, Zhang F, Tu YY, Hu YN, Zhang BG and Zhai QW, 2013. Profiling and Identification of Small rDNA‐Derived RNAs and Their Potential Biological Functions. PLoS ONE, 8, e56842–e56842. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1630. Wei JX, Yang J, Sun JF, Jia LT, Zhang Y, Zhang HZ, Li X, Meng YL, Yao LB and Yang AG, 2009. Both Strands of siRNA Have Potential to Guide Posttranscriptional Gene Silencing in Mammalian Cells. PLoS ONE, 4, e5382–e5382. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1631. Wei W, Ba ZQ, Gao M, Wu Y, Ma YT, Amiard S, White CI, Danielsen JMR, Yang YG and Qi YJ, 2012. A Role for Small RNAs in DNA Double‐Strand Break Repair. Cell, 149, 101–112. [DOI] [PubMed] [Google Scholar]
  1632. Weinberg MS, Villeneuve LM, Ehsani A, Amarzguioui M, Aagaard L, Chen ZX, Riggs AD, Rossi JJ and Morris KV, 2006. The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells. Rna, 12, 256–262. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1633. Weinmann L, Hock J, Ivacevic T, Ohrt T, Mutze J, Schwille P, Kremmer E, Benes V, Urlaub H and Meister G, 2009. Importin 8 is a gene silencing factor that targets argonaute proteins to distinct mRNAs. Cell, 136, 496–507. [DOI] [PubMed] [Google Scholar]
  1634. Weissbach R and Scadden ADJ, 2012. Tudor‐SN and ADAR1 are components of cytoplasmic stress granules. Rna, 18, 462–471. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1635. Weitz SH, Gong M, Barr I, Weiss S and Guo F, 2014. Processing of microRNA primary transcripts requires heme in mammalian cells. Proc Natl Acad Sci U S A, 111, 1861–1866. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1636. Wen JY, Ladewig E, Shenker S, Mohammed J and Lai EC, 2015. Analysis of Nearly One Thousand Mammalian Mirtrons Reveals Novel Features of Dicer Substrates. Plos Computational Biology, 11, e1004441–e1004441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1637. Westholm JO, Ladewig E, Okamura K, Robine N and Lai EC, 2012. Common and distinct patterns of terminal modifications to mirtrons and canonical microRNAs. Rna, 18, 177–192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1638. White E, Schlackow M, Kamieniarz‐Gdula K, Proudfoot NJ and Gullerova M, 2014. Human nuclear Dicer restricts the deleterious accumulation of endogenous double‐stranded RNA. Nature Structural & Molecular Biology, 21, 552–559. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1639. Wichroski MJ, Robb GB and Rana TM, 2006. Human retroviral host restriction factors APOBEC3G and APOBEC3F localize to mRNA processing bodies. Plos Pathogens, 2, 374–383. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1640. Wilkins C, Dishongh R, Moore SC, Whitt MA, Chow M and Machaca K, 2005. RNA interference is an antiviral defence mechanism in Caenorhabditis elegans. Nature, 436, 1044–1047. [DOI] [PubMed] [Google Scholar]
  1641. Wilson RC, Tambe A, Kidwell MA, Noland CL, Schneider CP and Doudna JA, 2015. Dicer‐TRBP Complex Formation Ensures Accurate Mammalian MicroRNA Biogenesis. Molecular Cell, 57, 397–407. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1642. Winter J, Link S, Witzigmann D, Hildenbrand C, Previti C and Diederichs S, 2013. Loop‐miRs: active microRNAs generated from single‐stranded loop regions. Nucleic Acids Research, 41, 5503–5512. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1643. Wolfrum C, Shi S, Jayaprakash KN, Jayaraman M, Wang G, Pandey RK, Rajeev KG, Nakayama T, Charrise K, Ndungo EM, Zimmermann T, Koteliansky V, Manoharan M and Stoffel M, 2007. Mechanisms and optimization of in vivo delivery of lipophilic siRNAs. Nature Biotechnology, 25, 1149–1157. [DOI] [PubMed] [Google Scholar]
  1644. Wong SK and Lazinski DW, 2002. Replicating hepatitis delta virus RNA is edited in the nucleus by the small form of ADAR1. Proc Natl Acad Sci U S A, 99, 15118–15123. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1645. Wu C, So J, Davis‐Dusenbery BN, Qi HH, Bloch DB, Shi Y, Lagna G and Hata A, 2011. Hypoxia Potentiates MicroRNA‐Mediated Gene Silencing through Posttranslational Modification of Argonaute2. Molecular and Cellular Biology, 31, 4760–4774. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1646. Wu GP, Yang GH, Zhang RX, Xu GY, Zhang L, Wen W, Lu JB, Liu JY and Yu Y, 2015a. Altered microRNA Expression Profiles of Extracellular Vesicles in Nasal Mucus From Patients With Allergic Rhinitis. Allergy Asthma & Immunology Research, 7, 449–457. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1647. Wu WX, Zhang W, Duggan ES, Booth JL, Zou MH and Metcalf JP, 2015b. RIG‐I and TLR3 are both required for maximum interferon induction by influenza virus in human lung alveolar epithelial cells. Virology, 482, 181–188. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1648. Xia J, Joyce CE, Bowcock AM and Zhang WX, 2013. Noncanonical microRNAs and endogenous siRNAs in normal and psoriatic human skin. Human Molecular Genetics, 22, 737–748. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1649. Xie MY, Li MF, Vilborg A, Lee N, Shu MD, Yartseva V, Sestan N and Steitz JA, 2013. Mammalian 5 ‘‐Capped MicroRNA Precursors that Generate a SingleMicroRNA. Cell, 155, 1568–1580. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1650. Xu N, Gkountela S, Saeed K and Akusjarvi G, 2009. The 5′‐end heterogeneity of adenovirus virus‐associated RNAI contributes to the asymmetric guide strand incorporation into the RNA‐induced silencing complex. Nucleic Acids Research, 37, 6950–6959. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1651. Xu S, Xue CY, Li JP, Bi YZ and Cao YC, 2011. Marek's Disease Virus Type 1 MicroRNA miR‐M3 Suppresses Cisplatin‐Induced Apoptosis by Targeting SMAD2 of the Transforming Growth Factor Beta Signal Pathway. Journal of Virology, 85, 276–285. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1652. Yang N and Kazazian HH Jr, 2006. L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells. Nature Structural & Molecular Biology, 13, 763–771. [DOI] [PubMed] [Google Scholar]
  1653. Yang S, Tutton S, Pierce E and Yoon K, 2001. Specific double‐stranded RNA interference in undifferentiated mouse embryonic stem cells. Molecular and Cellular Biology, 21, 7807–7816. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1654. Yang WD, Wang QD, Howell KL, Lee JT, Cho DSC, Murray JM and Nishikura K, 2005. ADAR1 RNA deaminase limits short interfering RNA efficacy in mammalian cells. Journal of Biological Chemistry, 280, 3946–3953. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1655. Yang WD, Chendrimada TP, Wang QD, Higuchi M, Seeburg PH, Shiekhattar R and Nishikura K, 2006a. Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nature Structural & Molecular Biology, 13, 13–21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1656. Yang X, Murthy V, Schultz K, Tatro JB, Fitzgerald KA and Beasley D, 2006b. Toll‐like receptor 3 signaling evokes a proinflammatory and proliferative phenotype in human vascular smooth muscle cells. American Journal of Physiology‐Heart and Circulatory Physiology, 291, H2334–H2343. [DOI] [PubMed] [Google Scholar]
  1657. Yao B, Li SQ, Lian SL, Fritzler MJ and Chan EKL, 2011. Mapping of Ago2‐GW182 Functional Interactions. Argonaute Proteins: Methods and Protocols., 45–62. [DOI] [PubMed] [Google Scholar]
  1658. Ye XC, Huang NA, Liu Y, Paroo Z, Huerta C, Li P, Chen S, Liu QH and Zhang H, 2011. Structure of C3PO and mechanism of human RISC activation. Nature Structural & Molecular Biology, 18, 650–U643. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1659. Yi CE, Bekker JM, Miller G, Hill KL and Crosbie RH, 2003. Specific and potent RNA interference in terminally differentiated myotubes. Journal of Biological Chemistry, 278, 934–939. [DOI] [PubMed] [Google Scholar]
  1660. Yoda M, Kawamata T, Paroo Z, Ye XC, Iwasaki S, Liu QH and Tomari Y, 2010. ATP‐dependent human RISC assembly pathways. Nature Structural & Molecular Biology, 17, 17–U29. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1661. Yoneyama M, Kikuchi M, Natsukawa T, Shinobu N, Imaizumi T, Miyagishi M, Taira K, Akira S and Fujita T, 2004. The RNA helicase RIG‐I has an essential function in double‐stranded RNA‐induced innate antiviral responses. Nature Immunology, 5, 730–737. [DOI] [PubMed] [Google Scholar]
  1662. Yoon YJ, Kim OY and Gho YS, 2014. Extracellular vesicles as emerging intercellular communicasomes. Bmb Reports, 47, 531–539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1663. Younger ST and Corey DR, 2011. Transcriptional gene silencing in mammalian cells by miRNA mimics that target gene promoters. Nucleic Acids Research, 39, 5682–5691. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1664. Yu JH, Yang WH, Gulick T, Bloch KD and Bloch DB, 2005. Ge‐1 is a central component of the mammalian cytoplasmic mRNA processing body. Rna, 11, 1795–1802. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1665. Yuan YR, Pei Y, Ma JB, Kuryavyi V, Zhadina M, Meister G, Chen HY, Dauter Z, Tuschl T and Patel DJ, 2005. Crystal structure of A‐aeolicus Argonaute, a site‐specific DNA‐guided endoribonuclease, provides insights into RISC‐mediated mRNA cleavage. Molecular Cell, 19, 405–419. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1666. Zamore PD, Tuschl T, Sharp PA and Bartel DP, 2000. RNAi: double‐stranded RNA directs the ATP‐dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell, 101, 25–33. [DOI] [PubMed] [Google Scholar]
  1667. Zekri L, Huntzinger E, Heimstadt S and Izaurralde E, 2009. The silencing domain of GW182 interacts with PABPC1 to promote translational repression and degradation of microRNA targets and is required for target release. Molecular and Cellular Biology, 29, 6220–6231. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1668. Zekri L, Kuzuoglu‐Ozturk D and Izaurralde E, 2013. GW182 proteins cause PABP dissociation from silenced miRNA targets in the absence of deadenylation. EMBO J, 32, 1052–1065. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1669. Zeng Y, Wagner EJ and Cullen BR, 2002. Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Molecular Cell, 9, 1327–1333. [DOI] [PubMed] [Google Scholar]
  1670. Zeng Y, Sankala H, Zhang XX and Graves PR, 2008. Phosphorylation of Argonaute 2 at serine‐387 facilitates its localization to processing bodies. Biochemical Journal, 413, 429–436. [DOI] [PubMed] [Google Scholar]
  1671. Zhang HD, Kolb FA, Brondani V, Billy E and Filipowicz W, 2002. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J, 21, 5875–5885. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1672. Zhang HD, Kolb FA, Jaskiewicz L, Westhof E and Filipowicz W, 2004. Single processing center models for human dicer and bacterial RNase III. Cell, 118, 57–68. [DOI] [PubMed] [Google Scholar]
  1673. Zhang L, Hou D, Chen X, Li D, Zhu L, Zhang Y, Li J, Bian Z, Liang X, Cai X, Yin Y, Wang C, Zhang T, Zhu D, Zhang D, Xu J, Chen Q, Ba Y, Liu J, Wang Q, Chen J, Wang J, Wang M, Zhang Q, Zhang J, Zen K and Zhang CY, 2012. Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross‐kingdom regulation by microRNA. Cell Research, 22, 107–126. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1674. Zhang MX, Zhang C, Shen YH, Wang J, Li XN, Chen L, Zhang Y, Coselli JS and Wang XL, 2008a. Effect of 27nt small RNA on endothelial nitric‐oxide synthase expression. Molecular Biology of the Cell, 19, 3997–4005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1675. Zhang MX, Zhang C, Shen YH, Wang J, Li XN, Zhang Y, Coselli J and Wang XL, 2008b. Biogenesis of short intronic repeat 27nt small RNA from endothelial nitric oxide synthase gene. Journal of Biological Chemistry. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1676. Zhang XZ, Li HT, Burnett JC and Rossi JJ, 2014. The role of antisense long noncoding RNA in small RNA‐triggered gene activation. Rna, 20, 1916–1928. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1677. Zheng XF and Bevilacqua PC, 2004. Activation of the protein kinase PKR by short double‐stranded RNAs with single‐stranded tails. Rna, 10, 1934–1945. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1678. Zheng ZM, Tang SA and Tao MF, 2005. Development of resistance to RNAi in mammalian cells. In: Strategies for Silencing Gene Expression. 105–118. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1679. Zhou HM, Yang L, Li HJ, Li LJ and Chen JM, 2009. Residues that affect human Argonaute2 concentration in cytoplasmic processing bodies. Biochem Biophys Res Commun, 378, 620–624. [DOI] [PubMed] [Google Scholar]
  1680. Zipprich JT, Bhattacharyya S, Mathys H and Filipowicz W, 2009. Importance of the C‐terminal domain of the human GW182 protein TNRC6C for translational repression. Rna, 15, 781–793. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1681. Zou J, Chang M, Nie P and Secombes CJ, 2009. Origin and evolution of the RIG‐I like RNA helicase gene family. Bmc Evolutionary Biology, 9, 85. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1682. Andermatt I, Wilson N and Stoeckli ET, 2014. In ovo electroporation of miRNA‐based‐plasmids to investigate gene function in the developing neural tube. Methods in Molecular Biology, 1101, 353–368. [DOI] [PubMed] [Google Scholar]
  1683. Baeriswyl T, Mauti O and Stoeckli ET, 2008. Temporal control of gene silencing by in ovo electroporation. Methods in Molecular Biology, 442, 231–244. [DOI] [PubMed] [Google Scholar]
  1684. Chen CH, Zhou YL, Wu YF, Cao Y, Gao JS and Tang JB, 2009a. Effectiveness of MicroRNA in Down‐Regulation of TGF‐beta Gene Expression in Digital Flexor Tendons of Chickens. In Vitro and In Vivo Study. Journal of Hand Surgery‐American, 34A, 1777–1784. [DOI] [PubMed] [Google Scholar]
  1685. Chen M, Payne WS, Hunt H, Zhang HM, Holmen SL and Dodgson JB, 2008. Inhibition of Marek's disease virus replication by retroviral vector‐based RNA interference. Virology, 377, 265–272. [DOI] [PubMed] [Google Scholar]
  1686. Chen M, Payne WS, Dunn JR, Chang S, Zhang HM, Hunt HD and Dodgson JB, 2009b. Retroviral delivery of RNA interference against Marek's disease virus in vivo. Poultry Science, 88, 1373–1380. [DOI] [PubMed] [Google Scholar]
  1687. Chen SCY, Stern P, Guo ZY and Chen JZ, 2011. Expression of Multiple Artificial MicroRNAs from a Chicken miRNA126‐Based Lentiviral Vector. Plos One, 6, e22437–e22437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1688. Chen Y, Huang ZY, Wang B, Yu QM, Liu R, Xu Q, Chang GB, Ding JT and Chen GH, 2015. Duck RIG‐I CARD Domain Induces the Chicken IFN‐beta by Activating NF‐kappa B. Biomed Research International, 2015, 348792–348792. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1689. Coupeau D, Dambrine G and Rasschaert D, 2012. Kinetic expression analysis of the cluster mdv1‐mir‐M9‐M4, genes meq and vIL‐8 differs between the lytic and latent phases of Marek's disease virus infection. Journal of General Virology, 93, 1519–1529. [DOI] [PubMed] [Google Scholar]
  1690. Dai FP, Yusuf F, Farjah GH and Brand‐Saberi B, 2005. RNAi‐induced targeted silencing of developmental control genes during chicken embryogenesis. Developmental Biology, 285, 80–90. [DOI] [PubMed] [Google Scholar]
  1691. Das RM, Van Hateren NJ, Howell GR, Farrell ER, Bangs FK, Porteous VC, Manning EM, McGrew MJ, Ohyama K, Sacco MA, Halley PA, Sang HM, Storey KG, Placzek M, Tickle C, Nair VK and Wilson SA, 2006. A robust system for RNA interference in the chicken using a modified microRNA operon. Developmental Biology, 294, 554–563. [DOI] [PubMed] [Google Scholar]
  1692. Deng JH, Deng P, Lin SL and Ying SY, 2015. Gene Silencing In Vitro and In Vivo Using Intronic MicroRNAs. RNA Interference: Challenges and Therapeutic Opportunities., 321–340. [DOI] [PubMed] [Google Scholar]
  1693. Dinh H, Hong YH and Lillehoj HS, 2014. Modulation of microRNAs in two genetically disparate chicken lines showing different necrotic enteritis disease susceptibility. Veterinary Immunology and Immunopathology, 159, 74–82. [DOI] [PubMed] [Google Scholar]
  1694. Flemr M, Malik R, Franke V, Nejepinska J, Sedlacek R, Vlahovicek K and Svoboda P, 2013. A retrotransposon‐driven dicer isoform directs endogenous small interfering RNA production in mouse oocytes. Cell, 155, 807–816. [DOI] [PubMed] [Google Scholar]
  1695. Fukagawa T, Nogami M, Yoshikawa M, Ikeno M, Okazaki T, Takami Y, Nakayama T and Oshimura M, 2004. Dicer is essential for formation of the heterochromatin structure in vertebrate cells. Nature Cell Biology, 6, 784–791. [DOI] [PubMed] [Google Scholar]
  1696. Giles KE, Ghirlando R and Felsenfeld G, 2010. Maintenance of a constitutive heterochromatin domain in vertebrates by a Dicer‐dependent mechanism. Nature Cell Biology, 12, 94–U246. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1697. Godnic I, Zorc M, Skok DJ, Calin GA, Horvat S, Dovc P, Kovac M and Kunej T, 2013. Genome‐Wide and Species‐Wide In Silico Screening for Intragenic MicroRNAs in Human, Mouse and Chicken. Plos One, 8, e65165–e65165. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1698. Gonzalez‐Lopez C, Martinez‐Costas J, Esteban M and Benavente J, 2003. Evidence that avian reovirus sigma A protein is an inhibitor of the double‐stranded RNA‐dependent protein kinase. Journal of General Virology, 84, 1629–1639. [DOI] [PubMed] [Google Scholar]
  1699. Gunaratne PH, Lin YC, Benham AL, Drnevich J, Coarfa C, Tennakoon JB, Creighton CJ, Kim JH, Milosavljevic A, Watson M, Griffiths‐Jones S and Clayton DF, 2011. Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain. Bmc Genomics, 12, 277–277. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1700. Haesler S, Rochefort C, Georgi B, Licznerski P, Osten P and Scharff C, 2007. Incomplete and inaccurate vocal imitation after knockdown of FoxP2 in songbird basal ganglia nucleus area X. Plos Biology, 5, 2885–2897. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1701. Han B, Lian L, Li X, Zhao C, Qu L, Liu C, Song J and Yang N, 2016. Chicken gga‐miR‐103‐3p Targets CCNE1 and TFDP2 and Inhibits MDCC‐MSB1 Cell Migration. G3‐Genes Genomes Genetics. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1702. Hayashi T, Watanabe C, Suzuki Y, Tanikawa T, Uchida Y and Saito T, 2014. Chicken MDA5 Senses Short Double‐Stranded RNA with Implications for Antiviral Response against Avian Influenza Viruses in Chicken. Journal of Innate Immunity, 6, 58–71. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1703. Herbert A, Lowenhaupt K, Spitzner J and Rich A, 1995. Double‐stranded RNA adenosine deaminase binds Z‐DNA in vitro. Nucleic Acids Symp Ser, 16–19. [PubMed] [Google Scholar]
  1704. Hu SQ, Cao W, Yang MJ, Liu HH, Li L and Wang JW, 2014. Molecular characterization, tissue distribution, and expression of two ovarian Dicer isoforms during follicle development in goose (Anser cygnoides). Biology, 170, 33–41. [DOI] [PubMed] [Google Scholar]
  1705. Hutcheson JM, Susta L, Stice SL, Afonso CL and West FD, 2015. Delayed Newcastle disease virus replication using RNA interference to target the nucleoprotein. Biologicals, 43, 274–280. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1706. International Chicken Genome Sequencing C , 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432, 695–716. [DOI] [PubMed] [Google Scholar]
  1707. Karpala AJ, Lowenthal JW and Bean AG, 2008. Activation of the TLR3 pathway regulates IFN beta production in chickens. Developmental and Comparative Immunology, 32, 435–444. [DOI] [PubMed] [Google Scholar]
  1708. Karpala AJ, Stewart C, McKay J, Lowenthal JW and Bean AG, 2011. Characterization of chicken Mda5 activity: regulation of IFN‐beta in the absence of RIG‐I functionality. J Immunol, 186, 5397–5405. [DOI] [PubMed] [Google Scholar]
  1709. Kim TH, Yun TW, Rengaraj D, Lee SI, Lim SM, Seo HW, Park TS and Han JY, 2012. Conserved functional characteristics of the PIWI family members in chicken germ cell lineage. Theriogenology, 78, 1948–1959. [DOI] [PubMed] [Google Scholar]
  1710. Kint J, Fernandez‐Gutierrez M, Maier HJ, Britton P, Langereis MA, Koumans J, Wiegertjes GF and Forlenza M, 2015. Activation of the chicken type I interferon response by infectious bronchitis coronavirus. Journal of Virology, 89, 1156–1167. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1711. Lambeth LS, Yao YX, Smith LP, Zhao YG and Nair V, 2009a. MicroRNAs 221 and 222 target p27(Kip1) in Marek's disease virus‐transformed tumour cell line MSB‐1. Journal of General Virology, 90, 1164–1171. [DOI] [PubMed] [Google Scholar]
  1712. Lambeth LS, Zhao YG, Smith LP, Kgosana L and Nair V, 2009b. Targeting Marek's disease virus by RNA interference delivered from a herpesvirus vaccine. Vaccine, 27, 298–306. [DOI] [PubMed] [Google Scholar]
  1713. Lee CC, Wu CC and Lin TL, 2012. Characterization of chicken melanoma differentiation‐associated gene 5 (MDA5) from alternative translation initiation. Comparative Immunology Microbiology and Infectious Diseases, 35, 335–343. [DOI] [PubMed] [Google Scholar]
  1714. Lee CC, Wu CC and Lin TL, 2014. Chicken melanoma differentiation‐associated gene 5 (MDA5) recognizes infectious bursal disease virus infection and triggers MDA5‐related innate immunity. Archives of Virology, 159, 1671–1686. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1715. Lee SH, Eldi P, Cho SY and Rangasamy D, 2009. Control of chicken CR1 retrotransposons is independent of Dicer‐mediated RNA interference pathway. Bmc Biology, 7, 53–53. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1716. Lee SI, Lee BR, Hwang YS, Lee HC, Rengaraj D, Song G, Park TS and Han JY, 2011. MicroRNA‐mediated posttranscriptional regulation is required for maintaining undifferentiated properties of blastoderm and primordial germ cells in chickens. Proc Natl Acad Sci U S A, 108, 10426–10431. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1717. Lee SI, Ji MR, Jang YJ, Jeon MH, Kim JS, Park JK, Jeon IS and Byun SJ, 2015. Characterization and miRNA‐mediated posttranscriptional regulation of vitelline membrane outer layer protein I in the adult chicken oviduct. In Vitro Cellular & Developmental Biology‐Animal, 51, 222–229. [DOI] [PubMed] [Google Scholar]
  1718. Li H, Sun GR, Tian YD, Han RL, Li GX and Kang XT, 2013. MicroRNAs‐1614‐3p gene seed region polymorphisms and association analysis with chicken production traits. Journal of Applied Genetics, 54, 209–213. [DOI] [PubMed] [Google Scholar]
  1719. Li WZ, Chen HJ, Sutton T, Obadan A and Perez DR, 2014a. Interactions between the Influenza A Virus RNA Polymerase Components and Retinoic Acid‐Inducible Gene I. Journal of Virology, 88, 10432–10447. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1720. Li X, Lian L, Zhang DX, Qu LJ and Yang N, 2014b. gga‐miR‐26a targets NEK6 and suppresses Marek's disease lymphoma cell proliferation. Poultry Science, 93, 1097–1105. [DOI] [PubMed] [Google Scholar]
  1721. Li ZJ, Zhang YP, Li Y, Zheng HW, Zheng YS and Liu CJ, 2014c. Distinct expression pattern of miRNAs in Marek's disease virus infected‐chicken splenic tumors and non‐tumorous spleen tissues. Research in Veterinary Science, 97, 156–161. [DOI] [PubMed] [Google Scholar]
  1722. Lian L, Li X, Zhao CF, Han B, Qu LJ, Song JZ, Liu CJ and Yang N, 2015a. Chicken gga‐miR‐181a targets MYBL1 and shows an inhibitory effect on proliferation of Marek's disease virus‐transformed lymphoid cell line. Poultry Science, 94, 2616–2621. [DOI] [PubMed] [Google Scholar]
  1723. Lian L, Zhang DX, Wang Q, Yang N and Qu LJ, 2015b. The inhibitory effects of gga‐miR‐199‐3p, gga‐miR‐140‐3p, and gga‐miR‐221‐5p in Marek's disease tumorigenesis. Poultry Science, 94, 2131–2135. [DOI] [PubMed] [Google Scholar]
  1724. Lim SL, Tsend‐Ayush E, Kortschak RD, Jacob R, Ricciardelli C, Oehler MK and Grutzner F, 2013. Conservation and Expression of PIWI‐Interacting RNA Pathway Genes in Male and Female Adult Gonad of Amniotes. Biology of Reproduction, 89, 136–136. [DOI] [PubMed] [Google Scholar]
  1725. Lin S‐L, Chang DC and Ying S‐Y, 2006a. Isolation and identification of gene‐specific microRNAs. In: Methods in Molecular Biology. 313–320. [DOI] [PubMed] [Google Scholar]
  1726. Lin S‐L, Chang S‐JE and Ying S‐Y, 2006b. Transgene‐like animal models using intronic microRNAs. In: Methods in Molecular Biology. 321–334. [DOI] [PubMed] [Google Scholar]
  1727. Lin S‐L and Ying S‐Y, 2006. Gene silencing in vitro and in vivo using intronic microRNAs. In: Methods in Molecular Biology. 295–312. [DOI] [PubMed] [Google Scholar]
  1728. Lin SL, Chang DC and Ying SY, 2013a. Isolation and identification of gene‐specific microRNAs. Methods in Molecular Biology, 936, 271–278. [DOI] [PubMed] [Google Scholar]
  1729. Lin SL, Chang SJ and Ying SY, 2013b. Transgene‐like animal models using intronic microRNAs. Methods in Molecular Biology, 936, 279–294. [DOI] [PubMed] [Google Scholar]
  1730. Lin SL and Ying SY, 2013. Gene silencing in vitro and in vivo using intronic microRNAs. Methods in Molecular Biology, 936, 209–229. [DOI] [PubMed] [Google Scholar]
  1731. Lostale‐Seijo I, Martinez‐Costas J and Benavente J, 2016. Interferon induction by avian reovirus. Virology, 487, 104–111. [DOI] [PubMed] [Google Scholar]
  1732. Luo GZ, Hafner M, Shi Z, Brown M, Feng GH, Tuschl T, Wang XJ and Li X, 2012. Genome‐wide annotation and analysis of zebra finch microRNA repertoire reveal sex‐biased expression. Bmc Genomics, 13, 727. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1733. Luo J, Sun AJ, Teng M, Zhou H, Cui ZZ, Qu LH and Zhang GP, 2011. Expression profiles of microRNAs encoded by the oncogenic Marek's disease virus reveal two distinct expression patterns in vivo during different phases of disease. Journal of General Virology, 92, 608–620. [DOI] [PubMed] [Google Scholar]
  1734. Mauti O, Baeriswyl T and Stoeckli ET, 2008. Gene Silencing by Injection and Electroporation of dsRNA in Avian Embryos. Cold Spring Harbor Protocols, 2008, pdb.prot5094–pdb.prot5094. [DOI] [PubMed] [Google Scholar]
  1735. Morgan R, Anderson A, Bernberg E, Kamboj S, Huang E, Lagasse G, Isaacs G, Parcells M, Meyers BC, Green PJ and Burnside J, 2008. Sequence Conservation and Differential Expression of Marek's Disease Virus MicroRNAs. Journal of Virology, 82, 12213–12220. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1736. Muylkens B, Coupeau D, Dambrine G, Trapp S and Rasschaert D, 2010. Marek's disease virus microRNA designated Mdv1‐pre‐miR‐M4 targets both cellular and viral genes. Archives of Virology, 155, 1823–1837. [DOI] [PubMed] [Google Scholar]
  1737. O'Neill G, 2007. Australia tackles bird flu using RNAi. Nature Biotechnology, 25, 605–606. [DOI] [PubMed] [Google Scholar]
  1738. Pekarik V, Bourikas D, Miglino N, Joset P, Preiswerk S and Stoeckli ET, 2003. Screening for gene function in chicken embryo using RNAi and electroporation. Nature Biotechnology, 21, 93–96. [DOI] [PubMed] [Google Scholar]
  1739. Sahare AA, Bedekar MK, Jain SK, Singh A, Singh S and Sarkhel BC, 2015. Inhibition of Infectious Bursal Disease Virus by Vector Delivered SiRNA in Cell Culture. Animal Biotechnology, 26, 58–64. [DOI] [PubMed] [Google Scholar]
  1740. Sato F, Nakagawa T, Ito M, Kitagawa Y and Hattori MA, 2004. Application of RNA interference to chicken embryos using small interferfing RNA. Journal of Experimental Zoology Part a‐Comparative Experimental Biology, 301A, 820–827. [DOI] [PubMed] [Google Scholar]
  1741. Sato H, Oshiumi H, Takaki H, Hikono H and Seya T, 2015. Evolution of the DEAD box helicase family in chicken: Chickens have no DHX9 ortholog. Microbiology and Immunology, 59, 633–640. [DOI] [PubMed] [Google Scholar]
  1742. Stewart CR, Karpala AJ, Lowther S, Lowenthal JW and Bean AG, 2011. Immunostimulatory Motifs Enhance Antiviral siRNAs Targeting Highly Pathogenic Avian Influenza H5N1. Plos One, 6, e21552–e21552. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1743. Stik G, Dambrine G, Pfeffer S and Rasschaert D, 2013. The Oncogenic MicroRNA OncomiR‐21 Overexpressed during Marek's Disease Lymphomagenesis Is Transactivated by the Viral Oncoprotein Meq. Journal of Virology, 87, 80–93. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1744. Strassheim S, Stik G, Rasschaert D and Laurent S, 2012. mdv1‐miR‐M7‐5p, located in the newly identified first intron of the latency‐associated transcript of Marek's disease virus, targets the immediate‐early genes ICP4 and ICP27. Journal of General Virology, 93, 1731–1742. [DOI] [PubMed] [Google Scholar]
  1745. Taft RJ, Glazov EA, Lassmann T, Hayashizaki Y, Carninci P and Mattick JS, 2009. Small RNAs derived from snoRNAs. RNA, 15, 1233–1240. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1746. Tian F, Luo J, Zhang HM, Chang S and Song JZ, 2012. MiRNA expression signatures induced by Marek's disease virus infection in chickens. Genomics, 99, 152–159. [DOI] [PubMed] [Google Scholar]
  1747. Tian Y, Lu LZ, Fu Y, Zhao J, Zhang C, Yuan QY and Shen JD, 2007. Assignment of Dicer gene to chicken chromosome 5 by radiation hybrid panel mapping. Biochemical Genetics, 45, 239–243. [DOI] [PubMed] [Google Scholar]
  1748. Villanueva AI, Kulkarni RR and Sharif S, 2011. Synthetic double‐stranded RNA oligonucleotides are immunostimulatory for chicken spleen cells. Developmental and Comparative Immunology, 35, 28–34. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1749. Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez‐Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER and Wilson RK, 2010. The genome of a songbird. Nature, 464, 757–762. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1750. Wei RR, Ma XQ, Wang GH, Guo HJ, Liu JZ, Fan LX and Cheng ZQ, 2015. Synergistic inhibition of avian leukosis virus subgroup J replication by miRNA‐embedded siRNA interference of double‐target. Virology Journal, 12, 45–45. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1751. Wilson NH and Stoeckli ET, 2011. Cell type specific, traceable gene silencing for functional gene analysis during vertebrate neural development. Nucleic Acids Research, 39, e133–e133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1752. Wilson NH and Stoeckli ET, 2012. In ovo Electroporation of miRNA‐based Plasmids in the Developing Neural Tube and Assessment of Phenotypes by DiI Injection in Open‐book Preparations. Jove‐Journal of Visualized Experiments. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1753. Xu HT, Yao YX, Smith LP and Nair V, 2010. MicroRNA‐26a‐mediated regulation of interleukin‐2 expression in transformed avian lymphocyte lines. Cancer Cell International, 10, 15–15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1754. Xu S, Xue CY, Li JP, Bi YZ and Cao YC, 2011. Marek's Disease Virus Type 1 MicroRNA miR‐M3 Suppresses Cisplatin‐Induced Apoptosis by Targeting SMAD2 of the Transforming Growth Factor Beta Signal Pathway. Journal of Virology, 85, 276–285. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1755. Xu WP, Shao Q, Zang YL, Guo Q, Zhang YC and Li ZD, 2015. Pigeon RIG‐I Function in Innate Immunity against H9N2 IAV and IBDV. Viruses‐Basel, 7, 4131–4151. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1756. Yao YX, Zhao YG, Xu HT, Smith LP, Lawrie CH, Watson M and Nair V, 2008. MicroRNA profile of Marek's disease virus‐transformed T‐cell line MSB‐1: Predominance of virus‐encoded microRNAs. Journal of Virology, 82, 4007–4015. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1757. Yin RF, Ding ZA, Liu XX, Mu LZ, Cong YL and Stoeger T, 2010. Inhibition of Newcastle disease virus replication by RNA interference targeting the matrix protein gene in chicken embryo fibroblasts. Journal of Virological Methods, 167, 107–111. [DOI] [PubMed] [Google Scholar]
  1758. Ying S‐Y and Lin S‐L, 2009. Intron‐Mediated RNA Interference and microRNA Biogenesis. In: Methods in Molecular Biology. 387–413. [DOI] [PubMed] [Google Scholar]
  1759. Ying SY, Chang CP and Lin SL, 2010. Intron‐Mediated RNA Interference, Intronic MicroRNAs, and Applications. In: RNA Therapeutics: Function, Design, and Delivery. 203–235. [DOI] [PubMed] [Google Scholar]
  1760. Zhang SL, Sun YJ, Chen HJ, Dai YB, Zhan Y, Yu SQ, Qiu XS, Tan L, Song CP and Ding C, 2014. Activation of the PKR/eIF2 alpha signaling cascade inhibits replication of Newcastle disease virus. Virology Journal, 11, 62–62. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1761. Zhao YG, Yao YX, Xu HT, Lambeth L, Smith LP, Kgosana L, Wang XW and Nair V, 2009. A Functional MicroRNA‐155 Ortholog Encoded by the Oncogenic Marek's Disease Virus. Journal of Virology, 83, 489–492. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1762. Zhao YG, Xu HT, Yao YX, Smith LP, Kgosana L, Green J, Petherbridge L, Baigent SJ and Nair V, 2011. Critical Role of the Virus‐Encoded MicroRNA‐155 Ortholog in the Induction of Marek's Disease Lymphomas. Plos Pathogens, 7, e1001305–e1001305. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1763. Zhou X, Guo H, Chen K, Cheng HH and Zhou RJ, 2010. Identification, chromosomal mapping and conserved synteny of porcine Argonaute family of genes. Genetica, 138, 805–812. [DOI] [PubMed] [Google Scholar]
  1764. Andrews OE, Cha DJ, Wei CY and Patton JG, 2014. RNAi‐Mediated Gene silencing in Zebrafish Triggered by Convergent Transcription. Scientific Reports, 4, 5222–5222. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1765. Bazzini AA, Lee MT and Giraldez AJ, 2012. Ribosome Profiling Shows That miR‐430 Reduces Translation Before Causing mRNA Decay in Zebrafish. Science, 336, 233–237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1766. Blum M, De Robertis EM, Wallingford JB and Niehrs C, 2015. Morpholinos: Antisense and Sensibility. Developmental Cell, 35, 145–149. [DOI] [PubMed] [Google Scholar]
  1767. Choi WY, Giraldez AJ and Schier AF, 2007. Target protectors reveal dampening and balancing of nodal agonist and antagonist by miR‐430. Science, 318, 271–274. [DOI] [PubMed] [Google Scholar]
  1768. Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson ND, Wolfe SA and Giraldez AJ, 2010. A novel miRNA processing pathway independent of dicer requires argonaute2 catalytic activity. Science, 328, 1694–1698. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1769. De Rienzo G, Gutzman JH and Sive H, 2012. Efficient shRNA‐Mediated Inhibition of Gene Expression in Zebrafish. Zebrafish, 9, 97–107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1770. Dong Z, Peng J and Guo S, 2013. Stable gene silencing in zebrafish with spatiotemporally targetable RNA interference. Genetics, 193, 1065–1071. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1771. Eisen JS and Smith JC, 2008. Controlling morpholino experiments: don't stop making antisense. Development, 135, 1735–1743. [DOI] [PubMed] [Google Scholar]
  1772. Francia S, Michelini F, Saxena A, Tang D, de Hoon M, Anelli V, Mione M, Carninci P and d'Adda di Fagagna F, 2012. Site‐specific DICER and DROSHA RNA products control the DNA‐damage response. Nature, 488, 231–235. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1773. Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, Inoue K, Enright AJ and Schier AF, 2006. Zebrafish MiR‐430 promotes deadenylation and clearance of maternal mRNAs. Science, 312, 75–79. [DOI] [PubMed] [Google Scholar]
  1774. Gotesman M, Soliman H, Besch R and El‐Matbouli M, 2014. In vitro inhibition of Cyprinid herpesvirus‐3 replication by RNAi. J Virol Methods, 206, 63–66. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1775. Guo S, Xu D, H‐x Xu, Wang T, J‐l Li and L‐q Lu, 2012. Suppression of RNA interference pathway in vitro by Grass carp reovirus. Virologica Sinica, 27, 109–119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1776. Heath G, Childs D, Docker MF, McCauley DW and Whyard S, 2014. RNA Interference Technology to Control Pest Sea Lampreys ‐ A Proof‐of‐Concept. Plos One, 9, e88387–e88387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1777. Houwing S, Kamminga LM, Berezikov E, Cronembold D, Girard A, van den Elst H, Filippov DV, Blaser H, Raz E, Moens CB, Plasterk RHA, Hannon GJ, Draper BW and Ketting RF, 2007. A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in zebrafish. Cell, 129, 69–82. [DOI] [PubMed] [Google Scholar]
  1778. Huang HY, Houwing S, Kaaij LJT, Meppelink A, Redl S, Gauci S, Vos H, Draper BW, Moens CB, Burgering BM, Ladurner P, Krijgsveld J, Berezikov E and Ketting RF, 2011. Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. EMBO J, 30, 3298–3308. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1779. Kamminga LM, Luteijn MJ, den Broeder MJ, Redl S, Kaaij LJT, Roovers EF, Ladurner P, Berezikov E and Ketting RF, 2010. Hen1 is required for oocyte development and piRNA stability in zebrafish. EMBO J, 29, 3688–3700. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1780. Kedde M, Strasser MJ, Boldajipour B, Vrielink J, Le Sage C, Nagel R, Voorhoeve PM, Van Duijse J, Orom UA, Lund AH, Perrakis A, Raz E, Agami R and Slanchev K, 2007. RNA‐binding protein Dnd1 inhibits microRNA access to target mRNA. Cell, 131, 1273–1286. [DOI] [PubMed] [Google Scholar]
  1781. Li YX, Farrell MJ, Liu RP, Mohanty N and Kirby ML, 2000. Double‐stranded RNA injection produces null phenotypes in zebrafish. Developmental Biology, 217, 394–405. [DOI] [PubMed] [Google Scholar]
  1782. Mangos S, Vanderbeld B, Krawetz R, Sudol K and Kelly GM, 2001. Ran binding protein RanBP1 in zebrafish embryonic development. Molecular Reproduction and Development, 59, 235–248. [DOI] [PubMed] [Google Scholar]
  1783. McFarlane L, Svingen T, Braasch I, Koopman P, Schartl M and Wilhelm D, 2011. Expansion of the Ago gene family in the teleost clade. Development Genes and Evolution, 221, 95–104. [DOI] [PubMed] [Google Scholar]
  1784. Mishima Y, Giraldez AJ, Takeda Y, Fujiwara T, Sakamoto H, Schier AF and Inoue K, 2006. Differential regulation of germline mRNAs in soma and germ cells by zebrafish miR‐430. Current Biology, 16, 2135–2142. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1785. Mishima Y, Fukao A, Kishimoto T, Sakamoto H, Fujiwara T and Inoue K, 2012. Translational inhibition by deadenylation‐independent mechanisms is central to microRNA‐mediated silencing in zebrafish. Proc Natl Acad Sci U S A, 109, 1104–1109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1786. Murphy D, Dancis B and Brown JR, 2008. The evolution of core proteins involved in microRNA biogenesis. Bmc Evolutionary Biology, 8, 92–92. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1787. Oates AC, Bruce AEE and Ho RK, 2000. Too much interference: Injection of double‐stranded RNA has nonspecific effects in the zebrafish embryo. Developmental Biology, 224, 20–28. [DOI] [PubMed] [Google Scholar]
  1788. Rothenburg S, Deigendesch N, Dey M, Dever TE and Tazi L, 2008. Double‐stranded RNA‐activated protein kinase PKR of fishes and amphibians: Varying the number of double‐stranded RNA binding domains and lineage‐specific duplications. Bmc Biology, 6, 12–12. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1789. Shen XB, Xu D, Li JL and Lu LQ, 2013. Molecular cloning and immune responsive expression of a ribonuclease III ortholog involved in RNA interference, dicer, in grass carp Ctenopharyngodon idella. Journal of Fish Biology, 83, 1234–1248. [DOI] [PubMed] [Google Scholar]
  1790. Svoboda P, Stein P, Hayashi H and Schultz RM, 2000. Selective reduction of dormant maternal mRNAs in mouse oocytes by RNA interference. Development, 127, 4147–4156. [DOI] [PubMed] [Google Scholar]
