Skip to main content
NCBI home page
Springer Nature - PMC COVID-19 Collection logoLink to Springer Nature - PMC COVID-19 Collection
. 2006;173:105–116. doi: 10.1007/3-540-27262-3_6

Antiviral Applications of RNAi

KV Morris 10, JJ Rossi 11
Editors: Volker Erdmann7, Jan Barciszewski8, Jürgen Brosius9
PMCID: PMC7122589  PMID: 16594613

Abstract

RNA interference is a natural mechanism by which small interfering (si)RNA operates to specifically and potently down-regulate the expression of a target gene. This down-regulation has been thought to predominantly function at the level of the messenger (m)RNA, post-transcriptional gene silencing (PTGS). Recently, the discovery that siRNAs can function to suppress a gene’s expression at the level of transcription, i.e., transcriptional gene silencing (TGS), has created a major paradigm shift in mammalian RNAi. These recent findings significantly broaden the role RNA, specifically siRNAs and potentially microRNAs, plays in the regulation of gene expression as well as the breadth of potential siRNA target sites. Indeed, the specificity and simplicity of design makes the use of siRNAs to target and suppress virtually any gene or gene promoter of interest a realized technology. Furthermore, since siRNAs are a small nucleic acid reagent, they are unlikely to elicit an immune response, making them a theoretically good future therapeutic. This review will focus on the development, delivery, and potential therapeutic use of antiviral siRNAs in treating viral infections as well as emerging viral threats.

Keywords: RNAi, siRNA, PTGS, TGS, HIV-1

Contributor Information

Volker Erdmann, Email: erdmann@chemie.fu-berlin.de.

Jan Barciszewski, Email: jan.barciszewski@ibch.poznan.pl.

Jürgen Brosius, Email: brosius@pop.uni-muenster.de.