  1791. Svoboda P and Flemr M, 2010. The role of miRNAs and endogenous siRNAs in maternal‐to‐zygotic reprogramming and the establishment of pluripotency. EMBO Rep, 11, 590–597. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1792. Thornton JE, Du P, Jing LL, Sjekloca L, Lin SB, Grossi E, Sliz P, Zon LI and Gregory RI, 2014. Selective microRNA uridylation by Zcchc6 (TUT7) and Zcchc11 (TUT4). Nucleic Acids Research, 42, 11777–11791. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1793. Wang L, Zhou JY, Yao JH, Lu DR, Qiao XJ and Jia W, 2010. U6 promoter‐driven siRNA injection has nonspecific effects in zebrafish. Biochem Biophys Res Commun, 391, 1363–1368. [DOI] [PubMed] [Google Scholar]
  1794. Wianny F and Zernicka‐Goetz M, 2000. Specific interference with gene function by double‐stranded RNA in early mouse development. Nature Cell Biology, 2, 70–75. [DOI] [PubMed] [Google Scholar]
  1795. Wienholds E, Koudijs MJ, van Eeden FJM, Cuppen E and Plasterk RHA, 2003. The microRNA‐producing enzyme Dicer1 is essential for zebrafish development. Nature Genetics, 35, 217–218. [DOI] [PubMed] [Google Scholar]
  1796. Yi TF, Arthanari H, Akabayov B, Song HD, Papadopoulos E, Qi HH, Jedrychowski M, Guttler T, Guo CC, Luna RE, Gygi SP, Huang SA and Wagner G, 2015. eIF1A augments Ago2‐mediated Dicer‐independent miRNA biogenesis and RNA interference. Nature Communications, 6, 7194–7194. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1797. Ying SY, Chang CP and Lin SL, 2010. Intron‐mediated RNA interference, intronic microRNAs, and applications. Methods Mol Biol, 629, 205–237. [DOI] [PubMed] [Google Scholar]
  1798. Zhao XF, Fjose A, Larsen N, Helvik JV and Drivenes O, 2008. Treatment with small interfering RNA affects the microRNA pathway and causes unspecific defects in zebrafish embryos. Febs Journal, 275, 2177–2184. [DOI] [PubMed] [Google Scholar]
  1799. Zhao ZX, Cao Y, Li M and Meng AM, 2001. Double‐stranded RNA injection produces nonspecific defects in zebrafish. Developmental Biology, 229, 215–223. [DOI] [PubMed] [Google Scholar]
  1800. Abe M, Naqvi A, Hendriks GJ, Feltzin V, Zhu YQ, Grigoriev A and Bonini NM, 2014. Impact of age‐associated increase in 2 ‘‐O‐methylation of miRNAs on aging and neurodegeneration in Drosophila. Genes & Development, 28, 44–57. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1801. Adelman ZN, Anderson MAE, Liu M, Zhang L and Myles KM, 2012. Sindbis virus induces the production of a novel class of endogenous siRNAs in Aedes aegypti mosquitoes. Insect Molecular Biology, 21, 357–368. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1802. Ameres SL, Horwich MD, Hung JH, Xu J, Ghildiyal M, Weng ZP and Zamore PD, 2010. Target RNA‐Directed Trimming and Tailing of Small Silencing RNAs. Science, 328, 1534–1539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1803. Antic S, Wolfinger MT, Skucha A, Hosiner S and Dorner S, 2015. General and MicroRNA‐Mediated mRNA Degradation Occurs on Ribosome Complexes in Drosophila Cells. Molecular and Cellular Biology, 35, 2309–2320. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1804. Azzam G, Smibert P, Lai EC and Liu JL, 2012. Drosophila Argonaute 1 and its miRNA biogenesis partners are required for oocyte formation and germline cell division. Developmental Biology, 365, 384–394. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1805. Bansal R and Michel AP, 2013. Core RNAi Machinery and Sid1, a Component for Systemic RNAi, in the Hemipteran Insect, Aphis glycines. International Journal of Molecular Sciences, 14, 3786–3801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1806. Barraud P, Heale BSE, O'Connell MA and Allain FHT, 2012. Solution structure of the N‐terminal dsRBD of Drosophila ADAR and interaction studies with RNA. Biochimie, 94, 1499–1509. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1807. Behm‐Ansmant I, Rehwinkel J, Doerks T, Stark A, Bork P and Izaurralde E, 2006. MRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1: DCP2 decapping complexes. Genes & Development, 20, 1885–1898. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1808. Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, Hung JH, Okamura K, Dai Q, Bortolamiol‐Becet D, Martin R, Zhao YJ, Zamore PD, Hannon GJ, Marra MA, Weng ZP, Perrimon N and Lai EC, 2011. Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Research, 21, 203–215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1809. Bernhardt SA, Simmons MP, Olson KE, Beaty BJ, Blair CD and Black WC, 2012. Rapid Intraspecific Evolution of miRNA and siRNA Genes in the Mosquito Aedes aegypti. Plos One, 7, e44198–e44198. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1810. Bernstein E, Caudy AA, Hammond SM and Hannon GJ, 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409, 363–366. [DOI] [PubMed] [Google Scholar]
  1811. Blandin S, Moita LF, Kocher T, Wilm M, Kafatos FC and Levashina EA, 2002. Reverse genetics in the mosquito Anopheles gambiae: targeted disruption of the Defensin gene. EMBO Rep, 3, 852–856. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1812. Bozzetti MP, Specchia V, Cattenoz PB, Laneve P, Geusa A, Sahin HB, Di Tommaso S, Friscini A, Massari S, Diebold C and Giangrande A, 2015. The Drosophila fragile X mental retardation protein participates in the piRNA pathway. Journal of Cell Science, 128, 2070–2084. [DOI] [PubMed] [Google Scholar]
  1813. Bucher G, Scholten J and Klingler M, 2002. Parental RNAi in Tribolium (Coleoptera). Curr Biol, 12, R85–86. [DOI] [PubMed] [Google Scholar]
  1814. Burroughs AM, Ando Y, de Hoon MJL, Tomaru Y, Nishibu T, Ukekawa R, Funakoshi T, Kurokawa T, Suzuki H, Hayashizaki Y and Daub CO, 2010. A comprehensive survey of 3 ‘ animal miRNA modification events and a possible role for 3 ‘ adenylation in modulating miRNA targeting effectiveness. Genome Research, 20, 1398–1410. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1815. Campbell CL, Keene KM, Brackney DE, Olson KE, Blair CD, Wilusz J and Foy BD, 2008. Aedes aegypti uses RNA interference in defense against Sindbis virus infection. Bmc Microbiology, 8, 47–47. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1816. Cappelle K, deOliveira CF , Van Eynde B, Christiaens O and Smagghe G, 2016. The involvement of clathrin‐mediated endocytosis and two Sid‐1‐like transmembrane proteins in double‐stranded RNA uptake in the Colorado potato beetle midgut. Insect Molecular Biology. [DOI] [PubMed] [Google Scholar]
  1817. Caudy AA, Myers M, Hannon GJ and Hammond SM, 2002. Fragile X‐related protein and VIG associate with the RNA interference machinery. Genes & Development, 16, 2491–2496. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1818. Caudy AA, Ketting RF, Hammond SM, Denli AM, Bathoorn AMP, Tops BBJ, Silva JM, Myers MM, Hannon GJ and Plasterk RHA, 2003. A micrococcal nuclease homolog in RNAi effector complexes. Nature, 425, 411–414. [DOI] [PubMed] [Google Scholar]
  1819. Cenik ES, Fukunaga R, Lu G, Dutcher R, Wang YM, Hall TMT and Zamore PD, 2011. Phosphate and R2D2 Restrict the Substrate Specificity of Dicer‐2, an ATP‐Driven Ribonuclease. Molecular Cell, 42, 172–184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1820. Cernilogar FM, Burroughs AM, Lanzuolo C, Breiling A, Imhof A and Orlando V, 2013. RNA‐Interference Components Are Dispensable for Transcriptional Silencing of the Drosophila Bithorax‐Complex. Plos One, 8, e65740–e65740. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1821. Cerutti H and Casas‐Mollano JA, 2006. On the origin and functions of RNA‐mediated silencing: from protists to man. Curr Genet, 50, 81–99. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1822. Chak LL, Mohammed J, Lai EC, Tucker‐Kellogg G and Okamura K, 2015. A deeply conserved, noncanonical miRNA hosted by ribosomal DNA. Rna, 21, 375–384. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1823. Chawla G and Sokol NS, 2014. ADAR mediates differential expression of polycistronic microRNAs. Nucleic Acids Research, 42, 5245–5255. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1824. Chekulaeva M, Filipowicz W and Parker R, 2009. Multiple independent domains of dGW182 function in miRNA‐mediated repression in Drosophila. Rna, 15, 794–803. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1825. Chekulaeva M, Parker R and Filipowicz W, 2010. The GW/WG repeats of Drosophila GW182 function as effector motifs for miRNA‐mediated repression. Nucleic Acids Research, 38, 6673–6683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1826. Chekulaeva M, Mathys H, Zipprich JT, Attig J, Colic M, Parker R and Filipowicz W, 2011. miRNA repression involves GW182‐mediated recruitment of CCR4‐NOT through conserved W‐containing motifs. Nature Structural & Molecular Biology, 18, 1218–U1262. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1827. Chen YH, Jia XT, Zhao L, Li CZ, Zhang SA, Chen YG, Weng SP and He JG, 2011. Identification and functional characterization of Dicer2 and five single VWC domain proteins of Litopenaeus vannamei. Developmental and Comparative Immunology, 35, 661–671. [DOI] [PubMed] [Google Scholar]
  1828. Chen YH, Zhao L, Jia XT, Li XY, Li CZ, Yan H, Weng SP and He JG, 2012. Isolation and characterization of cDNAs encoding Ars2 and Pasha homologs, two components of the RNA interference pathway in Litopenaeus vannamei. Fish & Shellfish Immunology, 32, 373–380. [DOI] [PubMed] [Google Scholar]
  1829. Chung WJ, Okamura K, Martin R and Lai EC, 2008. Endogenous RNA interference provides a somatic Defense against Drosophila transposons. Current Biology, 18, 795–802. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1830. Cui YL, Huang TZ and Zhang XB, 2015. RNA editing of microRNA prevents RNA‐induced silencing complex recognition of target mRNA. Open Biology, 5, 150126–150126. [DOI] [PMC free article] [PubMed] [Google Scholar] [Retracted]
  1831. Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C, Dus M, Perrimon N, Kellis M, Wohlschlegel JA, Sachidanandam R, Hannon GJ and Brennecke J, 2008. An endogenous small interfering RNA pathway in Drosophila. Nature, 453, 798–U797. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1832. Czech B, Zhou R, Erlich Y, Brennecke J, Binari R, Villalta C, Gordon A, Perrimon N and Hannon GJ, 2009. Hierarchical Rules for Argonaute Loading in Drosophila. Molecular Cell, 36, 445–456. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1833. Dechklar M, Udomkit A and Panyim S, 2008. Characterization of Argonaute cDNA from Penaeus monodon and implication of its role in RNA interference. Biochem Biophys Res Commun, 367, 768–774. [DOI] [PubMed] [Google Scholar]
  1834. Dekanty A, Romero NM, Bertolin AP, Thomas MG, Leishman CC, Perez‐Perri JI, Boccaccio GL and Wappner P, 2010. Drosophila Genome‐Wide RNAi Screen Identifies Multiple Regulators of HIF‐Dependent Transcription in Hypoxia. Plos Genetics, 6, e1000994–e1000994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1835. Denli AM, Tops BBJ, Plasterk RHA, Ketting RF and Hannon GJ, 2004. Processing of primary microRNAs by the Microprocessor complex. Nature, 432, 231–235. [DOI] [PubMed] [Google Scholar]
  1836. Deshpande G, Calhoun G and Schedl P, 2005. Drosophila argonaute‐2 is required early in embryogenesis for the assembly of centric/centromeric heterochromatin, nuclear division, nuclear migration, and germ‐cell formation. Genes & Development, 19, 1680–1685. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1837. Dong Y and Friedrich M, 2005. Nymphal RNAi: systemic RNAi mediated gene knockdown in juvenile grasshopper. Bmc Biotechnology, 5, 25–25. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1838. Dzitoyeva S, Dimitrijevic N and Manev H, 2003. Gamma‐aminobutyric acid B receptor 1 mediates behavior‐impairing actions of alcohol in Drosophila: adult RNA interference and pharmacological evidence. Proc Natl Acad Sci U S A, 100, 5485–5490. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1839. Eulalio A, Huntzinger E and Izaurralde E, 2008. GW182 interaction with Argonaute is essential for miRNA‐mediated translational repression and mRNA decay. Nature Structural & Molecular Biology, 15, 346–353. [DOI] [PubMed] [Google Scholar]
  1840. Eulalio A, Tritschler F, Buettner R, Weichenrieder O, Izaurralde E and Truffault V, 2009. The RRM domain in GW182 proteins contributes to miRNA‐mediated gene silencing. Nucleic Acids Research, 37, 2974–2983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1841. Fagegaltier D, Bouge AL, Berry B, Poisot E, Sismeiro O, Coppee JY, Theodore L, Voinnet O and Antoniewski C, 2009. The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila. Proc Natl Acad Sci U S A, 106, 21258–21263. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1842. Feinberg EH and Hunter CP, 2003. Transport of dsRNA into cells by the transmembrane protein SID‐1. Science, 301, 1545–1547. [DOI] [PubMed] [Google Scholar]
  1843. Feltzin VL, Khaladkar M, Abe M, Parisi M, Hendriks GJ, Kim J and Bonini NM, 2015. The exonuclease Nibbler regulates age‐associated traits and modulates piRNA length in Drosophila. Aging Cell, 14, 443–452. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1844. Filippov V, Solovyev V, Filippova M and Gill SS, 2000. A novel type of RNase III family proteins in eukaryotes. Gene, 245, 213–221. [DOI] [PubMed] [Google Scholar]
  1845. Flynt AS, Greimann JC, Chung WJ, Lima CD and Lai EC, 2010. MicroRNA Biogenesis via Splicing and Exosome‐Mediated Trimming in Drosophila. Molecular Cell, 38, 900–907. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1846. Forstemann K, Tomari Y, Du TT, Vagin VV, Denli AM, Bratu DP, Klattenhoff C, Theurkauf WE and Zamore PD, 2005. Normal microRNA maturation and germ‐line stem cell maintenance requires loquacious, a double‐stranded RNA‐binding domain protein. Plos Biology, 3, 1187–1201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1847. Forstemann K, Horwich MD, Wee L, Tomari Y and Zamore PD, 2007. Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by Dicer‐1. Cell, 130, 287–297. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1848. Fu Q and Wang PJ, 2014. Mammalian piRNAs: Biogenesis, function, and mysteries. Spermatogenesis, 4, e27889–e27889. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1849. Fukaya T and Tomari Y, 2011. PABP is not essential for microRNA‐mediated translational repression and deadenylation in vitro. EMBO J, 30, 4998–5009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1850. Fukaya T, H‐o Iwakawa and Tomari Y, 2014. MicroRNAs Block Assembly of eIF4F Translation Initiation Complex in Drosophila. Molecular Cell, 56, 67–78. [DOI] [PubMed] [Google Scholar]
  1851. Fukunaga R, Han BW, Hung JH, Xu J, Weng ZP and Zamore PD, 2012. Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals. Cell, 151, 533–546. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1852. Fukunaga R, Colpan C, Han BW and Zamore PD, 2014. Inorganic phosphate blocks binding of pre‐miRNA to Dicer‐2 via its PAZ domain. EMBO J, 33, 371–384. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1853. Galiana‐Arnoux D, Dostert C, Schneemann A, Hoffmann JA and Imler JL, 2006. Essential function in vivo for Dicer‐2 in host defense against RNA viruses in drosophila. Nature Immunology, 7, 590–597. [DOI] [PubMed] [Google Scholar]
  1854. Gandhi SG, Bag I, Sengupta S, Pal‐Bhadra M and Bhadra U, 2015. Drosophila oncogene Gas41 is an RNA interference modulator that intersects heterochromatin and the small interfering RNA pathway. Febs Journal, 282, 153–173. [DOI] [PubMed] [Google Scholar]
  1855. Gerbasi VR, Preall JB, Golden DE, Powell DW, Cummins TD and Sontheimer EJ, 2011. Blanks, a nuclear siRNA/dsRNA‐binding complex component, is required for Drosophila spermiogenesis. Proc Natl Acad Sci U S A, 108, 3204–3209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1856. Ghildiyal M, Seitz H, Horwich MD, Li CJ, Du TT, Lee S, Xu J, Kittler ELW, Zapp ML, Weng ZP and Zamore PD, 2008. Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science, 320, 1077–1081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1857. Ghildiyal M, Xu J, Seitz H, Weng ZP and Zamore PD, 2010. Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. Rna, 16, 43–56. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1858. Ghosh S, Kakumani PK, Kumar A, Malhotra P, Mukherjee SK and Bhatnagar RK, 2014. Genome wide screening of RNAi factors of Sf21 cells reveal several novel pathway associated proteins. Bmc Genomics, 15, 775–775. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1859. Gomez‐Orte E and Belles X, 2009. MicroRNA‐dependent metamorphosis in hemimetabolan insects. Proc Natl Acad Sci U S A, 106, 21678–21682. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1860. Gong L, Wang Z, Wang H, Qi J, Hu M and Hu Q, 2015. Core RNAi machinery and three Sid‐1 related genes in Spodoptera litura (Fabricius). International Journal of Agriculture and Biology, 17, 937–944. [Google Scholar]
  1861. Gracheva E, Dus M and Elgin SCR, 2009. Drosophila RISC Component VIG and Its Homolog Vig2 Impact Heterochromatin Formation. Plos One, 4, e6182–e6182. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1862. Haac ME, Anderson MAE, Eggleston H, Myles KM and Adelman ZN, 2015. The hub protein loquacious connects the microRNA and short interfering RNA pathways in mosquitoes. Nucleic Acids Research, 43, 3688–3700. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1863. Haase AD, 2016. A Small RNA‐Based Immune System Defends Germ Cells against Mobile Genetic Elements. Stem Cells International, 2016, 7595791–7595791. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1864. Han BW, Hung JH, Weng ZP, Zamore PD and Ameres SL, 2011. The 3 ‘‐to‐5 ‘ Exoribonuclease Nibbler Shapes the 3 ‘ Ends of MicroRNAs Bound to Drosophila Argonaute1. Current Biology, 21, 1878–1887. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1865. Han BW and Zamore PD, 2014. PiRNAs. Current Biology, 24, R730–R733. [DOI] [PubMed] [Google Scholar]
  1866. Hartig JV, Esslinger S, Bottcher R, Saito K and Forstemann K, 2009. Endo‐siRNAs depend on a new isoform of loquacious and target artificially introduced, high‐copy sequences. EMBO J, 28, 2932–2944. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1867. Hartig JV and Forstemann K, 2011. Loqs‐PD and R2D2 define independent pathways for RISC generation in Drosophila. Nucleic Acids Research, 39, 3836–3851. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1868. He YD and Zhang XB, 2012. Comprehensive characterization of viral miRNAs involved in white spot syndrome virus (WSSV) infection. RNA biology, 9, 1019–1029. [DOI] [PubMed] [Google Scholar]
  1869. Herbert KM, Pimienta G, DeGregorio SJ, Alexandrov A and Steitz JA, 2013. Phosphorylation of DGCR8 Increases Its Intracellular Stability and Induces a Progrowth miRNA Profile. Cell Reports, 5, 1070–1081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1870. Honeybee Genome Sequencing C, 2006. Insights into social insects from the genome of the honeybee Apis mellifera. Nature, 443, 931–949. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1871. Horwich MD, Li CJ, Matranga C, Vagin V, Farley G, Wang P and Zamore PD, 2007. The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single‐stranded siRNAs in RISC. Current Biology, 17, 1265–1272. [DOI] [PubMed] [Google Scholar]
  1872. Hoy MA, Waterhouse RM, Wu K, Estep AS, Ioannidis P, Palmer WJ, Pomerantz AF, Simao FA, Thomas J, Jiggins FM, Murphy TD, Pritham EJ, Robertson HM, Zdobnov EM, Gibbs RA and Richards S, 2016. Genome sequencing of the phytoseiid predatory mite Metaseiulus occidentalis reveals completely atomised Hox genes and super‐dynamic intron evolution. Genome biology and evolution. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1873. Huang HD, Li YJ, Szulwach KE, Zhang GQ, Jin P and Chen DH, 2014. AGO3 Slicer activity regulates mitochondria‐nuage localization of Armitage and piRNA amplification. Journal of Cell Biology, 206, 217–230. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1874. Huang TZ, Xu DD and Zhang XB, 2012. Characterization of shrimp Drosha in virus infection. Fish & Shellfish Immunology, 33, 575–581. [DOI] [PubMed] [Google Scholar]
  1875. Huang TZ and Zhang XB, 2013. Host defense against DNA virus infection in shrimp is mediated by the siRNA pathway. European Journal of Immunology, 43, 137–146. [DOI] [PubMed] [Google Scholar]
  1876. Huntzinger E, Braun JE, Heimstaedt S, Zekri L and Izaurralde E, 2010. Two PABPC1‐binding sites in GW182 proteins promote miRNA‐mediated gene silencing. EMBO J, 29, 4146–4160. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1877. Huntzinger E, Kuzuoglu‐Oeztuerk D, Braun JE, Eulalio A, Wohlbold L and Izaurralde E, 2013. The interactions of GW182 proteins with PABP and deadenylases are required for both translational repression and degradation of miRNA targets. Nucleic Acids Research, 41, 978–994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1878. Ishizuka A, Siomi MC and Siomi H, 2002. A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins. Genes & Development, 16, 2497–2508. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1879. Iwasaki S, Kawamata T and Tomari Y, 2009. Drosophila Argonaute1 and Argonaute2 Employ Distinct Mechanisms for Translational Repression. Molecular Cell, 34, 58–67. [DOI] [PubMed] [Google Scholar]
  1880. Iwasaki S, Sasaki HM, Sakaguchi Y, Suzuki T, Tadakuma H and Tomari Y, 2015. Defining fundamental steps in the assembly of the Drosophila RNAi enzyme complex. Nature, 521, 533–U274. [DOI] [PubMed] [Google Scholar]
  1881. Jariyapong P, Weerachatyanukul W, Direkbusarakom S, Hirono I, Wuthisuthimethavee S and Chotwiwatthanakun C, 2015. Enhancement of shrimp immunity against white spot syndrome virus by Macrobrachium rosenbergii nodavirus‐like particle encapsulated VP28 double‐stranded RNA. Aquaculture, 446, 325–332. [Google Scholar]
  1882. Jaskiewicz L and Filipowicz W, 2008. Role of Dicer in posttranscriptional RNA silencing. Curr Top Microbiol Immunol, 320, 77–97. [DOI] [PubMed] [Google Scholar]
  1883. Jaubert‐Possamai S, Rispe C, Tanguy S, Gordon K, Walsh T, Edwards O and Tagu D, 2010. Expansion of the miRNA Pathway in the Hemipteran Insect Acyrthosiphon pisum. Molecular Biology and Evolution, 27, 979–987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1884. Jiang F, Ye XC, Liu X, Fincher L, McKearin D and Liu QH, 2005. Dicer‐1 and R3D1‐L catalyze microRNA maturation in Drosophila. Genes & Development, 19, 1674–1679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1885. Jiang FF, Lu FL, Li PX, Liu W, Zhao L, Wang QF, Cao XF, Zhang L and Zhang YQ, 2016. Drosophila Homolog of FMRP Maintains Genome Integrity by Interacting with Piwi. Journal of Genetics and Genomics, 43, 11–24. [DOI] [PubMed] [Google Scholar]
  1886. Jin ZG and Xie T, 2007. Dcr‐1 maintains Drosophila ovarian stem cells. Current Biology, 17, 539–544. [DOI] [PubMed] [Google Scholar]
  1887. Kadener S, Rodriguez J, Abruzzi KC, Khodor YL, Sugino K, Marr MT, Nelson S and Rosbash M, 2009. Genome‐wide identification of targets of the drosha‐pasha/DGCR8 complex. Rna, 15, 537–545. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1888. Kavi HH and Birchler JA, 2009. Interaction of RNA polymerase II and the small RNA machinery affects heterochromatic silencing in Drosophila. Epigenetics & Chromatin, 2, 15–15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1889. Kawamata T, Seitz H and Tomari Y, 2009. Structural determinants of miRNAs for RISC loading and slicer‐independent unwinding. Nature Structural & Molecular Biology, 16, 953–U977. [DOI] [PubMed] [Google Scholar]
  1890. Kawamura Y, Saito K, Kin T, Ono Y, Asai K, Sunohara T, Okada TN, Siomi MC and Siomi H, 2008. Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells. Nature, 453, 793–U795. [DOI] [PubMed] [Google Scholar]
  1891. Keene KM, Foy BD, Sanchez‐Vargas I, Beaty BJ, Blair CD and Olson KE, 2004. RNA interference acts as a natural antiviral response to O'nyong‐nyong virus (Alphavirus; Togaviridae) infection of Anopheles gambiae. Proc Natl Acad Sci U S A, 101, 17240–17245. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1892. Kim K, Lee YS, Harris D, Nakahara K and Carthew RW, 2006. The RNAi pathway initiated by Dicer‐2 in Drosophila. Cold Spring Harbor Symposia on Quantitative Biology, 71, 39–44. [DOI] [PubMed] [Google Scholar]
  1893. Kim K, Lee YS and Carthew RW, 2007. Conversion of pre‐RISC to holo‐RISC by Ago2 during assembly of RNAi complexes. Rna, 13, 22–29. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1894. Kolliopoulou A and Swevers L, 2013. Functional analysis of the RNAi response in ovary‐derived silkmoth Bm5 cells. Insect Biochemistry and Molecular Biology, 43, 654–663. [DOI] [PubMed] [Google Scholar]
  1895. Ku HY, Gangaraju VK, Qi HY, Liu N and Lin HF, 2016. Tudor‐SN Interacts with Piwi Antagonistically in Regulating Spermatogenesis but Synergistically in Silencing Transposons in Drosophila. Plos Genetics, 12, e1005813–e1005813. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1896. Kurscheid S, Lew‐Tabor AE, Valle MR, Bruyeres AG, Doogan VJ, Munderloh UG, Guerrero FD, Barrero RA and Bellgard MI, 2009. Evidence of a tick RNAi pathway by comparative genomics and reverse genetics screen of targets with known loss‐of‐function phenotypes in Drosophila. Bmc Molecular Biology, 10, 26–26. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1897. Kuzuoglu‐Ozturk D, Bhandari D, Huntzinger E, Fauser M, Helms S and Izaurralde E, 2016. miRISC and the CCR4‐NOT complex silence mRNA targets independently of 43S ribosomal scanning. EMBO J. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1898. Labreuche Y, Veloso A, de la Vega E, Gross PS, Chapman RW, Browdy CL and Warr GW, 2010. Non‐specific activation of antiviral immunity and induction of RNA interference may engage the same pathway in the Pacific white leg shrimp Litopenaeus vannamei. Developmental and Comparative Immunology, 34, 1209–1218. [DOI] [PubMed] [Google Scholar]
  1899. Landthaler M, Yalcin A and Tuschl T, 2004. The human DiGeorge syndrome critical region gene 8 and its D‐melanogaster homolog are required for miRNA biogenesis. Current Biology, 14, 2162–2167. [DOI] [PubMed] [Google Scholar]
  1900. Lau PW, Guiley KZ, De N, Potter CS, Carragher B and MacRae IJ, 2012. The molecular architecture of human Dicer. Nature Structural & Molecular Biology, 19, 436–440. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1901. Lee M, Choi Y, Kim K, Jin H, Lim J, Nguyen TA, Yang J, Jeong M, Giraldez AJ, Yang H, Patel DJ and Kim VN, 2014. Adenylation of maternally inherited microRNAs by Wispy. Molecular Cell, 56, 696–707. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1902. Lee YS, Nakahara K, Pham JW, Kim K, He ZY, Sontheimer EJ and Carthew RW, 2004. Distinct roles for Drosophila Dicer‐1 and Dicer‐2 in the siRNA/miRNA silencing pathways. Cell, 117, 69–81. [DOI] [PubMed] [Google Scholar]
  1903. Leebonoi W, Sukthaworn S, Panyim S and Udomkit A, 2015. A novel gonad‐specific Argonaute 4 serves as a defense against transposons in the black tiger shrimp Penaeus monodon. Fish & Shellfish Immunology, 42, 280–288. [DOI] [PubMed] [Google Scholar]
  1904. Leger P, Lara E, Jagla B, Sismeiro O, Mansuroglu Z, Coppee JY, Bonnefoy E and Bouloy M, 2013. Dicer‐2‐and Piwi‐Mediated RNA Interference in Rift Valley Fever Virus‐Infected Mosquito Cells. Journal of Virology, 87, 1631–1648. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1905. Lewis SH, Salmela H and Obbard DJ, 2016. Duplication and Diversification of Dipteran Argonaute Genes, and the Evolutionary Divergence of Piwi and Aubergine. Genome biology and evolution, 8, 507–518. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1906. Li H, Li WX and Ding SW, 2002. Induction and suppression of RNA silencing by an animal virus. Science, 296, 1319–1321. [DOI] [PubMed] [Google Scholar]
  1907. Li WH, Prazak L, Chatterjee N, Gruninger S, Krug L, Theodorou D and Dubnau J, 2013. Activation of transposable elements during aging and neuronal decline in Drosophila. Nature Neuroscience, 16, 529–+. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1908. Lim SJ, Scott A, Xiong XP, Vahidpour S, Karijolich J, Guo DD, Pei SS, Yu YT, Zhou R and Li WX, 2014. Requirement for CRIF1 in RNA interference and Dicer‐2 stability. RNA biology, 11, 1171–1179. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1909. Lipardi C, Wei Q and Paterson BM, 2001. RNAi as random degradative PCR: siRNA primers convert mRNA into dsRNAs that are degraded to generate new siRNAs. Cell, 107, 297–307. [DOI] [PubMed] [Google Scholar]
  1910. Lipardi C and Paterson BM, 2009. Identification of an RNA‐dependent RNA polymerase in Drosophila involved in RNAi and transposon suppression (Retracted article. See vol. 108, pg. 15010, 2011). Proc Natl Acad Sci U S A, 106, 15645–15650. [DOI] [PMC free article] [PubMed] [Google Scholar] [Retracted]
  1911. Lipardi C and Paterson BM, 2011. Retraction for Lipardi and Paterson, “Identification of an RNA‐dependent RNA polymerase in Drosophila involved in RNAi and transposon suppression”. Proc Natl Acad Sci U S A, 108, 15010. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1912. Liu N, Abe M, Sabin LR, Hendriks GJ, Naqvi AS, Yu ZM, Cherry S and Bonini NM, 2011. The Exoribonuclease Nibbler Controls 3 ‘ End Processing of MicroRNAs in Drosophila. Current Biology, 21, 1888–1893. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1913. Liu QH, Rand TA, Kalidas S, Du FH, Kim HE, Smith DP and Wang XD, 2003. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science, 301, 1921–1925. [DOI] [PubMed] [Google Scholar]
  1914. Liu W, Liu JB, Lu YH, Gong YC, Zhu M, Chen F, Liang Z, Zhu LY, Kuang SL, Hu XL, Cao GL, Xue RY and Gong CL, 2015. Immune signaling pathways activated in response to different pathogenic micro‐organisms in Bombyx mori. Molecular Immunology, 65, 391–397. [DOI] [PubMed] [Google Scholar]
  1915. Liu Y, Ye XC, Jiang F, Liang CY, Chen DM, Peng JM, Kinch LN, Grishin NV and Liu QH, 2009. C3PO, an Endoribonuclease That Promotes RNAi by Facilitating RISC Activation. Science, 325, 750–753. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1916. Lozano J, Gomez‐Orte E, Lee HJ and Belles X, 2012. Super‐induction of Dicer‐2 expression by alien double‐stranded RNAs: an evolutionary ancient response to viral infection? Development Genes and Evolution, 222, 229–235. [DOI] [PubMed] [Google Scholar]
  1917. Lucchetta EM, Carthew RW and Ismagilov RF, 2009. The Endo‐siRNA Pathway Is Essential for Robust Development of the Drosophila Embryo. Plos One, 4, e7576–e7576. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1918. Luhur A, Chawla G, Wu YC, Li J and Sokol NS, 2014. Drosha‐independent DGCR8/Pasha pathway regulates neuronal morphogenesis. Proc Natl Acad Sci U S A, 111, 1421–1426. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1919. Luo Y, Wang XH, Yu D and Kang L, 2012. The SID‐1 double‐stranded RNA transporter is not required for systemic RNAi in the migratory locust. RNA biology, 9, 663–671. [DOI] [PubMed] [Google Scholar]
  1920. MacRae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD and Doudna JA, 2006. Structural basis for double‐stranded RNA processing by Dicer. Science, 311, 195–198. [DOI] [PubMed] [Google Scholar]
  1921. MacRae IJ, Zhou K and Doudna JA, 2007. Structural determinants of RNA recognition and cleavage by Dicer. Nature Structural and Molecular Biology, 14, 934–940. [DOI] [PubMed] [Google Scholar]
  1922. Maralit BA, Komatsu M, Hipolito SG, Hirono I and Kondo H, 2015. Microarray Analysis of Immunity Against WSSV in Response to Injection of Non‐specific Long dsRNA in Kuruma Shrimp, Marsupenaeus japonicus. Marine Biotechnology, 17, 493–501. [DOI] [PubMed] [Google Scholar]
  1923. Marques JT, Kim K, Wu PH, Alleyne TM, Jafari N and Carthew RW, 2010. Loqs and R2D2 act sequentially in the siRNA pathway in Drosophila. Nature Structural & Molecular Biology, 17, 24–U37. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1924. Martin R, Smibert P, Yalcin A, Tyler DM, Schafer U, Tuschl T and Lai EC, 2009. A Drosophila pasha Mutant Distinguishes the Canonical MicroRNA and Mirtron Pathways. Molecular and Cellular Biology, 29, 861–870. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1925. Matranga C, Tomari Y, Shin C, Bartel DP and Zamore PD, 2005. Passenger‐strand cleavage facilitates assembly of siRNA into Ago2‐containing RNAi enzyme complexes. Cell, 123, 607–620. [DOI] [PubMed] [Google Scholar]
  1926. Miyoshi K, Tsukumo H, Nagami T, Siomi H and Siomi MC, 2005. Slicer function of Drosophila Argonautes and its involvement in RISC formation. Genes & Development, 19, 2837–2848. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1927. Miyoshi K, Okada TN, Siomi H and Siomi MC, 2009. Characterization of the miRNA‐RISC loading complex and miRNA‐RISC formed in the Drosophila miRNA pathway. Rna, 15, 1282–1291. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1928. Miyoshi K, Miyoshi T, Hartig JV, Siomi H and Siomi MC, 2010a. Molecular mechanisms that funnel RNA precursors into endogenous small‐interfering RNA and microRNA biogenesis pathways in Drosophila. Rna, 16, 506–515. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1929. Miyoshi T, Takeuchi A, Siomi H and Siomi MC, 2010b. A direct role for Hsp90 in pre‐RISC formation in Drosophila. Nature Structural & Molecular Biology, 17, 1024–1026. [DOI] [PubMed] [Google Scholar]
  1930. Mon H, Li Z, Kobayashi I, Tomita S, Lee J, Sezutsu H, Tamura T and Kusakabe T, 2013. Soaking RNAi in Bombyx mori BmN4‐SID1 cells arrests cell cycle progression. Journal of Insect Science, 13, 155–155. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1931. Morazzani EM, Wiley MR, Murreddu MG, Adelman ZN and Myles KM, 2012. Production of Virus‐Derived Ping‐Pong‐Dependent piRNA‐like Small RNAs in the Mosquito Soma. Plos Pathogens, 8, e1002470–e1002470. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1932. Moretti F, Kaiser C, Zdanowicz‐Specht A and Hentze MW, 2012. PABP and the poly(A) tail augment microRNA repression by facilitated miRISC binding. Nature Structural & Molecular Biology, 19, 603–+. [DOI] [PubMed] [Google Scholar]
  1933. Moshkovich N, Nisha P, Boyle PJ, Thompson BA, Dale RK and Lei EP, 2011. RNAi‐independent role for Argonaute2 in CTCF/CP190 chromatin insulator function. Genes & Development, 25, 1686–1701. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1934. Mugat B, Akkouche A, Serrano V, Armenise C, Li B, Brun C, Fulga TA, Van Vactor D, Pelisson A and Chambeyron S, 2015. MicroRNA‐Dependent Transcriptional Silencing of Transposable Elements in Drosophila Follicle Cells. Plos Genetics, 11, e1005194–e1005194. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1935. Murota Y, Ishizu H, Nakagawa S, Iwasaki YW, Shibata S, Kamatani MK, Saito K, Okano H, Siomi H and Siomi MC, 2014. Yb Integrates piRNA Intermediates and Processing Factors into Perinuclear Bodies to Enhance piRISC Assembly. Cell Reports, 8, 103–113. [DOI] [PubMed] [Google Scholar]
  1936. Murphy D, Dancis B and Brown JR, 2008. The evolution of core proteins involved in microRNA biogenesis. Bmc Evolutionary Biology, 8, 92–92. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1937. Nagao A, Mituyama T, Huang HD, Chen DH, Siomi MC and Siomi H, 2010. Biogenesis pathways of piRNAs loaded onto AGO3 in the Drosophila testis. Rna, 16, 2503–2515. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1938. Nayak A, Berry B, Tassetto M, Kunitomi M, Acevedo A, Deng CH, Krutchinsky A, Gross J, Antoniewski C and Andino R, 2010. Cricket paralysis virus antagonizes Argonaute 2 to modulate antiviral defense in Drosophila. Nature Structural & Molecular Biology, 17, 547–U541. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1939. Nishida KM, Miyoshi K, Ogino A, Miyoshi T, Siomi H and Siomi MC, 2013. Roles of R2D2, a Cytoplasmic D2 Body Component, in the Endogenous siRNA Pathway in Drosophila. Molecular Cell, 49, 680–691. [DOI] [PubMed] [Google Scholar]
  1940. Niu JZ, Smagghe G, De Coninck DIM, Van Nieuwerburgh F, Deforce D and Meeus I, 2016. In vivo study of Dicer‐2‐mediated immune response of the small interfering RNA pathway upon systemic infections of virulent and avirulent viruses in Bombus terrestris. Insect Biochemistry and Molecular Biology, 70, 127–137. [DOI] [PubMed] [Google Scholar]
  1941. Nykanen A, Haley B and Zamore PD, 2001. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell, 107, 309–321. [DOI] [PubMed] [Google Scholar]
  1942. Okamura K, Hagen JW, Duan H, Tyler DM and Lai EC, 2007. The mirtron pathway generates microRNA‐class regulatory RNAs in Drosophila. Cell, 130, 89–100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1943. Okamura K, Balla S, Martin R, Liu N and Lai EC, 2008a. Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster. Nature Structural & Molecular Biology, 15, 581–590. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1944. Okamura K, Chung WJ and Lai EC, 2008b. The long and short of inverted repeat genes in animals ‐ microRNAs, mirtrons and hairpin RNAs. Cell Cycle, 7, 2840–2845. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1945. Okamura K, Chung WJ, Ruby JG, Guo HL, Bartel DP and Lai EC, 2008c. The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature, 453, 803–U808. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1946. Okamura K, Liu N and Lai EC, 2009. Distinct Mechanisms for MicroRNA Strand Selection by Drosophila Argonautes. Molecular Cell, 36, 431–444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1947. Okamura K, Robine N, Liu Y, Liu QH and Lai EC, 2011. R2D2 Organizes Small Regulatory RNA Pathways in Drosophila. Molecular and Cellular Biology, 31, 884–896. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1948. Okamura K, Ladewig E, Zhou L and Lai EC, 2013. Functional small RNAs are generated from select miRNA hairpin loops in flies and mammals. Genes & Development, 27, 778–792. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1949. Ortiz‐Rivas B, Jaubert‐Possamai S, Tanguy S, Gauthier JP, Tagu D and Claude R, 2012. Evolutionary study of duplications of the miRNA machinery in aphids associated with striking rate acceleration and changes in expression profiles. Bmc Evolutionary Biology, 12, 216–216. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1950. Palladino MJ, Keegan LP, O'Connell MA and Reenan RA, 2000. dADAR, a Drosophila double‐stranded RNA‐specific adenosine deaminase is highly developmentally regulated and is itself a target for RNA editing. Rna, 6, 1004–1018. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1951. Palmer WJ and Jiggins FM, 2015. Comparative Genomics Reveals the Origins and Diversity of Arthropod Immune Systems. Molecular Biology and Evolution, 32, 2111–2129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1952. Paradkar PN, Trinidad L, Voysey R, Duchemin JB and Walker PJ, 2012. Secreted Vago restricts West Nile virus infection in Culex mosquito cells by activating the Jak‐STAT pathway. Proc Natl Acad Sci U S A, 109, 18915–18920. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1953. Paro S, Li XH, O'Connell MA and Keegan LP, 2012. Regulation and Functions of ADAR in Drosophila. In: Adenosine Deaminases Acting on Rna. 221–236. [DOI] [PubMed] [Google Scholar]
  1954. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Muller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E and Ruvkun G, 2000. Conservation of the sequence and temporal expression of let‐7 heterochronic regulatory RNA. Nature, 408, 86–89. [DOI] [PubMed] [Google Scholar]
  1955. Peters L and Meister G, 2007. Argonaute proteins: mediators of RNA silencing. Molecular Cell, 26, 611–623. [DOI] [PubMed] [Google Scholar]
  1956. Peters NT, Rohrbach JA, Zalewski BA, Byrkett CM and Vaughn JC, 2003. RNA editing and regulation of Drosophila 4f‐rnp expression by sas‐10 antisense readthrough mRNA transcripts. Rna, 9, 698–710. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1957. Pham JW, Pellino JL, Lee YS, Carthew RW and Sontheimer EJ, 2004. A Dicer‐2‐dependent 80S complex cleaves targeted mRNAs during RNAi in Drosophila. Cell, 117, 83–94. [DOI] [PubMed] [Google Scholar]
  1958. Phetrungnapha A, Ho T, Udomkit A, Panyim S and Ongvarrasopone C, 2013. Molecular cloning and functional characterization of Argonaute‐3 gene from Penaeus monodon. Fish & Shellfish Immunology, 35, 874–882. [DOI] [PubMed] [Google Scholar]
  1959. Pinder BD and Smibert CA, 2013. microRNA‐independent recruitment of Argonaute 1 to nanos mRNA through the Smaug RNA‐binding protein. EMBO Rep, 14, 80–86. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1960. Pressman S, Reinke CA, Wang XH and Carthew RW, 2012. A Systematic Genetic Screen to Dissect the MicroRNA Pathway in Drosophila. G3‐Genes Genomes. Genetics, 2, 437–448. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1961. Provost P, Dishart D, Doucet J, Frendewey D, Samuelsson B and Radmark O, 2002. Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J, 21, 5864–5874. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1962. Pushpavalli S, Bag I, Pal‐Bhadra M and Bhadra U, 2012. Drosophila Argonaute‐1 is critical for transcriptional cosuppression and heterochromatin formation. Chromosome Research, 20, 333–351. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1963. Qi H, Watanabe T, Ku H‐Y, Liu N, Zhong M and Lin H, 2011. The Yb Body, a Major Site for Piwi‐associated RNA Biogenesis and a Gateway for Piwi Expression and Transport to the Nucleus in Somatic Cells. Journal of Biological Chemistry, 286, 3789–3797. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1964. Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, Wetzer R, Martin JW and Cunningham CW, 2010. Arthropod relationships revealed by phylogenomic analysis of nuclear protein‐coding sequences. Nature, 463, 1079–1083. [DOI] [PubMed] [Google Scholar]
  1965. Rehwinkel J, Behm‐Ansmant I, Gatfield D and Izaurralde E, 2005. A crucial role for GW182 and the DCP1: DCP2 decapping complex in miRNA‐mediated gene silencing. Rna, 11, 1640–1647. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1966. Reimao‐Pinto MM, Ignatova V, Burkard TR, Hung JH, Manzenreither RA, Sowemimo I, Herzog VA, Reichholf B, Farina‐Lopez S and Ameres SL, 2015. Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila. Molecular Cell, 59, 203–216. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1967. Roignant JY, Carre C, Mugat B, Szymczak D, Lepesant JA and Antoniewski C, 2003. Absence of transitive and systemic pathways allows cell‐specific and isoform‐specific RNAi in Drosophila. Rna, 9, 299–308. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1968. Ruby JG, Jan CH and Bartel DP, 2007. Intronic microRNA precursors that bypass Drosha processing. Nature, 448, 83–86. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1969. Sabin LR and Cherry S, 2013. Small creatures use small RNAs to direct antiviral defenses. European Journal of Immunology, 43, 27–33. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1970. Saito K, Ishizuka A, Siomi H and Siomi MC, 2005. Processing of pre‐microRNAs by the Dicer‐1‐Loquacious complex in Drosophila cells. Plos Biology, 3, 1202–1212. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1971. Saito K, Sakaguchi Y, Suzuki T, Suzuki T, Siomi H and Siomi MC, 2007. Pimet, the Drosophila homolog of HEN1, mediates 2 ‘‐O‐methylation of PIWI‐interacting RNAs at their 3 ‘ ends. Genes & Development, 21, 1603–1608. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1972. Saito K, Ishizu H, Komai M, Kotani H, Kawamura Y, Nishida KM, Siomi H and Siomi MC, 2010. Roles for the Yb body components Armitage and Yb in primary piRNA biogenesis in Drosophila. Genes & Development, 24, 2493–2498. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1973. Saleh MC, Tassetto M, van Rij RP, Goic B, Gausson V, Berry B, Jacquier C, Antoniewski C and Andino R, 2009. Antiviral immunity in Drosophila requires systemic RNA interference spread. Nature, 458, 346–350. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1974. Sanchez‐Vargas I, Scott JC, Poole‐Smith BK, Franz AWE, Barbosa‐Solomieu V, Wilusz J, Olson KE and Blair CD, 2009. Dengue Virus Type 2 Infections of Aedes aegypti Are Modulated by the Mosquito's RNA Interference Pathway. Plos Pathogens, 5, e1000299–e1000299. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1975. Sato K and Siomi MC, 2013. Piwi‐interacting RNAs: biological functions and biogenesis. Essays in biochemistry, 54, 39–52. [DOI] [PubMed] [Google Scholar]
  1976. Schnettler E, Donald CL, Human S, Watson M, Siu RWC, McFarlane M, Fazakerley JK, Kohl A and Fragkoudis R, 2013a. Knockdown of piRNA pathway proteins results in enhanced Semliki Forest virus production in mosquito cells. Journal of General Virology, 94, 1680–1689. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1977. Schnettler E, Ratinier M, Watson M, Shaw AE, McFarlane M, Varela M, Elliott RM, Palmarini M and Kohl A, 2013b. RNA Interference Targets Arbovirus Replication in Culicoides Cells. Journal of Virology, 87, 2441–2454. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1978. Schnettler E, Tykalova H, Watson M, Sharma M, Sterken MG, Obbard DJ, Lewis SH, McFarlane M, Bell‐Sakyi L, Barry G, Weisheit S, Best SM, Kuhn RJ, Pijlman GP, Chase‐Topping ME, Gould EA, Grubhoffer L, Fazakerley JK and Kohl A, 2014. Induction and suppression of tick cell antiviral RNAi responses by tick‐borne flaviviruses. Nucleic Acids Research, 42, 9436–9446. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1979. Schuster S, Zirkel F, Kurth A, van Cleef KWR, Drosten C, van Rij RP and Junglen S, 2014. A Unique Nodavirus with Novel Features: Mosinovirus Expresses Two Subgenomic RNAs, a Capsid Gene of Unknown Origin, and a Suppressor of the Antiviral RNA Interference Pathway. Journal of Virology, 88, 13447–13459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1980. Schwarz DS, Hutvagner G, Haley B and Zamore PD, 2002. Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways. Molecular Cell, 10, 537–548. [DOI] [PubMed] [Google Scholar]
  1981. Schwarz DS, Tomari Y and Zamore PD, 2004. The RNA‐induced silencing complex is a Mg2+‐dependent endonuclease. Current Biology, 14, 787–791. [DOI] [PubMed] [Google Scholar]
  1982. Shih JD and Hunter CP, 2011. SID‐1 is a dsRNA‐selective dsRNA‐gated channel. Rna, 17, 1057–1065. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1983. Shreve JT, Shukle RH, Subramanyam S, Johnson AJ, Schemerhorn BJ, Williams CE and Stuart JJ, 2013. A genome‐wide survey of small interfering RNA and microRNA pathway genes in a galling insect. Journal of Insect Physiology, 59, 367–376. [DOI] [PubMed] [Google Scholar]
  1984. Sinha NK, Trettin KD, Aruscavage PJ and Bass BL, 2015. Drosophila Dicer‐2 Cleavage Is Mediated by Helicase‐ and dsRNA Termini‐Dependent States that Are Modulated by Loquacious‐PD. Molecular Cell, 58, 406–417. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1985. Smibert P, Bejarano F, Wang D, Garaulet DL, Yang JS, Martin R, Bortolamiol‐Becet D, Robine N, Hiesinger PR and Lai EC, 2011. A Drosophila genetic screen yields allelic series of core microRNA biogenesis factors and reveals post‐developmental roles for microRNAs. Rna, 17, 1997–2010. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1986. Song JS, Guo W, Jiang F, Kang L and Zhou ST, 2013. Argonaute 1 is indispensable for juvenile hormone mediated oogenesis in the migratory locust, Locusta migratoria. Insect Biochemistry and Molecular Biology, 43, 879–887. [DOI] [PubMed] [Google Scholar]
  1987. Su JS, Oanh DTH, Lyons RE, Leeton L, van Hulten MCW, Tan SH, Song L, Rajendran KV and Walker PJ, 2008. A key gene of the RNA interference pathway in the black tiger shrimp, Penaeus monodon: Identification and functional characterisation of Dicer‐1. Fish & Shellfish Immunology, 24, 223–233. [DOI] [PubMed] [Google Scholar]
  1988. Taliaferro JM, Aspden JL, Bradley T, Marwha D, Blanchette M and Rio DC, 2013. Two new and distinct roles for Drosophila Argonaute‐2 in the nucleus: alternative pre‐mRNA splicing and transcriptional repression. Genes & Development, 27, 378–389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1989. Tomari Y, Du TT, Haley B, Schwarz DS, Bennett R, Cook HA, Koppetsch BS, Theurkauf WE and Zamore PD, 2004a. RISC assembly defects in the Drosophila RNAi mutant armitage. Cell, 116, 831–841. [DOI] [PubMed] [Google Scholar]
  1990. Tomari Y, Matranga C, Haley B, Martinez N and Zamore PD, 2004b. A protein sensor for siRNA asymmetry. Science, 306, 1377–1380. [DOI] [PubMed] [Google Scholar]
  1991. Tomari Y and Zamore PD, 2005. Perspective: machines for RNAi. Genes Dev, 19, 517–529. [DOI] [PubMed] [Google Scholar]
  1992. Tomari Y, Du T and Zamore PD, 2007. Sorting of Drosophila small silencing RNAs. Cell, 130, 299–308. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1993. Tomoyasu Y, Miller SC, Tomita S, Schoppmeier M, Grossmann D and Bucher G, 2008. Exploring systemic RNA interference in insects: a genome‐wide survey for RNAi genes in Tribolium. Genome Biology, 9, R10–R10. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1994. Tsutsumi A, Kawamata T, Izumi N, Seitz H and Tomari Y, 2011. Recognition of the pre‐miRNA structure by Drosophila Dicer‐1. Nature Structural & Molecular Biology, 18, 1153–U1189. [DOI] [PubMed] [Google Scholar]
  1995. van Cleef KWR, van Mierlo JT, Miesen P, Overheul GJ, Fros JJ, Schuster S, Marklewitz M, Pijlman GP, Junglen S and van Rij RP, 2014. Mosquito and Drosophila entomobirnaviruses suppress dsRNA‐ and siRNA‐induced RNAi. Nucleic Acids Research, 42, 8732–8744. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1996. van Rij RP, Saleh MC, Berry B, Foo C, Houk A, Antoniewski C and Andino R, 2006. The RNA silencing endonuclease Argonaute 2 mediates specific antiviral immunity in Drosophila melanogaster. Genes & Development, 20, 2985–2995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1997. Vodovar N, Bronkhorst AW, van Cleef KWR, Miesen P, Blanc H, van Rij RP and Saleh MC, 2012. Arbovirus‐Derived piRNAs Exhibit a Ping‐Pong Signature in Mosquito Cells. Plos One, 7, e30861–e30861. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1998. Wang H, Ma ZJ, Niu KY, Xiao Y, Wu XF, Pan CY, Zhao Y, Wang K, Zhang YY and Liu N, 2016. Antagonistic roles of Nibbler and Hen1 in modulating piRNA 3 ‘ ends in Drosophila. Development, 143, 530–539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  1999. Wang HD, Gong L, Qi JW, Hu MY, Zhong GH and Gong L, 2014. Molecular cloning and characterization of a SID‐1‐like gene in Plutella xylostella. Archives of Insect Biochemistry and Physiology, 87, 164–176. [DOI] [PubMed] [Google Scholar]
  2000. Wang PH, Yang LS, Gu ZH, Weng SP, Yu XQ and He JG, 2013. Nucleic acid‐induced antiviral immunity in shrimp. Antiviral Research, 99, 270–280. [DOI] [PubMed] [Google Scholar]
  2001. Wang PH, Weng SP and He JG, 2015a. Nucleic acid‐induced antiviral immunity in invertebrates: An evolutionary perspective. Developmental and Comparative Immunology, 48, 291–296. [DOI] [PubMed] [Google Scholar]
  2002. Wang XH, Aliyari R, Li WX, Li HW, Kim K, Carthew R, Atkinson P and Ding SW, 2006. RNA interference directs innate immunity against viruses in adult Drosophila. Science, 312, 452–454. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2003. Wang Z, Wu D, Liu Y, Xia X, Gong W, Qiu Y, Yang J, Zheng Y, Li J, Wang YF, Xiang Y, Hu Y and Zhou X, 2015b. Drosophila Dicer‐2 has an RNA interference‐independent function that modulates Toll immune signaling. Science advances, 1, e1500228–e1500228. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2004. Welker NC, Maity TS, Ye XC, Aruscavage PJ, Krauchuk AA, Liu QH and Bass BL, 2011. Dicer's Helicase Domain Discriminates dsRNA Termini to Promote an Altered Reaction Mode. Molecular Cell, 41, 589–599. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2005. Wen JY, Duan H, Bejarano F, Okamura K, Fabian L, Brill JA, Bortolamiol‐Becet D, Martin R, Ruby JG and Lai EC, 2015. Adaptive Regulation of Testis Gene Expression and Control of Male Fertility by the Drosophila Harpin RNA Pathway. Molecular Cell, 57, 165–178. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2006. Westholm JO, Ladewig E, Okamura K, Robine N and Lai EC, 2012. Common and distinct patterns of terminal modifications to mirtrons and canonical microRNAs. Rna, 18, 177–192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2007. Winter F, Edaye S, Huttenhofer A and Brunel C, 2007. Anopheles gambiae miRNAs as actors of defence reaction against Plasmodium invasion. Nucleic Acids Research, 35, 6953–6962. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2008. Wynant N, Santos D, Subramanyam SH, Verlinden H and Broeck JV, 2015. Drosha, Dicer‐1 and Argonaute‐1 in the desert locust: Phylogenetic analyses, transcript profiling and regulation during phase transition and feeding. Journal of Insect Physiology, 75, 20–29. [DOI] [PubMed] [Google Scholar]
  2009. Xiong XP, Vogler G, Kurthkoti K, Samsonova A and Zhou R, 2015. SmD1 Modulates the miRNA Pathway Independently of Its Pre‐mRNA Splicing Function. Plos Genetics, 11, e1005475–e1005475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2010. Xu HJ, Chen T, Ma XF, Xue J, Pan PL, Zhang XC, Cheng JA and Zhang CX, 2013. Genome‐wide screening for components of small interfering RNA (siRNA) and micro‐RNA (miRNA) pathways in the brown planthopper, Nilaparvata lugens (Hemiptera: Delphacidae). Insect Molecular Biology, 22, 635–647. [DOI] [PubMed] [Google Scholar]
  2011. Xu KY, Bogert BA, Li WJ, Su K, Lee A and Gao FB, 2004. The fragile X‐related gene affects the crawling behavior of Drosophila larvae by regulating the mRNA level of the DEG/ENaC protein pickpocket1. Current Biology, 14, 1025–1034. [DOI] [PubMed] [Google Scholar]
  2012. Xu W and Han Z, 2008. Cloning and phylogenetic analysis of sid‐1‐like genes from aphids. Journal of insect science (Online), 8, 1–6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2013. Yang JS, Smibert P, Westholm JO, Jee D, Maurin T and Lai EC, 2014a. Intertwined pathways for Argonaute‐mediated microRNA biogenesis in Drosophila. Nucleic Acids Research, 42, 1987–2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2014. Yang LL, Chen DS, Duan RH, Xia LX, Wang J, Qurashi A, Jin P and Chen DH, 2007. Argonaute 1 regulates the fate of germline stem cells in Drosophila. Development, 134, 4265–4272. [DOI] [PubMed] [Google Scholar]
  2015. Yang LS, Li XL, Jiang S, Qiu LH, Zhou FL, Liu WJ and Jiang SG, 2014b. Characterization of Argonaute2 gene from black tiger shrimp (Penaeus monodon) and its responses to immune challenges. Fish & Shellfish Immunology, 36, 261–269. [DOI] [PubMed] [Google Scholar]
  2016. Ye XC, Paroo Z and Liu QH, 2007. Functional anatomy of the Drosophila MicroRNA‐ generating enzyme. Journal of Biological Chemistry, 282, 28373–28378. [DOI] [PubMed] [Google Scholar]
  2017. Yoda M, Kawamata T, Paroo Z, Ye XC, Iwasaki S, Liu QH and Tomari Y, 2010. ATP‐dependent human RISC assembly pathways. Nature Structural & Molecular Biology, 17, 17–U29. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2018. Zambon RA, Vakharia VN and Wu LP, 2006. RNAi is an antiviral immune response against a dsRNA virus in Drosophila melanogaster. Cellular Microbiology, 8, 880–889. [DOI] [PubMed] [Google Scholar]
  2019. Zhang H, Kolb FA, Brondani V, Billy E and Filipowicz W, 2002. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J, 21, 5875–5885. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2020. Zhang XY, Lu K, Zhou JL and Zhou Q, 2013. Molecular characterization and gene functional analysis of Dicer‐2 gene from Nilaparvata lugens (Hemiptera: Geometroidea). Insect Science, 20, 61–68. [DOI] [PubMed] [Google Scholar]
  2021. Zhao CY, Gonzales MAA, Poland TM and Mittapalli O, 2015. Core RNAi machinery and gene knockdown in the emerald ash borer (Agrilus planipennis). Journal of Insect Physiology, 72, 70–78. [DOI] [PubMed] [Google Scholar]
  2022. Zhou R, Czech B, Brennecke J, Sachidanandam R, Wohlschlegel JA, Perrimon N and Hannon GJ, 2009. Processing of Drosophila endo‐siRNAs depends on a specific Loquacious isoform. Rna, 15, 1886–1895. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2023. Zhu L, Tatsuke T, Li ZQ, Mon H, Xu J, Lee JM and Kusakabe T, 2012. Molecular cloning of BmTUDOR‐SN and analysis of its role in the RNAi pathway in the silkworm, Bombyx mori (Lepidoptera: Bombycidae). Applied Entomology and Zoology, 47, 207–215. [Google Scholar]
  2024. Zografidis A, Van Nieuwerburgh F, Kolliopoulou A, Apostolou‐Karampelis K, Head SR, Deforce D, Smagghe G and Swevers L, 2015. Viral Small‐RNA Analysis of Bombyx mori Larval Midgut during Persistent and Pathogenic Cytoplasmic Polyhedrosis Virus Infection. Journal of Virology, 89, 11473–11486. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2025. Biggar KK, Kornfeld SF, Maistrovski Y and Storey KB, 2012. MicroRNA Regulation in Extreme Environments: Differential Expression of MicroRNAs in the Intertidal Snail Littorina littorea During Extended Periods of Freezing and Anoxia. Genomics Proteomics & Bioinformatics, 10, 302–309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2026. Bitel CL, Singh V and Frederikse PH, 2012. miR‐124, miR‐125b, let‐7 and Vesicle Transport Proteins in Squid Lenses in L. pealei. Current Eye Research, 37, 388–394. [DOI] [PubMed] [Google Scholar]
  2027. Chen GF, Zhang CY, Jiang FJ, Wang YY, Xu Z and Wang CM, 2014. Bioinformatics analysis of hemocyte miRNAs of scallop Chlamys farreri against acute viral necrobiotic virus (AVNV). Fish & Shellfish Immunology, 37, 75–86. [DOI] [PubMed] [Google Scholar]
  2028. Cheng W, Tsai RT and Chang CC, 2012. Dietary sodium alginate administration enhances Mx gene expression of the tiger grouper, Epinephelus fuscoguttatus receiving poly I:C. Aquaculture, 324, 201–208. [Google Scholar]
  2029. Choi SH, Jee BY, Lee SJ, Cho MY, Lee SJ, Kim JW, Do Jeong H and Kim KH, 2013. Effects of RNA interference‐mediated knock‐down of hypoxia‐inducible factor‐alpha on respiratory burst activity of the Pacific oyster Crassostrea gigas hemocytes. Fish & Shellfish Immunology, 35, 476–479. [DOI] [PubMed] [Google Scholar]
  2030. De Zoysa M, Kang HS, Song YB, Jee Y, Lee YD and Lee J, 2007. First report of invertebrate Mx: Cloning, characterization and expression analysis of Mx cDNA in disk abalone (Haliotis discus discus). Fish & Shellfish Immunology, 23, 86–96. [DOI] [PubMed] [Google Scholar]
  2031. Fabioux C, Corporeau C, Quillien V, Favrel P and Huvet A, 2009. In vivo RNA interference in oyster ‐vasa silencing inhibits germ cell development. Febs Journal, 276, 2566–2573. [DOI] [PubMed] [Google Scholar]
  2032. Fei GH, Guo CH, Sun HS and Feng ZP, 2007. Chronic hypoxia stress‐induced differential modulation of heat‐shock protein 70 and presynaptic proteins. Journal of Neurochemistry, 100, 50–61. [DOI] [PubMed] [Google Scholar]
  2033. Green TJ and Barnes AC, 2009. Inhibitor of REL/NF‐B‐K is regulated in Sydney rock oysters in response to specific double‐stranded RNA and Vibrio alginolyticus, but the major immune anti‐oxidants EcSOD and Prx6 are non‐inducible. Fish & Shellfish Immunology, 27, 260–265. [DOI] [PubMed] [Google Scholar]
  2034. Green TJ and Montagnani C, 2013. Poly I: C induces a protective antiviral immune response in the Pacific oyster (Crassostrea gigas) against subsequent challenge with Ostreid herpesvirus (OsHV‐1 mu var). Fish & Shellfish Immunology, 35, 382–388. [DOI] [PubMed] [Google Scholar]
  2035. Green TJ, Benkendorff K, Robinson N, Raftos D and Speck P, 2014. Anti‐viral gene induction is absent upon secondary challenge with double‐stranded RNA in the Pacific oyster, Crassostrea gigas. Fish & Shellfish Immunology, 39, 492–497. [DOI] [PubMed] [Google Scholar]
  2036. Green TJ, Raftos D, Speck P and Montagnani C, 2015a. Antiviral immunity in marine molluscs. Journal of General Virology, 96, 2471–2482. [DOI] [PubMed] [Google Scholar]
  2037. Green TJ, Rolland JL, Vergnes A, Raftos D and Montagnani C, 2015b. OsHV‐1 countermeasures to the Pacific oyster's anti‐viral response. Fish & Shellfish Immunology, 47, 435–443. [DOI] [PubMed] [Google Scholar]
  2038. Guo CH, Senzel A, Li K and Feng ZP, 2010. De Novo Protein Synthesis of Syntaxin‐1 and Dynamin‐1 in Long‐Term Memory Formation Requires CREB1 Gene Transcription in Lymnaea stagnalis. Behavior Genetics, 40, 680–693. [DOI] [PubMed] [Google Scholar]
  2039. Hashimoto N, Kurita Y and Wada H, 2012. Developmental role of dpp in the gastropod shell plate and co‐option of the dpp signaling pathway in the evolution of the operculum. Developmental Biology, 366, 367–373. [DOI] [PubMed] [Google Scholar]
  2040. Hui K, Fei GH, Saab BJ, Su J, Roder JC and Feng ZP, 2007. Neuronal calcium sensor‐1 modulation of optimal calcium level for neurite outgrowth. Development, 134, 4479–4489. [DOI] [PubMed] [Google Scholar]
  2041. Huvet A, Fleury E, Corporeau C, Quillien V, Daniel JY, Riviere G, Boudry P and Fabioux C, 2012. In Vivo RNA Interference of a Gonad‐Specific Transforming Growth Factor‐beta in the Pacific Oyster Crassostrea gigas. Marine Biotechnology, 14, 402–410. [DOI] [PubMed] [Google Scholar]
  2042. Huvet A, Beguel JP, Cavaleiro NP, Thomas Y, Quillien V, Boudry P, Alunno‐Bruscia M and Fabioux C, 2015. Disruption of amylase genes by RNA interference affects reproduction in the Pacific oyster Crassostrea gigas. Journal of Experimental Biology, 218, 1740–1747. [DOI] [PubMed] [Google Scholar]
  2043. Jiang YG, Loker ES and Zhang SM, 2006. In vivo and in vitro knockdown of FREP2 gene expression in the snail Biomphalaria glabrata using RNA interference. Developmental and Comparative Immunology, 30, 855–866. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2044. Jiao Y, Zheng Z, Du XD, Wang QH, Huang RL, Deng YW, Shi SL and Zhao XX, 2014. Identification and Characterization of MicroRNAs in Pearl Oyster Pinctada martensii by Solexa Deep Sequencing. Marine Biotechnology, 16, 54–62. [DOI] [PubMed] [Google Scholar]
  2045. Jiao Y, Zheng Z, Tian RR, Du XD, Wang QH and Huang RL, 2015. MicroRNA, Pm‐miR‐2305, Participates in Nacre Formation by Targeting Pearlin in Pearl Oyster Pinctada martensii. International Journal of Molecular Sciences, 16, 21442–21453. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2046. Kenny NJ, Namigai EKO, Marletaz F, Hui JHL and Shimeld SM, 2015. Draft genome assemblies and predicted microRNA complements of the intertidal lophotrochozoans Patella vulgata (Mollusca, Patellogastropoda) and Spirobranchus (Pomatoceros) lamarcki (Annelida, Serpulida). Marine Genomics, 24, 139–146. [DOI] [PubMed] [Google Scholar]
  2047. Kjaer KH, Poulsen JB, Reintamm T, Saby E, Martensen PM, Kelve M and Justesen J, 2009. Evolution of the 2′‐5′‐Oligoadenylate Synthetase Family in Eukaryotes and Bacteria. Journal of Molecular Evolution, 69, 612–624. [DOI] [PubMed] [Google Scholar]
  2048. Knight M, Miller A, Liu YJ, Scaria P, Woodle M and Ittiprasert W, 2011. Polyethyleneimine (PEI) Mediated siRNA Gene Silencing in the Schistosoma mansoni Snail Host, Biomphalaria glabrata. Plos Neglected Tropical Diseases, 5, e1212–e1212. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2049. Lee JA, Kim HK, Kim KH, Han JH, Lee YS, Lim CS, Chang DJ, Kubo T and Kaang BK, 2001. Overexpression of and RNA interference with the CCAAT enhancer‐binding protein on long‐term facilitation of Aplysia sensory to motor synapses. Learning & Memory, 8, 220–226. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2050. Lyles V, Zhao YL and Martin KC, 2006. Synapse formation and mRNA localization in cultured Aplysia neurons. Neuron, 49, 349–356. [DOI] [PubMed] [Google Scholar]
  2051. Martin‐Gomez L, Villalba A, Kerkhoven RH and Abollo E, 2014. Role of microRNAs in the immunity process of the flat oyster Ostrea edulis against bonamiosis. Infection Genetics and Evolution, 27, 40–50. [DOI] [PubMed] [Google Scholar]
  2052. Masood M, Raftos DA and Nair SV, 2016. Two oyster species that show differential susceptibility to virus infection also show differential proteomic responses to generic dsRNA. Journal of proteome research. [DOI] [PubMed] [Google Scholar]
  2053. Miao G, Qi H, Li L, Que H and Zhang G, 2016. Characterization and functional analysis of two inhibitor of apoptosis genes in Zhikong scallop Chlamys farreri. Developmental and Comparative Immunology, 60, 1–11. [DOI] [PubMed] [Google Scholar]
  2054. Millan MJ, 2011. MicroRNA in the regulation and expression of serotonergic transmission in the brain and other tissues. Current Opinion in Pharmacology, 11, 11–22. [DOI] [PubMed] [Google Scholar]
  2055. Ormond J, Hislop J, Zhao YL, Webb N, Vaillaincourt F, Dyer JR, Ferraro G, Barker P, Martin KC and Sossin WS, 2004. ApTrkl, a Trk‐like receptor, mediates serotonin‐dependent ERK activation and long‐term facilitation in Aplysia sensory neurons. Neuron, 44, 715–728. [DOI] [PubMed] [Google Scholar]
  2056. Pari M, Kuusksalu A, Lopp A, Kjaer KH, Justesen J and Kelve M, 2014. Enzymatically active 2 ‘,5 ‘‐oligoadenylate synthetases are widely distributed among Metazoa, including protostome lineage. Biochimie, 97, 200–209. [DOI] [PubMed] [Google Scholar]
  2057. Rajasethupathy P, Fiumara F, Sheridan R, Betel D, Puthanveettil SV, Russo JJ, Sander C, Tuschl T and Kandel E, 2009. Characterization of Small RNAs in Aplysia Reveals a Role for miR‐124 in Constraining Synaptic Plasticity through CREB. Neuron, 63, 803–817. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2058. Rajasethupathy P, Antonov I, Sheridan R, Frey S, Sander C, Tuschl T and Kandel ER, 2012. A Role for Neuronal piRNAs in the Epigenetic Control of Memory‐Related Synaptic Plasticity. Cell, 149, 693–707. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2059. Rosani U, Pallavicini A and Venice P, 2016. The miRNA biogenesis in marine bivalves. Peerj, 4, e1763–e1763. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2060. Tian RR, Zheng Z, Huang RL, Jiao Y and Du XD, 2015. miR‐29a Participated in Nacre Formation and Immune Response by Targeting Y2R in Pinctada martensii. International Journal of Molecular Sciences, 16, 29436–29445. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2061. Wang GD, Li N, Zhang LL, Zhang LH, Zhang ZP and Wang YL, 2015a. IGFBP7 promotes hemocyte proliferation in small abalone Haliotis diversicolor, proved by dsRNA and cap mRNA exposure. Gene, 571, 65–70. [DOI] [PubMed] [Google Scholar]
  2062. Wang GD, Li N, Zhang LL, Zhang LH, Zhang ZP and Wang YL, 2016a. IGFBP7 is involved in abalone metamorphosis. Aquaculture, 451, 377–384. [Google Scholar]
  2063. Wang M, Wang L, Xin L, Wang X, Wang L, Xu J, Jia Z, Yue F, Wang H and Song L, 2016b. Two novel LRR‐only proteins in Chlamys farreri: Similar in structure, yet different in expression profile and pattern recognition. Developmental and Comparative Immunology, 59, 99–109. [DOI] [PubMed] [Google Scholar]
  2064. Wang MQ, Wang LL, Guo Y, Yi QL and Song LS, 2016c. An LRR‐only protein representing a new type of pattern recognition receptor in Chlamys farreri. Developmental and Comparative Immunology, 54, 145–155. [DOI] [PubMed] [Google Scholar]
  2065. Wang PH, Weng SP and He JG, 2015b. Nucleic acid‐induced antiviral immunity in invertebrates: An evolutionary perspective. Developmental and Comparative Immunology, 48, 291–296. [DOI] [PubMed] [Google Scholar]
  2066. Xu F, Wang XT, Feng Y, Huang W, Wang W, Li L, Fang XD, Que HY and Zhang GF, 2014. Identification of Conserved and Novel MicroRNAs in the Pacific Oyster Crassostrea gigas by Deep Sequencing. PLoS ONE, 9, e104371–e104371. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2067. Zhang Y, Yu F, Li J, Tong Y, Zhang YH and Yu ZN, 2014. The first invertebrate RIG‐I‐like receptor (RLR) homolog gene in the pacific oyster Crassostrea gigas. Fish & Shellfish Immunology, 40, 466–471. [DOI] [PubMed] [Google Scholar]
  2068. Zhao XL, Yu H, Kong LF, Liu SK and Li Q, 2016. High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response. Scientific Reports, 6, 22687–22687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2069. Zheng Z, Jiao Y, Du XD, Tian QL, Wang QH, Huang RL and Deng YW, 2016a. Computational prediction of candidate miRNAs and their potential functions in biomineralization in pearl oyster Pinctada martensii. Saudi Journal of Biological Sciences, 23, 372–378. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2070. Zheng Z, Liang J, Huang R, Du X, Wang Q, Deng Y and Jiao Y, 2016b. Identification of a novel miR‐146a from Pinctada martensii involved in the regulation of the inflammatory response. Fish and Shellfish Immunology, 54, 40–45. [DOI] [PubMed] [Google Scholar]
  2071. Zhou Z, Wang LL, Song LS, Liu R, Zhang H, Huang MM and Chen H, 2014. The Identification and Characteristics of Immune‐Related MicroRNAs in Haemocytes of Oyster Crassostrea gigas. PLoS ONE, 9, e88397–e88397. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2072. Christodoulou F, Raible F, Tomer R, Simakov O, Trachana K, Klaus S, Snyman H, Hannon GJ, Bork P and Arendt D, 2010. Ancient animal microRNAs and the evolution of tissue identity. Nature, 463, 1084–U1105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2073. Flemr M, Malik R, Franke V, Nejepinska J, Sedlacek R, Vlahovicek K and Svoboda P, 2013. A Retrotransposon‐Driven Dicer Isoform Directs Endogenous Small Interfering RNA Production in Mouse Oocytes. Cell, 155, 807–816. [DOI] [PubMed] [Google Scholar]
  2074. Giani VC, Yamaguchi E, Boyle MJ and Seaver EC, 2011. Somatic and germline expression of piwi during development and regeneration in the marine polychaete annelid Capitella teleta. Evodevo, 2, 10–10. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2075. Gong P, Xie FL, Zhang BH and Perkins EJ, 2010. In silico identification of conserved microRNAs and their target transcripts from expressed sequence tags of three earthworm species. Computational Biology and Chemistry, 34, 313–319. [DOI] [PubMed] [Google Scholar]
  2076. Helm C, Bernhart SH, Siederdissen CHZ, Nickel B and Bleidorn C, 2012. Deep sequencing of small RNAs confirms an annelid affinity of Myzostomida. Molecular Phylogenetics and Evolution, 64, 198–203. [DOI] [PubMed] [Google Scholar]
  2077. Huang XM, Tian QN, Bao ZX, Qin YF, Chen SJ, Lu P, Zhang XL, Zhang YZ and Zhang ST, 2012. Cloning and Identification of MicroRNAs in Earthworm (Eisenia fetida). Biochemical Genetics, 50, 1–11. [DOI] [PubMed] [Google Scholar]
  2078. Kenny NJ, Namigai EKO, Marletaz F, Hui JHL and Shimeld SM, 2015. Draft genome assemblies and predicted microRNA complements of the intertidal lophotrochozoans Patella vulgata (Mollusca, Patellogastropoda) and Spirobranchus (Pomatoceros) lamarcki (Annelida, Serpulida). Marine Genomics, 24, 139–146. [DOI] [PubMed] [Google Scholar]
  2079. Kjaer KH, Poulsen JB, Reintamm T, Saby E, Martensen PM, Kelve M and Justesen J, 2009. Evolution of the 2′‐5′‐Oligoadenylate Synthetase Family in Eukaryotes and Bacteria. Journal of Molecular Evolution, 69, 612–624. [DOI] [PubMed] [Google Scholar]
  2080. Kozin VV and Kostyuchenko RP, 2015. Vasa, PL10, and Piwi gene expression during caudal regeneration of the polychaete annelid Alitta virens. Development Genes and Evolution, 225, 129–138. [DOI] [PubMed] [Google Scholar]
  2081. Ozpolat BD and Bely AE, 2015. Gonad establishment during asexual reproduction in the annelid Pristina leidyi. Developmental Biology, 405, 123–136. [DOI] [PubMed] [Google Scholar]
  2082. Rosani U, Pallavicini A and Venier P, 2016. The miRNA biogenesis in marine bivalves. PeerJ, 4, e1763. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2083. Sperling EA, Vinther J, Moy VN, Wheeler BM, Semon M, Briggs DEG and Peterson KJ, 2009. MicroRNAs resolve an apparent conflict between annelid systematics and their fossil record. Proceedings of the Royal Society B‐Biological Sciences, 276, 4315–4322. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2084. Sugio M, Takeuchi K, Kutsuna J, Tadokoro R, Takahashi Y, Yoshida‐Noro C and Tochinai S, 2008. Exploration of embryonic origins of germline stem cells and neoblasts in Enchytraeus japonensis (Oligochaeta, Annelida). Gene Expression Patterns, 8, 227–236. [DOI] [PubMed] [Google Scholar]
  2085. Takeo M, Yoshida‐Noro C and Tochinai S, 2010. Functional analysis of grimp, a novel gene required for mesodermal cell proliferation at an initial stage of regeneration in Enchytraeus japonensis (Enchytraeidae, Oligochaete). International Journal of Developmental Biology, 54, 151–160. [DOI] [PubMed] [Google Scholar]
  2086. Tessmar‐Raible K, Raible F, Christodoulou F, Guy K, Rembold M, Hausen H and Arendt D, 2007. Conserved sensory‐neurosecretory cell types in annelid and fish forebrain: Insights into hypothalamus evolution. Cell, 129, 1389–1400. [DOI] [PubMed] [Google Scholar]
  2087. Weigert A, Helm C, Hausen H, Zakrzewski AC and Bleidorn C, 2013. Expression pattern of Piwi‐like genes in adult Myzostoma cirriferum (Annelida). Development Genes and Evolution, 223, 329–334. [DOI] [PubMed] [Google Scholar]
  2088. Yoshida‐Noro C and Tochinai S, 2010. Stem cell system in asexual and sexual reproduction of Enchytraeus japonensis (Oligochaeta, Annelida). Development Growth & Differentiation, 52, 43–55. [DOI] [PubMed] [Google Scholar]
  2089. Allo M and Kornblihtt AR, 2010. Gene Silencing: Small RNAs Control RNA Polymerase II Elongation. Current Biology, 20, R704–R707. [DOI] [PubMed] [Google Scholar]
  2090. Ambros V, Lee RC, Lavanway A, Williams PT and Jewell D, 2003. MicroRNAs and other tiny endogenous RNAs in C‐elegans. Current Biology, 13, 807–818. [DOI] [PubMed] [Google Scholar]
  2091. Aoki K, Moriguchi H, Yoshioka T, Okawa K and Tabara H, 2007. In vitro analyses of the production and activity of secondary small interfering RNAs in C‐elegans. Embo J, 26, 5007–5019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2092. Ashe A, Bélicard T, Le Pen J, Sarkies P, Frézal L, Lehrbach NJ, Félix MA and Miska EA, 2013. A deletion polymorphism in the Caenorhabditis elegans RIG‐I homolog disables viral RNA dicing and antiviral immunity. eLife, 2013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2093. Asikainen S, Heikkinen L, Wong G and Storvik M, 2008. Functional characterization of endogenous siRNA target genes in Caenorhabditis elegans. Bmc Genomics, 9, 270–270. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2094. Beshore EL, McEwen T, Marshall J and Bennett K, 2009. Activating interactions between GLH‐1, microRNAs and Dicer in C. elegans. Developmental Biology, 331, 418–418. [Google Scholar]
  2095. Beshore EL, McEwen TJ, Jud MC, Marshall JK, Schisa JA and Bennett KL, 2011. C. elegans Dicer interacts with the P‐granule component GLH‐1 and both regulate germline RNPs. Developmental Biology, 350, 370–381. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2096. Blanchard D, Parameswaran P, Lopez‐Molina J, Gent J, Saynuk JF and Fire A, 2011. On the nature of in vivo requirements for rde‐4 in RNAi and developmental pathways in C‐elegans. Rna Biology, 8, 458–467. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2097. Bouasker S and Simard MJ, 2012. The slicing activity of miRNA‐specific Argonautes is essential for the miRNA pathway in C. elegans. Nucleic Acids Research, 40, 10452–10462. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2098. Buck AH and Blaxter M, 2013. Functional diversification of Argonautes in nematodes: an expanding universe. Biochemical Society Transactions, 41, 881–886. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2099. Buckley BA, Burkhart KB, Gu SG, Spracklin G, Kershner A, Fritz H, Kimble J, Fire A and Kennedy S, 2012. A nuclear Argonaute promotes multigenerational epigenetic inheritance and germline immortality. Nature, 489, 447–451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2100. Burton NO, Burkhart KB and Kennedy S, 2011. Nuclear RNAi maintains heritable gene silencing in Caenorhabditis elegans. Proc Natl Acad Sci U S A, 108, 19683–19688. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2101. Campbell AC and Updike DL, 2015. CSR‐1 and P granules suppress sperm‐specific transcription in the C. elegans germline. Development, 142, 1745–1755. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2102. Cecere G, Hoersch S, O'Keeffe S, Sachidanandam R and Grishok A, 2014. Global effects of the CSR‐1 RNA interference pathway on the transcriptional landscape. Nature Structural & Molecular Biology, 21, 358–U394. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2103. Chatterjee S and Grosshans H, 2009. Active turnover modulates mature microRNA activity in Caenorhabditis elegans. Nature, 461, 546–U120. [DOI] [PubMed] [Google Scholar]
  2104. Chiliveri SC and Deshmukh MV, 2014. Structure of RDE‐4 dsRBDs and mutational studies provide insights into dsRNA recognition in the Caenorhabditis elegans RNAi pathway. Biochemical Journal, 458, 119–130. [DOI] [PubMed] [Google Scholar]
  2105. Chu YD, Wang WC, Chen SAA, Hsu YT, Yeh MW, Slack FJ and Chan SP, 2014. RACK‐1 regulates let‐7 microRNA expression and terminal cell differentiation in Caenorhabditis elegans. Cell Cycle, 13, 1995–2009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2106. Claycomb JM, Batista PJ, Pang KM, Gu WF, Vasale JJ, van Wolfswinkel JC, Chaves DA, Shirayama M, Mitani S, Ketting RF, Conte D and Mello CC, 2009. The Argonaute CSR‐1 and Its 22G‐RNA Cofactors Are Required for Holocentric Chromosome Segregation. Cell, 139, 123–134. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2107. Conine CC, Batista PJ, Gu WF, Claycomb JM, Chaves DA, Shirayama M and Mello CC, 2010. Argonautes ALG‐3 and ALG‐4 are required for spermatogenesis‐specific 26G‐RNAs and thermotolerant sperm in Caenorhabditis elegans. Proc Natl Acad Sci U S A, 107, 3588–3593. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2108. Conine CC, Moresco JJ, Gu W, Shirayama M, Conte D Jr, Yates JR III and Mello CC, 2013. Argonautes Promote Male Fertility and Provide a Paternal Memory of Germline Gene Expression in C. elegans. Cell, 155, 1532–1544. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2109. Correa RL, Steiner FA, Berezikov E and Ketting RF, 2010. MicroRNA‐Directed siRNA Biogenesis in Caenorhabditis elegans. Plos Genetics, 6, e1000903–e1000903. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2110. Dalzell JJ, McVeigh P, Warnock ND, Mitreva M, Bird DM, Abad P, Fleming CC, Day TA, Mousley A, Marks NJ and Maule AG, 2011. RNAi Effector Diversity in Nematodes. Plos Neglected Tropical Diseases, 5, e1176–e1176. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2111. Denli AM, Tops BBJ, Plasterk RHA, Ketting RF and Hannon GJ, 2004. Processing of primary microRNAs by the Microprocessor complex. Nature, 432, 231–235. [DOI] [PubMed] [Google Scholar]