J.J. Rossi, Email: JRossi@coh.org

References

  1. Banerjea A., Li M.J., Bauer G., Remling L., Lee N.S., Rossi J., Akkina R. Inhibition of HIV-1 by lentiviral vector-transduced siRNAs in T lymphocytes differentiated in SCID-hu mice and CD34+ progenitor cell-derived macrophages. Mol Ther. 2003;8:62–71. doi: 10.1016/S1525-0016(03)00140-0. [DOI] [PubMed] [Google Scholar]
  2. Bennasser Y., Le S.Y., Benkirane M., Jeang K.T. Evidence that HIV-1 encodes an siRNA and a suppressor of RNA silencing. Immunology. 2005;22:607–619. doi: 10.1016/j.immuni.2005.03.010. [DOI] [PubMed] [Google Scholar]
  3. Bernstein E., Caudy A.A., Hammond S.M., Hannon G.J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature. 2001;409:363–366. doi: 10.1038/35053110. [DOI] [PubMed] [Google Scholar]
  4. Bernstein E., Kim S.Y., Carmell M.A., Murchison E.P., Alcorn H., Li M.Z., Mills A.A., Elledge S.J., Anderson K.V., Hannon G.J. Dicer is essential for mouse development. Nat Genet. 2003;35:215–217. doi: 10.1038/ng1253. [DOI] [PubMed] [Google Scholar]
  5. Boerger A.L., Snitkovsky S., Young J.A.T. Retroviral vectors preloaded with a viral receptor-ligand bridge protein are targeted to specific cell types. Proc Natl Acad Sci USA. 1999;96:9867–9872. doi: 10.1073/pnas.96.17.9867. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bosher J.M., Dugourcq P., Sookhareea S., Labouesse M. RNA interference can target pre-mRNA: consequences for gene expression in a Caenorhabditis elegans operon. Genetics. 1999;153:1245–1256. doi: 10.1093/genetics/153.3.1245. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Browning M.T., Schmidt R.D., Lew K.A., Rizvi T.A. Primate and feline lentivirus vector RNA packaging and propagation by heterologous lentivirus virions. J Virol. 2001;75:5129–5140. doi: 10.1128/JVI.75.11.5129-5140.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Buchschacher G.L., Wong-Staal F. Development of lentiviral vectors for gene therapy for human diseases. Blood. 2000;95:2499–2504. [PubMed] [Google Scholar]
  9. Castanotto D., Rossi J.J. Construction and transfection of PCR products expressing siRNAs or shRNAs in mammalian cells. Methods Mol Biol. 2004;252:509–514. doi: 10.1385/1-59259-746-7:509. [DOI] [PubMed] [Google Scholar]
  10. Coburn G.A., Cullen B.R. Potent and specific inhibition of human immunodeficiency virus type 1 replication by RNA interference. J Virol. 2002;76:9225–9231. doi: 10.1128/JVI.76.18.9225-9231.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., Mello C.C. Potent and specific genetic interference by double stranded RNA in Caenorhabditis elegans. Nature. 1998;391:806–811. doi: 10.1038/35888. [DOI] [PubMed] [Google Scholar]
  12. Gervaix A., West D., Leoni L.M., Richman D.D., Wong-Staal F., Corbeil J. A new reporter cell line to monitor HIV infection and drug susceptibility in vitro. Proc Natl Acad Sci U S A. 1997;94:4653–4658. doi: 10.1073/pnas.94.9.4653. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Gitlin L., Karelsky S., Andino R. Short interfering RNA confers intracellular antiviral immunity in human cells. Nature. 2002;26:1–5. doi: 10.1038/nature00873. [DOI] [PubMed] [Google Scholar]
  14. Goujon C., Jarrosson-Wuilleme L., Bernaud J., Rigal D., Darlix J., Cimarelli A. Heterologous human immunodeficiency virus type 1 lentiviral vectors packaging a simian immunodeficiency virus-derived genome display a specific postentry transduction defect in dendritic cells. J Virol. 2003;787:9295–9304. doi: 10.1128/JVI.77.17.9295-9304.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hamada M., Ohtsuka T., Kawaida R., Koizumi M., Morita K., Furukawa H., Imanishi T., Miyagishi M., Taira K. Effects on RNA interference in gene expression (RNAi) in cultured mammalian cells of mismatches and the introduction of chemical modifications at the 3′-ends of siRNAs. Antisense Nucleic Acid Drug Dev. 2002;12:301–309. doi: 10.1089/108729002761381285. [DOI] [PubMed] [Google Scholar]