  2112. Ding L, Spencer A, Morita K and Han M, 2005. The developmental timing regulator AIN‐1 interacts with miRISCs and may target the argonaute protein ALG‐1 to cytoplasmic P bodies in C. elegans. Molecular Cell, 19, 437–447. [DOI] [PubMed] [Google Scholar]
  2113. Ding XC and Grosshans H, 2009. Repression of C‐elegans microRNA targets at the initiation level of translation requires GW182 proteins. Embo J, 28, 213–222. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2114. Drake M, Furuta T, Suen KM, Gonzalez G, Liu B, Kalia A, Ladbury JE, Fire AZ, Skeath JB and Arur S, 2014. A Requirement for ERK‐Dependent Dicer Phosphorylation in Coordinating Oocyte‐to‐Embryo Transition in C. elegans. Developmental Cell, 31, 614–628. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2115. Duchaine TF, Wohlschlegel JA, Kennedy S, Bei YX, Conte D, Pang KM, Brownell DR, Harding S, Mitani S, Ruvkun G, Yates JR and Mello CC, 2006. Functional proteomics reveals the biochemical niche of C‐elegans DCR‐1 in multiple small‐RNA‐mediated pathways. Cell, 124, 343–354. [DOI] [PubMed] [Google Scholar]
  2116. Etheridge T, Nemoto K, Hashizume T, Mori C, Sugimoto T, Suzuki H, Fukui K, Yamazaki T, Higashibata A, Szewczyk NJ and Higashitani A, 2011. The Effectiveness of RNAi in Caenorhabditis elegans Is Maintained during Spaceflight. Plos One, 6, e20459–e20459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2117. Feinberg EH and Hunter CP, 2003. Transport of dsRNA into cells by the transmembrane protein SID‐1. Science, 301, 1545–1547. [DOI] [PubMed] [Google Scholar]
  2118. Felix MA, Ashe A, Piffaretti J, Wu G, Nuez I, Belicard T, Jiang Y, Zhao G, Franz CJ, Goldstein LD, Sanroman M, Miska EA and Wang D, 2011. Natural and experimental infection of Caenorhabditis nematodes by novel viruses related to nodaviruses. Plos Biology, 9, e1000586. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2119. Fischer SEJ, Montgomery TA, Zhang C, Fahlgren N, Breen PC, Hwang A, Sullivan CM, Carrington JC and Ruvkun G, 2011. The ERI‐6/7 Helicase Acts at the First Stage of an siRNA Amplification Pathway That Targets Recent Gene Duplications. Plos Genetics, 7, e1002369–e1002369. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2120. Fischer SEJ, Pan Q, Breen PC, Qi Y, Shi Z, Zhang C and Ruvkun G, 2013. Multiple small RNA pathways regulate the silencing of repeated and foreign genes in C. elegans. Genes & Development, 27, 2678–2695. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2121. Fitzgerald ME, Vela A and Pyle AM, 2014. Dicer‐related helicase 3 forms an obligate dimer for recognizing 22G‐RNA. Nucleic Acids Research, 42, 3919–3930. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2122. Frezal L and Felix MA, 2015. C. elegans outside the Petri dish. eLife, 4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2123. Gao ZQ, Wang M, Blair D, Zheng YD and Dou YX, 2014. Phylogenetic Analysis of the Endoribonuclease Dicer Family. Plos One, 9, e95350–e95350. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2124. Ge X, Zhao X, Nakagawa A, Gong XQ, Skeen‐Gaar RR, Shi Y, Gong HP, Wang XQ and Xue D, 2014. A novel mechanism underlies caspase‐dependent conversion of the dicer ribonuclease into a deoxyribonuclease during apoptosis. Cell Research, 24, 218–232. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2125. Gent JI, Schvarzstein M, Villeneuve AM, Gu SG, Jantsch V, Fire AZ and Baudrimont A, 2009. A Caenorhabditis elegans RNA‐Directed RNA Polymerase in Sperm Development and Endogenous RNA Interference. Genetics, 183, 1297–1314. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2126. Gent JI, Lamm AT, Pavelec DM, Maniar JM, Parameswaran P, Tao L, Kennedy S and Fire AZ, 2010. Distinct Phases of siRNA Synthesis in an Endogenous RNAi Pathway in C. elegans Soma. Molecular Cell, 37, 679–689. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2127. Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A, Ruvkun G and Mello CC, 2001. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C‐elegans developmental timing. Cell, 106, 23–34. [DOI] [PubMed] [Google Scholar]
  2128. Gu WF, Shirayama M, Conte D, Vasale J, Batista PJ, Claycomb JM, Moresco JJ, Youngman EM, Keys J, Stoltz MJ, Chen CCG, Chaves DA, Duan SH, Kasschau KD, Fahlgren N, Yates JR, Mitani S, Carrington JC and Mello CC, 2009. Distinct Argonaute‐Mediated 22G‐RNA Pathways Direct Genome Surveillance in the C. elegans Germline. Molecular Cell, 36, 231–244. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2129. Guo XY, Zhang R, Wang J, Ding SW and Lu R, 2013a. Homologous RIG‐I‐like helicase proteins direct RNAi‐mediated antiviral immunity in C. elegans by distinct mechanisms. Proc Natl Acad Sci U S A, 110, 16085–16090. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2130. Guo XY, Zhang R, Wang J and Lu R, 2013b. Antiviral RNA Silencing Initiated in the Absence of RDE‐4, a Double‐Stranded RNA Binding Protein, in Caenorhabditis elegans. Journal of Virology, 87, 10721–10729. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2131. Habig JW, Aruscavage PJ and Bass BL, 2008. In C. elegans, High Levels of dsRNA Allow RNAi in the Absence of RDE‐4. Plos One, 3, e4052–e4052. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2132. Han T, Manoharan AP, Harkins TT, Bouffard P, Fitzpatrick C, Chu DS, Thierry‐Mieg D, Thierry‐Mieg J and Kim JK, 2009. 26G endo‐siRNAs regulate spermatogenic and zygotic gene expression in Caenorhabditis elegans. Proc Natl Acad Sci U S A, 106, 18674–18679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2133. Han W, Sundaram P, Kenjale H, Grantham J and Timmons L, 2008. The Caenorhabditis elegans rsd‐2 and rsd‐6 genes are required for chromosome functions during exposure to unfavorable environments. Genetics, 178, 1875–1893. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2134. Hellwig S and Bass BL, 2008. A starvation‐induced noncoding RNA modulates expression of Dicer‐regulated genes. Proc Natl Acad Sci U S A, 105, 12897–12902. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2135. Hinas A, Wright AJ and Hunter CP, 2012. SID‐5 Is an Endosome‐Associated Protein Required for Efficient Systemic RNAi in C. elegans. Current Biology, 22, 1938–1943. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2136. Hundley HA, Krauchuk AA and Bass BL, 2008. C‐elegans and H‐sapiens mRNAs with edited 3 ‘ UTRs are present on polysomes. Rna, 14, 2050–2060. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2137. Iatsenko I, Sinha A, Rodelsperger C and Sommer RJ, 2013. New Role for DCR‐1/Dicer in Caenorhabditis elegans Innate Immunity against the Highly Virulent Bacterium Bacillus thuringiensis DB27. Infection and Immunity, 81, 3942–3957. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2138. Jannot G, Boisvert MEL, Banville IH and Simard MJ, 2008. Two molecular features contribute to the Argonaute specificity for the microRNA and RNAi pathways in C‐elegans. Rna, 14, 829–835. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2139. Jaskiewicz L and Filipowicz W, 2008. Role of Dicer in posttranscriptional RNA silencing. Curr Top Microbiol Immunol, 320, 77–97. [DOI] [PubMed] [Google Scholar]
  2140. Jose AM, Garcia GA and Hunter CP, 2011. Two classes of silencing RNAs move between Caenorhabditis elegans tissues. Nature Structural & Molecular Biology, 18, 1183–U1111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2141. Jose AM, Kim YA, Leal‐Ekman S and Hunter CP, 2012. Conserved tyrosine kinase promotes the import of silencing RNA into Caenorhabditis elegans cells. Proc Natl Acad Sci U S A, 109, 14520–14525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2142. Kennedy S, Wang D and Ruvkun G, 2004. A conserved siRNA‐degrading RNase negatively regulates RNA interference in C. elegans. Nature, 427, 645–649. [DOI] [PubMed] [Google Scholar]
  2143. Ketting RF, Fischer SEJ, Bernstein E, Sijen T, Hannon GJ and Plasterk RHA, 2001. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C‐elegans. Genes & Development, 15, 2654–2659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2144. Knight SW and Bass BL, 2001. A role for the RNase III enzyme DCR‐1 in RNA interference and germ line development in Caenorhabditis elegans. Science, 293, 2269–2271. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2145. Kuzuoglu‐Oeztuerk D, Huntzinger E, Schmidt S and Izaurralde E, 2012. The Caenorhabditis elegans GW182 protein AIN‐1 interacts with PAB‐1 and subunits of the PAN2‐PAN3 and CCR4‐NOT deadenylase complexes. Nucleic Acids Research, 40, 5651–5665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2146. Lambert NJ, Gu SG and Zahler AM, 2011. The conformation of microRNA seed regions in native microRNPs is prearranged for presentation to mRNA targets. Nucleic Acids Research, 39, 4827–4835. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2147. Lee RC, Feinbaum RL and Ambros V, 1993. The C. elegans heterochronic gene lin‐4 encodes small RNAs with antisense complementarity to lin‐14. Cell, 75, 843–854. [DOI] [PubMed] [Google Scholar]
  2148. Lee RC, Hammell CM and Ambros V, 2006. Interacting endogenous and exogenous RNAi pathways in Caenorhabditis elegans. Rna, 12, 589–597. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2149. Lee YS, Nakahara K, Pham JW, Kim K, He Z, Sontheimer EJ and Carthew RW, 2004. Distinct roles for Drosophila Dicer‐1 and Dicer‐2 in the siRNA/miRNA silencing pathways. Cell, 117, 69–81. [DOI] [PubMed] [Google Scholar]
  2150. Lehrbach NJ, Armisen J, Lightfoot HL, Murfitt KJ, Bugaut A, Balasubramanian S and Miska EA, 2009. LIN‐28 and the poly(U) polymerase PUP‐2 regulate let‐7 microRNA processing in Caenorhabditis elegans. Nature Structural & Molecular Biology, 16, 1016–U1027. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2151. Lu R, Maduro M, Li F, Li HW, Broitman‐Maduro G, Li WX and Ding SW, 2005. Animal virus replication and RNAi‐mediated antiviral silencing in Caenorhabditis elegans. Nature, 436, 1040–1043. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2152. Mao H, Zhu CM, Zong DD, Weng CC, Yang XW, Huang H, Liu D, Feng XZ and Guang SH, 2015. The Nrde Pathway Mediates Small‐RNA‐Directed Histone H3 Lysine 27 Trimethylation in Caenorhabditis elegans. Current Biology, 25, 2398–2403. [DOI] [PubMed] [Google Scholar]
  2153. Massirer KB and Pasquinelli AE, 2013. MicroRNAs that interfere with RNAi. Worm, 2, e21835–e21835. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2154. Matranga C and Pyle AM, 2010. Double‐stranded RNA‐dependent ATPase DRH‐3 INSIGHT INTO ITS ROLE IN RNA SILENCING IN CAENORHABDITIS ELEGANS. Journal of Biological Chemistry, 285, 25363–25371. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2155. McEwan DL, Weisman AS and Huntert CP, 2012. Uptake of Extracellular Double‐Stranded RNA by SID‐2. Molecular Cell, 47, 746–754. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2156. Mon H, Kobayashi I, Ohkubo S, Tomita S, Lee JM, Sezutsu H, Tamura T and Kusakabe T, 2012. Effective RNA interference in cultured silkworm cells mediated by overexpression of Caenorhabditis elegans SID‐1. Rna Biology, 9, 40–46. [DOI] [PubMed] [Google Scholar]
  2157. Mon H, Li Z, Kobayashi I, Tomita S, Lee J, Sezutsu H, Tamura T and Kusakabe T, 2013. Soaking RNAi in Bombyx mori BmN4‐SID1 cells arrests cell cycle progression. Journal of Insect Science, 13, 155–155. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2158. Morita K and Han M, 2006. Multiple mechanisms are involved in regulating the expression of the developmental timing regulator lin‐28 in Caenorhabditis elegans. Embo J, 25, 5794–5804. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2159. Morse DP and Bass BL, 1999. Long RNA hairpins that contain inosine are present in Caenorhabditis elegans poly(A)(+) RNA. Proc Natl Acad Sci U S A, 96, 6048–6053. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2160. Morse DP, Aruscavage PJ and Bass BL, 2002. RNA hairpins in noncoding regions of human brain and Caenorhabditis elegans mRNA are edited by adenosine deaminases that act on RNA. Proc Natl Acad Sci U S A, 99, 7906–7911. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2161. Nakagawa A, Shi Y, Kage‐Nakadai E, Mitani S and Xue D, 2010. Caspase‐Dependent Conversion of Dicer Ribonuclease into a Death‐Promoting Deoxyribonuclease. Science, 328, 327–334. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2162. Nakamura M, Ando R, Nakazawa T, Yudazono T, Tsutsumi N, Hatanaka N, Ohgake T, Hanaoka F and Eki T, 2007. Dicer‐related drh‐3 gene functions in germ‐line development by maintenance of chromosomal integrity in Caenorhabditis elegans. Genes to Cells, 12, 997–1010. [DOI] [PubMed] [Google Scholar]
  2163. Newman MA, Thomson JM and Hammond SM, 2008. Lin‐28 interaction with the Let‐7 precursor loop mediates regulated microRNA processing. Rna, 14, 1539–1549. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2164. Okamura K, Ishizuka A, Siomi H and Siomi MC, 2004. Distinct roles for Argonaute proteins in small RNA‐directed RNA cleavage pathways. Genes Dev, 18, 1655–1666. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2165. Ouchi Y, Yamamoto J and Iwamoto T, 2014. The Heterochronic Genes lin‐28a and lin‐28b Play an Essential and Evolutionarily Conserved Role in Early Zebrafish Development. Plos One, 9, e88086–e88086. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2166. Pak J and Fire A, 2007. Distinct populations of primary and secondary effectors during RNAi in C‐elegans. Science, 315, 241–244. [DOI] [PubMed] [Google Scholar]
  2167. Palladino MJ, Keegan LP, O'Connell MA and Reenan RA, 2000. A‐to‐I pre‐mRNA editing in Drosophila is primarily involved in adult nervous system function and integrity. Cell, 102, 437–449. [DOI] [PubMed] [Google Scholar]
  2168. Parker GS, Eckert DM and Bass BL, 2006. RDE‐4 preferentially binds long dsRNA and its dimerization is necessary for cleavage of dsRNA to siRNA. Rna, 12, 807–818. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2169. Parker GS, Maity TS and Bass BL, 2008. dsRNA Binding Properties of RDE‐4 and TRBP Reflect Their Distinct Roles in RNAi. Journal of Molecular Biology, 384, 967–979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2170. Parrish S and Fire A, 2001. Distinct roles for RDE‐1 and RDE‐4 during RNA interference in Caenorhabditis elegans. Rna, 7, 1397–1402. [PMC free article] [PubMed] [Google Scholar]
  2171. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Muller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E and Ruvkun G, 2000. Conservation of the sequence and temporal expression of let‐7 heterochronic regulatory RNA. Nature, 408, 86–89. [DOI] [PubMed] [Google Scholar]
  2172. Pavelec DM, Lachowiec J, Duchaine TF, Smith HE and Kennedy S, 2009. Requirement for the ERI/DICER Complex in Endogenous RNA Interference and Sperm Development in Caenorhabditis elegans. Genetics, 183, 1283–1295. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2173. Racen EL, McEwen TJ and Bennett KL, 2008. The intriguing interaction of Dicer (DCR‐1) with GLH‐1, a P granule component in Caenorhabditis elegans. Developmental Biology, 319, 547–547. [Google Scholar]
  2174. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR and Ruvkun G, 2000. The 21‐nucleotide let‐7 RNA regulates developmental timing in Caenorhabditis elegans. Nature, 403, 901–906. [DOI] [PubMed] [Google Scholar]
  2175. Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H and Bartel DP, 2006. Large‐scale sequencing reveals 21U‐RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell, 127, 1193–1207. [DOI] [PubMed] [Google Scholar]
  2176. Ruby JG, Jan CH and Bartel DP, 2007. Intronic microRNA precursors that bypass Drosha processing. Nature, 448, 83–86. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2177. Rybak‐Wolf A, Jens M, Murakawa Y, Herzog M, Landthaler M and Rajewsky N, 2014. A Variety of Dicer Substrates in Human and C‐elegans. Cell, 159, 1153–1167. [DOI] [PubMed] [Google Scholar]
  2178. Sarkies P, Ashe A, Le Pen J, McKie MA and Miska EA, 2013. Competition between virus‐derived and endogenous small RNAs regulates gene expression in Caenorhabditis elegans. Genome Research, 23, 1258–1270. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2179. Sawh AN and Duchaine TF, 2013. A Truncated Form of Dicer Tilts the Balance of RNA Interference Pathways. Cell Reports, 4, 454–463. [DOI] [PubMed] [Google Scholar]
  2180. Schott DH, Cureton DK, Whelan SP and Hunter CP, 2005. An antiviral role for the RNA interference machinery in Caenorhabditis elegans. Proc Natl Acad Sci U S A, 102, 18420–18424. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2181. Seth M, Shirayama M, Gu WF, Ishidate T, Conte D and Mello CC, 2013. The C. elegans CSR‐1 Argonaute Pathway Counteracts Epigenetic Silencing to Promote Germline Gene Expression. Developmental Cell, 27, 656–663. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2182. Shih JD, Fitzgerald MC, Sutherlin M and Hunter CP, 2009. The SID‐1 double‐stranded RNA transporter is not selective for dsRNA length. Rna, 15, 384–390. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2183. Shih JD and Hunter CP, 2011. SID‐1 is a dsRNA‐selective dsRNA‐gated channel. Rna, 17, 1057–1065. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2184. Shirayama M, Stanney W, Gu WF, Seth M and Mello CC, 2014. The Vasa Homolog RDE‐12 Engages Target mRNA and Multiple Argonaute Proteins to Promote RNAi in C. elegans. Current Biology, 24, 845–851. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2185. Sijen T, Fleenor J, Simmer F, Thijssen KL, Parrish S, Timmons L, Plasterk RHA and Fire A, 2001. On the role of RNA amplification in dsRNA‐triggered gene silencing. Cell, 107, 465–476. [DOI] [PubMed] [Google Scholar]
  2186. Sijen T, Steiner FA, Thijssen KL and Plasterk RHA, 2007. Secondary siRNAs result from unprimed RNA synthesis and form a distinct class. Science, 315, 244–247. [DOI] [PubMed] [Google Scholar]
  2187. Simmer F, Tijsterman M, Parrish S, Koushika SP, Nonet ML, Fire A, Ahringer J and Plasterk RHA, 2002. Loss of the putative RNA‐directed RNA polymerase RRF‐3 makes C. elegans hypersensitive to RNAi. Current Biology, 12, 1317–1319. [DOI] [PubMed] [Google Scholar]
  2188. Smardon A, Spoerke JM, Stacey SC, Klein ME, Mackin N and Maine EM, 2000. EGO‐1 is related to RNA‐directed RNA polymerase and functions in germ‐line development and RNA interference in C‐elegans. Current Biology, 10, 169–178. [DOI] [PubMed] [Google Scholar]
  2189. Stefani G, Chen XW, Zhao HY and Slack FJ, 2015. A novel mechanism of LIN‐28 regulation of let‐7 microRNA expression revealed by in vivo HITS‐CLIP in C. elegans. Rna, 21, 985–996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2190. Steiner FA, Hoogstrate SW, Okihara KL, Thijssen KL, Ketting RF, Plasterk RHA and Sijen T, 2007. Structural features of small RNA precursors determine Argonaute loading in Caenorhabditis elegans. Nature Structural & Molecular Biology, 14, 927–933. [DOI] [PubMed] [Google Scholar]
  2191. Steiner FA, Okihara KL, Hoogstrate SW, Sijen T and Ketting RF, 2009. RDE‐1 slicer activity is required only for passenger‐strand cleavage during RNAi in Caenorhabditis elegans. Nature Structural & Molecular Biology, 16, 207–211. [DOI] [PubMed] [Google Scholar]
  2192. Tabara H, Grishok A and Mello CC, 1998. RNAi in C. elegans: soaking in the genome sequence. Science, 282, 430–431. [DOI] [PubMed] [Google Scholar]
  2193. Tabara H, Sarkissian M, Kelly WG, Fleenor J, Grishok A, Timmons L, Fire A and Mello CC, 1999. The rde‐1 gene, RNA interference, and transposon silencing in C‐elegans. Cell, 99, 123–132. [DOI] [PubMed] [Google Scholar]
  2194. Tabara H, Yigit E, Siomi H and Mello CC, 2002. The dsRNA binding protein RDE‐4 interacts with RDE‐1, DCR‐1, and a DExX‐box helicase to direct RNAi in C‐elegans. Cell, 109, 861–871. [DOI] [PubMed] [Google Scholar]
  2195. Thivierge C, Makil N, Flamand M, Vasale JJ, Mello CC, Wohlschlegel J, Conte D and Duchaine TF, 2012. Tudor domain ERI‐5 tethers an RNA‐dependent RNA polymerase to DCR‐1 to potentiate endo‐RNAi. Nature Structural & Molecular Biology, 19, 90–U114. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2196. Tijsterman M, Okihara KL, Thijssen K and Plasterk RHA, 2002. PPW‐1, a PAZ/PIWI protein required for efficient germline RNAi, is defective in a natural isolate of C‐elegans. Current Biology, 12, 1535–1540. [DOI] [PubMed] [Google Scholar]
  2197. Tonkin LA, Saccomanno L, Morse DP, Brodigan T, Krause M and Bass BL, 2002. RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans. Embo J, 21, 6025–6035. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2198. Tonkin LA and Bass BL, 2003. Mutations in RNAi rescue aberrant chemotaxis of ADAR mutants. Science, 302, 1725. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2199. Tops BBJ, Plasterk RHA and Ketting RF, 2006. The Caenorhabditis elegans argonautes ALG‐1 and ALG‐2: Almost identical yet different. Cold Spring Harbor Symposia on Quantitative Biology, 71, 189–194. [DOI] [PubMed] [Google Scholar]
  2200. Tsai HY, Chen CCG, Conte D, Moresco JJ, Chaves DA, Mitani S, Yates JR, Tsai MD and Mello CC, 2015. A Ribonuclease Coordinates siRNA Amplification and mRNA Cleavage during RNAi. Cell, 160, 407–419. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2201. Tu SK, Wu MZ, Wang J, Cutter AD, Weng ZP and Claycomb JM, 2015. Comparative functional characterization of the CSR‐1 22G‐RNA pathway in Caenorhabditis nematodes. Nucleic Acids Research, 43, 208–224. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2202. Vadla B, Kemper K, Alaimo J, Heine C and Moss EG, 2012. lin‐28 Controls the Succession of Cell Fate Choices via Two Distinct Activities. Plos Genetics, 8, e1002588–e1002588. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2203. Van Wynsberghe PM, Kai ZS, Massirer KB, Burton VH, Yeo GW and Pasquinelli AE, 2011. LIN‐28 co‐transcriptionally binds primary let‐7 to regulate miRNA maturation in Caenorhabditis elegans. Nature Structural & Molecular Biology, 18, 302–U386. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2204. Vasale JJ, Gu WF, Thivierge C, Batista PJ, Claycomb JM, Youngman EM, Duchaine TF, Mello CC and Conte D, 2010. Sequential rounds of RNA‐dependent RNA transcription drive endogenous small‐RNA biogenesis in the ERGO‐1/Argonaute pathway. Proc Natl Acad Sci U S A, 107, 3582–3587. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2205. Vasquez‐Rifo A, Jannot G, Armisen J, Labouesse M, Irfan S, Bukhari A, Rondeau EL, Miska EA and Simard MJ, 2012. Developmental Characterization of the MicroRNA‐Specific C. elegans Argonautes alg‐1 and alg‐2. Plos One, 7, e33750–e33750. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2206. Vasquez‐Rifo A, Bosse GD, Rondeau EL, Jannot G, Dallaire A and Simard MJ, 2013. A New Role for the GARP Complex in MicroRNA‐Mediated Gene Regulation. Plos Genetics, 9, e1003961–e1003961. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2207. Warf MB, Johnson WE and Bass BL, 2011. Improved annotation of C. elegans microRNAs by deep sequencing reveals structures associated with processing by Drosha and Dicer. Rna, 17, 563–577. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2208. Warf MB, Shepherd BA, Johnson WE and Bass BL, 2012. Effects of ADARs on small RNA processing pathways in C. elegans. Genome Research, 22, 1488–1498. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2209. Wedeles CJ, Wu MZ and Claycomb JM, 2013a. Protection of Germline Gene Expression by the C. elegans Argonaute CSR‐1. Developmental Cell, 27, 664–671. [DOI] [PubMed] [Google Scholar]
  2210. Wedeles CJ, Wu MZ and Claycomb JM, 2013b. A multitasking Argonaute: exploring the many facets of C‐elegans CSR‐1. Chromosome Research, 21, 573–586. [DOI] [PubMed] [Google Scholar]
  2211. Welker NC, Habig JW and Bass BL, 2007. Genes misregulated in C. elegans deficient in Dicer, RDE‐4, or RDE‐1 are enriched for innate immunity genes. Rna, 13, 1090–1102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2212. Welker NC, Pavelec DM, Nix DA, Duchaine TF, Kennedy S and Bass BL, 2010. Dicer's helicase domain is required for accumulation of some, but not all, C‐elegans endogenous siRNAs. Rna, 16, 893–903. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2213. Welker NC, Maity TS, Ye XC, Aruscavage PJ, Krauchuk AA, Liu QH and Bass BL, 2011. Dicer's Helicase Domain Discriminates dsRNA Termini to Promote an Altered Reaction Mode. Molecular Cell, 41, 589–599. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2214. Whipple JM, Youssef OA, Aruscavage PJ, Nix DA, Hong CJ, Johnson WE and Bass BL, 2015. Genome‐wide profiling of the C. elegans dsRNAome. Rna, 21, 786–800. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2215. Wilkins C, Dishongh R, Moore SC, Whitt MA, Chow M and Machaca K, 2005. RNA interference is an antiviral defence mechanism in Caenorhabditis elegans. Nature, 436, 1044–1047. [DOI] [PubMed] [Google Scholar]
  2216. Winston WM, Molodowitch C and Hunter CP, 2002. Systemic RNAi in C‐elegans requires the putative transmembrane protein SID‐1. Science, 295, 2456–2459. [DOI] [PubMed] [Google Scholar]
  2217. Winston WM, Sutherlin M, Wright AJ, Feinberg EH and Hunter CP, 2007. Caenorhabditis elegans SID‐2 is required for environmental RNA interference. Proc Natl Acad Sci U S A, 104, 10565–10570. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2218. Wu D, Lamm AT and Fire AZ, 2011. Competition between ADAR and RNAi pathways for an extensive class of RNA targets. Nature Structural & Molecular Biology, 18, 1094–U1024. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2219. Xu J, Mon H, Kusakabe T, Li ZQ, Zhu L, Iiyama K, Masuda A, Mitsudome T and Lee JM, 2013a. Establishment of a soaking RNA interference and Bombyx mori nucleopolyhedrovirus (BmNPV)‐hypersensitive cell line using Bme21 cell. Applied Microbiology and Biotechnology, 97, 10435–10444. [DOI] [PubMed] [Google Scholar]
  2220. Xu J, Nagata Y, Mon H, Li ZQ, Zhu L, Iiyama K, Kusakabe T and Lee JM, 2013b. Soaking RNAi‐mediated modification of Sf9 cells for baculovirus expression system by ectopic expression of Caenorhabditis elegans SID‐1. Applied Microbiology and Biotechnology, 97, 5921–5931. [DOI] [PubMed] [Google Scholar]
  2221. Yang YZ, Jittayasothorn Y, Chronis D, Wang XH, Cousins P and Zhong GY, 2013. Molecular Characteristics and Efficacy of 16D10 siRNAs in Inhibiting Root‐Knot Nematode Infection in Transgenic Grape Hairy Roots. Plos One, 8, e69463–e69463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2222. Yigit E, Batista PJ, Bei YX, Pang KM, Chen CCG, Tolia NH, Joshua‐Tor L, Mitani S, Simard MJ and Mello CC, 2006. Analysis of the C‐elegans argonaute family reveals that distinct argonautes act sequentially during RNAi. Cell, 127, 747–757. [DOI] [PubMed] [Google Scholar]
  2223. Zhang C, Montgomery TA, Gabel HW, Fischer SEJ, Phillips CM, Fahlgren N, Sullivan CM, Carrington JC and Ruvkun G, 2011. mut‐16 and other mutator class genes modulate 22G and 26G siRNA pathways in Caenorhabditis elegans. Proc Natl Acad Sci U S A, 108, 1201–1208. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2224. Zhang C, Montgomery TA, Fischer SEJ, Garcia S, Riedel CG, Fahlgren N, Sullivan CM, Carrington JC and Ruvkun G, 2012. The Caenorhabditis elegans RDE‐10/RDE‐11 Complex Regulates RNAi by Promoting Secondary siRNA Amplification. Current Biology, 22, 881–890. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2225. Zhang L, Ding L, Cheung TH, Dong MQ, Chen J, Sewell AK, Liu X, Yates JR and Han M, 2007. Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN‐1 and AIN‐2. Molecular Cell, 28, 598–613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2226. Zhang PP and Zhang H, 2013. Autophagy modulates miRNA‐mediated gene silencing and selectively degrades AIN‐1/GW182 in C‐elegans. EMBO Rep, 14, 568–576. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2227. Zhuang JJ and Hunter CP, 2012. The Influence of Competition Among C. elegans Small RNA Pathways on Development. Genes, 3, 671–685. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2228. Zinovyeva AY, Bouasker S, Simard MJ, Hammell CM and Ambros V, 2014. Mutations in Conserved Residues of the C. elegans microRNA Argonaute ALG‐1 Identify Separable Functions in ALG‐1 miRISC Loading and Target Repression. Plos Genetics, 10, e1004286–e1004286. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2229. Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE and Yeo GW, 2010. Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nature Structural & Molecular Biology, 17, 173–U176. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2230. Abe M, Yoshikawa T, Nosaka M, Sakakibara H, Sato Y, Nagato Y and Itoh J, 2010. WAVY LEAF1, an Ortholog of Arabidopsis HEN1, Regulates Shoot Development by Maintaining MicroRNA and Trans‐Acting Small Interfering RNA Accumulation in Rice. Plant Physiology, 154, 1335–1346. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2231. Agorio A and Vera P, 2007. ARGONAUTE4 is required for resistance to Pseudomonas syringae in Arabidopsis . Plant Cell, 19, 3778–3790. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2232. Akbergenov R, Si‐Ammour A, Blevins T, Amin I, Kutter C, Vanderschuren H, Zhang P, Gruissem W, Meins F, Hohn T and Pooggin MM, 2006. Molecular characterization of geminivirus‐derived small RNAs in different plant species. Nucleic Acids Research, 34, 462–471. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2233. Ali E, Kobayashi K, Yamaoka N, Ishikawa M and Nishiguchi M, 2013. Graft transmission of RNA silencing to non‐transgenic scions for conferring virus resistance in tobacco. Plos One, 8, e63257. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2234. Allen E, Xie Z, Gustafson AM, Sung GH, Spatafora JW and Carrington JC, 2004. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana . Nature Genetics, 36, 1282–1290. [DOI] [PubMed] [Google Scholar]
  2235. Aregger M, Borah BK, Seguin J, Rajeswaran R, Gubaeva EG, Zvereva AS, Windels D, Vazquez F, Blevins T, Farinelli L and Pooggin MM, 2012. Primary and Secondary siRNAs in Geminivirus‐induced Gene Silencing. Plos Pathogens, 8, e1002941–e1002941. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2236. Aufsatz W, Mette MF, van der Winden J, Matzke AJ and Matzke M, 2002a. RNA‐directed DNA methylation in Arabidopsis . Proc Natl Acad Sci U S A, 99(Suppl 4), 16499–16506. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2237. Aufsatz W, Mette MF, van der Winden J, Matzke M and Matzke AJ, 2002b. HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double‐stranded RNA. EMBO J, 21, 6832–6841. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2238. Aufsatz W, Mette MF, Matzke AJ and Matzke M, 2004. The role of MET1 in RNA‐directed de novo and maintenance methylation of CG dinucleotides. Plant Molecular Biology, 54, 793–804. [DOI] [PubMed] [Google Scholar]
  2239. Axtell MJ, Jan C, Rajagopalan R and Bartel DP, 2006. A two‐hit trigger for siRNA biogenesis in plants. Cell, 127, 565–577. [DOI] [PubMed] [Google Scholar]
  2240. Axtell MJ, Westholm JO and Lai EC, 2011. Vive la difference: biogenesis and evolution of microRNAs in plants and animals. Genome Biology, 12, 221. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2241. Axtell MJ, 2013. Classification and comparison of small RNAs from plants. Annu Rev Plant Biol, 64, 137–159. [DOI] [PubMed] [Google Scholar]
  2242. Bai M, Yang G‐S, Chen W‐T, Mao Z‐C, Kang H‐X, Chen G‐H, Yang Y‐H and Xie B‐Y, 2012. Genome‐wide identification of Dicer‐like, Argonaute and RNA‐dependent RNA polymerase gene families and their expression analyses in response to viral infection and abiotic stresses in Solanum lycopersicum. Gene, 501, 52–62. [DOI] [PubMed] [Google Scholar]
  2243. Baranauske S, Mickute M, Plotnikova A, Finke A, Venclovas C, Klimasauskas S and Vilkaitis G, 2015. Functional mapping of the plant small RNA methyltransferase: HEN1 physically interacts with HYL1 and DICER‐LIKE 1 proteins. Nucleic Acids Research, 43, 2802–2812. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2244. Bartee L, Malagnac F and Bender J, 2001. Arabidopsis cmt3 chromomethylase mutations block non‐CG methylation and silencing of an endogenous gene. Genes Dev, 15, 1753–1758. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2245. Baumberger N and Baulcombe DC, 2005. Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proc Natl Acad Sci U S A, 102, 11928–11933. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2246. Beauclair L, Yu A and Bouche N, 2010. microRNA‐directed cleavage and translational repression of the copper chaperone for superoxide dismutase mRNA in Arabidopsis . Plant Journal, 62, 454–462. [DOI] [PubMed] [Google Scholar]
  2247. Beclin C, Boutet S, Waterhouse P and Vaucheret H, 2002. A branched pathway for transgene‐induced RNA silencing in plants. Current Biology, 12, 684–688. [DOI] [PubMed] [Google Scholar]
  2248. Blevins T, Rajeswaran R, Aregger M, Borah BK, Schepetilnikov M, Baerlocher L, Farinelli L, Meins F, Hohn T and Pooggin MM, 2011. Massive production of small RNAs from a non‐coding region of Cauliflower mosaic virus in plant defense and viral counter‐defense. Nucleic Acids Research, 39, 5003–5014. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2249. Bohmert K, Camus I, Bellini C, Bouchez D, Caboche M and Benning C, 1998. AGO1 defines a novel locus of Arabidopsis controlling leaf development. EMBO J, 17, 170–180. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2250. Bologna NG, Mateos JL, Bresso EG and Palatnik JF, 2009. A loop‐to‐base processing mechanism underlies the biogenesis of plant microRNAs miR319 and miR159. EMBO J, 28, 3646–3656. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2251. Bologna NG and Voinnet O, 2014. The Diversity, Biogenesis, and Activities of Endogenous Silencing Small RNAs in Arabidopsis . Annual Review of Plant Biology, 65, 473–503. [DOI] [PubMed] [Google Scholar]
  2252. Bonnet E, Van de Peer Y and Rouze P, 2006. The small RNA world of plants. New Phytologist, 171, 451–468. [DOI] [PubMed] [Google Scholar]
  2253. Bonnet E, He Y, Billiau K and Van de Peer Y, 2010. TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics, 26, 1566–1568. [DOI] [PubMed] [Google Scholar]
  2254. Borges F and Martienssen RA, 2015. The expanding world of small RNAs in plants. Nature Reviews Molecular Cell Biology, 16, 727–741. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2255. Bouche N, Lauressergues D, Gasciolli V and Vaucheret H, 2006. An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs. EMBO J, 25, 3347–3356. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2256. Bowman JL, 2004. Class III HD‐Zip gene regulation, the golden fleece of ARGONAUTE activity? Bioessays, 26, 938–942. [DOI] [PubMed] [Google Scholar]
  2257. Boyko A and Kovalchuk I, 2010. Transgenerational response to stress in Arabidopsis thaliana . Plant Signaling and Behavior, 5, 995–998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2258. Bozorov TA, Pandey SP, Dinh ST, Kim SG, Heinrich M, Gase K and Baldwin IT, 2012. DICER‐like Proteins and Their Role in Plant‐herbivore Interactions in Nicotiana attenuata. Journal of Integrative Plant Biology, 54, 189–206. [DOI] [PubMed] [Google Scholar]
  2259. Brandt R, Xie YK, Musielak T, Graeff M, Stierhof YD, Huang H, Liu CM and Wenkel S, 2013. Control of stem cell homeostasis via interlocking microRNA and microProtein feedback loops. Mechanisms of Development, 130, 25–33. [DOI] [PubMed] [Google Scholar]
  2260. Brodersen P, Sakvarelidze‐Achard L, Bruun‐Rasmussen M, Dunoyer P, Yamamoto YY, Sieburth L and Voinnet O, 2008. Widespread translational inhibition by plant miRNAs and siRNAs. Science, 320, 1185–1190. [DOI] [PubMed] [Google Scholar]
  2261. Brosnan CA, Mitter N, Christie M, Smith NA, Waterhouse PM and Carroll BJ, 2007. Nuclear gene silencing directs reception of long‐distance mRNA silencing in Arabidopsis . Proc Natl Acad Sci U S A, 104, 14741–14746. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2262. Brosseau C and Moffett P, 2015. Functional and Genetic Analysis Identify a Role for Arabidopsis ARGONAUTE5 in Antiviral RNA Silencing. Plant Cell, 27, 1742–1754. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2263. Cao MJ, Du P, Wang XB, Yu YQ, Qiu YH, Li WX, Gal‐On A, Zhou CY, Li Y and Ding SW, 2014. Virus infection triggers widespread silencing of host genes by a distinct class of endogenous siRNAs in Arabidopsis . Proc Natl Acad Sci U S A, 111, 14613–14618. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2264. Cao X and Jacobsen SE, 2002. Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Current Biology, 12, 1138–1144. [DOI] [PubMed] [Google Scholar]
  2265. Carbonell A, Fahlgren N, Garcia‐Ruiz H, Gilbert KB, Montgomery TA, Nguyen T, Cuperus JT and Carrington JC, 2012. Functional Analysis of Three Arabidopsis ARGONAUTES Using Slicer‐Defective Mutants. Plant Cell, 24, 3613–3629. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2266. Carbonell A and Carrington JC, 2015. Antiviral roles of plant ARGONAUTES. Current Opinion in Plant Biology, 27, 111–117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2267. Chan SW, Zilberman D, Xie Z, Johansen LK, Carrington JC and Jacobsen SE, 2004. RNA silencing genes control de novo DNA methylation. Science, 303, 1336. [DOI] [PubMed] [Google Scholar]
  2268. Chellappan P, Xia J, Zhou XF, Gao S, Zhang XM, Coutino G, Vazquez F, Zhang WX and Jin HL, 2010. siRNAs from miRNA sites mediate DNA methylation of target genes. Nucleic Acids Research, 38, 6883–6894. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2269. Chen DJ, Meng YJ, Yuan CH, Bai L, Huang DL, Lv SL, Wu P, Chen LL and Chen M, 2011. Plant siRNAs from introns mediate DNA methylation of host genes. Rna, 17, 1012–1024. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2270. Chen XM, 2009. Small RNAs and Their Roles in Plant Development. In: Annual Review of Cell and Developmental Biology. 21–44. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2271. Clavel M, Pelissier T, Descombin J, Jean V, Picart C, Charbonel C, Saez‐Vasquez J, Bousquet‐Antonelli C and Deragon J‐M, 2015. Parallel action of AtDRB2 and RdDM in the control of transposable element expression. BMC plant biology, 15, 455–455. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2272. Clavel M, Pelissier T, Montavon T, Tschopp MA, Pouch‐Pelissier MN, Descombin J, Jean V, Dunoyer P, Bousquet‐Antonelli C and Deragon JM, 2016. Evolutionary history of double‐stranded RNA binding proteins in plants: identification of new cofactors involved in easiRNA biogenesis. Plant Molecular Biology, 91, 131–147. [DOI] [PubMed] [Google Scholar]
  2273. Coruh C, Cho SH, Shahid S, Liu QK, Wierzbicki A and Axtella MJ, 2015. Comprehensive Annotation of Physcomitrella patens Small RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants. Plant Cell, 27, 2148–2162. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2274. Curtin SJ, Watson JM, Smith NA, Eamens AL, Blanchard CL and Waterhouse PM, 2008. The roles of plant dsRNA‐binding proteins in RNAi‐like pathways. Febs Letters, 582, 2753–2760. [DOI] [PubMed] [Google Scholar]
  2275. Curtin SJ, Kantar MB, Yoon HW, Whaley AM, Schlueter JA and Stupar RM, 2012. Co‐expression of soybean Dicer‐like genes in response to stress and development. Functional & Integrative Genomics, 12, 671–682. [DOI] [PubMed] [Google Scholar]
  2276. Dalmay T, Hamilton A, Rudd S, Angell S and Baulcombe DC, 2000. An RNA‐dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell, 101, 543–553. [DOI] [PubMed] [Google Scholar]
  2277. Datta R and Paul S, 2015. Plant microRNAs: master regulator of gene expression mechanism. Cell Biology International, 39, 1185–1190. [DOI] [PubMed] [Google Scholar]
  2278. Daxinger L, Kanno T, Bucher E, van der Winden J, Naumann U, Matzke AJM and Matzke M, 2009. A stepwise pathway for biogenesis of 24‐nt secondary siRNAs and spreading of DNA methylation. EMBO J, 28, 48–57. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2279. Debernardi JM, Rodriguez RE, Mecchia MA and Palatnik JF, 2012. Functional specialization of the plant miR396 regulatory network through distinct microRNA‐target interactions. PLoS Genetics, 8, e1002419. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2280. Debernardi JM, Mecchia MA, Vercruyssen L, Smaczniak C, Kaufmann K, Inze D, Rodriguez RE and Palatnik JF, 2014. Post‐transcriptional control of GRF transcription factors by microRNA miR396 and GIF co‐activator affects leaf size and longevity. Plant Journal, 79, 413–426. [DOI] [PubMed] [Google Scholar]
  2281. Deleris A, Gallego‐Bartolome J, Bao JS, Kasschau KD, Carrington JC and Voinnet O, 2006. Hierarchical action and inhibition of plant Dicer‐like proteins in antiviral defense. Science, 313, 68–71. [DOI] [PubMed] [Google Scholar]
  2282. Di Serio F, Gisel A, Navarro B, Delgado S, de Alba A‐EM, Donvito G and Flores R, 2009. Deep Sequencing of the Small RNAs Derived from Two Symptomatic Variants of a Chloroplastic Viroid: Implications for Their Genesis and for Pathogenesis. Plos One, 4, e7539–e7539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2283. Diaz‐Pendon JA, Li F, Li WX and Ding SW, 2007. Suppression of antiviral silencing by cucumber mosaic virus 2b protein in Arabidopsis is associated with drastically reduced accumulation of three classes of viral small interfering RNAs. Plant Cell, 19, 2053–2063. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2284. Dolgosheina EV, Morin RD, Aksay G, Sahinalp SC, Magrini V, Mardis ER, Mattsson J and Unrau PJ, 2008. Conifers have a unique small RNA silencing signature. Rna, 14, 1508–1515. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2285. Donaire L, Barajas D, Martinez‐Garcia B, Martinez‐Priego L, Pagan I and Llave C, 2008. Structural and genetic requirements for the biogenesis of tobacco rattle virus‐derived small interfering RNAs. Journal of Virology, 82, 5167–5177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2286. Douglas RN, Wiley D, Sarkar A, Springer N, Timmermans MCP and Scanlon MJ, 2010. ragged seedling2 Encodes an ARGONAUTE7‐Like Protein Required for Mediolateral Expansion, but Not Dorsiventrality, of Maize Leaves. Plant Cell, 22, 1441–1451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2287. Dunoyer P, Himber C and Voinnet O, 2005. DICER‐LIKE 4 is required for RNA interference and produces the 21‐nucleotide small interfering RNA component of the plant cell‐to‐cell silencing signal. Nature Genetics, 37, 1356–1360. [DOI] [PubMed] [Google Scholar]
  2288. Dunoyer P, Schott G, Himber C, Meyer D, Takeda A, Carrington JC and Voinnet O, 2010. Small RNA Duplexes Function as Mobile Silencing Signals Between Plant Cells. Science, 328, 912–916. [DOI] [PubMed] [Google Scholar]
  2289. Eamens AL, Smith NA, Curtin SJ, Wang MB and Waterhouse PM, 2009. The Arabidopsis thaliana double‐stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes. Rna, 15, 2219–2235. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2290. Eamens AL, Kim KW, Curtin SJ and Waterhouse PM, 2012a. DRB2 Is Required for MicroRNA Biogenesis in Arabidopsis thaliana . Plos One, 7, e35933–e35933. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2291. Eamens AL, Wook Kim K and Waterhouse PM, 2012b. DRB2, DRB3 and DRB5 function in a non‐canonical microRNA pathway in Arabidopsis thaliana . Plant Signaling and Behavior, 7, 1224–1229. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2292. Earley KW and Poethig RS, 2011. Binding of the cyclophilin 40 ortholog SQUINT to Hsp90 protein is required for SQUINT function in Arabidopsis . Journal of Biological Chemistry, 286, 38184–38189. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2293. Eun C, Lorkovic ZJ, Naumann U, Long Q, Havecker ER, Simon SA, Meyers BC, Matzke AJM and Matzke M, 2011. AGO6 Functions in RNA‐Mediated Transcriptional Gene Silencing in Shoot and Root Meristems in Arabidopsis thaliana . Plos One, 6, e25730–e25730. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2294. Fang Y and Spector DL, 2007. Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants. Current Biology, 17, 818–823. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2295. Fatyol K, Ludman M and Burgyan J, 2016. Functional dissection of a plant Argonaute. Nucleic Acids Research, 44, 1384–1397. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2296. Finnegan EJ, Margis R and Waterhouse PM, 2003. Posttranscriptional gene silencing is not compromised in the Arabidopsis CARPEL FACTORY (DICER‐LIKE1) mutant, a homolog of dicer‐1 from Drosophila. Current Biology, 13, 236–240. [DOI] [PubMed] [Google Scholar]
  2297. Franco‐Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, Rubio‐Somoza I, Leyva A, Weigel D, Garcia JA and Paz‐Ares J, 2007. Target mimicry provides a new mechanism for regulation of microRNA activity. Nature Genetics, 39, 1033–1037. [DOI] [PubMed] [Google Scholar]
  2298. Fusaro AF, Matthew L, Smith NA, Curtin SJ, Dedic‐Hagan J, Ellacott GA, Watson JM, Wang MB, Brosnan C, Carroll BJ and Waterhouse PM, 2006. RNA interference‐inducing hairpin RNAs in plants act through the viral defence pathway. EMBO Rep, 7, 1168–1175. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2299. Galun E, 2005. RNA silencing in plants. In Vitro Cellular & Developmental Biology‐Plant, 41, 113–123. [Google Scholar]
  2300. Garcia‐Ruiz H, Takeda A, Chapman EJ, Sullivan CM, Fahlgren N, Brempelis KJ and Carrington JC, 2010. Arabidopsis RNA‐Dependent RNA Polymerases and Dicer‐Like Proteins in Antiviral Defense and Small Interfering RNA Biogenesis during Turnip Mosaic Virus Infection. Plant Cell, 22, 481–496. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2301. Garcia D, Collier SA, Byrne ME and Martienssen RA, 2006. Specification of leaf polarity in Arabidopsis via the trans‐acting siRNA pathway. Current Biology, 16, 933–938. [DOI] [PubMed] [Google Scholar]
  2302. German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R, De Paoli E, Lu C, Schroth G, Meyers BC and Green PJ, 2008. Global identification of microRNA‐target RNA pairs by parallel analysis of RNA ends. Nature Biotechnology, 26, 941–946. [DOI] [PubMed] [Google Scholar]
  2303. Giner A, Lakatos L, Garcia‐Chapa M, Lopez‐Moya JJ and Burgyan J, 2010. Viral Protein Inhibits RISC Activity by Argonaute Binding through Conserved WG/GW Motifs. Plos Pathogens, 6, 1–13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2304. Guo XY, Zhang ZL, Gerstein MB and Zheng DY, 2009. Small RNAs Originated from Pseudogenes: cis‐ or trans‐Acting? Plos Computational Biology, 5, e1000449–e1000449. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2305. Hall IM, Shankaranarayana GD, Noma K, Ayoub N, Cohen A and Grewal SI, 2002. Establishment and maintenance of a heterochromatin domain. Science, 297, 2232–2237. [DOI] [PubMed] [Google Scholar]
  2306. Havecker ER, Wallbridge LM, Hardcastle TJ, Bush MS, Kelly KA, Dunn RM, Schwach F, Doonan JH and Baulcombe DC, 2010. The Arabidopsis RNA‐Directed DNA Methylation Argonautes Functionally Diverge Based on Their Expression and Interaction with Target Loci. Plant Cell, 22, 321–334. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2307. He XJ, Hsu YF, Zhu SH, Wierzbicki AT, Pontes O, Pikaard CS, Liu HL, Wang CS, Jin HL and Zhu JK, 2009. An Effector of RNA‐Directed DNA Methylation in Arabidopsis Is an ARGONAUTE 4‐and RNA‐Binding Protein. Cell, 137, 498–508. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2308. Henderson IR, Zhang X, Lu C, Johnson L, Meyers BC, Green PJ and Jacobsen SE, 2006. Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nature Genetics, 38, 721–725. [DOI] [PubMed] [Google Scholar]
  2309. Herr AJ, Jensen MB, Dalmay T and Baulcombe DC, 2005. RNA polymerase IV directs silencing of endogenous DNA. Science, 308, 118–120. [DOI] [PubMed] [Google Scholar]
  2310. Himber C, Dunoyer P, Moissiard G, Ritzenthaler C and Voinnet O, 2003. Transitivity‐dependent and ‐independent cell‐to‐cell movement of RNA silencing. EMBO J, 22, 4523–4533. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2311. Horwich MD, Li CJ, Matranga C, Vagin V, Farley G, Wang P and Zamore PD, 2007. The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single‐stranded siRNAs in RISC. Current Biology, 17, 1265–1272. [DOI] [PubMed] [Google Scholar]
  2312. Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, Kasschau KD and Carrington JC, 2007. Genome‐wide analysis of the RNA‐DEPENDENT RNA POLYMERASE6/DICER‐LIKE4 pathway in Arabidopsis reveals dependency on miRNA‐ and tasiRNA‐directed targeting. Plant Cell, 19, 926–942. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2313. Huang SQ, Peng J, Qiu CX and Yang ZM, 2009. Heavy metal‐regulated new microRNAs from rice. J Inorg Biochem, 103, 282–287. [DOI] [PubMed] [Google Scholar]
  2314. Hunter C, Sun H and Poethig RS, 2003. The Arabidopsis heterochronic gene ZIPPY is an ARGONAUTE family member. Current Biology, 13, 1734–1739. [DOI] [PubMed] [Google Scholar]
  2315. Iki T, Yoshikawa M, Meshi T and Ishikawa M, 2012. Cyclophilin 40 facilitates HSP90‐mediated RISC assembly in plants. EMBO J, 31, 267–278. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2316. Jackson JP, Lindroth AM, Cao X and Jacobsen SE, 2002. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature, 416, 556–560. [DOI] [PubMed] [Google Scholar]
  2317. Jakubiec A, Yang SW and Chua NH, 2012. Arabidopsis DRB4 protein in antiviral defense against Turnip yellow mosaic virus infection. Plant Journal, 69, 14–25. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2318. Jaskiewicz L and Filipowicz W, 2008. Role of Dicer in posttranscriptional RNA silencing. Curr Top Microbiol Immunol, 320, 77–97. [DOI] [PubMed] [Google Scholar]
  2319. Jaubert M, Bhattacharjee S, Mello AFS, Perry KL and Moffett P, 2011. ARGONAUTE2 Mediates RNA‐Silencing Antiviral Defenses against Potato virus X in Arabidopsis . Plant Physiology, 156, 1556–1564. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2320. Jeong DH, Thatcher SR, Brown RSH, Zhai JX, Park S, Rymarquis LA, Meyers BC and Green PJ, 2013. Comprehensive Investigation of MicroRNAs Enhanced by Analysis of Sequence Variants, Expression Patterns, ARGONAUTE Loading, and Target Cleavage. Plant Physiology, 162, 1225–1245. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2321. Ji LJ, Liu XG, Yan J, Wang WM, Yumul RE, Kim YJ, Dinh TT, Liu J, Cui X, Zheng BL, Agarwal M, Liu CY, Cao XF, Tang GL and Chen XM, 2011. ARGONAUTE10 and ARGONAUTE1 Regulate the Termination of Floral Stem Cells through Two MicroRNAs in Arabidopsis . PLoS Genetics, 7, e1001358–e1001358. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2322. Jones L, Ratcliff F and Baulcombe DC, 2001. RNA‐directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance. Current Biology, 11, 747–757. [DOI] [PubMed] [Google Scholar]
  2323. Jones L, Keining T, Eamens A and Vaistij FE, 2006. Virus‐induced gene silencing of Argonaute genes in Nicotiana benthamiana demonstrates that extensive systemic silencing requires Argonaute1‐like and Argonaute4‐like genes. Plant Physiology, 141, 598–606. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2324. Jover‐Gil S, Candela H, Robles P, Aguilera V, Barrero JM, Micol JL and Ponce MR, 2012. The MicroRNA Pathway Genes AGO1, HEN1 and HYL1 Participate in Leaf Proximal‐Distal, Venation and Stomatal Patterning in Arabidopsis . Plant and Cell Physiology, 53, 1322–1333. [DOI] [PubMed] [Google Scholar]
  2325. Kanno T, Mette MF, Kreil DP, Aufsatz W, Matzke M and Matzke AJ, 2004. Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA‐directed DNA methylation. Current Biology, 14, 801–805. [DOI] [PubMed] [Google Scholar]
  2326. Kanno T, Aufsatz W, Jaligot E, Mette MF, Matzke M and Matzke AJ, 2005a. A SNF2‐like protein facilitates dynamic control of DNA methylation. EMBO Rep, 6, 649–655. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2327. Kanno T, Huettel B, Mette MF, Aufsatz W, Jaligot E, Daxinger L, Kreil DP, Matzke M and Matzke AJ, 2005b. Atypical RNA polymerase subunits required for RNA‐directed DNA methylation. Nature Genetics, 37, 761–765. [DOI] [PubMed] [Google Scholar]
  2328. Kapoor M, Arora R, Lama T, Nijhawan A, Khurana JP, Tyagi AK and Kapoor S, 2008. Genome‐wide identification, organization and phylogenetic analysis of Dicer‐like, Argonaute and RNA‐dependent RNA Polymerase gene families and their expression analysis during reproductive development and stress in rice. Bmc Genomics, 9, 451–451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2329. Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA and Carrington JC, 2007. Genome‐wide profiling and analysis of Arabidopsis siRNAs. Plos Biology, 5, e57. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2330. Kidner CA and Martienssen RA, 2004. Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature, 428, 81–84. [DOI] [PubMed] [Google Scholar]
  2331. Komiya R, Ohyanagi H, Niihama M, Watanabe T, Nakano M, Kurata N and Nonomura K, 2014. Rice germline‐specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs. Plant Journal, 78, 385–397. [DOI] [PubMed] [Google Scholar]
  2332. Kravchik M, Damodharan S, Stav R and Arazi T, 2014a. Generation and characterization of a tomato DCL3‐silencing mutant. Plant Science, 221, 81–89. [DOI] [PubMed] [Google Scholar]
  2333. Kravchik M, Sunkar R, Damodharan S, Stav R, Zohar M, Isaacson T and Arazi T, 2014b. Global and local perturbation of the tomato microRNA pathway by a trans‐activated DICER‐LIKE 1 mutant. Journal of Experimental Botany, 65, 725–739. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2334. Kumar SP, Pandya HA and Jasrai YT, 2014. A computational model for non‐conserved mature miRNAs from the rice genome. Sar and Qsar in Environmental Research, 25, 205–220. [DOI] [PubMed] [Google Scholar]
  2335. Lee WC, Lu SH, Lu MH, Yang CJ, Wu SH and Chen HM, 2015. Asymmetric bulges and mismatches determine 20‐nt microRNA formation in plants. RNA biology, 12, 1054–1066. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2336. Leibman D, Wolf D, Saharan V, Zelcer A, Arazi T, Yoel S, Gaba V and Gal‐On A, 2011. A High Level of Transgenic Viral Small RNA Is Associated with Broad Potyvirus Resistance in Cucurbits. Molecular Plant‐Microbe Interactions, 24, 1220–1238. [DOI] [PubMed] [Google Scholar]
  2337. Li CF, Pontes O, El‐Shami M, Henderson IR, Bernatavichute YV, Chan SW, Lagrange T, Pikaard CS and Jacobsen SE, 2006. An ARGONAUTE4‐containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana . Cell, 126, 93–106. [DOI] [PubMed] [Google Scholar]
  2338. Li H, Xu L, Wang H, Yuan Z, Cao XF, Yang ZN, Zhang DB, Xu YQ and Huang H, 2005a. The putative RNA‐dependent RNA polymerase RDR6 acts synergistically with ASYMMETRIC LEAVES1 and 2 to repress BREVIPEDICELLUS and MicroRNA165/166 in Arabidopsis leaf development. Plant Cell, 17, 2157–2171. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2339. Li J, Yang Z, Yu B, Liu J and Chen X, 2005b. Methylation protects miRNAs and siRNAs from a 3′‐end uridylation activity in Arabidopsis . Current Biology, 15, 1501–1507. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2340. Li J, Reichel M and Millar AA, 2014. Determinants beyond both complementarity and cleavage govern microR159 efficacy in Arabidopsis . PLoS Genetics, 10, e1004232. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2341. Li SB, Liu L, Zhuang XH, Yu Y, Liu XG, Cui X, Ji LJ, Pan ZQ, Cao XF, Mo BX, Zhang FC, Raikhel N, Jiang LW and Chen XM, 2013. MicroRNAs Inhibit the Translation of Target mRNAs on the Endoplasmic Reticulum in Arabidopsis . Cell, 153, 562–574. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2342. Liang D, White RG and Waterhouse PM, 2012. Gene silencing in Arabidopsis spreads from the root to the shoot, through a gating barrier, by template‐dependent, nonvascular, cell‐to‐cell movement. Plant Physiology, 159, 984–1000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2343. Lin D, Xiang Y, Xian Z and Li Z, 2016. Ectopic expression of SlAGO7 alters leaf pattern and inflorescence architecture and increases fruit yield in tomato. Physiologia plantarum. [DOI] [PubMed] [Google Scholar]
  2344. Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S and Jacobsen SE, 2001. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science, 292, 2077–2080. [DOI] [PubMed] [Google Scholar]
  2345. Liu B, Chen ZY, Song XW, Liu CY, Cui X, Zhao XF, Fang J, Xu WY, Zhang HY, Wang XJ, Chu CC, Deng XW, Xue YB and Cao XF, 2007. Oryza sativa dicer‐like4 reveals a key role for small interfering RNA silencing in plant development. Plant Cell, 19, 2705–2718. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2346. Liu Q, Wang F and Axtell MJ, 2014. Analysis of complementarity requirements for plant microRNA targeting using a Nicotiana benthamiana quantitative transient assay. Plant Cell, 26, 741–753. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2347. Liu QL, Yao XZ, Pi LM, Wang H, Cui XF and Huang H, 2009a. The ARGONAUTE10 gene modulates shoot apical meristem maintenance and establishment of leaf polarity by repressing miR165/166 in Arabidopsis . Plant Journal, 58, 27–40. [DOI] [PubMed] [Google Scholar]
  2348. Liu QP, Feng Y and Zhu ZJ, 2009b. Dicer‐like (DCL) proteins in plants. Functional & Integrative Genomics, 9, 277–286. [DOI] [PubMed] [Google Scholar]
  2349. Llave C, Xie Z, Kasschau KD and Carrington JC, 2002. Cleavage of Scarecrow‐like mRNA targets directed by a class of Arabidopsis miRNA. Science, 297, 2053–2056. [DOI] [PubMed] [Google Scholar]
  2350. Lobbes D, Rallapalli G, Schmidt DD, Martin C and Clarke J, 2006. SERRATE: a new player on the plant microRNA scene. EMBO Rep, 7, 1052–1058. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2351. Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC and Green PJ, 2005. Elucidation of the small RNA component of the transcriptome. Science, 309, 1567–1569. [DOI] [PubMed] [Google Scholar]
  2352. Ma XF, Nicole MC, Meteignier LV, Hong N, Wang GP and Moffett P, 2015. Different roles for RNA silencing and RNA processing components in virus recovery and virus‐induced gene silencing in plants. Journal of Experimental Botany, 66, 919–932. [DOI] [PubMed] [Google Scholar]
  2353. Malagnac F, Bartee L and Bender J, 2002. An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO J, 21, 6842–6852. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2354. Mallory AC, Reinhart BJ, Jones‐Rhoades MW, Tang G, Zamore PD, Barton MK and Bartel DP, 2004. MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5′ region. EMBO J, 23, 3356–3364. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2355. Mallory AC and Bouche N, 2008. MicroRNA‐directed regulation: to cleave or not to cleave. Trends in Plant Science, 13, 359–367. [DOI] [PubMed] [Google Scholar]
  2356. Mallory AC, Elmayan T and Vaucheret H, 2008. MicroRNA maturation and action ‐ the expanding roles of ARGONAUTEs. Current Opinion in Plant Biology, 11, 560–566. [DOI] [PubMed] [Google Scholar]
  2357. Manavella PA, Hagmann J, Ott F, Laubinger S, Franz M, Macek B and Weigel D, 2012. Fast‐Forward Genetics Identifies Plant CPL Phosphatases as Regulators of miRNA Processing Factor HYL1. Cell, 151, 859–870. [DOI] [PubMed] [Google Scholar]
  2358. Margis R, Fusaro AF, Smith NA, Curtin SJ, Watson JM, Finnegan EJ and Waterhouse PM, 2006. The evolution and diversification of Dicers in plants. Febs Letters, 580, 2442–2450. [DOI] [PubMed] [Google Scholar]
  2359. Marin‐Gonzalez E and Suarez‐Lopez P, 2012. “And yet it moves”: Cell‐to‐cell and long‐distance signaling by plant microRNAs. Plant Science, 196, 18–30. [DOI] [PubMed] [Google Scholar]
  2360. Marrocco K, Criqui MC, Zervudacki J, Schott G, Eisler H, Parnet A, Dunoyer P and Genschik P, 2012. APC/C‐Mediated Degradation of dsRNA‐Binding Protein 4 (DRB4) Involved in RNA Silencing. Plos One, 7, e35173–e35173. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2361. Matzke MA and Birchler JA, 2005. RNAi‐mediated pathways in the nucleus. Nature Reviews Genetics, 6, 24–35. [DOI] [PubMed] [Google Scholar]
  2362. Matzke MA, Kanno T and Matzke AJ, 2015. RNA‐Directed DNA Methylation: The Evolution of a Complex Epigenetic Pathway in Flowering Plants. Annu Rev Plant Biol, 66, 243–267. [DOI] [PubMed] [Google Scholar]
  2363. McCue AD, Panda K, Nuthikattu S, Choudury SG, Thomas EN and Slotkin RK, 2015. ARGONAUTE 6 bridges transposable element mRNA‐derived siRNAs to the establishment of DNA methylation. EMBO J, 34, 20–35. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2364. McHale NA and Koning RE, 2004. MicroRNA‐directed cleavage of Nicoltiana sylvestris PHAVOLUTA mRNA regulates the vascular cambium and structure of apical Meristems. Plant Cell, 16, 1730–1740. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2365. Meng Y and Shao C, 2012. Large‐scale identification of mirtrons in Arabidopsis and rice. Plos One, 7, e31163. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2366. Mette MF, Aufsatz W, van der Winden J, Matzke MA and Matzke AJ, 2000. Transcriptional silencing and promoter methylation triggered by double‐stranded RNA. EMBO J, 19, 5194–5201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2367. Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C, Chen S, Hannon GJ and Qi Y, 2008. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell, 133, 116–127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2368. Migicovsky Z and Kovalchuk I, 2014. Transgenerational changes in plant physiology and in transposon expression in response to UV‐C stress in Arabidopsis thaliana . Plant Signaling and Behavior, 9, e976490–e976490. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2369. Migicovsky Z, Yao Y and Kovalchuk I, 2014. Transgenerational phenotypic and epigenetic changes in response to heat stress in Arabidopsis thaliana . Plant Signaling and Behavior, 9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2370. Migicovsky Z and Kovalchuk I, 2015. Transgenerational inheritance of epigenetic response to cold in Arabidopsis thaliana . Biocatalysis and Agricultural Biotechnology, 4, 1–10. [Google Scholar]
  2371. Minoia S, Carbonell A, Di Serio F, Gisel A, Carrington JC, Navarro B and Flores R, 2014. Specific Argonautes Selectively Bind Small RNAs Derived from Potato Spindle Tuber Viroid and Attenuate Viroid Accumulation In Vivo. Journal of Virology, 88, 11933–11945. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2372. Mirzaei K, Bahramnejad B, Shamsifard MH and Zamani W, 2014. In Silico Identification, Phylogenetic and Bioinformatic Analysis of Argonaute Genes in Plants. International Journal of Genomics, 2014, 967461–967461. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2373. Mlotshwa S, Pruss GJ, Peragine A, Endres MW, Li JJ, Chen XM, Poethig RS, Bowman LH and Vance V, 2008. DICER‐LIKE2 Plays a Primary Role in Transitive Silencing of Transgenes in Arabidopsis . Plos One, 3, e1755–e1755. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2374. Moissiard G and Voinnet O, 2006. RNA silencing of host transcripts by cauliflower mosaic virus requires coordinated action of the four Arabidopsis Dicer‐like proteins (Retracted article. See vol. 112, pg. E4818, 2015). Proc Natl Acad Sci U S A, 103, 19593–19598. [DOI] [PMC free article] [PubMed] [Google Scholar] [Retracted]
  2375. Moissiard G, Parizotto EA, Himber C and Voinnet O, 2007. Transitivity in Arabidopsis can be primed, requires the redundant action of the antiviral Dicer‐like 4 and Dicer‐like 2, and is compromised by viral‐encoded suppressor proteins. Rna, 13, 1268–1278. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2376. Montgomery TA, Howell MD, Cuperus JT, Li DW, Hansen JE, Alexander AL, Chapman EJ, Fahlgren N, Allen E and Carrington JC, 2008. Specificity of ARGONAUTE7‐miR390 interaction and dual functionality in TAS3 trans‐acting siRNA formation. Cell, 133, 128–141. [DOI] [PubMed] [Google Scholar]
  2377. Morel JB, Godon C, Mourrain P, Beclin C, Boutet S, Feuerbach F, Proux F and Vaucheret H, 2002. Fertile hypomorphic ARGONAUTE (ago1) mutants impaired in post‐transcriptional gene silencing and virus resistance. Plant Cell, 14, 629–639. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2378. Mourrain P, Beclin C, Elmayan T, Feuerbach F, Godon C, Morel JB, Jouette D, Lacombe AM, Nikic S, Picault N, Remoue K, Sanial M, Vo TA and Vaucheret H, 2000. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell, 101, 533–542. [DOI] [PubMed] [Google Scholar]
  2379. Muangsan N, Beclin C, Vaucheret H and Robertson D, 2004. Geminivirus VIGS of endogenous genes requires SGS2/SDE1 and SGS3 and defines a new branch in the genetic pathway for silencing in plants. Plant Journal, 38, 1004–1014. [DOI] [PubMed] [Google Scholar]
  2380. Mukherjee K, Campos H and Kolaczkowski B, 2013. Evolution of Animal and Plant Dicers: Early Parallel Duplications and Recurrent Adaptation of Antiviral RNA Binding in Plants. Molecular Biology and Evolution, 30, 627–641. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2381. Nagano H, Fukudome A, Hiraguri A, Moriyama H and Fukuhara T, 2014. Distinct substrate specificities of Arabidopsis DCL3 and DCL4. Nucleic Acids Research, 42, 1845–1856. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2382. Nagasaki H, Itoh J‐I, Hayashi K, Hibara K‐I, Satoh‐Nagasawa N, Nosaka M, Mukouhata M, Ashikari M, Kitano H, Matsuoka M, Nagato Y and Sato Y, 2007. The small interfering RNA production pathway is required for shoot meristern initiation in rice. Proc Natl Acad Sci U S A, 104, 14867–14871. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2383. Nakazawa Y, Hiraguri A, Moriyama H and Fukuhara T, 2007. The dsRNA‐binding protein DRB4 interacts with the Dicer‐like protein DCL4 in vivo and functions in the trans‐acting siRNA pathway. Plant Molecular Biology, 63, 777–785. [DOI] [PubMed] [Google Scholar]
  2384. Odokonyero D, Mendoza MR, Alvarado VY, Zhang JT, Wang XF and Scholthof HB, 2015. Transgenic down‐regulation of ARGONAUTE2 expression in Nicotiana benthamiana interferes with several layers of antiviral defenses. Virology, 486, 209–218. [DOI] [PubMed] [Google Scholar]
  2385. Ogwok E, Ilyas M, Alicai T, Rey MEC and Taylor NJ, 2016. Comparative analysis of virus‐derived small RNAs within cassava (Manihot esculenta Crantz) infected with cassava brown streak viruses. Virus Research, 215, 1–11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2386. Oliver C, Santos JL and Pradillo M, 2014. On the role of some ARGONAUTE proteins in meiosis and DNA repair in Arabidopsis thaliana . Frontiers in Plant Science, 5, 177–177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2387. Olmedo‐Monfil V, Duran‐Figueroa N, Arteaga‐Vazquez M, Demesa‐Arevalo E, Autran D, Grimanelli D, Slotkin RK, Martienssen RA and Vielle‐Calzada JP, 2010. Control of female gamete formation by a small RNA pathway in Arabidopsis . Nature, 464, 628–U200. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2388. Onodera Y, Haag JR, Ream T, Nunes PC, Pontes O and Pikaard CS, 2005. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation‐dependent heterochromatin formation. Cell, 120, 613–622. [DOI] [PubMed] [Google Scholar]
  2389. Palmer JD, Soltis DE and Chase MW, 2004. The plant tree of life: an overview and some points of view. Am J Bot, 91, 1437–1445. [DOI] [PubMed] [Google Scholar]
  2390. Papp I, Mette MF, Aufsatz W, Daxinger L, Schauer SE, Ray A, van der Winden J, Matzke M and Matzke AJM, 2003. Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiology, 132, 1382–1390. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2391. Parent JS, Bouteiller N, Elmayan T and Vaucheret H, 2015. Respective contributions of Arabidopsis DCL2 and DCL4 to RNA silencing. Plant Journal, 81, 223–232. [DOI] [PubMed] [Google Scholar]
  2392. Park MY, Wu G, Gonzalez‐Sulser A, Vaucheret H and Poethig RS, 2005. Nuclear processing and export of microRNAs in Arabidopsis . Proc Natl Acad Sci U S A, 102, 3691–3696. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2393. Park W, Li JJ, Song RT, Messing J and Chen XM, 2002. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana . Current Biology, 12, 1484–1495. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2394. Pelissier T, Thalmeir S, Kempe D, Sanger HL and Wassenegger M, 1999. Heavy de novo methylation at symmetrical and non‐symmetrical sites is a hallmark of RNA‐directed DNA methylation. Nucleic Acids Research, 27, 1625–1634. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2395. Pelissier T and Wassenegger M, 2000. A DNA target of 30 bp is sufficient for RNA‐directed DNA methylation. Rna, 6, 55–65. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2396. Pelissier T, Clavel M, Chaparro C, Pouch‐Pelissier MN, Vaucheret H and Deragon JM, 2011. Double‐stranded RNA binding proteins DRB2 and DRB4 have an antagonistic impact on polymerase IV‐dependent siRNA levels in Arabidopsis . Rna, 17, 1502–1510. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2397. Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S and Fischer RL, 2007. DNA demethylation in the Arabidopsis genome. Proc Natl Acad Sci U S A, 104, 6752–6757. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2398. Peragine A, Yoshikawa M, Wu G, Albrecht HL and Poethig RS, 2004. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans‐acting siRNAs in Arabidopsis . Genes & Development, 18, 2368–2379. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2399. Pontes O, Li CF, Nunes PC, Haag J, Ream T, Vitins A, Jacobsen SE and Pikaard CS, 2006. The Arabidopsis chromatin‐modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell, 126, 79–92. [DOI] [PubMed] [Google Scholar]
  2400. Pontier D, Picart C, Roudier F, Garcia D, Lahmy S, Azevedo J, Alart E, Laudie M, Karlowski WM, Cooke R, Colot V, Voinnet O and Lagrange T, 2012. NERD, a Plant‐Specific GW Protein, Defines an Additional RNAi‐Dependent Chromatin‐Based Pathway in Arabidopsis . Molecular Cell, 48, 121–132. [DOI] [PubMed] [Google Scholar]
  2401. Pouch‐Pelissier M‐N, Pelissier T, Elmayan T, Vaucheret H, Boko D, Jantsch MF and Deragon J‐M, 2008. SINE RNA Induces Severe Developmental Defects in Arabidopsis thaliana and Interacts with HYL1 (DRB1), a Key Member of the DCL1 Complex. PLoS Genetics, 4, e1000096–e1000096. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2402. Qu F, Ye XH, Hou GC, Sato S, Clemente TE and Morris TJ, 2005. RDR6 has a broad‐spectrum but temperature‐dependent antiviral defense role in Nicotiana benthamiana . Journal of Virology, 79, 15209–15217. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2403. Qu F, Ye XH and Morris TJ, 2008. Arabidopsis DRB4, AG01, AG07, and RDR6 participate in a DCL4‐initiated antiviral RNA silencing pathway negatively regulated by DCL1. Proc Natl Acad Sci U S A, 105, 14732–14737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2404. Raghuram B, Sheikh AH, Rustagi Y and Sinha AK, 2015. MicroRNA biogenesis factor DRB1 is a phosphorylation target of mitogen activated protein kinase MPK3 in both rice and Arabidopsis . Febs Journal, 282, 521–536. [DOI] [PubMed] [Google Scholar]
  2405. Raja P, Jackel JN, Li SZ, Heard IM and Bisaro DM, 2014. Arabidopsis Double‐Stranded RNA Binding Protein DRB3 Participates in Methylation‐Mediated Defense against Geminiviruses. Journal of Virology, 88, 2611–2622. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2406. Rajagopalan R, Vaucheret H, Trejo J and Bartel DP, 2006. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana . Genes & Development, 20, 3407–3425. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2407. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B and Bartel DP, 2002. MicroRNAs in plants. Genes & Development, 16, 1616–1626. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2408. Reis RS, Eamens AL and Waterhouse PM, 2015a. Missing Pieces in the Puzzle of Plant MicroRNAs. Trends in Plant Science, 20, 721–728. [DOI] [PubMed] [Google Scholar]
  2409. Reis RS, Hart‐Smith G, Eamens AL, Wilkins MR and Waterhouse PM, 2015b. MicroRNA Regulatory Mechanisms Play Different Roles in Arabidopsis . Journal of Proteome Research, 14, 4743–4751. [DOI] [PubMed] [Google Scholar]
  2410. Reis RS, Hart‐Smith G, Eamens AL, Wilkins MR and Waterhouse PM, 2015c. Gene regulation by translational inhibition is determined by Dicer partnering proteins. Nature Plants, 1. [DOI] [PubMed] [Google Scholar]
  2411. Reis RS, Eamens AL, Roberts TH and Waterhouse PM, 2016. Chimeric DCL1‐Partnering Proteins Provide Insights into the MicroRNA Pathway. Frontiers in Plant Science, 6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2412. Ren GD, Xie M, Zhang SX, Vinovskis C, Chen XM and Yu B, 2014. Methylation protects microRNAs from an AGO1‐associated activity that uridylates 5′ RNA fragments generated by AGO1 cleavage. Proc Natl Acad Sci U S A, 111, 6365–6370. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2413. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B and Bartel DP, 2002. Prediction of plant microRNA targets. Cell, 110, 513–520. [DOI] [PubMed] [Google Scholar]
  2414. Rodriguez RE, Mecchia MA, Debernardi JM, Schommer C, Weigel D and Palatnik JF, 2010. Control of cell proliferation in Arabidopsis thaliana by microRNA miR396. Development, 137, 103–112. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2415. Rogers K and Chen XM, 2013. Biogenesis, Turnover, and Mode of Action of Plant MicroRNAs. Plant Cell, 25, 2383–2399. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2416. Roodbarkelari F, Du F, Truernit E and Laux T, 2015. ZLL/AGO10 maintains shoot meristem stem cells during Arabidopsis embryogenesis by down‐regulating ARF2‐mediated auxin response. Bmc Biology, 13, 74–74. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2417. Salgado PS, Koivunen MRL, Makeyev EV, Bamford DH, Stuart DI and Grimes JM, 2006. The structure of an RNAi polymerase links RNA silencing and transcription. Plos Biology, 4, 2274–2281. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2418. Schauer SE, Jacobsen SE, Meinke DW and Ray A, 2002. DICER‐LIKE1: blind men and elephants in Arabidopsis development. Trends in Plant Science, 7, 487–491. [DOI] [PubMed] [Google Scholar]
  2419. Schiebel W, Haas B, Marinkovic S, Klanner A and Sanger HL, 1993. RNA‐directed RNA polymerase from tomato leaves. II. Catalytic in vitro properties. Journal of Biological Chemistry, 268, 11858–11867. [PubMed] [Google Scholar]
  2420. Schiebel W, Pelissier T, Riedel L, Thalmeir S, Schiebel R, Kempe D, Lottspeich F, Sanger HL and Wassenegger M, 1998. Isolation of an RNA‐Directed RNA polymerase‐specific cDNA clone from tomato. Plant Cell, 10, 2087–2101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2421. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M and Weigel D, 2005. Specific effects of microRNAs on the plant transcriptome. Developmental Cell, 8, 517–527. [DOI] [PubMed] [Google Scholar]
  2422. Shao CG, Chen M and Meng YJ, 2013. A reversed framework for the identification of microRNA‐target pairs in plants. Briefings in Bioinformatics, 14, 293–301. [DOI] [PubMed] [Google Scholar]
  2423. Shao FJ and Lu SF, 2013. Genome‐wide identification, molecular cloning, expression profiling and posttranscriptional regulation analysis of the Argonaute gene family in Salvia miltiorrhiza, an emerging model medicinal plant. Bmc Genomics, 14, 512–512. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2424. Shao FJ and Lu SF, 2014. Identification, Molecular Cloning and Expression Analysis of Five RNA‐Dependent RNA Polymerase Genes in Salvia miltiorrhiza. Plos One, 9, e95117–e95117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2425. Shi ZY, Wang J, Wan XS, Shen GZ, Wang XQ and Zhang JL, 2007. Over‐expression of rice OsAGO7 gene induces upward curling of the leaf blade that enhanced erect‐leaf habit. Planta, 226, 99–108. [DOI] [PubMed] [Google Scholar]
  2426. Shivaprasad PV, Rajeswaran R, Blevins T, Schoelz J, Meins F, Hohn T and Pooggin MM, 2008. The CaMV transactivator/viroplasmin interferes with RDR6‐dependent trans‐acting and secondary siRNA pathways in Arabidopsis . Nucleic Acids Research, 36, 5896–5909. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2427. Silva TF, Romanel EAC, Andrade RRS, Farinelli L, Osteras M, Deluen C, Correa RL, Schrago CEG and Vaslin MFS, 2011. Profile of small interfering RNAs from cotton plants infected with the polerovirus Cotton leafroll dwarf virus. Bmc Molecular Biology, 12, 40–40. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2428. Singh M, Goel S, Meeley RB, Dantec C, Parrinello H, Michaud C, Leblanc O and Grimanelli D, 2011. Production of Viable Gametes without Meiosis in Maize Deficient for an ARGONAUTE Protein. Plant Cell, 23, 443–458. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2429. Smith MR, Willmann MR, Wu G, Berardini TZ, Moller B, Weijers D and Poethig RS, 2009. Cyclophilin 40 is required for microRNA activity in Arabidopsis . Proc Natl Acad Sci U S A, 106, 5424–5429. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2430. Song XW, Li PC, Zhai JX, Zhou M, Ma LJ, Liu B, Jeong DH, Nakano M, Cao SY, Liu CY, Chu CC, Wang XJ, Green PJ, Meyers BC and Cao XF, 2012. Roles of DCL4 and DCL3b in rice phased small RNA biogenesis. Plant Journal, 69, 462–474. [DOI] [PubMed] [Google Scholar]
  2431. Souret FF, Kastenmayer JP and Green PJ, 2004. AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Molecular Cell, 15, 173–183. [DOI] [PubMed] [Google Scholar]
  2432. Sunkar R and Zhu JK, 2004. Novel and stress‐regulated microRNAs and other small RNAs from Arabidopsis . Plant Cell, 16, 2001–2019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2433. Takeda A, Iwasaki S, Watanabe T, Utsumi M and Watanabe Y, 2008. The mechanism selecting the guide strand from small RNA duplexes is different among Argonaute proteins. Plant and Cell Physiology, 49, 493–500. [DOI] [PubMed] [Google Scholar]
  2434. Thomas CL, Jones L, Baulcombe DC and Maule AJ, 2001. Size constraints for targeting post‐transcriptional gene silencing and for RNA‐directed methylation in Nicotiana benthamiana using a potato virus X vector. Plant Journal, 25, 417–425. [DOI] [PubMed] [Google Scholar]