  16. Hamilton A., Voinnet O., Chappell L., Baulcombe D. Two classes of short interfering RNA in RNA silencing. EMBO J. 2002;21:4671–4679. doi: 10.1093/emboj/cdf464. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Holen T., Amarzguioui M., Wiiger M.T., Babaie E., Prydz H. Positional effects of short interfering RNAs targeting the human coagulation trigger tissue factor. Nucleic Acids Res. 2002;30:1757–1766. doi: 10.1093/nar/30.8.1757. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Jacque J., Triques K., Stevenson M. Modulation of HIV-1 replication by RNA interference. Nature. 2002;26:1–4. doi: 10.1038/nature00896. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Jeffery L., Nakielny S. Components of the DNA methylation system of chromatin control are RNA-binding proteins. J Biol Chem. 2004;279:49479–49487. doi: 10.1074/jbc.M409070200. [DOI] [PubMed] [Google Scholar]
  20. Johansen L.K., Carrington J.C. Silencing on the spot. Induction and suppression of RNA silencing in the Agrobacterium-mediated transient expression system. Plant Physiol. 2001;126:930–938. doi: 10.1104/pp.126.3.930. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kawasaki H., Taira K. Induction of DNA methylation and gene silencing by short interfering RNAs in human cells. Nature. 2004;9:211–217. doi: 10.1038/nature02889. [DOI] [PubMed] [Google Scholar]
  22. Kawasaki H., Taira K., Morris K.V. siRNA induced transcriptional gene silencing in mammalian cells. Cell Cycle. 2005;3:442–448. doi: 10.4161/cc.4.3.1520. [DOI] [PubMed] [Google Scholar]
  23. Kobinger G.P., Weiner D.J., Yu Q., Wilson J.M. Filovirus-pseudotyped lentiviral vector can efficiently and stably transduce airway epithelia in vivo. Nat Biotechnol. 2001;19:225–230. doi: 10.1038/85664. [DOI] [PubMed] [Google Scholar]
  24. Lee N.S., Rossi J.J. Control of HIV-1 replication by RNA interference. Virus Res. 2004;102:53–58. doi: 10.1016/j.virusres.2004.01.015. [DOI] [PubMed] [Google Scholar]
  25. Lee N.S., Dohjima T., Bauer G., Li H., Li M., Ehsani A., Salvaterra P., Rossi J. Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nat Biotechnol. 2002;19:500–505. doi: 10.1038/nbt0502-500. [DOI] [PubMed] [Google Scholar]
  26. Lee Y., Ahn C., Han J., Choi H., Kim J., Yim J., Lee J., Provost P., Radmark O., Kim S., Kim V.N. The nuclear RNase III Drosha initiates microRNA processing. Nature. 2003;425:415–419. doi: 10.1038/nature01957. [DOI] [PubMed] [Google Scholar]
  27. Li H., Li W.X., Ding S.W. Induction and suppression of RNA silencing by an animal virus. Science. 2002;296:1319–1321. doi: 10.1126/science.1070948. [DOI] [PubMed] [Google Scholar]
  28. Liu J., Carmell M.A., Rivas F.V., Marsden C.G., Thomson J.M., Song J.J., Hammond S.M., Joshua-Tor L., Hannon G.J. Argonaute2 is the catalytic engine of mammalian RNAi. Science. 2004;305:1437–1441. doi: 10.1126/science.1102513. [DOI] [PubMed] [Google Scholar]
  29. Llave C., Kasschau K.D., Carrington J.C. Virus-encoded suppressor of posttranscriptional gene silencing targets amaintenance step in the silencing pathway. Proc Natl Acad Sci USA. 2000;97:13401–13406. doi: 10.1073/pnas.230334397. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Lund E., Guttinger S., Calado A., Dahlberg J.E., Kutay U. Nuclear export of microRNA precursors. Science. 2004;303:95–98. doi: 10.1126/science.1090599. [DOI] [PubMed] [Google Scholar]
  31. Mallory A.C., Ely L., Smith T.H., Marathe R., Anandalakshmi R., Fagard M., Vaucheret H., Pruss G., Bowman L., Vance V.B. HC-Pro suppression of transgene silencing eliminates the small RNAs but not transgene methylation or the mobile signal. Plant Cell. 2001;13:571–583. doi: 10.1105/tpc.13.3.571. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Mallory A.C., Reinhart B.J., Bartel D., Vance V.B., Bowman L.H. A viral suppressor of RNA silencing differentially regulates the accumulation of short interfering RNAs and micro-RNAs in tobacco. Proc Natl Acad Sci U S A. 2002;99:15228–15233. doi: 10.1073/pnas.232434999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Martinez J., Patkaniowska A., Urlaub H., Luhrmann R., Tuschl T. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell. 2002;110:563–574. doi: 10.1016/S0092-8674(02)00908-X. [DOI] [PubMed] [Google Scholar]