  2435. Tkaczuk KL, Obarska A and Bujnicki JM, 2006. Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis. Bmc Evolutionary Biology, 6, 6–6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2436. Tucker MR, Okada T, Hu Y, Scholefield A, Taylor JM and Koltunow AM, 2012. Somatic small RNA pathways promote the mitotic events of megagametogenesis during female reproductive development in Arabidopsis . Development, 139, 1399–1404. [DOI] [PubMed] [Google Scholar]
  2437. Tucker MR, Roodbarkelari F, Truernit E, Adamski NM, Hinze A, Lohmuller B, Wurschum T and Laux T, 2013. Accession‐specific modifiers act with ZWILLE/ARGONAUTE10 to maintain shoot meristem stem cells during embryogenesis in Arabidopsis . Bmc Genomics, 14, 809–809. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2438. Tworak A, Urbanowicz A, Podkowinski J, Kurzynska‐Kokorniak A, Koralewska N and Figlerowicz M, 2016. Six Medicago truncatula Dicer‐like protein genes are expressed in plant cells and upregulated in nodules. Plant Cell Reports, 35, 1043–1052. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2439. Urayama S, Moriyama H, Aoki N, Nakazawa Y, Okada R, Kiyota E, Miki D, Shimamoto K and Fukuhara T, 2010. Knock‐down of OsDCL2 in Rice Negatively Affects Maintenance of the Endogenous dsRNA Virus, Oryza sativa Endornavirus. Plant and Cell Physiology, 51, 58–67. [DOI] [PubMed] [Google Scholar]
  2440. Vaistij FE, Jones L and Baulcombe DC, 2002. Spreading of RNA targeting and DNA methylation in RNA silencing requires transcription of the target gene and a putative RNA‐dependent RNA polymerase. Plant Cell, 14, 857–867. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2441. Van Ex F, Jacob Y and Martienssen RA, 2011. Multiple roles for small RNAs during plant reproduction. Current Opinion in Plant Biology, 14, 588–593. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2442. Vaucheret H, Vazquez F, Crete P and Bartel DP, 2004. The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes & Development, 18, 1187–1197. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2443. Vaucheret H, 2005. MicroRNA‐dependent trans‐acting siRNA production. Science's STKE: signal transduction knowledge environment, 2005, pe43–pe43. [DOI] [PubMed] [Google Scholar]
  2444. Vaucheret H, 2008. Plant ARGONAUTES. Trends in Plant Science, 13, 350–358. [DOI] [PubMed] [Google Scholar]
  2445. Vazquez F, Gasciolli V, Crete P and Vaucheret H, 2004. The nuclear dsRNA binding protein HYL1 is required for MicroRNA accumulation and plant development, but not posttranscriptional transgene silencing. Current Biology, 14, 346–351. [DOI] [PubMed] [Google Scholar]
  2446. Vazquez F, 2006. Arabidopsis endogenous small RNAs: highways and byways. Trends in Plant Science, 11, 460–468. [DOI] [PubMed] [Google Scholar]
  2447. Vongs A, Kakutani T, Martienssen RA and Richards EJ, 1993. Arabidopsis thaliana DNA methylation mutants. Science, 260, 1926–1928. [DOI] [PubMed] [Google Scholar]
  2448. Wang XB, Wu QF, Ito T, Cillo F, Li WX, Chen XM, Yu JL and Ding SW, 2010. RNAi‐mediated viral immunity requires amplification of virus‐derived siRNAs in Arabidopsis thaliana . Proc Natl Acad Sci U S A, 107, 484–489. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2449. Wang XB, Jovel J, Udomporn P, Wang Y, Wu QF, Li WX, Gasciolli V, Vaucheret H and Ding SW, 2011. The 21‐Nucleotide, but Not 22‐Nucleotide, Viral Secondary Small Interfering RNAs Direct Potent Antiviral Defense by Two Cooperative Argonautes in Arabidopsis thaliana . Plant Cell, 23, 1625–1638. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2450. Wassenegger M, Heimes S, Riedel L and Sanger HL, 1994. RNA‐directed de novo methylation of genomic sequences in plants. Cell, 76, 567–576. [DOI] [PubMed] [Google Scholar]
  2451. Wassenegger M and Krczal G, 2006. Nomenclature and functions of RNA‐directed RNA polymerases. Trends in Plant Science, 11, 142–151. [DOI] [PubMed] [Google Scholar]
  2452. Wei LY, Gu LF, Song XW, Cui XK, Lu ZK, Zhou M, Wang LL, Hu FY, Zhai JX, Meyers BC and Cao XF, 2014. Dicer‐like 3 produces transposable element‐associated 24‐nt siRNAs that control agricultural traits in rice. Proc Natl Acad Sci U S A, 111, 3877–3882. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2453. Wei W, Ba Z, Gao M, Wu Y, Ma Y, Amiard S, White CI, Rendtlew Danielsen JM, Yang YG and Qi Y, 2012. A role for small RNAs in DNA double‐strand break repair. Cell, 149, 101–112. [DOI] [PubMed] [Google Scholar]
  2454. Wu JG, Yang ZR, Wang Y, Zheng LJ, Ye RQ, Ji YH, Zhao SS, Ji SY, Liu RF, Xu L, Zheng H, Zhou YJ, Zhang X, Cao XF, Xie LH, Wu ZJ, Qi YJ and Li Y, 2015. Viral‐Inducible Argonaute18 Confers Broad‐Spectrum Virus Resistance in Rice by Sequestering A Host MicroRNA. Elife, 4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2455. Wu L, Zhang QQ, Zhou HY, Ni FR, Wu XY and Qi YJ, 2009. Rice MicroRNA Effector Complexes and Targets. Plant Cell, 21, 3421–3435. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2456. Wu L, Zhou HY, Zhang QQ, Zhang JG, Ni FR, Liu C and Qi YJ, 2010. DNA Methylation Mediated by a MicroRNA Pathway. Molecular Cell, 38, 465–475. [DOI] [PubMed] [Google Scholar]
  2457. Wu L, Mao L and Qi YJ, 2012. Roles of DICER‐LIKE and ARGONAUTE Proteins in TAS‐Derived Small Interfering RNA‐Triggered DNA Methylation. Plant Physiology, 160, 990–999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2458. Xie M and Yu B, 2015. siRNA‐directed DNA Methylation in Plants. Current genomics, 16, 23–31. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2459. Xie ZX, Kasschau KD and Carrington JC, 2003. Negative feedback regulation of Dicer‐Like1 in Arabidopsis by microRNA‐guided mRNA degradation. Current Biology, 13, 784–789. [DOI] [PubMed] [Google Scholar]
  2460. Xie ZX, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE and Carrington JC, 2004. Genetic and functional diversification of small RNA pathways in plants. Plos Biology, 2, 642–652. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2461. Xie ZX, Allen E, Wilken A and Carrington JC, 2005. DICER‐LIKE 4 functions in trans‐acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana . Proc Natl Acad Sci U S A, 102, 12984–12989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2462. Xie ZX, Khanna K and Ruan SL, 2010. Expression of microRNAs and its regulation in plants. Seminars in Cell & Developmental Biology, 21, 790–797. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2463. Yang L, Liu ZQ, Lu F, Dong AW and Huang H, 2006. SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis . Plant Journal, 47, 841–850. [DOI] [PubMed] [Google Scholar]
  2464. Yang L, Wu G and Poethig RS, 2012. Mutations in the GW‐repeat protein SUO reveal a developmental function for microRNA‐mediated translational repression in Arabidopsis . Proc Natl Acad Sci U S A, 109, 315–320. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2465. Yang SJ, Carter SA, Cole AB, Cheng NH and Nelson RS, 2004. A natural variant of a host RNA‐dependent RNA polymerase is associated with increased susceptibility to viruses by Nicotiana benthamiana . Proc Natl Acad Sci U S A, 101, 6297–6302. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2466. You CX, Zhao Q, Wang XF, Xie XB, Feng XM, Zhao LL, Shu HR and Hao YJ, 2014. A dsRNA‐binding protein MdDRB1 associated with miRNA biogenesis modifies adventitious rooting and tree architecture in apple. Plant Biotechnology Journal, 12, 183–192. [DOI] [PubMed] [Google Scholar]
  2467. Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett RW, Steward R and Chen X, 2005. Methylation as a crucial step in plant microRNA biogenesis. Science, 307, 932–935. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2468. Yu DQ, Fan BF, MacFarlane SA and Chen ZX, 2003. Analysis of the involvement of an inducible Arabidopsis RNA‐dependent RNA polymerase in antiviral defense. Molecular Plant‐Microbe Interactions, 16, 206–216. [DOI] [PubMed] [Google Scholar]
  2469. Zhai L, Sun W, Zhang K, Jia H, Liu L, Liu Z, Teng F and Zhang Z, 2014. Identification and characterization of Argonaute gene family and meiosis‐enriched Argonaute during sporogenesis in maize. J Integr Plant Biol, 56, 1042–1052. [DOI] [PubMed] [Google Scholar]
  2470. Zhang H, Xia R, Meyers BC and Walbot V, 2015. Evolution, functions, and mysteries of plant ARGONAUTE proteins. Current Opinion in Plant Biology, 27, 84–90. [DOI] [PubMed] [Google Scholar]
  2471. Zhang WX, Gao S, Zhou XF, Xia J, Chellappan P, Zhou XA, Zhang XM and Jin HL, 2010. Multiple distinct small RNAs originate from the same microRNA precursors. Genome Biology, 11, R81–R81. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2472. Zhang X, Henderson IR, Lu C, Green PJ and Jacobsen SE, 2007. Role of RNA polymerase IV in plant small RNA metabolism. Proc Natl Acad Sci U S A, 104, 4536–4541. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2473. Zhang X, Zhao H, Gao S, Wang WC, Katiyar‐Agarwal S, Huang HD, Raikhel N and Jin H, 2011. Arabidopsis Argonaute 2 regulates innate immunity via miRNA393(*)‐mediated silencing of a Golgi‐localized SNARE gene, MEMB12. Molecular Cell, 42, 356–366. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2474. Zhang XC, Zhang XF, Singh J, Li DW and Qu F, 2012. Temperature‐Dependent Survival of Turnip Crinkle Virus‐Infected Arabidopsis Plants Relies on an RNA Silencing‐Based Defense That Requires DCL2, AG02, and HEN1. Journal of Virology, 86, 6847–6854. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2475. Zhao X, Zhang H and Li L, 2013. Identification and analysis of the proximal promoters of microRNA genes in Arabidopsis . Genomics, 101, 187–194. [DOI] [PubMed] [Google Scholar]
  2476. Zheng B, Wang Z, Li S, Yu B, Liu J‐Y and Chen X, 2009. Intergenic transcription by RNA Polymerase II coordinates Pol IV and Pol V in siRNA‐directed transcriptional gene silencing in Arabidopsis . Genes & Development, 23, 2850–2860. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2477. Zheng XW, Zhu JH, Kapoor A and Zhu JK, 2007. Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing. EMBO J, 26, 1691–1701. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2478. Zhou C, Han L, Fu C, Wen J, Cheng X, Nakashima J, Ma J, Tang Y, Tan Y, Tadege M, Mysore KS, Xia G and Wang Z‐Y, 2013. The Trans‐Acting Short Interfering RNA3 Pathway and NO APICAL MERISTEM Antagonistically Regulate Leaf Margin Development and Lateral Organ Separation, as Revealed by Analysis of an argonaute7/lobed leaflet1 Mutant in Medicago truncatula. Plant Cell, 25, 4845–4862. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2479. Zhou Y, Honda M, Zhu H, Zhang Z, Guo X, Li T, Li Z, Peng X, Nakajima K, Duan L and Zhang X, 2015. Spatiotemporal Sequestration of miR165/166 by Arabidopsis Argonaute10 Promotes Shoot Apical Meristem Maintenance. Cell Reports, 10, 1819–1827. [DOI] [PubMed] [Google Scholar]
  2480. Zhu H, Zhou Y, Castillo‐Gonzalez C, Lu A, Ge C, Zhao YT, Duan L, Li Z, Axtell MJ, Wang XJ and Zhang X, 2013. Bidirectional processing of pri‐miRNAs with branched terminal loops by Arabidopsis Dicer‐like1. Nature Structural & Molecular Biology, 20, 1106–1115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2481. Zhu HL, Hu FQ, Wang RH, Zhou X, Sze SH, Liou LW, Barefoot A, Dickman M and Zhang XR, 2011. Arabidopsis Argonaute10 Specifically Sequesters miR166/165 to Regulate Shoot Apical Meristem Development. Cell, 145, 242–256. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2482. Zilberman D, Cao XF, Johansen LK, Xie ZX, Carrington JC and Jacobsen SE, 2004. Role of arabidopsis ARGONAUTE4 in RNA‐directed DNA methylation triggered by inverted repeats. Current Biology, 14, 1214–1220. [DOI] [PubMed] [Google Scholar]
  2483. Adams R, Nicke B, Pohlenz HD and Sohler F, 2015. Deciphering Seed Sequence Based Off‐Target Effects in a Large‐Scale RNAi Reporter Screen for E‐Cadherin Expression. PLoS ONE, 10, e0137640–e0137640. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2484. Afonso‐Grunz F and Muller S, 2015. Principles of miRNA‐mRNA interactions: beyond sequence complementarity. Cellular and Molecular Life Sciences, 72, 3127–3141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2485. Agarwal V, Bell GW, Nam JW and Bartel DP, 2015. Predicting effective microRNA target sites in mammalian mRNAs. Elife, 4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2486. Ahmed F, Dai XB and Zhao PX, 2015. Bioinformatics Tools for Achieving Better Gene Silencing in Plants. In: Plant Gene Silencing: Methods and Protocols. 43–60. [DOI] [PubMed] [Google Scholar]
  2487. Aleman LM, Doench J and Sharp PA, 2007. Comparison of siRNA‐induced off‐target RNA and protein effects. Rna‐a Publication of the Rna Society, 13, 385–395. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2488. Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M and Hatzigeorgiou AG, 2009. Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics, 25, 3049–3055. [DOI] [PubMed] [Google Scholar]
  2489. Alexiou P, Vergoulis T, Gleditzsch M, Prekas G, Dalamagas T, Megraw M, Grosse I, Sellis T and Hatzigeorgiou AG, 2010. miRGen 2.0: a database of microRNA genomic information and regulation. Nucleic Acids Research, 38, D137–D141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2490. Allen E, Xie ZX, Gustafson AM, Sung GH, Spatafora JW and Carrington JC, 2004. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana . Nature Genetics, 36, 1282–1290. [DOI] [PubMed] [Google Scholar]
  2491. Ameres SL, Martinez J and Schroeder R, 2007. Molecular basis for target RNA recognition and cleavage by human RISC. Cell, 130, 101–112. [DOI] [PubMed] [Google Scholar]
  2492. Amirkhah R, Farazmand A, Gupta SK, Ahmadi H, Wolkenhauer O and Schmitz U, 2015. Naive Bayes classifier predicts functional microRNA target interactions in colorectal cancer. Molecular Biosystems, 11, 2126–2134. [DOI] [PubMed] [Google Scholar]
  2493. Anderson EM, Birmingham A, Baskerville S, Reynolds A, Maksimova E, Leake D, Fedorov Y, Karpilow J and Khvorova A, 2008. Experimental validation of the importance of seed complement frequency to siRNA specificity. Rna‐a Publication of the Rna Society, 14, 853–861. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2494. Andres‐Leon E, Pena DG, Gomez‐Lopez G and Pisano DG, 2015. miRGate: a curated database of human, mouse and rat miRNA‐mRNA targets. Database‐the Journal of Biological Databases and Curation, 2015, bav035–bav035. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2495. Androsavich JR and Chau BN, 2014. Non‐inhibited miRNAs shape the cellular response to anti‐miR. Nucleic Acids Research, 42, 6945–6955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2496. Arroyo JD, Gallichotte EN and Tewari M, 2014. Systematic design and functional analysis of artificial microRNAs. Nucleic Acids Research, 42, 6064–6077. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2497. Axtell MJ, 2013. Classification and comparison of small RNAs from plants. Annu Rev Plant Biol, 64, 137–159. [DOI] [PubMed] [Google Scholar]
  2498. Baigude H, Ahsanullah Li Z, Zhou Y and Rana TM, 2012. miR‐TRAP: a benchtop chemical biology strategy to identify microRNA targets. Angew Chem Int Ed Engl, 51, 5880–5883. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2499. Balaga O, Friedman Y and Linial M, 2012. Toward a combinatorial nature of microRNA regulation in human cells. Nucleic Acids Research, 40, 9404–9416. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2500. Bandyopadhyay S, Ghosh D, Mitra R and Zhao ZM, 2015. MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets. Scientific Reports, 5, 8004–8004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2501. Bartel DP, 2009. MicroRNAs: Target Recognition and Regulatory Functions. Cell, 136, 215–233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2502. Batista PJ, Ruby JG, Claycomb JM, Chiang R, Fahlgren N, Kasschau KD, Chaves DA, Gu W, Vasale JJ, Duan S, Conte D Jr, Luo S, Schroth GP, Carrington JC, Bartel DP and Mello CC, 2008. PRG‐1 and 21U‐RNAs interact to form the piRNA complex required for fertility in C. elegans. Mol Cell, 31, 67–78. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2503. Betel D, Wilson M, Gabow A, Marks DS and Sander C, 2008. The microRNA.org resource: targets and expression. Nucleic Acids Research, 36, D149–D153. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2504. Betel D, Koppal A, Agius P, Sander C and Leslie C, 2010. Comprehensive modeling of microRNA targets predicts functional non‐conserved and non‐canonical sites. Genome Biology, 11, R90–R90. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2505. Bhandare V and Ramaswamy A, 2016. Structural dynamics of human argonaute2 and its interaction with siRNAs designed to target mutant tdp43. Advances in Bioinformatics, 2016, 8792814–8792814. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2506. Birmingham A, Anderson EM, Reynolds A, Ilsley‐Tyree D, Leake D, Fedorov Y, Baskerville S, Maksimova E, Robinson K, Karpilow J, Marshall WS and Khvorova A, 2006. 3′ UTR seed matches, but not overall identity, are associated with RNAi off‐targets. Nature Methods, 3, 199–204. [DOI] [PubMed] [Google Scholar]
  2507. Bisognin A, Sales G, Coppe A, Bortoluzzi S and Romualdi C, 2012. MAGIA(2): from miRNA and genes expression data integrative analysis to microRNA‐transcription factor mixed regulatory circuits (2012 update). Nucleic Acids Research, 40, W13–W21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2508. Brennecke J, Stark A, Russell RB and Cohen SM, 2005. Principles of MicroRNA‐target recognition. Plos Biology, 3, 404–418. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2509. Broughton JP and Pasquinelli AE, 2016. A tale of two sequences: microRNA‐target chimeric reads. Genetics, selection, evolution: GSE, 48, 31–31. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2510. Brousse C, Liu QK, Beauclair L, Deremetz A, Axtell MJ and Bouche N, 2014. A non‐canonical plant microRNA target site. Nucleic Acids Research, 42, 5270–5279. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2511. Buckley BA, Burkhart KB, Gu SG, Spracklin G, Kershner A, Fritz H, Kimble J, Fire A and Kennedy S, 2012. A nuclear Argonaute promotes multigenerational epigenetic inheritance and germline immortality. Nature, 489, 447–451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2512. Cao W, Hunter R, Strnatka D, McQueen CA and Erickson RP, 2005. DNA constructs designed to produce short hairpin, interfering RNAs in transgenic mice sometimes show early lethality and an interferon response. J Appl Genet, 46, 217–225. [PubMed] [Google Scholar]
  2513. Chandradoss SD, Schirle NT, Szczepaniak M, MacRae IJ and Joo C, 2015. A Dynamic Search Process Underlies MicroRNA Targeting. Cell, 162, 96–107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2514. Chen L, Hou J and Liu L, 2015. High‐Throughput Techniques for Identifying microRNA Target Genes. Current Bioinformatics, 10, 370–376. [Google Scholar]
  2515. Chen PY, Weinmann L, Gaidatzis D, Pei Y, Zavolan M, Tuschl T and Meister G, 2008. Strand‐specific 5 ‘‐O‐methylation of siRNA duplexes controls guide strand selection and targeting specificity. Rna‐a Publication of the Rna Society, 14, 263–274. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2516. Cheng S, Guo M, Wang C, Liu X, Liu Y and Wu X, 2015. MiRTDL: a deep learning approach for miRNA target prediction. ACM, IEEE/ACM transactions on computational biology and bioinformatics / IEEE. [DOI] [PubMed] [Google Scholar]
  2517. Chi SW, Zang JB, Mele A and Darnell RB, 2009. Argonaute HITS‐CLIP decodes microRNA‐mRNA interaction maps. Nature, 460, 479–486. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2518. Chi SW, Hannon GJ and Darnell RB, 2012. An alternative mode of microRNA target recognition. Nature Structural & Molecular Biology, 19, 321–U380. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2519. Chiu HS, Llobet‐Navas D, Yang XR, Chung WJ, Ambesi‐Impiombato A, Lyer A, Kim HR, Seviour EG, Luo ZJ, Sehga V, Moss T, Lu YL, Ram P, Silva J, Mills GB, Califano A and Sumazin P, 2015. Cupid: simultaneous reconstruction of microRNA‐target and ceRNA networks. Genome Research, 25, 257–267. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2520. Chiu YL and Rana TM, 2003. siRNA function in RNAi: A chemical modification analysis. Rna‐a Publication of the Rna Society, 9, 1034–1048. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2521. Chou CH, Lin FM, Chou MT, Hsu SD, Chang TH, Weng SL, Shrestha S, Hsiao CC, Hung JH and Huang HD, 2013. A computational approach for identifying microRNA‐target interactions using high‐throughput CLIP and PAR‐CLIP sequencing. BMC Genomics, 14, S2–S2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2522. Chu TJ, Mouillet JF, Hood BL, Conrads TP and Sadovsky Y, 2015. The assembly of miRNA‐mRNA‐protein regulatory networks using high‐throughput expression data. Bioinformatics, 31, 1780–1787. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2523. Cipolla GA, 2014. A non‐canonical landscape of the microRNA system. Frontiers in Genetics, 5, 337–337. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2524. Clark PM, Loher P, Quann K, Brody J, Londin ER and Rigoutsos I, 2014. Argonaute CLIP‐Seq reveals miRNA targetome diversity across tissue types. Scientific Reports, 4, 5947–5947. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2525. Dai XB and Zhao PX, 2011. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Research, 39, W155–W159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2526. Das PP, Bagijn MP, Goldstein LD, Woolford JR, Lehrbach NJ, Sapetschnig A, Buhecha HR, Gilchrist MJ, Howe KL, Stark R, Matthews N, Berezikov E, Ketting RF, Tavare S and Miska EA, 2008. Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Mol Cell, 31, 79–90. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2527. Das S, Ghosal S, Chakrabarti J and Kozak K, 2013. SeedSeq: Off‐Target Transcriptome Database. Biomed Research International, 2013, 905429–905429. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2528. Das S, Ghosal S, Kozak K and Chakrabarti J, 2013b. An siRNA designing tool with a unique functional off‐target filtering approach. Journal of Biomolecular Structure & Dynamics, 31, 1343–1357. [DOI] [PubMed] [Google Scholar]
  2529. De N, Young L, Lau PW, Meisner NC, Morrissey DV and MacRae IJ, 2013. Highly Complementary Target RNAs Promote Release of Guide RNAs from Human Argonaute2. Molecular Cell, 50, 344–355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2530. Deerberg A, Willkomm S and Restle T, 2013. Minimal mechanistic model of siRNA‐dependent target RNA slicing by recombinant human Argonaute 2 protein. America, 110, 17850–17855. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2531. Didiano D and Hobert O, 2006. Perfect seed pairing is not a generally reliable predictor for miRNA‐target interactions. Nature Structural & Molecular Biology, 13, 849–851. [DOI] [PubMed] [Google Scholar]
  2532. Ding J, Zhou S and Guan J, 2012a. Finding microRNA targets in plants: current status and perspectives. Genomics, proteomics & bioinformatics, 10, 264–275. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2533. Ding JD, Li DQ, Ohler U, Guan JH and Zhou SG, 2012b. Genome‐wide search for miRNA‐target interactions in Arabidopsis thaliana with an integrated approach. BMC Genomics, 13, S3–S3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2534. Ding XL, Li JJ, Zhang H, He TT, Han SH, Li YW, Yang SP and Gai JY, 2016. Identification of miRNAs and their targets by high‐throughput sequencing and degradome analysis in cytoplasmic male‐sterile line NJCMS1A and its maintainer NJCMS1B of soybean. BMC Genomics, 17, 24–24. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2535. Doench JG, Petersen CP and Sharp PA, 2003. siRNAs can function as miRNAs. Genes & Development, 17, 438–442. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2536. Du Q, Thonberg H, Wang J, Wahlestedt C and Liang ZC, 2005. A systematic analysis of the silencing effects of an active siRNA at all single‐nucleotide mismatched target sites. Nucleic Acids Research, 33, 1671–1677. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2537. Dua P, Yoo JW, Kim S and Lee DK, 2011. Modified siRNA Structure With a Single Nucleotide Bulge Overcomes Conventional siRNA‐mediated Off‐target Silencing. Molecular Therapy, 19, 1676–1687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2538. Duran‐Figueroa N and Vielle‐Calzada JP, 2010. ARGONAUTE9‐dependent silencing of transposable elements in pericentromeric regions of Arabidopsis . Plant Signal Behav, 5, 1476–1479. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2539. Easow G, Teleman AA and Cohen SM, 2007. Isolation of microRNA targets by miRNP immunopurification. Rna‐a Publication of the Rna Society, 13, 1198–1204. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2540. Echeverri CJ, Beachy PA, Baum B, Boutros M, Buchholz F, Chanda SK, Downward J, Ellenberg J, Fraser AG, Hacohen N, Hahn WC, Jackson AL, Kiger A, Linsley PS, Lum L, Ma Y, Mathey‐Prevot B, Root DE, Sabatini DM, Taipale J, Perrimon N and Bernards R, 2006. Minimizing the risk of reporting false positives in large‐scale RNAi screens. Nat Methods, 3, 777–779. [DOI] [PubMed] [Google Scholar]
  2541. Elkayam E, Kuhn CD, Tocilj A, Haase AD, Greene EM, Hannon GJ and Joshua‐Tor L, 2012. The structure of human argonaute‐2 in complex with miR‐20a. Cell, 150, 100–110. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2542. Ellwanger DC, Buttner FA, Mewes HW and Stumpflen V, 2011. The sufficient minimal set of miRNA seed types. Bioinformatics, 27, 1346–1350. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2543. Elton TS and Yalowich JC, 2015. Experimental procedures to identify and validate specific mRNA targets of miRNAs. EXCLI journal, 14, 758–790. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2544. Engels JW, 2013. Gene silencing by chemically modified siRNAs. New Biotechnology, 30, 302–307. [DOI] [PubMed] [Google Scholar]
  2545. Enright AJ, John B, Gaul U, Tuschl T, Sander C and Marks DS, 2003. MicroRNA targets in Drosophila. Genome Biology, 5, R1–R1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2546. Erhard F, Dolken L, Jaskiewicz L and Zimmer R, 2013. PARma: identification of microRNA target sites in AGO‐PAR‐CLIP data. Genome Biology, 14, R79–R79. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2547. Faehnle CR and Joshua‐Tor L, 2007. Argonautes confront new small RNAs. Curr Opin Chem Biol, 11, 569–577. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2548. Faehnle CR, Elkayam E, Haase AD, Hannon GJ and Joshua‐Tor L, 2013. The making of a slicer: activation of human Argonaute‐1. Cell Rep, 3, 1901–1909. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2549. Fan GQ, Li XY, Deng MJ, Zhao ZL and Yang L, 2016. Comparative Analysis and Identification of miRNAs and Their Target Genes Responsive to Salt Stress in Diploid and Tetraploid Paulownia fortunei Seedlings. PLoS ONE, 11, e0149617–e0149617. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2550. Fedorov Y, Anderson EM, Birmingham A, Reynolds A, Karpilow J, Robinson K, Leake D, Marshall WS and Khvorova A, 2006. Off‐target effects by siRNA can induce toxic phenotype. Rna‐a Publication of the Rna Society, 12, 1188–1196. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2551. Fischer SE, Montgomery TA, Zhang C, Fahlgren N, Breen PC, Hwang A, Sullivan CM, Carrington JC and Ruvkun G, 2011. The ERI‐6/7 helicase acts at the first stage of an siRNA amplification pathway that targets recent gene duplications. PLoS Genet, 7, e1002369. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2552. Flores O, Kennedy EM, Skalsky RL and Cullen BR, 2014. Differential RISC association of endogenous human microRNAs predicts their inhibitory potential. Nucleic Acids Research, 42, 4629–4639. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2553. Fluiter K, Mook ORF and Baas F, 2009. The Therapeutic Potential of LNA‐Modified siRNAs: Reduction of Off‐Target Effects by Chemical Modification of the siRNA Sequence. In: Methods in Molecular Biology. 189–203. [DOI] [PubMed] [Google Scholar]
  2554. Folkes L, Moxon S, Woolfenden HC, Stocks MB, Szittya G, Dalmay T and Moulton V, 2012. PAREsnip: a tool for rapid genome‐wide discovery of small RNA/target interactions evidenced through degradome sequencing. Nucleic Acids Research, 40, e103–e103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2555. Forstemann K, Horwich MD, Wee L, Tomari Y and Zamore PD, 2007. Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by dicer‐1. Cell, 130, 287–297. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2556. Friedman RC, Farh KKH, Burge CB and Bartel DP, 2009. Most mammalian mRNAs are conserved targets of microRNAs. Genome Research, 19, 92–105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2557. Friedman Y, Naamati G and Linial M, 2010. MiRror: a combinatorial analysis web tool for ensembles of microRNAs and their targets. Bioinformatics, 26, 1920–1921. [DOI] [PubMed] [Google Scholar]
  2558. Gan HH and Gunsalus KC, 2015. Assembly and analysis of eukaryotic Argonaute‐RNA complexes in microRNA‐target recognition. Nucleic Acids Research, 43, 9613–9625. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2559. Ghosal S, Saha S, Das S, Sen R, Goswami S, Jana SS and Chakrabarti J, 2016. miRepress: modelling gene expression regulation by microRNA with non‐conventional binding sites. Scientific Reports, 6, 22334–22334. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2560. Ghoshal A, Shankar R, Bagchi S, Grama A and Chaterji S, 2015. MicroRNA target prediction using thermodynamic and sequence curves. BMC Genomics, 16, 999–999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2561. Grimm D, Streetz KL, Jopling CL, Storm TA, Pandey K, Davis CR, Marion P, Salazar F and Kay MA, 2006. Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature, 441, 537–541. [DOI] [PubMed] [Google Scholar]
  2562. Grimson A, Farh KKH, Johnston WK, Garrett‐Engele P, Lim LP and Bartel DP, 2007. MicroRNA targeting specificity in mammals: Determinants beyond seed pairing. Molecular Cell, 27, 91–105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2563. Grosswendt S, Filipchyk A, Manzano M, Klironomos F, Schilling M, Herzog M, Gottwein E and Rajewsky N, 2014. Unambiguous Identification of miRNA: Target Site Interactions by Different Types of Ligation Reactions. Molecular Cell, 54, 1042–1054. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2564. Grun D, Wang YL, Langenberger D, Gunsalus KC and Rajewsky N, 2005. MicroRNA target predictions across seven Drosophila species and comparison to mammalian targets. Plos Computational Biology, 1, 51–66. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2565. Gu S, Zhang Y, Jin L, Huang Y, Zhang FJ, Bassik MC, Kampmann M and Kay MA, 2014. Weak base pairing in both seed and 3 ‘ regions reduces RNAi off‐targets and enhances si/shRNA designs. Nucleic Acids Research, 42, 12169–12176. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2566. Gumienny R and Zavolan M, 2015. Accurate transcriptome‐wide prediction of microRNA targets and small interfering RNA off‐targets with MIRZA‐G. Nucleic Acids Research, 43, 1380–1391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2567. Guo ZW, Xie C, Yang JR, Li JH, Yang JH and Zheng LM 2015. MtiBase: a database for decoding microRNA target sites located within CDS and 5 ‘ UTR regions from CLIP‐Seq and expression profile datasets. Database‐the Journal of Biological Databases and Curation, 2015. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2568. Guzman F, Almerao MP, Korbes AP, Christoff AP, Zanella CM, Bered F and Margis R, 2013. Identification of potential miRNAs and their targets in Vriesea carinata (Poales, Bromeliaceae). Plant Science, 210, 214–223. [DOI] [PubMed] [Google Scholar]
  2569. Haecker I and Renne R, 2014. HITS‐CLIP and PAR‐CLIP advance viral miRNA targetome analysis. Critical Reviews in Eukaryotic Gene Expression, 24, 101–116. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2570. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M and Tuschl T, 2010. Transcriptome‐wide identification of RNA‐binding protein and microRNA target sites by PAR‐CLIP. Cell, 141, 129–141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2571. Hafner M, Lianoglou S, Tuschl T and Betel D, 2012. Genome‐wide identification of miRNA targets by PAR‐CLIP. Methods, 58, 94–105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2572. Haley B and Zamore PD, 2004. Kinetic analysis of the RNAi enzyme complex. Nature Structural & Molecular Biology, 11, 599–606. [DOI] [PubMed] [Google Scholar]
  2573. Hanning JE, Saini HK, Murray MJ, van Dongen S, Davis MPA, Barker EM, Ward DM, Scarpini CG, Enright AJ, Pett MR and Coleman N, 2013. Lack of correlation between predicted and actual off‐target effects of short‐interfering RNAs targeting the human papillomavirus type 16 E7 oncogene. British Journal of Cancer, 108, 450–460. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2574. Hannus M, Beitzinger M, Engelmann JC, Weickert MT, Spang R, Hannus S and Meister G, 2014. siPools: highly complex but accurately defined siRNA pools eliminate off‐target effects. Nucleic Acids Research, 42, 8049–8061. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2575. Hausser J, Berninger P, Rodak C, Jantscher Y, Wirth S and Zavolan M, 2009. MirZ: an integrated microRNA expression atlas and target prediction resource. Nucleic Acids Research, 37, W266–W272. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2576. Heale BSE, Soifer HS, Bowers C and Rossi JJ, 2005. siRNA target site secondary structure predictions using local stable substructures. Nucleic Acids Research, 33, 1–10. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2577. Heale BSE, Soifer HS, Bowers C and Rossi JJ, 2006. siRNA target site secondary structure predictions using local stable substructures (vol 33, pg 30, 2005). Nucleic Acids Research, 34, 4653–4653. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2578. Helwak A, Kudla G, Dudnakova T and Tollervey D, 2013. Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding. Cell, 153, 654–665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2579. Helwak A and Tollervey D, 2014. Mapping the miRNA interactome by cross‐linking ligation and sequencing of hybrids (CLASH). Nature Protocols, 9, 711–728. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2580. Hendrickson DG, Hogan DJ, Herschlag D, Ferrell JE and Brown PO, 2008. Systematic Identification of mRNAs Recruited to Argonaute 2 by Specific microRNAs and Corresponding Changes in Transcript Abundance. PLoS ONE, 3, e2126–e2126. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2581. Hill CG, Jabbari N, Matyunina LV and McDonald JF, 2014. Functional and Evolutionary Significance of Human MicroRNA Seed Region Mutations. PLoS ONE, 9, e115241–e115241. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2582. Holen T, Moe SE, Sorbo JG, Meza TJ, Ottersen OP and Klungland A, 2005. Tolerated wobble mutations in siRNAs decrease specificity, but can enhance activity in vivo. Nucleic Acids Research, 33, 4704–4710. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2583. Hon LS and Zhang ZM, 2007. The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression. Genome Biology, 8, R166–R166. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2584. Hsieh WJ and Wang HY, 2011. Human microRNA target identification by RRSM. Journal of Theoretical Biology, 286, 79–84. [DOI] [PubMed] [Google Scholar]
  2585. Hsu PWC, Huang HD, Hsu SD, Lin LZ, Tsou AP, Tseng CP, Stadler PF, Washietl S and Hofacker IL, 2006. miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Research, 34, D135–D139. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2586. Hsu SD, Huang HY, Chou CH, Sun YM, Hsu MT and Tsou AP, 2015. Integrated analyses to reconstruct microRNA‐mediated regulatory networks in mouse liver using high‐throughput profiling. BMC Genomics, 16, S12–S12. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2587. Huang JC, Morris QD and Frey BJ, 2007. Bayesian inference of microRNA targets from sequence and expression data. Journal of Computational Biology, 14, 550–563. [DOI] [PubMed] [Google Scholar]
  2588. Huang Y, Zou Q, Sun XH and Zhao LP, 2014a. Computational Identification of MicroRNAs and Their Targets in Perennial Ryegrass (Lolium perenne). Applied Biochemistry and Biotechnology, 173, 1011–1022. [DOI] [PubMed] [Google Scholar]
  2589. Huang Y, Zou Q and Wang ZB, 2014b. Computational identification of miRNA genes and their targets in mulberry. Russian Journal of Plant Physiology, 61, 537–542. [Google Scholar]
  2590. Huang Y, Cheng JH, Luo FN, Pan H, Sun XJ, Diao LY and Qin XJ, 2016. Genome‐wide identification and characterization of microRNA genes and their targets in large yellow croaker (Larimichthys crocea). Gene, 576, 261–267. [DOI] [PubMed] [Google Scholar]
  2591. Imig J, Brunschweiger A, Brummer A, Guennewig B, Mittal N, Kishore S, Tsikrika P, Gerber AP, Zavolan M and Hall J, 2015. miR‐CLIP capture of a miRNA targetome uncovers a lincRNA H19‐miR‐106a interaction. Nature Chemical Biology, 11, 107–U143. [DOI] [PubMed] [Google Scholar]
  2592. Iwasaki YW, Siomi MC and Siomi H, 2015. PIWI‐Interacting RNA: Its Biogenesis and Functions. Annu Rev Biochem, 84, 405–433. [DOI] [PubMed] [Google Scholar]
  2593. Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, Mao M, Li B, Cavet G and Linsley PS, 2003. Expression profiling reveals off‐target gene regulation by RNAi. Nature Biotechnology, 21, 635–637. [DOI] [PubMed] [Google Scholar]
  2594. Jackson AL, Burchard J, Leake D, Reynolds A, Schelter J, Guo J, Johnson JM, Lim L, Karpilow J, Nichols K, Marshall W, Khvorova A and Linsley PS, 2006a. Position‐specific chemical modification of siRNAs reduces “off‐target’’ transcript silencing. Rna‐a Publication of the Rna Society, 12, 1197–1205. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2595. Jackson AL, Burchard J, Schelter J, Chau BN, Cleary M, Lim L and Linsley PS, 2006b. Widespread siRNA “off‐target’’ transcript silencing mediated by seed region sequence complementarity. Rna‐a Publication of the Rna Society, 12, 1179–1187. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2596. Jagla B, Aulner N, Kelly PD, Song D, Volchuk A, Zatorski A, Shum D, Mayer T, De Angelis DA, Ouerfelli O, Rutishauser U and Rothman JE, 2005. Sequence characteristics of functional siRNAs. Rna‐a Publication of the Rna Society, 11, 864–872. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2597. Janas MM, Wang B, Harris AS, Aguiar M, Shaffer JM, Subrahmanyam YV, Behlke MA, Wucherpfennig KW, Gygi SP, Gagnon E and Novina CD, 2012. Alternative RISC assembly: binding and repression of microRNA‐mRNA duplexes by human Ago proteins. Rna, 18, 2041–2055. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2598. Jaskiewicz L, Bilen B, Hausser J and Zavolan M, 2012. Argonaute CLIP ‐ A method to identify in vivo targets of miRINAs. Methods, 58, 106–112. [DOI] [PubMed] [Google Scholar]
  2599. Jinek M and Doudna JA, 2009. A three‐dimensional view of the molecular machinery of RNA interference. Nature, 457, 405–412. [DOI] [PubMed] [Google Scholar]
  2600. Jo MH, Shin S, Jung SR, Kim E, Song JJ and Hohng S, 2015a. Human Argonaute 2 Has Diverse Reaction Pathways on Target RNAs. Molecular Cell, 59, 117–124. [DOI] [PubMed] [Google Scholar]
  2601. Jo MH, Song J‐J and Hohng S, 2015b. Single‐molecule fluorescence measurements reveal the reaction mechanisms of the core‐RISC, composed of human Argonaute 2 and a guide RNA. Bmb Reports, 48, 643–644. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2602. John B, Enright AJ, Aravin A, Tuschl T, Sander C and Marks DS, 2004. Human MicroRNA targets. Plos Biology, 2, 1862–1879. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2603. Jones‐Rhoades MW and Bartel DP, 2004. Computational identification of plant microRNAs and their targets, including a stress‐induced miRNA. Mol Cell, 14, 787–799. [DOI] [PubMed] [Google Scholar]
  2604. Jones‐Rhoades MW, Bartel DP and Bartel B, 2006. MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol, 57, 19–53. [DOI] [PubMed] [Google Scholar]
  2605. Jung D, Kim B, Freishtat RJ, Giri M, Hoffman E and Seo J, 2015. miRTarVis: an interactive visual analysis tool for microRNA‐mRNA expression profile data. BMC proceedings, 9, S2–S2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2606. Kakrana A, Hammond R, Patel P, Nakano M and Meyers BC, 2014. sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target‐identification software. Nucleic Acids Research, 42, e139–e139. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2607. Kamola PJ, Nakano Y, Takahashi T, Wilson PA and Uitei K, 2015. The siRNA Non‐seed Region and Its Target Sequences Are Auxiliary Determinants of Off‐Target Effects. Plos Computational Biology, 11, e1004656–e1004656. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2608. Karathanou K, Theofilatos K, Kleftogiannis D, Alexakos C, Likothanassis S, Tsakalidis A and Mavroudi S, 2015. ncRNAclass: A Web Platform for Non‐Coding RNA Feature Calculation and MicroRNAs and Targets Prediction. International Journal on Artificial Intelligence Tools, 24. [Google Scholar]
  2609. Karginov FV, Conaco C, Xuan Z, Schmidt BH, Parker JS, Mandel G and Hannon GJ, 2007. A biochemical approach to identifying microRNA targets. America, 104, 19291–19296. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2610. Katanforoush A and Mahdavi E, 2015. miRNA target recognition using features of suboptimal alignments. International Journal of Data Mining and Bioinformatics, 13, 171–180. [DOI] [PubMed] [Google Scholar]
  2611. Katoh T and Suzuki T, 2007. Specific residues at every third position of siRNA shape its efficient RNAi activity. Nucleic Acids Research, 35, e27–e27. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2612. Kertesz M, Iovino N, Unnerstall U, Gaul U and Segal E, 2007. The role of site accessibility in microRNA target recognition. Nature Genetics, 39, 1278–1284. [DOI] [PubMed] [Google Scholar]
  2613. Khan AA, Betel D, Miller ML, Sander C, Leslie CS and Marks DS, 2009. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nature Biotechnology, 27, 549–U592. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2614. Khorshid M, Hausser J, Zavolan M and Van Nimwegen E, 2013. A biophysical miRNA‐mRNA interaction model infers canonical and noncanonical targets. Nature Methods, 10, 253–255. [DOI] [PubMed] [Google Scholar]
  2615. Kim MS, Hur B and Kim S, 2016. RDDpred: A condition‐specific RNA‐editing prediction model from RNA‐seq data. BMC Genomics, 17, 5–5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2616. Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z and Hatzigeorgiou A, 2004. A combined computational‐experimental approach predicts human microRNA targets. Genes & Development, 18, 1165–1178. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2617. Korfiati A, Theofilatos K, Kleftogiannis D, Alexakos C, Likothanassis S and Mavroudi S, 2015. Predicting human miRNA target genes using a novel computational intelligent framework. Information Sciences, 294, 576–585. [Google Scholar]
  2618. Kozomara A and Griffiths‐Jones S, 2014. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res, 42, D68–73. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2619. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M and Rajewsky N, 2005. Combinatorial microRNA target predictions. Nature Genetics, 37, 495–500. [DOI] [PubMed] [Google Scholar]
  2620. Krutzfeldt J, Rajewsky N, Braich R, Rajeev KG, Tuschl T, Manoharan M and Stoffel M, 2005. Silencing of microRNAs in vivo with ‘antagomirs’. Nature, 438, 685–689. [DOI] [PubMed] [Google Scholar]
  2621. Kumar D, Singh D, Kanodia P, Prabhu KV, Kumar M and Mukhopadhyay K, 2014. Discovery of novel leaf rust responsive microRNAs in wheat and prediction of their target genes. Journal of Nucleic Acids, 2014, 570176–570176. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2622. Kumar D, 2015. Synthetic Gene Complementation to Determine Off‐Target Silencing. In: Plant Gene Silencing: Methods and Protocols. 281–293. [DOI] [PubMed]
  2623. Kurubanjerdjit N, Huang CH, Lee YL, Tsai JJP and Ng KL, 2013. Prediction of microRNA‐regulated protein interaction pathways in Arabidopsis using machine learning algorithms. Computers in Biology and Medicine, 43, 1645–1652. [DOI] [PubMed] [Google Scholar]
  2624. Lagana A, 2015. Computational Prediction of microRNA Targets. In: Microrna: Basic Science: From Molecular Biology to Clinical Practice. 231–252. [DOI] [PubMed] [Google Scholar]
  2625. Lagos‐Quintana M, Rauhut R, Lendeckel W and Tuschl T, 2001. Identification of novel genes coding for small expressed RNAs. Science, 294, 853–858. [DOI] [PubMed] [Google Scholar]
  2626. Lau NC, Lim LP, Weinstein EG and Bartel DP, 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science, 294, 858–862. [DOI] [PubMed] [Google Scholar]
  2627. Law PT, Qin H, Chan TF and Wong N, 2013. Experimental verification of microRNA targets is essential, prediction alone is insufficient. Carcinogenesis, 34, 723–723. [DOI] [PubMed] [Google Scholar]
  2628. Le TD, Zhang JP, Liu L and Li JY, 2015a. Ensemble Methods for MiRNA Target Prediction from Expression Data. PLoS ONE, 10, e0131627–e0131627. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2629. Le TD, Zhang JP, Liu L, Liu HW and Li JY, 2015b. miRLAB: An R Based Dry Lab for Exploring miRNA‐mRNA Regulatory Relationships. PLoS ONE, 10, e0145386–e0145386. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2630. Lee E, Ito K, Zhao Y, Schadt EE, Irie HY and Zhu J, 2016. Inferred miRNA activity identifies miRNA‐mediated regulatory networks underlying multiple cancers. Bioinformatics, 32, 96–105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2631. Lee RC and Ambros V, 2001. An extensive class of small RNAs in Caenorhabditis elegans. Science, 294, 862–864. [DOI] [PubMed] [Google Scholar]
  2632. Leoni G and Tramontano A, 2016. A structural view of microRNA‐target recognition. Nucleic Acids Research. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2633. Leung AKL, Young AG, Bhutkar A, Zheng GX, Bosson AD, Nielsen CB and Sharp PA, 2011. Genome‐wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs. Nature Structural & Molecular Biology, 18, 237–U309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2634. Lewis BP, Shih IH, Jones‐Rhoades MW, Bartel DP and Burge CB, 2003. Prediction of mammalian microRNA targets. Cell, 115, 787–798. [DOI] [PubMed] [Google Scholar]
  2635. Lewis BP, Burge CB and Bartel DP, 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15–20. [DOI] [PubMed] [Google Scholar]
  2636. Li C, Liu Z, Yang F, Liu W, Wang D, Dong E, Wang Y, Wu CI and Lu X, 2015. siRNAs with decreased off‐target effect facilitate the identification of essential genes in cancer cells. [DOI] [PMC free article] [PubMed]
  2637. Li JJ, Kim TH, Nutiu R, Ray D, Hughes TR and Zhang ZL, 2014. Identifying mRNA sequence elements for target recognition by human Argonaute proteins. Genome Research, 24, 775–785. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2638. Li Y and Zhang CY, 2012. Analysis of MicroRNA‐Induced Silencing Complex‐Involved MicroRNA‐Target Recognition by Single‐Molecule Fluorescence Resonance Energy Transfer. Analytical Chemistry, 84, 5097–5102. [DOI] [PubMed] [Google Scholar]
  2639. Li Y and Zhang ZL, 2015. Computational Biology in microRNA. Wiley Interdisciplinary Reviews‐Rna, 6, 435–452. [DOI] [PubMed] [Google Scholar]
  2640. Li YF and Sunkar R, 2013. Global identification of small RNA targets in plants by sequencing sliced ends of messenger RNAs. [DOI] [PubMed]
  2641. Lim LP, Lau NC, Garrett‐Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS and Johnson JM, 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature, 433, 769–773. [DOI] [PubMed] [Google Scholar]
  2642. Lin X, Morgan‐Lappe S, Huang X, Li L, Zakula DM, Vernetti LA, Fesik SW and Shen Y, 2007. ‘Seed’ analysis of off‐target siRNAs reveals an essential role of Mcl‐1 in resistance to the small‐molecule Bcl‐2/Bcl‐X‐L inhibitor ABT‐737. Oncogene, 26, 3972–3979. [DOI] [PubMed] [Google Scholar]
  2643. Lin XY, Ruan X, Anderson MG, McDowell JA, Kroeger PE, Fesik SW and Shen Y, 2005. siRNA‐mediated off‐target gene silencing triggered by a 7 nt complementation. Nucleic Acids Research, 33, 4527–4535. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2644. Liu CC, Mallick B, Long D, Rennie WA, Wolenc A, Carmack CS and Ding Y, 2013. CLIP‐based prediction of mammalian microRNA binding sites. Nucleic Acids Research, 41, e138–e138. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2645. Liu CC, Rennie WA, Mallick B, Kanoria S, Long D, Wolenc A, Carmack CS and Ding Y, 2014a. MicroRNA binding sites in C. elegans 3 ‘ UTRs. RNA Biology, 11, 693–701. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2646. Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, Song JJ, Hammond SM, Joshua‐Tor L and Hannon GJ, 2004. Argonaute2 is the catalytic engine of mammalian RNAi. Science, 305, 1437–1441. [DOI] [PubMed] [Google Scholar]
  2647. Liu Q, Yao X, Pi L, Wang H, Cui X and Huang H, 2009. The ARGONAUTE10 gene modulates shoot apical meristem maintenance and establishment of leaf polarity by repressing miR165/166 in Arabidopsis . Plant J, 58, 27–40. [DOI] [PubMed] [Google Scholar]
  2648. Liu QK, Wang F and Axtell MJ, 2014b. Analysis of Complementarity Requirements for Plant MicroRNA Targeting Using a Nicotiana benthamiana Quantitative Transient Assay. Plant Cell, 26, 741–753. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2649. Liu Y, Baker S, Jiang H, Stuart G and Bai Y, 2015. Correlating Bladder Cancer Risk Genes with Their Targeting MicroRNAs Using MMiRNA‐Tar. Genomics, Proteomics and Bioinformatics, 13, 177–182. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2650. Llave C, Xie Z, Kasschau KD and Carrington JC, 2002. Cleavage of Scarecrow‐like mRNA targets directed by a class of Arabidopsis miRNA. Science, 297, 2053–2056. [DOI] [PubMed] [Google Scholar]
  2651. Long D, Lee R, Williams P, Chan CY, Ambros V and Ding Y, 2007. Potent effect of target structure on microRNA function. Nature Structural & Molecular Biology, 14, 287–294. [DOI] [PubMed] [Google Scholar]
  2652. Lu S and Cullen BR, 2004. Adenovirus VA1 noncoding RNA can inhibit small interfering RNA and MicroRNA biogenesis. J Virol, 78, 12868–12876. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2653. Lytle JR, Yario TA and Steitz JA, 2007. Target mRNAs are repressed as efficiently by microRNA‐binding sites in the 5 ‘ UTR as in the 3 ‘ UTR. America, 104, 9667–9672. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2654. Ma JB, Yuan YR, Meister G, Pei Y, Tuschl T and Patel DJ, 2005. Structural basis for 5 ‘‐end‐specific recognition of guide RNA by the A‐fulgidus Piwi protein. Nature, 434, 666–670. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2655. Ma Y, Creanga A, Lum L and Beachy PA, 2006. Prevalence of off‐target effects in Drosophila RNA interference screens. Nature, 443, 359–363. [DOI] [PubMed] [Google Scholar]
  2656. Majoros WH and Ohler U, 2007. Spatial preferences of microRNA targets in 3 ‘ untranslated regions. BMC Genomics, 8, 152–152. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2657. Majoros WH, Lekprasert P, Mukherjee N, Skalsky RL, Corcoran DL, Cullen BR and Ohler U, 2013. MicroRNA target site identification by integrating sequence and binding information. Nat Methods, 10, 630–633. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2658. Maragkakis M, Reczko M, Simossis VA, Alexiou P, Papadopoulos GL, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Vergoulis T, Koziris N, Sellis T, Tsanakas P and Hatzigeorgiou AG, 2009. DIANA‐microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Research, 37, W273–W276. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2659. Maragkakis M, Vergoulis T, Alexiou P, Reczko M, Plomaritou K, Gousis M, Kourtis K, Koziris N, Dalamagas T and Hatzigeorgiou AG, 2011. DIANA‐microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association. Nucleic Acids Research, 39, W145–W148. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2660. Marin RM, Voellmy F, von Erlach T and Vanicek J, 2012. Analysis of the accessibility of CLIP bound sites reveals that nucleation of the miRNA:mRNA pairing occurs preferentially at the 3 ‘‐end of the seed match. Rna‐a Publication of the Rna Society, 18, 1760–1770. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2661. Martin HC, Wani S, Steptoe AL, Krishnan K, Nones K, Nourbakhsh E, Vlassov A, Grimmond SM and Cloonan N, 2014. Imperfect centered miRNA binding sites are common and can mediate repression of target mRNAs. Genome Biology, 15, R51–R51. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2662. Martin SE and Caplen NJ, 2006. Mismatched siRNAs downregulate mRNAs as a function of target site location. Febs Letters, 580, 3694–3698. [DOI] [PubMed] [Google Scholar]
  2663. Maxwell EK, Campbell JD, Spira A and Baxevanis AD, 2015. SubmiRine: assessing variants in microRNA targets using clinical genomic data sets. Nucleic Acids Research, 43, 3886–3898. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2664. Megraw M, Sethupathy P, Corda B and Hatzigeorgiou AG, 2007. miRGen: a database for the study of animal microRNA genomic organization and function. Nucleic Acids Research, 35, D149–D155. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2665. Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G and Tuschl T, 2004. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol Cell, 15, 185–197. [DOI] [PubMed] [Google Scholar]
  2666. Menezes RX, Mohammadi L, Goeman JJ and Boer JM, 2016. Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack. BMC Bioinformatics, 17, 77–77. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2667. Mishra AK, Duraisamy GS and Matousek J, 2015. Discovering MicroRNAs and Their Targets in Plants. Critical Reviews in Plant Sciences, 34, 553–571. [Google Scholar]
  2668. Mohr SE, Smith JA, Shamu CE, Neumuller RA and Perrimon N, 2014. RNAi screening comes of age: improved techniques and complementary approaches. Nature Reviews Molecular Cell Biology, 15, 591–600. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2669. Moore MJ, Scheel TKH, Luna JM, Park CY, Fak JJ, Nishiuchi E, Rice CM and Darnell RB, 2015. miRNA‐target chimeras reveal miRNA 3 ‘‐end pairing as a major determinant of Argonaute target specificity. Nature Communications, 6, 8864–8864. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2670. Mousavi R, Eftekhari M and Haghighi MG, 2015. A new approach to human microRNA target prediction using ensemble pruning and rotation foreste. Journal of Bioinformatics and Computational Biology, 13, 1550017–1550017. [DOI] [PubMed] [Google Scholar]
  2671. Muckstein U, Tafer H, Hackermuller J, Bernhart SH, Stadler PF and Hofacker IL, 2006. Thermodynamics of RNA‐RNA binding. Bioinformatics, 22, 1177–1182. [DOI] [PubMed] [Google Scholar]
  2672. Mullany LE, Herrick JS, Wolff RK and Slattery ML, 2016. MicroRNA Seed Region Length Impact on Target Messenger RNA Expression and Survival in Colorectal Cancer. PLoS ONE, 11, e0154177–e0154177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2673. Naito Y, Yoshimura J, Morishita S and Ui‐Tei K, 2009. siDirect 2.0: updated software for designing functional siRNA with reduced seed‐dependent off‐target effect. BMC Bioinformatics, 10, 392–392. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2674. Naito Y and Ui‐Tei K, 2013. Designing functional siRNA with reduced off‐target effects. Methods in Molecular Biology, 942, 57–68. [DOI] [PubMed] [Google Scholar]
  2675. Nakanishi K, Ascano M, Gogakos T, Ishibe‐Murakami S, Serganov AA, Briskin D, Morozov P, Tuschl T and Patel DJ, 2013. Eukaryote‐Specific Insertion Elements Control Human ARGONAUTE Slicer Activity. Cell Reports, 3, 1893–1900. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2676. Nam JW, Rissland OS, Koppstein D, Abreu‐Goodger C, Jan CH, Agarwal V, Yildirim MA, Rodriguez A and Bartel DP, 2014a. Global Analyses of the Effect of Different Cellular Contexts on MicroRNA Targeting. Molecular Cell, 53, 1031–1043. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2677. Nam S, Kim B, Shin S and Lee S, 2008. miRGator: an integrated system for functional annotation of microRNAs. Nucleic Acids Research, 36, D159–D164. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2678. Nam S, Li M, Choi KM, Balch C, Kim S and Nephew KP, 2009. MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Research, 37, W356–W362. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2679. Nam S, Ryu H, Son WJ, Kim YH, Kim KT, Balch C, Nephew KP and Lee J, 2014b. Mg2+ Effect on Argonaute and RNA Duplex by Molecular Dynamics and Bioinformatics Implications. PLoS ONE, 9, e109745–e109745. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2680. Nielsen CB, Shomron N, Sandberg R, Hornstein E, Kitzman J and Burge CB, 2007. Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. Rna‐a Publication of the Rna Society, 13, 1894–1910. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2681. Nithin C, Patwa N, Thomas A, Bahadur RP and Basak J, 2015. Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures. Bmc Plant Biology, 15, 140–140. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2682. Nolte A, Ott K, Rohayem J, Walker T, Schlensak C and Wendel HP, 2013. Modification of small interfering RNAs to prevent off‐target effects by the sense strand. New Biotechnology, 30, 159–165. [DOI] [PubMed] [Google Scholar]
  2683. Orom UA and Lund AH, 2007. Isolation of microRNA targets using biotinylated synthetic microRNAs. Methods, 43, 162–165. [DOI] [PubMed] [Google Scholar]
  2684. Paraskevopoulou MD, Georgakilas G, Kostoulas N, Reczko M, Maragkakis M, Dalamagas TM and Hatzigeorgiou AG, 2013a. DIANA‐LncBase: experimentally verified and computationally predicted microRNA targets on long non‐coding RNAs. Nucleic Acids Research, 41, D239–D245. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2685. Paraskevopoulou MD, Georgakilas G, Kostoulas N, Vlachos IS, Vergoulis T, Reczko M, Filippidis C, Dalamagas T and Hatzigeorgiou AG, 2013b. DIANA‐microT web server v5.0: service integration into miRNA functional analysis workflows. Nucleic Acids Research, 41, W169–W173. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2686. Paraskevopoulou MD, Vlachos IS, Karagkouni D, Georgakilas G, Kanellos I, Vergoulis T, Zagganas K, Tsanakas P, Floros E, Dalamagas T and Hatzigeorgiou AG, 2016. DIANA‐LncBase v2: indexing microRNA targets on non‐coding transcripts. Nucleic Acids Research, 44, D231–D238. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2687. Park JH, Ahn S, Kim S, Lee J, Nam JW and Shin C, 2013. Degradome sequencing reveals an endogenous microRNA target in C. elegans. Febs Letters, 587, 964–969. [DOI] [PubMed] [Google Scholar]
  2688. Parker JS, Roe SM and Barford D, 2004. Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. Embo Journal, 23, 4727–4737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2689. Parker JS, Roe SM and Barford D, 2005. Structural insights into mRNA recognition from a PIWI domain‐siRNA guide complex. Nature, 434, 663–666. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2690. Pasquinelli AE, 2012. MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. Nat Rev Genet, 13, 271–282. [DOI] [PubMed] [Google Scholar]
  2691. Peacock H, Kannan A, Beal PA and Burrows CJ, 2011. Chemical Modification of siRNA Bases To Probe and Enhance RNA Interference. Journal of Organic Chemistry, 76, 7295–7300. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2692. Peterson SM, Thompson JA, Ufkin ML, Sathyanarayana P, Liaw L and Congdon CB, 2014. Common features of microRNA target prediction tools. Frontiers in Genetics, 5, 23–23. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2693. Petri S, Dueck A, Lehmann G, Putz N, Rudel S, Kremmer E and Meister G, 2011. Increased siRNA duplex stability correlates with reduced off‐target and elevated on‐target effects. Rna, 17, 737–749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2694. Petri S and Meister G, 2013. siRNA design principles and off‐target effects. Methods in molecular biology (Clifton, N.J.), 986, 59–71. [DOI] [PubMed] [Google Scholar]
  2695. Pio G, Ceci M, Malerba D and D'Elia D, 2015. ComiRNet: a web‐based system for the analysis of miRNA‐gene regulatory networks. BMC Bioinformatics, 16, S7–S7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2696. Qiu SB, Lane TR and Yang CD, 2007. Efficient search algorithms for RNAi target detection. Journal of Supercomputing, 42, 303–319. [Google Scholar]
  2697. Rabiee‐Ghahfarrokhi B, Rafiei F, Niknafs AA and Zamani B, 2015. Prediction of microRNA target genes using an efficient genetic algorithm‐based decision tree. Febs Open Bio, 5, 877–884. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2698. Reczko M, Maragkakis M, Alexiou P, Papadopoulos GL and Hatzigeorgiou AG, 2011. Accurate microRNA Target Prediction Using Detailed Binding Site Accessibility and Machine Learning on Proteomics Data. Frontiers in Genetics, 2, 103–103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2699. Rennie W, Liu CC, Carmack CS, Wolenc A, Kanoria S, Lu J, Long D and Ding Y, 2014. STarMir: a web server for prediction of microRNA binding sites. Nucleic Acids Research, 42, W114–W118. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2700. Reyes‐Herrera PH, Ficarra E, Acquaviva A and Macii E, 2011. miREE: miRNA recognition elements ensemble. BMC Bioinformatics, 12, 454–454. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2701. Rhee S, Chae H and Kim S, 2015. PlantMirnaT: miRNA and mRNA integrated analysis fully utilizing characteristics of plant sequencing data. Methods, 83, 80–87. [DOI] [PubMed] [Google Scholar]
  2702. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B and Bartel DP, 2002. Prediction of plant microRNA targets. Cell, 110, 513–520. [DOI] [PubMed] [Google Scholar]
  2703. Ristevski B, 2015. Overview of Computational Approaches for Inference of MicroRNA‐Mediated and Gene Regulatory Networks. Advances in Computers, 97, 111–145. [Google Scholar]
  2704. Rueda A, Barturen G, Lebron R, Gomez‐Martin C, Alganza A, Oliver JL and Hackenberg M, 2015. sRNAtoolbox: an integrated collection of small RNA research tools. Nucleic Acids Research, 43, W467–W473. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2705. Ryan BC, Werner TS, Howard PL and Chow RL, 2016. ImiRP: a computational approach to microRNA target site mutation. BMC Bioinformatics, 17, 190–190. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2706. Saetrom O, Snove O and Saetrom P, 2005. Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms. Rna‐a Publication of the Rna Society, 11, 995–1003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2707. Salomon WE, Jolly SM, Moore MJ, Zamore PD and Serebrov V, 2015. Single‐Molecule Imaging Reveals that Argonaute Reshapes the Binding Properties of Its Nucleic Acid Guides. Cell, 162, 84–95. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2708. Sass S, Pitea A, Unger K, Hess J, Mueller NS and Theis FJ, 2015. MicroRNA‐Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma. International Journal of Molecular Sciences, 16, 30204–30222. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2709. Saxena S, Jonsson ZO and Dutta A, 2003. Small RNAs with imperfect match to endogenous mRNA repress translation ‐ Implications for off‐target activity of small inhibitory RNA in mammalian cells. Journal of Biological Chemistry, 278, 44312–44319. [DOI] [PubMed] [Google Scholar]
  2710. Scacheri PC, Rozenblatt‐Rosen O, Caplen NJ, Wolfsberg TG, Umayam L, Lee JC, Hughes CM, Shanmugam KS, Bhattacharjee A, Meyerson M and Collins FS, 2004. Short interfering RNAs can induce unexpected and divergent changes in the levels of untargeted proteins in mammalian cells. America, 101, 1892–1897. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2711. Schirle NT and MacRae IJ, 2012. The Crystal Structure of Human Argonaute2. Science, 336, 1037–1040. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2712. Schirle NT, Sheu‐Gruttadauria J and MacRae IJ, 2014. Structural basis for microRNA targeting. Science, 346, 608–613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2713. Schirle NT, Sheu‐Gruttadauria J, Chandradoss SD, Joo C and MacRae IJ, 2015. Water‐mediated recognition of t1‐adenosine anchors Argonaute2 to microRNA targets. Elife, 4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2714. Schirle NT, Kinberger GA, Murray HF, Lima WF, Prakash TP and MacRae IJ, 2016. Structural Analysis of Human Argonaute‐2 Bound to a Modified siRNA Guide. J Am Chem Soc, 138, 8694–8697. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2715. Schmich F, Szczurek E, Kreibich S, Dilling S, Andritschke D, Casanova A, Low SH, Eicher S, Muntwiler S, Emmenlauer M, Ramo P, Conde‐Alvarez R, von Mering C, Hardt WD, Dehio C and Beerenwinkel N, 2015. gespeR: a statistical model for deconvoluting off‐target‐confounded RNA interference screens. Genome Biology, 16, 220–220. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2716. Schubert S, Grunweller A, Erdmann VA and Kurreck J, 2005. Local RNA target structure influences siRNA efficacy: systematic analysis of intentionally designed binding regions. Journal of Molecular Biology, 348, 883–893. [DOI] [PubMed] [Google Scholar]
  2717. Schwarz DS, Ding HL, Kennington L, Moore JT, Schelter J, Burchard J, Linsley PS, Aronin N, Xu ZS and Zamore PD, 2006. Designing siRNA that distinguish between genes that differ by a single nucleotide. PLoS Genetics, 2, 1307–1318. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2718. Seok H and Ham J, 2016a. Jang ES and Chi SW. MicroRNA Target Recognition, Insights from Transcriptome‐Wide Non‐Canonical Interactions. Molecules and Cells. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2719. Seok H, Jang E‐S and Chi SW, 2016b. Rationally designed siRNAs without miRNA‐like off‐target repression. Bmb Reports, 49, 135–136. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2720. Sethupathy P, Corda B and Hatzigeorgiou AG, 2006. TarBase: A comprehensive database of experimentally supported animal microRNA targets. Rna‐a Publication of the Rna Society, 12, 192–197. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2721. Shao CG, Chen M and Meng YJ, 2013. A reversed framework for the identification of microRNA‐target pairs in plants. Briefings in Bioinformatics, 14, 293–301. [DOI] [PubMed] [Google Scholar]
  2722. Shao Y, Chan CY, Maliyekkel A, Lawrence CE, Roninson IB and Ding Y, 2007. Effect of target secondary structure on RNAi efficiency. Rna‐a Publication of the Rna Society, 13, 1631–1640. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2723. Shweta and Khan JA , 2014. In silico prediction of cotton (Gossypium hirsutum) encoded microRNAs targets in the genome of Cotton leaf curl Allahabad virus. Bioinformation, 10, 251–255. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2724. Singh N, Srivastava S and Sharma A, 2016. Identification and analysis of miRNAs and their targets in ginger using bioinformatics approach. Gene, 575, 570–576. [DOI] [PubMed] [Google Scholar]
  2725. Singh S, Wu XY, Ljosa V, Bray MA, Piccioni F, Root DE, Doench JG, Boehm JS and Carpenter AE, 2015. Morphological Profiles of RNAi‐Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects. PLoS ONE, 10, e0131370–e0131370. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2726. Snead NM, Escamilla‐Powers JR, Rossi JJ and McCaffrey AP, 2013. 5 ‘ Unlocked Nucleic Acid Modification Improves siRNA Targeting. Molecular Therapy‐Nucleic Acids, 2, e103–e103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2727. Snove O and Holen T, 2004. Many commonly used siRNAs risk off‐target activity. Biochemical and Biophysical Research Communications, 319, 256–263. [DOI] [PubMed] [Google Scholar]
  2728. Snove O and Rossi JJ, 2006. Chemical modifications rescue off‐target effects of RNAi. Acs Chemical Biology, 1, 274–276. [DOI] [PubMed] [Google Scholar]
  2729. Song JJ, Smith SK, Hannon GJ and Joshua‐Tor L, 2004. Crystal structure of Argonaute and its implications for RISC slicer activity. Science, 305, 1434–1437. [DOI] [PubMed] [Google Scholar]
  2730. Sood P, Krek A, Zavolan M, Macino G and Rajewsky N, 2006. Cell‐type‐specific signatures of microRNAs on target mRNA expression. America, 103, 2746–2751. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2731. Srivastava PK, Moturu TR, Pandey P, Baldwin IT and Pandey SP, 2014. A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome‐wide target prediction. BMC Genomics, 15, 348–348. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2732. Stalder L, Heusermann W, Sokol L, Trojer D, Wirz J, Hean J, Fritzsche A, Aeschimann F, Pfanzagl V, Basselet P, Weiler J, Hintersteiner M, Morrissey DV and Meisner‐Kober NC, 2013. The rough endoplasmatic reticulum is a central nucleation site of siRNA‐mediated RNA silencing. EMBO J, 32, 1115–1127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2733. Stark A, Brennecke J, Russell RB and Cohen SM, 2003. Identification of Drosophila MicroRNA targets. Plos Biology, 1, 397–409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2734. Sturm M, Hackenberg M, Langenberger D and Frishman D, 2010. TargetSpy: a supervised machine learning approach for microRNA target prediction. BMC Bioinformatics, 11, 292–292. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2735. Su XP, Wang HM, Ge W, Yang MJ, Hou J, Chen TY, Li N and Cao XT, 2015. An In Vivo Method to Identify microRNA Targets Not Predicted by Computation Algorithms: p21 Targeting by miR‐92a in Cancer. Cancer Research, 75, 2875–2885. [DOI] [PubMed] [Google Scholar]
  2736. Sulc M, Marin RM, Robins HS and Vanicek J, 2015. PACCMIT/PACCMIT‐CDS: identifying microRNA targets in 3 ‘ UTRs and coding sequences. Nucleic Acids Research, 43, W474–W479. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2737. Svoboda P, 2007. Off‐targeting and other non‐specific effects of RNAi experiments in mammalian cells. Curr Opin Mol Ther, 9, 248–257. [PubMed] [Google Scholar]
  2738. Svoboda P, 2014. Renaissance of mammalian endogenous RNAi. FEBS Lett, 588, 2550–2556. [DOI] [PubMed] [Google Scholar]
  2739. Svoboda P, 2015. A toolbox for miRNA analysis. FEBS Lett, 589, 1694–1701. [DOI] [PubMed] [Google Scholar]
  2740. Tafer H, Ameres SL, Obernosterer G, Gebeshuber CA, Schroeder R, Martinez J and Hofacker IL, 2008. The impact of target site accessibility on the design of effective siRNAs. Nature Biotechnology, 26, 578–583. [DOI] [PubMed] [Google Scholar]
  2741. Tafer H, 2014. Bioinformatics of sirna design. Methods in Molecular Biology, 1097, 477–490. [DOI] [PubMed] [Google Scholar]
  2742. Tan SM and Lieberman J, 2016. Capture and Identification of miRNA Targets by Biotin Pulldown and RNA‐seq. In: Post‐Transcriptional Gene Regulation, 2nd Edition. 211–228. [DOI] [PubMed] [Google Scholar]
  2743. Tarang S and Weston MD, 2014. Macros in microRNA target identification A comparative analysis of in silico, in vitro, and in vivo approaches to microRNA target identification. RNA Biology, 11, 324–333. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2744. Thang BN, Ho TB and Kanda T, 2015. A semi‐supervised tensor regression model for siRNA efficacy prediction. BMC Bioinformatics, 16, 80–80. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2745. Thomson DW, Bracken CP and Goodall GJ, 2011. Experimental strategies for microRNA target identification. Nucleic Acids Research, 39, 6845–6853. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2746. Tijsterman M, Ketting RF and Plasterk RH, 2002a. The genetics of RNA silencing. Annu Rev Genet, 36, 489–519. [DOI] [PubMed] [Google Scholar]
  2747. Tijsterman M, Okihara KL, Thijssen K and Plasterk RH, 2002b. PPW‐1, a PAZ/PIWI protein required for efficient germline RNAi, is defective in a natural isolate of C. elegans. Curr Biol, 12, 1535–1540. [DOI] [PubMed] [Google Scholar]
  2748. Urgese G, Paciello G, Acquaviva A and Ficarra E, 2016. isomiR‐SEA: an RNA‐Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA‐mRNA interaction sites evaluation. BMC Bioinformatics, 17, 148–148. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2749. Vasale JJ, Gu W, Thivierge C, Batista PJ, Claycomb JM, Youngman EM, Duchaine TF, Mello CC and Conte D Jr, 2010. Sequential rounds of RNA‐dependent RNA transcription drive endogenous small‐RNA biogenesis in the ERGO‐1/Argonaute pathway. Proc Natl Acad Sci U S A, 107, 3582–3587. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2750. Vatolin S, Navaratne K and Weil RJ, 2006. A novel method to detect functional microRNA targets. Journal of Molecular Biology, 358, 983–996. [DOI] [PubMed] [Google Scholar]
  2751. Vencken S, Hassan T, McElvaney NG, Smith SGJ and Greene CM, 2015. miR‐CATCH: MicroRNA Capture Affinity Technology. In: Rna Interference: Challenges and Therapeutic Opportunities. 365–373. [DOI] [PubMed] [Google Scholar]
  2752. Vergoulis T, Vlachos IS, Alexiou P, Georgakilas G, Maragkakis M, Reczko M, Gerangelos S, Koziris N, Dalamagas T and Hatzigeorgiou AG, 2012. TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Research, 40, D222–D229. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2753. Vila‐Casadesus M, Gironella M and Lozano JJ, 2016. MiRComb: An R Package to Analyse miRNA‐mRNA Interactions. Examples across Five Digestive Cancers. PLoS ONE, 11, e0151127–e0151127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2754. Vlachos IS, Kostoulas N, Vergoulis T, Georgakilas G, Reczko M, Maragkakis M, Paraskevopoulou MD, Prionidis K, Dalamagas T and Hatzigeorgiou AG, 2012. DIANA miRPath v. 2.0: investigating the combinatorial effect of microRNAs in pathways. Nucleic Acids Research, 40, W498–W504. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2755. Vosa U, Esko T, Kasela S and Annilo T, 2015. Altered Gene Expression Associated with microRNA Binding Site Polymorphisms. PLoS ONE, 10, e0141351–e0141351. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2756. Vourekas A, Zheng Q, Alexiou P, Maragkakis M, Kirino Y, Gregory BD and Mourelatos Z, 2012. Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis. Nat Struct Mol Biol, 19, 773–781. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2757. Wang F, Polydore S and Axtell MJ, 2015a. More than meets the eye? Factors that affect target selection by plant miRNAs and heterochromatic siRNAs. Current Opinion in Plant Biology, 27, 118–124. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2758. Wang G and Reinke V, 2008. A C. elegans Piwi, PRG‐1, regulates 21U‐RNAs during spermatogenesis. Curr Biol, 18, 861–867. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2759. Wang P, Ning SW, Wang QH, Li RH, Ye JR, Zhao ZXL, Li Y, Huang T and Li X, 2013. mirTarPri: Improved Prioritization of MicroRNA Targets through Incorporation of Functional Genomics Data. PLoS ONE, 8, e53685–e53685. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2760. Wang T, Chen BB, Kim MS, Xie Y and Xiao GH, 2014. A Model‐Based Approach to Identify Binding Sites in CLIP‐Seq Data. PLoS ONE, 9, e93248–e93248. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2761. Wang X, 2016. Improving microRNA target prediction by modeling with unambiguously identified microRNA‐target pairs from CLIP‐Ligation studies. Bioinformatics (Oxford, England). [DOI] [PMC free article] [PubMed] [Google Scholar]
  2762. Wang XW and El Naqa IM, 2008. Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics, 24, 325–332. [DOI] [PubMed] [Google Scholar]
  2763. Wang XW, 2014. Composition of seed sequence is a major determinant of microRNA targeting patterns. Bioinformatics, 30, 1377–1383. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2764. Wang Y, Li L, Tang S, Liu J, Zhang H, Zhi H, Jia G and Diao X, 2016. Combined small RNA and degradome sequencing to identify miRNAs and their targets in response to drought in foxtail millet. BMC Genetics, 17, 57–57. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2765. Wang YL, Juranek S, Li HT, Sheng G, Tuschl T and Patel DJ, 2008. Structure of an argonaute silencing complex with a seed‐containing guide DNA and target RNA duplex. Nature, 456, 921–U972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2766. Wang YL, Juranek S, Li HT, Sheng G, Wardle GS, Tuschl T and Patel DJ, 2009. Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Nature, 461, 754–U753. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2767. Wang ZX, Xu WL and Liu Y, 2015b. Integrating full spectrum of sequence features into predicting functional microRNA‐mRNA interactions. Bioinformatics, 31, 3529–3536. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2768. Wee LM, Flores‐Jasso CF, Salomon WE and Zamore PD, 2012. Argonaute Divides Its RNA Guide into Domains with Distinct Functions and RNA‐Binding Properties. Cell, 151, 1055–1067. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2769. Wei K, Yan F, Xiao H, Yang XX, Xie GE, Xiao Y, Wang TT, Xun Y, Huang ZQ, Han M, Zhang J and Xiang SL, 2014. Affinity Purification of Binding miRNAs for Messenger RNA Fused with a Common Tag. International Journal of Molecular Sciences, 15, 14753–14765. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2770. Weill N, Lisi V, Scott N, Dallaire P, Pelloux J and Major F, 2015. MiRBooking simulates the stoichiometric mode of action of microRNAs. Nucleic Acids Research, 43, 6730–6738. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2771. Wong N and Wang XW, 2015. miRDB: an online resource for microRNA target prediction and functional annotations. Nucleic Acids Research, 43, D146–D152. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2772. Wu C, Bardes EE, Jegga AG and Aronow BJ, 2014. ToppMiR: ranking microRNAs and their mRNA targets based on biological functions and context. Nucleic Acids Research, 42, W107–W113. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2773. Xiao FF, Zuo ZX, Cai GS, Kang SL, Gao XL and Li TB, 2009. miRecords: an integrated resource for microRNA‐target interactions. Nucleic Acids Research, 37, D105–D110. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2774. Xie P, Liu Y, Li YD, Zhang MQ and Wang XW, 2014. MIROR: a method for cell‐type specific microRNA occupancy rate prediction. Molecular Biosystems, 10, 1377–1384. [DOI] [PubMed] [Google Scholar]