  34. Matzke M.A., Primig M., Trnovsky J., Matzke A.J.M. Reversible methylation and inactivation of marker genes in sequentially transformed tobacco plants. EMBO J. 1989;8:643–649. doi: 10.1002/j.1460-2075.1989.tb03421.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Meissner W., Rothfels H., Schafer B., Seifart K. Development of an inducible pol III transcription system essentially requiring a mutated form of the TAT-binding protein. Nucleic Acids Res. 2001;29:1672–1682. doi: 10.1093/nar/29.8.1672. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Montgomery M.K., Xu S., Fire A. RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegans. Proc Natl Acad Sci USA. 1998;95:15502–15507. doi: 10.1073/pnas.95.26.15502. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Morris K.V., Chung C., Witke W., Looney D.J. Inhibition of HIV-1 replication by siRNA targeting conserved regions of gag/pol. RNA Biol. 2004;1:114–117. doi: 10.4161/rna.2.1.1198. [DOI] [PubMed] [Google Scholar]
  38. Morris K.V., Chan S.W., Jacobsen S.E., Looney D.J. Small interfering RNA-induced transcriptional gene silencing in human cells. Science. 2004;305:1289–1292. doi: 10.1126/science.1101372. [DOI] [PubMed] [Google Scholar]
  39. Morris K.V., Gilbert J., Wong-Staal F., Gasmi M., Looney D.J. Transduction of cell lines and primary cells by FIV-packaged HIV vectors. Mol Ther. 2004;10:181–190. doi: 10.1016/j.ymthe.2004.03.019. [DOI] [PubMed] [Google Scholar]
  40. Ngo H., Tschudi C., Gull K., Ullu E. Double-stranded RNA induces mRNA degradation in Trypanosoma brucei. Proc Natl Acad Sci USA. 1998;95:14687–14692. doi: 10.1073/pnas.95.25.14687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Nishikura K. A short primer on RNAi: RNA-directed RNA polymerase acts as a key catalyst. Cell. 2001;107:415–418. doi: 10.1016/S0092-8674(01)00581-5. [DOI] [PubMed] [Google Scholar]
  42. Novina C.D., Murray M.F., Dykxhoorn D.M., Beresford P.J., Riess J., Lee S., Collman R.G., Leiberman J., Shankar P., Sharp P.A. siRNA-directed inhibition of HIV-1 infection. Nat Med. 2002;8:681–686. doi: 10.1038/nm725. [DOI] [PubMed] [Google Scholar]
  43. Pasquinelli A.E. MicroRNAs: deviants no longer. Trends Genet. 2002;18:171–173. doi: 10.1016/S0168-9525(01)02624-5. [DOI] [PubMed] [Google Scholar]
  44. Pasquinelli A.E., Ruvkun G. Control of developmental timing by micrornas and their targets. Annu Rev Cell Dev Biol. 2002;18:495–513. doi: 10.1146/annurev.cellbio.18.012502.105832. [DOI] [PubMed] [Google Scholar]
  45. Poeschla E., Corbeau P., Wong-Staal F. Development of HIV vectors for anti-HIV gene therapy. Proc Natl Acad Sci U S A. 1996;93:11395–11399. doi: 10.1073/pnas.93.21.11395. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Price M.A., Case S.S., Carbonaro D.A., Yu X.J., Petersen D., Sabo K.M., Curran M.A., Engel B.C., Margarian H., Abkowitz J.L., Nolan G.P., Kohn D.B. Expression from second-generation feline immunodeficiency virus vectors is impaired in human hematopoietic cells. Mol Ther. 2002;6:645–652. doi: 10.1016/S1525-0016(02)90725-2. [DOI] [PubMed] [Google Scholar]
  47. Qin X., An D., Chen I.S.Y., Baltimore D. Inhibiting HIV-1 infection in human T cells by lentiviral mediated delivery of small interfering RNA against CCR5. Proc Natl Acad Sci USA. 2002;100:183–188. doi: 10.1073/pnas.232688199. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Quinonez R., Sutton R.E. Lentiviral Vectors for gene delivery into cells. DNA Cell Biol. 2002;12:937–951. doi: 10.1089/104454902762053873. [DOI] [PubMed] [Google Scholar]
  49. Radhakrishnan S., Gordon J., Del Valle L., Cui J., Khalili K. Intracellular approach for blocking JC virus gene expression by using RNA interference during viral infection. J Virol. 2004;78:7264–7269. doi: 10.1128/JVI.78.13.7264-7269.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Richman D.D., Havlir D., Corbeil J., Looney D., Ignacio C., Spector S.A., Sullivan J., Cheeseman S., Barringer K., Pauletti D. Nevirapine resistance mutations of human immunodeficiency virus type 1 selected during therapy. J Virol. 1994;68:1660–1666. doi: 10.1128/jvi.68.3.1660-1666.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Sandrin V., Russell S.J., Cosset F.L. Targeting retroviral and lentiviral vectors. Curr Top Microbiol Immunol. 2003;281:137–178. doi: 10.1007/978-3-642-19012-4_4. [DOI] [PubMed] [Google Scholar]
  52. Scherr M., Rossi J.J. Rapid determination and quantitation of the accessibility to native RNAs by antisense oligodeoxynucleotides in murine cell extracts. Nucleic Acids Res. 1998;26:5079–5085. doi: 10.1093/nar/26.22.5079. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Schwarz D.S., Hutvagner G., Du T., Xu Z., Aronin N., Zamore P.D. Asymmetry in the assembly of the RNAi enzyme complex. Cell. 2003;115:199–208. doi: 10.1016/S0092-8674(03)00759-1. [DOI] [PubMed] [Google Scholar]