  2775. Xing LB, Zhang D, Li YM, Zhao CP, Zhang SW, Shen YW, An N and Han MY, 2014. Genome‐wide identification of vegetative phase transition‐associated microRNAs and target predictions using degradome sequencing in Malus hupehensis. BMC Genomics, 15, 1125–1125. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2776. Xu P, Zhang YJ, Kang L, Roossinck MJ and Mysore KS, 2006. Computational estimation and experimental verification of off‐target silencing during posttranscriptional gene silencing in plants. Plant Physiology, 142, 429–440. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2777. Xu WL, San Lucas A, Wang ZX and Liu Y, 2014a. Identifying microRNA targets in different gene regions. BMC Bioinformatics, 15, S4–S4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2778. Xu WL, Wang ZX and Liu Y, 2014b. The Characterization of microRNA‐Mediated Gene Regulation as Impacted by Both Target Site Location and Seed Match Type. PLoS ONE, 9, e108260–e108260. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2779. Yamada T and Morishita S, 2005. Accelerated off‐target search algorithm for siRNA. Bioinformatics, 21, 1316–1324. [DOI] [PubMed] [Google Scholar]
  2780. Yang JH, Li JH, Shao P, Zhou H, Chen YQ and Qu LH, 2011. starBase: a database for exploring microRNA‐mRNA interaction maps from Argonaute CLIP‐Seq and Degradome‐Seq data. Nucleic Acids Research, 39, D202–D209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2781. Yao CY, Sasaki HM, Ueda T, Tomari Y and Tadakuma H, 2015. Single‐Molecule Analysis of the Target Cleavage Reaction by the Drosophila RNAi Enzyme Complex. Molecular Cell, 59, 125–132. [DOI] [PubMed] [Google Scholar]
  2782. Yekta S, Shih IH and Bartel DP, 2004. MicroRNA‐directed cleavage of HOXB8 mRNA. Science, 304, 594–596. [DOI] [PubMed] [Google Scholar]
  2783. Yi R, Doehle BP, Qin Y, Macara IG and Cullen BR, 2005. Overexpression of exportin 5 enhances RNA interference mediated by short hairpin RNAs and microRNAs. Rna, 11, 220–226. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2784. Yigit E, Batista PJ, Bei Y, Pang KM, Chen CC, Tolia NH, Joshua‐Tor L, Mitani S, Simard MJ and Mello CC, 2006. Analysis of the C. elegans Argonaute family reveals that distinct Argonautes act sequentially during RNAi. Cell, 127, 747–757. [DOI] [PubMed] [Google Scholar]
  2785. Yilmazel B, Hu YH, Sigoillot F, Smith JA, Shamu CE, Perrimon N and Mohr SE, 2014. Online GESS: prediction of miRNA‐like off‐target effects in large‐scale RNAi screen data by seed region analysis. BMC Bioinformatics, 15, 192–192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2786. Yousef M, Jung S, Kossenkov AV, Showe LC and Showe MK, 2007. Nave Bayes for microRNA target predictionsmachine learning for microRNA targets. Bioinformatics, 23, 2987–2992. [DOI] [PubMed] [Google Scholar]
  2787. Yu S, Kim J, Min H and Yoon S, 2014. Ensemble learning can significantly improve human microRNA target prediction. Methods, 69, 220–229. [DOI] [PubMed] [Google Scholar]
  2788. Yuan YR, Pei Y, Ma JB, Kuryavyi V, Zhadina M, Meister G, Chen HY, Dauter Z, Tuschl T and Patel DJ, 2005. Crystal structure of A. aeolicus argonaute, a site‐specific DNA‐guided endoribonuclease, provides insights into RISC‐mediated mRNA cleavage. Mol Cell, 19, 405–419. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2789. Zander A, Holzmeister P, Klose D, Tinnefeld P and Grohmann D, 2014. Single‐molecule FRET supports the two‐state model of argonaute action. RNA Biology, 11, 45–56. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2790. Zeng Y, Yi R and Cullen BR, 2003. MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. America, 100, 9779–9784. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2791. Zhang W, Le TD, Liu L, Zhou ZH and Li J, 2016a. Predicting miRNA targets by integrating gene Regulatory knowledge with Expression profiles. PLoS ONE, 11, e0152860–e0152860. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2792. Zhang Z, Liu X, Guo X, Wang XJ and Zhang X, 2016b. Arabidopsis AGO3 predominantly recruits 24‐nt small RNAs to regulate epigenetic silencing. Nat Plants, 2, 16049. [DOI] [PubMed] [Google Scholar]
  2793. Zheng X, Zhu J, Kapoor A and Zhu JK, 2007. Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing. EMBO J, 26, 1691–1701. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2794. Zhong R, Kim J, Kim HS, Kim M, Lum L, Levine B, Xiao GH, White MA and Xie Y, 2014. Computational detection and suppression of sequence‐specific off‐target phenotypes from whole genome RNAi screens. Nucleic Acids Research, 42, 8214–8222. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2795. Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE and Yeo GW, 2010. Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nature Structural & Molecular Biology, 17, 173–U176. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2796. Alsaweed M, Lai CT, Hartmann PE, Geddes DT and Kakulas F, 2016a. Human milk miRNAs primarily originate from the mammary gland resulting in unique miRNA profiles of fractionated milk. Scientific Reports, 6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2797. Alsaweed M, Lai CT, Hartmann PE, Geddes DT and Kakulas F, 2016b. Human Milk Cells and Lipids Conserve Numerous Known and Novel miRNAs. Some of Which Are Differentially Expressed during Lactation, Plos One: p. 11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2798. Alsaweed M, Lai CT, Hartmann PE, Geddes DT and Kakulas F, 2016c. Human Milk Cells Contain Numerous miRNAs that May Change with Milk Removal and Regulate Multiple Physiological Processes. International Journal of Molecular Sciences, 17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2799. Arroyo JD, Chevillet JR, Kroh EM, Ruf IK, Pritchard CC, Gibson DF, Mitchell PS, Bennett CF, Pogosova‐Agadjanyan EL, Stirewalt DL, Tait JF and Tewari M, 2011. Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc Natl Acad Sci U S A, 108, 5003–5008. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2800. Atkins CA, Smith PM and Rodriguez‐Medina C, 2011. Macromolecules in phloem exudates–a review. Protoplasma, 248, 165–172. [DOI] [PubMed] [Google Scholar]
  2801. Baglio SR, Rooijers K, Koppers‐Lalic D, Verweij FJ, Pérez Lanzón M, Zini N, Naaijkens B, Perut F, Niessen HWM, Baldini N and Pegtel DM, 2015. Human bone marrow‐ and adipose‐mesenchymal stem cells secrete exosomes enriched in distinctive miRNA and tRNA species. Stem Cell Research and Therapy, 6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2802. Baier SR, Nguyen C, Xie F, Wood JR and Zempleni J, 2014. MicroRNAs Are Absorbed in Biologically Meaningful Amounts from Nutritionally Relevant Doses of Cow Milk and Affect Gene Expression in Peripheral Blood Mononuclear Cells, HEK‐293 Kidney Cell Cultures, and Mouse Livers. Journal of Nutrition, 144, 1495–1500. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2803. Baum JA, Bogaert T, Clinton W, Heck GR, Feldmann P, Ilagan O, Johnson S, Plaetinck G, Munyikwa T, Pleau M, Vaughn T and Roberts J, 2007. Control of coleopteran insect pests through RNA interference. Nat Biotechnol, 25, 1322–1326. [DOI] [PubMed] [Google Scholar]
  2804. Baurle I, Smith L, Baulcombe DC and Dean C, 2007. Widespread role for the flowering‐time regulators FCA and FPA in RNA‐mediated chromatin silencing. Science, 318, 109–112. [DOI] [PubMed] [Google Scholar]
  2805. Beclin C, Berthome R, Palauqui JC, Tepfer M and Vaucheret H, 1998. Infection of tobacco or Arabidopsis plants by CMV counteracts systemic post‐transcriptional silencing of nonviral (trans)genes. Virology, 252, 313–317. [DOI] [PubMed] [Google Scholar]
  2806. Benmoussa A, Lee CHC, Laffont B, Savard P, Laugier J, Boilard E, Gilbert C, Fliss I and Provost P, 2016. Commercial Dairy Cow Milk microRNAs Resist Digestion under Simulated Gastrointestinal Tract Conditions. Journal of Nutrition, 146, 2206–2215. [DOI] [PubMed] [Google Scholar]
  2807. Bhatia V, Bhattacharya R, Uniyal PL, Singh R and Niranjan RS, 2012. Host Generated siRNAs Attenuate Expression of Serine Protease Gene in Myzus persicae. Plos One, 7, e46343–e46343. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2808. Bissels U, Wild S, Tomiuk S, Holste A, Hafner M, Tuschl T and Bosio A, 2009. Absolute quantification of microRNAs by using a universal reference. Rna, 15, 2375–2384. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2809. Boccara M, Sarazin A, Billoud B, Bulski A, Chapell L, Baulcombe D and Colot V, 2010. Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays. In: Plant Epigenetics: Methods and Protocols. 75–86. [DOI] [PubMed] [Google Scholar]
  2810. Brosnan CA, Mitter N, Christie M, Smith NA, Waterhouse PM and Carroll BJ, 2007. Nuclear gene silencing directs reception of long‐distance mRNA silencing in Arabidopsis . America, 104, 14741–14746. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2811. Brosnan CA and Voinnet O, 2011. Cell‐to‐cell and long‐distance siRNA movement in plants: mechanisms and biological implications. Curr Opin Plant Biol, 14, 580–587. [DOI] [PubMed] [Google Scholar]
  2812. Brown BD, Gentner B, Cantore A, Colleoni S, Amendola M, Zingale A, Baccarini A, Lazzari G, Galli C and Naldini L, 2007. Endogenous microRNA can be broadly exploited to regulate transgene expression according to tissue, lineage and differentiation state. Nat Biotechnol, 25, 1457–1467. [DOI] [PubMed] [Google Scholar]
  2813. Buck AH, Coakley G, Simbari F, McSorley HJ, Quintana JF, Le Bihan T, Kumar S, Abreu‐Goodger C, Lear M, Harcus Y, Ceroni A, Babayan SA, Blaxter M, Ivens A and Maizels RM, 2014. Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity. Nature Communications, 5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2814. Buhtz A, Springer F, Chappell L, Baulcombe DC and Kehr J, 2008. Identification and characterization of small RNAs from the phloem of Brassica napus. Plant J, 53, 739–749. [DOI] [PubMed] [Google Scholar]
  2815. Buhtz A, Pieritz J, Springer F and Kehr J, 2010. Phloem small RNAs, nutrient stress responses, and systemic mobility. BMC Plant Biol, 10, 64. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2816. Chen X, Zen K and Zhang C‐Y, 2013. Lack of detectable oral bioavailability of plant microRNAs after feeding in mice Reply. Nature Biotechnology, 31, 967–969. [DOI] [PubMed] [Google Scholar]
  2817. Chevillet JR, Kang Q, Ruf IK, Briggs HA, Vojtech LN, Hughes SM, Cheng HH, Arroyo JD, Meredith EK, Gallichotte EN, Pogosova‐Agadjanyan EL, Morrissey C, Stirewalt DL, Hladik F, Yu EY, Higano CS and Tewari M, 2014. Quantitative and stoichiometric analysis of the microRNA content of exosomes. Proc Natl Acad Sci U S A, 111, 14888–14893. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2818. Chim SS, Shing TK, Hung EC, Leung TY, Lau TK, Chiu RW and Lo YM, 2008. Detection and characterization of placental microRNAs in maternal plasma. Clin Chem, 54, 482–490. [DOI] [PubMed] [Google Scholar]
  2819. Chin AR, Fong MY, Somlo G, Wu J, Swiderski P, Wu X and Wang SE, 2016. Cross‐kingdom inhibition of breast cancer growth by plant miR159. Cell Research, 26, 217–228. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2820. Chitwood DH, Nogueira FT, Howell MD, Montgomery TA, Carrington JC and Timmermans MC, 2009. Pattern formation via small RNA mobility. Genes Dev, 23, 549–554. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2821. de Felippes FF, Ott F and Weigel D, 2011. Comparative analysis of non‐autonomous effects of tasiRNAs and miRNAs in Arabidopsis thaliana . Nucleic Acids Research, 39, 2880–2889. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2822. De Schepper V, De Swaef T, Bauweraerts I and Steppe K, 2013. Phloem transport: a review of mechanisms and controls. J Exp Bot, 64, 4839–4850. [DOI] [PubMed] [Google Scholar]
  2823. Denzler R, Agarwal V, Stefano J, Bartel DP and Stoffel M, 2014. Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance. Mol Cell, 54, 766–776. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2824. Dickinson B, Zhang Y, Petrick JS, Heck G, Ivashuta S and Marshall WS, 2013. Lack of detectable oral bioavailability of plant microRNAs after feeding in mice. Nature Biotechnology, 31, 965–967. [DOI] [PubMed] [Google Scholar]
  2825. Dismuke WM, Challa P, Navarro I, Stamer WD and Liu YT, 2015. Human aqueous humor exosomes. Experimental Eye Research, 132, 73–77. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2826. Dunoyer P, Himber C and Voinnet O, 2005. DICER‐LIKE 4 is required for RNA interference and produces the 21‐nucleotide small interfering RNA component of the plant cell‐to‐cell silencing signal. Nature Genetics, 37, 1356–1360. [DOI] [PubMed] [Google Scholar]
  2827. Dunoyer P, Himber C, Ruiz‐Ferrer V, Alioua A and Voinnet O, 2007. Intra‐ and intercellular RNA interference in Arabidopsis thaliana requires components of the microRNA and heterochromatic silencing pathways. Nature Genetics, 39, 848–856. [DOI] [PubMed] [Google Scholar]
  2828. Fei Q, Yang L, Liang W, Zhang D and Meyers BC, 2016. Dynamic changes of small RNAs in rice spikelet development reveal specialized reproductive phasiRNA pathways. J Exp Bot, 67, 6037–6049. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2829. Flachowsky H, Trankner C, Szankowski I, Waidmann S, Hanke MV, Treutter D and Fischer TC, 2012. RNA‐mediated gene silencing signals are not graft transmissible from the rootstock to the scion in greenhouse‐grown apple plants Malus sp. Int J Mol Sci, 13, 9992–10009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2830. Ghoshroy S, Freedman K, Lartey R and Citovsky V, 1998. Inhibition of plant viral systemic infection by non‐toxic concentrations of cadmium. Plant J, 13, 591–602. [DOI] [PubMed] [Google Scholar]
  2831. Grant‐Downton R, Le Trionnaire G, Schmid R, Rodriguez‐Enriquez J, Hafidh S, Mehdi S, Twell D and Dickinson H, 2009. MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana . Bmc Genomics, 10, 643–643. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2832. Guan D, Yan B, Thieme C, Hua J, Zhu H, Boheler KR, Zhao Z, Kragler F, Xia Y and Zhang S, 2017. PlaMoM: a comprehensive database compiles plant mobile macromolecules. Nucleic Acids Res, 45, D1021–D1028. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2833. Hafner M, Renwick N, Brown M, Mihailovic A, Holoch D, Lin C, Pena JT, Nusbaum JD, Morozov P, Ludwig J, Ojo T, Luo S, Schroth G and Tuschl T, 2011. RNA‐ligase‐dependent biases in miRNA representation in deep‐sequenced small RNA cDNA libraries. Rna, 17, 1697–1712. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2834. Ham BK, Li G, Jia W, Leary JA and Lucas WJ, 2014. Systemic delivery of siRNA in pumpkin by a plant PHLOEM SMALL RNA‐BINDING PROTEIN 1‐ribonucleoprotein complex. Plant J, 80, 683–694. [DOI] [PubMed] [Google Scholar]
  2835. Hamilton A, Voinnet O, Chappell L and Baulcombe D, 2002. Two classes of short interfering RNA in RNA silencing. Embo Journal, 21, 4671–4679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2836. Hannapel DJ, Sharma P and Lin T, 2013. Phloem‐mobile messenger RNAs and root development. Front Plant Sci, 4, 257. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2837. Hardcastle TJ, Kelly KA and Baulcombe DC, 2012. Identifying small interfering RNA loci from high‐throughput sequencing data. Bioinformatics, 28, 457–463. [DOI] [PubMed] [Google Scholar]
  2838. Heisel SE, Zhang YJ, Allen E, Guo L, Reynolds TL, Yang X, Kovalic D and Roberts JK, 2008. Characterization of Unique Small RNA Populations from Rice Grain. Plos One, 3, e2871–e2871. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2839. Himber C, Dunoyer P, Moissiard G, Ritzenthaler C and Voinnet O, 2003. Transitivity‐dependent and ‐independent cell‐to‐cell movement of RNA silencing. EMBO J, 22, 4523–4533. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2840. Hournard NM, Mainville JL, Bonin CP, Huang S, Luethy MH and Malvar TM, 2007. High‐lysine corn generated by endosperm‐specific suppression of lysine catabolism using RNAi. Plant Biotechnology Journal, 5, 605–614. [DOI] [PubMed] [Google Scholar]
  2841. Huang G, Allen R, Davis EL, Baum TJ and Hussey RS, 2006. Engineering broad root‐knot resistance in transgenic plants by RNAi silencing of a conserved and essential root‐knot nematode parasitism gene. Proc Natl Acad Sci U S A, 103, 14302–14306. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2842. Huang XY, Yuan TZ, Tschannen M, Sun ZF, Jacob H, Du MJ, Liang MH, Dittmar RL, Liu Y, Liang MY, Kohli M, Thibodeau SN, Boardman L and Wang L, 2013. Characterization of human plasma‐derived exosomal RNAs by deep sequencing. BMC Genomics, 14, 319–319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2843. Izumi H, Kosaka N, Shimizu T, Sekine K, Ochiya T and Takase M, 2012. Bovine milk contains microRNA and messenger RNA that are stable under degradative conditions. Journal of Dairy Science, 95, 4831–4841. [DOI] [PubMed] [Google Scholar]
  2844. Izumi H, Tsuda M, Sato Y, Kosaka N, Ochiya T, Iwamoto H, Namba K and Takeda Y, 2015. Bovine milk exosomes contain microRNA and mRNA and are taken up by human macrophages. Journal of Dairy Science, 98, 2920–2933. [DOI] [PubMed] [Google Scholar]
  2845. Jauvion V, Elmayan T and Vaucheret H, 2010. The conserved RNA trafficking proteins HPR1 and TEX1 are involved in the production of endogenous and exogenous small interfering RNA in Arabidopsis . Plant Cell, 22, 2697–2709. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2846. Jeong DH, Park S, Zhai J, Gurazada SG, De Paoli E, Meyers BC and Green PJ, 2011. Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage. Plant Cell, 23, 4185–4207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2847. Jeong DH, Thatcher SR, Brown RSH, Zhai JX, Park S, Rymarquis LA, Meyers BC and Green PJ, 2013. Comprehensive Investigation of MicroRNAs Enhanced by Analysis of Sequence Variants, Expression Patterns, ARGONAUTE Loading, and Target Cleavage. Plant Physiology, 162, 1225–1245. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2848. Jorgensen RA, 1995. Cosuppression, flower color patterns, and metastable gene expression States. Science, 268, 686–691. [DOI] [PubMed] [Google Scholar]
  2849. Kalantidis K, Tsagris M and Tabler M, 2006. Spontaneous short‐range silencing of a GFP transgene in Nicotiana benthamiana is possibly mediated by small quantities of siRNA that do not trigger systemic silencing. Plant Journal, 45, 1006–1016. [DOI] [PubMed] [Google Scholar]
  2850. Kapoor M, Arora R, Lama T, Nijhawan A, Khurana JP, Tyagi AK and Kapoor S, 2008. Genome‐wide identification, organization and phylogenetic analysis of Dicer‐like, Argonaute and RNA‐dependent RNA Polymerase gene families and their expression analysis during reproductive development and stress in rice. Bmc Genomics, 9, 451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2851. Kasai A, Bai SL, Li TZ and Harada T, 2011. Graft‐Transmitted siRNA Signal from the Root Induces Visual Manifestation of Endogenous Post‐Transcriptional Gene Silencing in the Scion. Plos One, 6, e16895–e16895. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2852. Kasai A, Sano T and Harada T, 2013. Scion on a Stock Producing siRNAs of Potato Spindle Tuber Viroid (PSTVd) Attenuates Accumulation of the Viroid. Plos One, 8, e57736–e57736. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2853. Knauer S, Holt AL, Rubio‐Somoza I, Tucker EJ, Hinze A, Pisch M, Javelle M, Timmermans MC, Tucker MR and Laux T, 2013. A Protodermal miR394 Signal Defines a Region of Stem Cell Competence in the Arabidopsis Shoot Meristem. Developmental Cell, 24, 125–132. [DOI] [PubMed] [Google Scholar]
  2854. Kobayashi K and Zambryski P, 2007. RNA silencing and its cell‐to‐cell spread during Arabidopsis embryogenesis. Plant Journal, 50, 597–604. [DOI] [PubMed] [Google Scholar]
  2855. Kola VSR, Renuka P, Padmakumari AP, Mangrauthia SK, Balachandran SM, Babu VR and Madhav MS, 2016. Silencing of CYP6 and APN Genes Affects the Growth and Development of Rice Yellow Stem Borer, Scirpophaga incertulas. Frontiers in Physiology, 7, 20–20. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2856. Kropp J, Salih SM and Khatib H, 2014. Expression of microRNAs in bovine and human pre‐implantation embryo culture media. Frontiers in Genetics, 5, 91–91. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2857. Kumar L, Verma S, Vaidya B and Gupta V, 2015. Exosomes: Natural Carriers for siRNA Delivery. Current Pharmaceutical Design, 21, 4556–4565. [DOI] [PubMed] [Google Scholar]
  2858. Kuruppath S, Kumar A, Modepalli VN, Ngo Khanh P, Gras SL and Lefevre C, 2013. Buffalo Milk Transcriptomics. Buffalo. Bulletin, 32, 796–804. [Google Scholar]
  2859. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M and Tuschl T, 2007. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell, 129, 1401–1414. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2860. Lasser C, 2012. Exosomal RNA as biomarkers and the therapeutic potential of exosome vectors. Expert Opinion on Biological Therapy, 12, S189–S197. [DOI] [PubMed] [Google Scholar]
  2861. Lawrie CH, Gal S, Dunlop HM, Pushkaran B, Liggins AP, Pulford K, Banham AH, Pezzella F, Boultwood J, Wainscoat JS, Hatton CS and Harris AL, 2008. Detection of elevated levels of tumour‐associated microRNAs in serum of patients with diffuse large B‐cell lymphoma. British Journal of Haematology, 141, 672–675. [DOI] [PubMed] [Google Scholar]
  2862. Lewsey MG, Hardcastle TJ, Melnyk CW, Molnar A, Valli A, Urich MA, Nery JR, Baulcombe DC and Ecker JR, 2016. Mobile small RNAs regulate genome‐wide DNA methylation. America, 113, E801–E810. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2863. Li J, Yang Z, Yu B, Liu J and Chen X, 2005. Methylation protects miRNAs and siRNAs from a 3′‐end uridylation activity in Arabidopsis . Curr Biol, 15, 1501–1507. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2864. Li S, Tighe SW, Nicolet CM, Grove D, Levy S, Farmerie W, Viale A, Wright C, Schweitzer PA, Gao Y, Kim D, Boland J, Hicks B, Kim R, Chhangawala S, Jafari N, Raghavachari N, Gandara J, Garcia‐Reyero N, Hendrickson C, Roberson D, Rosenfeld J, Smith T, Underwood JG, Wang M, Zumbo P, Baldwin DA, Grills GS and Mason CE, 2014. Multi‐platform assessment of transcriptome profiling using RNA‐seq in the ABRF next‐generation sequencing study. Nat Biotechnol, 32, 915–925. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2865. Liang DC, White RG and Waterhouse PM, 2012. Gene Silencing in Arabidopsis Spreads from the Root to the Shoot, through a Gating Barrier, by Template‐Dependent, Nonvascular, Cell‐to‐Cell Movement. Plant Physiology, 159, 984–1000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2866. Lin SI, Chiang SF, Lin WY, Chen JW, Tseng CY, Wu PC and Chiou TJ, 2008. Regulatory network of microRNA399 and PHO2 by systemic signaling. Plant Physiology, 147, 732–746. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2867. Linsen SE, de Wit E, Janssens G, Heater S, Chapman L, Parkin RK, Fritz B, Wyman SK, de Bruijn E, Voest EE, Kuersten S, Tewari M and Cuppen E, 2009. Limitations and possibilities of small RNA digital gene expression profiling. Nat Methods, 6, 474–476. [DOI] [PubMed] [Google Scholar]
  2868. Mansoor S, Amin I, Hussain M, Zafar Y and Briddon RW, 2006. Engineering novel traits in plants through RNA interference. Trends Plant Sci, 11, 559–565. [DOI] [PubMed] [Google Scholar]
  2869. Manzano D, Marquardt S, Jones AM, Baurle I, Liu F and Dean C, 2009. Altered interactions within FY/AtCPSF complexes required for Arabidopsis FCA‐mediated chromatin silencing. Proc Natl Acad Sci U S A, 106, 8772–8777. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2870. Mao YB, Cai WJ, Wang JW, Hong GJ, Tao XY, Wang LJ, Huang YP and Chen XY, 2007. Silencing a cotton bollworm P450 monooxygenase gene by plant‐mediated RNAi impairs larval tolerance of gossypol. Nat Biotechnol, 25, 1307–1313. [DOI] [PubMed] [Google Scholar]
  2871. Marin E, Jouannet V, Herz A, Lokerse AS, Weijers D, Vaucheret H, Nussaume L, Crespi MD and Maizel A, 2010. miR390, Arabidopsis TAS3 tasiRNAs, and their AUXIN RESPONSE FACTOR targets define an autoregulatory network quantitatively regulating lateral root growth. Plant Cell, 22, 1104–1117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2872. Maule AJ, 2008. Plasmodesmata: structure, function and biogenesis. Curr Opin Plant Biol, 11, 680–686. [DOI] [PubMed] [Google Scholar]
  2873. Maule AJ, Benitez‐Alfonso Y and Faulkner C, 2011. Plasmodesmata ‐ membrane tunnels with attitude. Curr Opin Plant Biol, 14, 683–690. [DOI] [PubMed] [Google Scholar]
  2874. McHale M, Eamens AL, Finnegan EJ and Waterhouse PM, 2013. A 22‐nt artificial microRNA mediates widespread RNA silencing in Arabidopsis . Plant Journal, 76, 519–529. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2875. Melnyk CW, Molnar A, Bassett A and Baulcombe DC, 2011a. Mobile 24 nt Small RNAs Direct Transcriptional Gene Silencing in the Root Meristems of Arabidopsis thaliana . Current Biology, 21, 1678–1683. [DOI] [PubMed] [Google Scholar]
  2876. Melnyk CW, Molnar A and Baulcombe DC, 2011b. Intercellular and systemic movement of RNA silencing signals. EMBO J, 30, 3553–3563. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2877. Mittal D, Mukherjee SK, Vasudevan M and Mishra NS, 2013. Identification of Tissue‐Preferential Expression Patterns of Rice miRNAs. Journal of Cellular Biochemistry, 114, 2071–2081. [DOI] [PubMed] [Google Scholar]
  2878. Miyashima S, Koi S, Hashimoto T and Nakajima K, 2011. Non‐cell‐autonomous microRNA165 acts in a dose‐dependent manner to regulate multiple differentiation status in the Arabidopsis root. Development, 138, 2303–2313. [DOI] [PubMed] [Google Scholar]
  2879. Mlotshwa S, Pruss GJ, MacArthur JL, Endres MW, Davis C, Hofseth LJ, Pena MM and Vance V, 2015. A novel chemopreventive strategy based on therapeutic microRNAs produced in plants. Cell Research, 25, 521–524. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2880. Molnar A, Melnyk CW, Bassett A, Hardcastle TJ, Dunn R and Baulcombe DC, 2010. Small Silencing RNAs in Plants Are Mobile and Direct Epigenetic Modification in Recipient Cells. Science, 328, 872–875. [DOI] [PubMed] [Google Scholar]
  2881. Nakano M, Nobuta K, Vemaraju K, Tej SS, Skogen JW and Meyers BC, 2006. Plant MPSS databases: signature‐based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res, 34, D731–735. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2882. Napoli C, Lemieux C and Jorgensen R, 1990. Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co‐Suppression of Homologous Genes in trans. Plant Cell, 2, 279–289. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2883. Nobuta K, Venu RC, Lu C, Belo A, Vemaraju K, Kulkarni K, Wang WZ, Pillay M, Green PJ, Wang GL and Meyers BC, 2007. An expression atlas of rice mRNAs and small RNAs. Nature Biotechnology, 25, 473–477. [DOI] [PubMed] [Google Scholar]
  2884. Nowara D, Gay A, Lacomme C, Shaw J, Ridout C, Douchkov D, Hensel G, Kumlehn J and Schweizer P, 2010. HIGS: host‐induced gene silencing in the obligate biotrophic fungal pathogen Blumeria graminis. Plant Cell, 22, 3130–3141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2885. Olmedo‐Monfil V, Duran‐Figueroa N, Arteaga‐Vazquez M, Demesa‐Arevalo E, Autran D, Grimanelli D, Slotkin RK, Martienssen RA and Vielle‐Calzada JP, 2010. Control of female gamete formation by a small RNA pathway in Arabidopsis . Nature, 464, 628–U200. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2886. Palauqui JC, Elmayan T, Pollien JM and Vaucheret H, 1997. Systemic acquired silencing: transgene‐specific post‐transcriptional silencing is transmitted by grafting from silenced stocks to non‐silenced scions. EMBO J, 16, 4738–4745. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2887. Pant BD, Buhtz A, Kehr J and Scheible WR, 2008. MicroRNA399 is a long‐distance signal for the regulation of plant phosphate homeostasis. Plant Journal, 53, 731–738. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2888. Peggion C, Bertoli A and Sorgato MC, 2016. Almost a century of prion protein(s): From pathology to physiology, and back to pathology. Biochem Biophys Res Commun. [DOI] [PubMed] [Google Scholar]
  2889. Pegtel DM, van de Garde MDB and Middeldorp JM, 2011. Viral miRNAs exploiting the endosomal‐exosomal pathway for intercellular cross‐talk and immune evasion. Biochimica Et Biophysica Acta‐Gene Regulatory Mechanisms, 1809, 715–721. [DOI] [PubMed] [Google Scholar]
  2890. Peters L and Meister G, 2007. Argonaute proteins: Mediators of RNA silencing. Molecular Cell, 26, 611–623. [DOI] [PubMed] [Google Scholar]
  2891. Rak J, 2013. Extracellular vesicles ‐ biomarkers and effectors of the cellular interactome in cancer. Frontiers in Pharmacology, 4, 21–21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2892. Ratcliff F, Harrison BD and Baulcombe DC, 1997. A similarity between viral defense and gene silencing in plants. Science, 276, 1558–1560. [DOI] [PubMed] [Google Scholar]
  2893. Rio DC, 2014. Northern blots for small RNAs and microRNAs. Cold Spring Harb Protoc, 2014, 793–797. [DOI] [PubMed] [Google Scholar]
  2894. Ryabov EV, van Wezel R, Walsh J and Hong Y, 2004. Cell‐to‐cell, but not long‐distance, spread of RNA silencing that is induced in individual epidermal cells. Journal of Virology, 78, 3149–3154. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2895. Schwab R, Maizel A, Ruiz‐Ferrer V, Garcia D, Bayer M, Crespi M, Voinnet O and Martienssen RA, 2009. Endogenous TasiRNAs Mediate Non‐Cell Autonomous Effects on Gene Regulation in Arabidopsis thaliana . Plos One, 4, e5980–e5980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2896. Schwach F, Vaistij FE, Jones L and Baulcombe DC, 2005. An RNA‐dependent RNA polymerase prevents meristem invasion by potato virus X and is required for the activity but not the production of a systemic silencing signal. Plant Physiology, 138, 1842–1852. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2897. Searle IR, Pontes O, Melnyk CW, Smith LM and Baulcombe DC, 2010. JMJ14, a JmjC domain protein, is required for RNA silencing and cell‐to‐cell movement of an RNA silencing signal in Arabidopsis . Genes & Development, 24, 986–991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2898. Shimamura K, Oka S, Shimotori Y, Ohmori T and Kodama H, 2007. Generation of secondary small interfering RNA in cell‐autonomous and non‐cell autonomous RNA silencing in tobacco. Plant Molecular Biology, 63, 803–813. [DOI] [PubMed] [Google Scholar]
  2899. Smith LM, Pontes O, Searle L, Yelina N, Yousafzai FK, Herr AJ, Pikaard CS and Baulcombe DC, 2007. An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis . Plant Cell, 19, 1507–1521. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2900. Snow JW, Hale AE, Isaacs SK, Baggish AL and Chan SY, 2013. Ineffective delivery of diet‐derived microRNAs to recipient animal organisms. Rna Biology, 10, 1107–1116. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2901. Sun Q, Chen X, Yu J, Zen K, Zhang C‐Y and Li L, 2013. Immune modulatory function of abundant immune‐related microRNAs in microvesicles from bovine colostrum. Protein & Cell, 4, 197–210. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2902. Svoboda P, 2007. Off‐targeting and other non‐specific effects of RNAi experiments in mammalian cells. Curr Opin Mol Ther, 9, 248–257. [PubMed] [Google Scholar]
  2903. Svoboda P, 2015. A toolbox for miRNA analysis. Febs Letters, 589, 1694–1701. [DOI] [PubMed] [Google Scholar]
  2904. Tabara H, Grishok A and Mello CC, 1998. RNAi in C. elegans: soaking in the genome sequence. Science, 282, 430–431. [DOI] [PubMed] [Google Scholar]
  2905. Tian Y, Simanshu DK, Ma JB and Patel DJ, 2011. Structural basis for piRNA 2′‐O‐methylated 3′‐end recognition by Piwi PAZ (Piwi/Argonaute/Zwille) domains. Proc Natl Acad Sci U S A, 108, 903–910. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2906. Timmons L and Fire A, 1998. Specific interference by ingested dsRNA. Nature, 395, 854. [DOI] [PubMed] [Google Scholar]
  2907. Tosar JP, Rovira C, Naya H and Cayota A, 2014. Mining of public sequencing databases supports a non‐dietary origin for putative foreign miRNAs: underestimated effects of contamination in NGS. Rna‐a Publication of the Rna Society, 20, 754–757. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2908. Tournier B, Tabler M and Kalantidis K, 2006. Phloem flow strongly influences the systemic spread of silencing in GFP Nicotiana benthamiana plants. Plant Journal, 47, 383–394. [DOI] [PubMed] [Google Scholar]
  2909. Turchinovich A, Weiz L, Langheinz A and Burwinkel B, 2011. Characterization of extracellular circulating microRNA. Nucleic Acids Research, 39, 7223–7233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2910. Turchinovich A, Tonevitsky AG and Burwinkel B, 2016. Extracellular miRNA: A Collision of Two Paradigms. Trends Biochem Sci, 41, 883–892. [DOI] [PubMed] [Google Scholar]
  2911. Turgeon R and Wolf S, 2009. Phloem transport: cellular pathways and molecular trafficking. Annu Rev Plant Biol, 60, 207–221. [DOI] [PubMed] [Google Scholar]
  2912. Tuteja JH, Zabala G, Varala K, Hudson M and Vodkin LO, 2009. Endogenous, Tissue‐Specific Short Interfering RNAs Silence the Chalcone Synthase Gene Family in Glycine max Seed Coats. Plant Cell, 21, 3063–3077. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2913. Vaistij FE, Jones L and Baulcombe DC, 2002. Spreading of RNA targeting and DNA methylation in RNA silencing requires transcription of the target gene and a putative RNA‐dependent RNA polymerase. Plant Cell, 14, 857–867. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2914. Valoczi A, Varallyay E, Kauppinen S, Burgyan J and Havelda Z, 2006. Spatio‐temporal accumulation of microRNAs is highly coordinated in developing plant tissues. Plant Journal, 47, 140–151. [DOI] [PubMed] [Google Scholar]
  2915. Voinnet O and Baulcombe DC, 1997. Systemic signalling in gene silencing. Nature, 389, 553. [DOI] [PubMed] [Google Scholar]
  2916. Voinnet O, Vain P, Angell S and Baulcombe DC, 1998. Systemic spread of sequence‐specific transgene RNA degradation in plants is initiated by localized introduction of ectopic promoterless DNA. Cell, 95, 177–187. [DOI] [PubMed] [Google Scholar]
  2917. Voinnet O, Vain P, Angell S and Baulcombe DC, 2016. Systemic Spread of Sequence‐Specific Transgene RNA Degradation in Plants Is Initiated by Localized Introduction of Ectopic Promoterless DNA. Cell, 166, 779. [DOI] [PubMed] [Google Scholar]
  2918. Wang H, Zhang XR, Liu J, Kiba T, Woo J, Ojo T, Hafner M, Tuschl T, Chua NH and Wang XJ, 2011. Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions. Plant Journal, 67, 292–304. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2919. Wang K, Li H, Yuan Y, Etheridge A, Zhou Y, Huang D, Wilmes P and Galas D, 2012. The Complex Exogenous RNA Spectra in Human Plasma: An Interface with Human Gut Biota? Plos One, 7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2920. Wee LM, Flores‐Jasso CF, Salomon WE and Zamore PD, 2012. Argonaute Divides Its RNA Guide into Domains with Distinct Functions and RNA‐Binding Properties. Cell, 151, 1055–1067. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2921. Williams Z, Ben‐Dov IZ, Elias R, Mihailovic A, Brown M, Rosenwaks Z and Tuschl T, 2013. Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations. Proc Natl Acad Sci U S A, 110, 4255–4260. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2922. Witwer KW, McAlexander MA, Queen SE and Adams RJ, 2013. Real‐time quantitative PCR and droplet digital PCR for plant miRNAs in mammalian blood provide little evidence for general uptake of dietary miRNAs Limited evidence for general uptake of dietary plant xenomiRs. Rna Biology, 10, 1080–1086. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2923. Wu GP, Yang GH, Zhang RX, Xu GY, Zhang L, Wen W, Lu JB, Liu JY and Yu Y, 2015. Altered microRNA Expression Profiles of Extracellular Vesicles in Nasal Mucus From Patients With Allergic Rhinitis. Allergy Asthma & Immunology Research, 7, 449–457. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2924. Xi Y, Jiang X, Li R, Chen M, Song W and Li X, 2016. The levels of human milk microRNAs and their association with maternal weight characteristics. European Journal of Clinical Nutrition, 70, 445–449. [DOI] [PubMed] [Google Scholar]
  2925. Yelina NE, Smith LM, Jones AM, Patel K, Kelly KA and Baulcombe DC, 2010. Putative Arabidopsis THO/TREX mRNA export complex is involved in transgene and endogenous siRNA biosynthesis. Proc Natl Acad Sci U S A, 107, 13948–13953. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2926. Yoo BC, Kragler F, Varkonyi‐Gasic E, Haywood V, Archer‐Evans S, Lee YM, Lough TJ and Lucas WJ, 2004. A systemic small RNA signaling system in plants. Plant Cell, 16, 1979–2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2927. Yoon YJ, Kim OY and Gho YS, 2014. Extracellular vesicles as emerging intercellular communicasomes. Bmb Reports, 47, 531–539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2928. Zabala G, Campos E, Varala KK, Bloomfield S, Jones SI, Win H, Tuteja JH, Calla B, Clough SJ, Hudson M and Vodkin LO, 2012. Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max. Bmc Plant Biology, 12, 177–177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2929. Zhang H, Li Y, Liu Y, Liu H, Wang H, Jin W, Zhang Y, Zhang C and Xu D, 2016. Role of plant MicroRNA in cross‐species regulatory networks of humans. Bmc Systems Biology, 10. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2930. Zhang L, Hou DX, Chen X, Li DH, Zhu LY, Zhang YJ, Li J, Bian Z, Liang XY, Cai X, Yin Y, Wang C, Zhang TF, Zhu DH, Zhang DM, Xu J, Chen Q, Ba Y, Liu J, Wang Q, Chen JQ, Wang J, Wang M, Zhang QP, Zhang JF, Zen K and Zhang CY, 2012a. Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross‐kingdom regulation by microRNA. Cell Research, 22, 107–126. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2931. Zhang WN, Kollwig G, Stecyk E, Apelt F, Dirks R and Kragler F, 2014. Graft‐transmissible movement of inverted‐repeat‐induced siRNA signals into flowers. Plant Journal, 80, 106–121. [DOI] [PubMed] [Google Scholar]
  2932. Zhang Y, Wiggins BE, Lawrence C, Petrick J, Ivashuta S and Heck G, 2012b. Analysis of plant‐derived miRNAs in animal small RNA datasets. Bmc Genomics, 13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2933. Zhao D and Song GQ, 2014. Rootstock‐to‐scion transfer of transgene‐derived small interfering RNAs and their effect on virus resistance in nontransgenic sweet cherry. Plant Biotechnol J, 12, 1319–1328. [DOI] [PubMed] [Google Scholar]
  2934. Zhou Z, Li X, Liu J, Dong L, Chen Q, Liu J, Kong H, Zhang Q, Qi X, Hou D, Zhang L, Zhang G, Liu Y, Zhang Y, Li J, Wang J, Chen X, Wang H, Zhang J, Chen H, Zen K and Zhang C‐Y, 2015. Honeysuckle‐encoded atypical microRNA2911 directly targets influenza A viruses. Cell Research, 25, 39–49. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2935. Zhu QH, Spriggs A, Matthew L, Fan LJ, Kennedy G, Gubler F and Helliwell C, 2008. A diverse set of microRNAs and microRNA‐like small RNAs in developing rice grains. Genome Research, 18, 1456–1465. [DOI] [PMC free article] [PubMed] [Google Scholar]

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