  54. Sharp P.A. RNA interference. Genes Dev. 2001;15:485–490. doi: 10.1101/gad.880001. [DOI] [PubMed] [Google Scholar]
  55. Sioud M., Sorensen D.R. Cationic liposome-mediated delivery of siRNAs in adult mice. Biochem Biophys Res Commun. 2003;312:1220–1225. doi: 10.1016/j.bbrc.2003.11.057. [DOI] [PubMed] [Google Scholar]
  56. Sledz C.A., Holko M., de Veer M.J., Silverman R.H., Williams B.R. Activation of the interferon system by short-interfering RNAs. Nat Cell Biol. 2003;5:834–839. doi: 10.1038/ncb1038. [DOI] [PubMed] [Google Scholar]
  57. Song E., Lee S., Dykxhoorn D.M., Novina C., Zhang D., Crawford K., Cerny J., Sharp P.A., Leiberman J., Manjunath N., Shankar P. Sustained small interfering RNA-mediated human immunodeficiency virus type 1 inhibition in primary macrophages. J Virol. 2003;77:7174–7181. doi: 10.1128/JVI.77.13.7174-7181.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Sorensen D.R., Leirdal M., Sioud M. Gene silencing by systemic delivery of synthetic siRNAs in adult mice. J Mol Biol. 2003;327:761–766. doi: 10.1016/s0022-2836(03)00181-5. [DOI] [PubMed] [Google Scholar]
  59. Sui G., Soohoo C., Affar E., Gay F., Shi Y., Forrester W.C., Shi Y. A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc Natl Acad Sci USA. 2002;99:5515–5520. doi: 10.1073/pnas.082117599. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Sumimoto H., Miyagishi M., Miyoshi H., Taira K., Kawakami Y. Development of an efficient small interfering RNA (siRNA) expression system with a lentiviral vector. Mol Ther. 2003;7:S34. [Google Scholar]
  61. Surabhi R.M., Gaynor R.B. RNA interference directed against viral and cellular targets inhibits human immunodeficiency virus type 1 replication. J Virol. 2002;76:12963–12973. doi: 10.1128/JVI.76.24.12963-12973.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Tijsterman M., Ketting R.F., Plasterk R.H. The genetics of RNA silencing. Annu Rev Genet. 2002;36:489–519. doi: 10.1146/annurev.genet.36.043002.091619. [DOI] [PubMed] [Google Scholar]
  63. Tuschl T. Expanding small RNA interference. Nat Biotechnol. 2002;20:446–448. doi: 10.1038/nbt0502-446. [DOI] [PubMed] [Google Scholar]
  64. Volpe T.A., Kidner C., Hall I.M., Teng G., Grewal S.I.S., Martienssen R.A. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science. 2002;297:1833–1837. doi: 10.1126/science.1074973. [DOI] [PubMed] [Google Scholar]
  65. Wassenegger M. RNA-directed DNA methylation. Plant Mol Biol. 2000;43:203–220. doi: 10.1023/A:1006479327881. [DOI] [PubMed] [Google Scholar]
  66. Wassenegger M., Graham M.W., Wang M.D. RNA-directed de novo methylation of genomic sequences in plants. Cell. 1994;76:567–576. doi: 10.1016/0092-8674(94)90119-8. [DOI] [PubMed] [Google Scholar]
  67. Westerhout E.M., Ooms M., Vink M., Das A.T., Berkhout B. HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome. Nucleic Acids Res. 2005;33:796–804. doi: 10.1093/nar/gki220. [DOI] [PMC free article] [PubMed] [Google Scholar]
  68. White S.M., Renda M., Nam N.Y., Klimatcheva E., Zhu Y., Fisk J., Halterman M., Rimel B.J., Federoff H., Pandya S., Rosenblatt J.R., Planelles V. Lentivirus vectors using human and simian immunodeficiency virus elements. J Virol. 1999;73:2832–2840. doi: 10.1128/jvi.73.4.2832-2840.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Wu X., Li Y., Crise B., Burgess S.M. Transcription start regions in the human genome are favored targets for MLV integration. Science. 2003;300:1749–1751. doi: 10.1126/science.1083413. [DOI] [PubMed] [Google Scholar]
  70. Yam P.Y., Li S., Wu J.U., Hu J., Zaia J.A., Yee J. Design of HIV vectors for efficient gene delivery into human hematopoietic cells. Mol Ther. 2002;5:479–484. doi: 10.1006/mthe.2002.0558. [DOI] [PubMed] [Google Scholar]
  71. Zeng Y., Cullen B.R. RNA interference in human cells is restricted to the cytoplasm. RNA. 2002;8:855–860. doi: 10.1017/S1355838202020071. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from RNA Towards Medicine are provided here courtesy of Nature Publishing Group

RESOURCES