Skip to main content
NCBI home page
Comparative and Functional Genomics logoLink to Comparative and Functional Genomics
. 2003 Apr;4(2):194–202. doi: 10.1002/cfg.260

Caenorhabditis Elegans—Applications to Nematode Genomics

William F Gregory 1,✉, John Parkinson 1
PMCID: PMC2447415  PMID: 18629128

Abstract

The complete genome sequence of the free-living nematode Caenorhabditis elegans was published 4 years ago. Since then, we have seen great strides in technologies that seek to exploit this data. Here we describe the application of some of these techniques and other advances that are helping us to understand about not only the biology of this important model organism but also the entire phylum Nematoda.

Full Text

The Full Text of this article is available as a PDF (136.5 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Ashrafi Kaveh, Chang Francesca Y., Watts Jennifer L., Fraser Andrew G., Kamath Ravi S., Ahringer Julie, Ruvkun Gary. Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes. Nature. 2003 Jan 16;421(6920):268–272. doi: 10.1038/nature01279. [DOI] [PubMed] [Google Scholar]
  2. Blaxter M. Caenorhabditis elegans is a nematode. Science. 1998 Dec 11;282(5396):2041–2046. doi: 10.1126/science.282.5396.2041. [DOI] [PubMed] [Google Scholar]
  3. Blumenthal T. Gene clusters and polycistronic transcription in eukaryotes. Bioessays. 1998 Jun;20(6):480–487. doi: 10.1002/(SICI)1521-1878(199806)20:6<480::AID-BIES6>3.0.CO;2-Q. [DOI] [PubMed] [Google Scholar]
  4. Blumenthal Thomas, Evans Donald, Link Christopher D., Guffanti Alessandro, Lawson Daniel, Thierry-Mieg Jean, Thierry-Mieg Danielle, Chiu Wei Lu, Duke Kyle, Kiraly Moni. A global analysis of Caenorhabditis elegans operons. Nature. 2002 Jun 20;417(6891):851–854. doi: 10.1038/nature00831. [DOI] [PubMed] [Google Scholar]
  5. Boulton Simon J., Gartner Anton, Reboul Jérôme, Vaglio Philippe, Dyson Nick, Hill David E., Vidal Marc. Combined functional genomic maps of the C. elegans DNA damage response. Science. 2002 Jan 4;295(5552):127–131. doi: 10.1126/science.1065986. [DOI] [PubMed] [Google Scholar]
  6. Brenner S. The genetics of Caenorhabditis elegans. Genetics. 1974 May;77(1):71–94. doi: 10.1093/genetics/77.1.71. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Britton C., Redmond D. L., Knox D. P., McKerrow J. H., Barry J. D. Identification of promoter elements of parasite nematode genes in transgenic Caenorhabditis elegans. Mol Biochem Parasitol. 1999 Oct 15;103(2):171–181. doi: 10.1016/s0166-6851(99)00121-8. [DOI] [PubMed] [Google Scholar]
  8. Britton Collette, Murray Linda. A cathepsin L protease essential for Caenorhabditis elegans embryogenesis is functionally conserved in parasitic nematodes. Mol Biochem Parasitol. 2002 Jun;122(1):21–33. doi: 10.1016/s0166-6851(02)00066-x. [DOI] [PubMed] [Google Scholar]
  9. C. elegans Sequencing Consortium Genome sequence of the nematode C. elegans: a platform for investigating biology. Science. 1998 Dec 11;282(5396):2012–2018. doi: 10.1126/science.282.5396.2012. [DOI] [PubMed] [Google Scholar]
  10. Coates Juliet C., de Bono Mario. Antagonistic pathways in neurons exposed to body fluid regulate social feeding in Caenorhabditis elegans. Nature. 2002 Oct 31;419(6910):925–929. doi: 10.1038/nature01170. [DOI] [PubMed] [Google Scholar]
  11. Coghlan Avril, Wolfe Kenneth H. Fourfold faster rate of genome rearrangement in nematodes than in Drosophila. Genome Res. 2002 Jun;12(6):857–867. doi: 10.1101/gr.172702. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Davis R. E., Parra A., LoVerde P. T., Ribeiro E., Glorioso G., Hodgson S. Transient expression of DNA and RNA in parasitic helminths by using particle bombardment. Proc Natl Acad Sci U S A. 1999 Jul 20;96(15):8687–8692. doi: 10.1073/pnas.96.15.8687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Davy A., Bello P., Thierry-Mieg N., Vaglio P., Hitti J., Doucette-Stamm L., Thierry-Mieg D., Reboul J., Boulton S., Walhout A. J. A protein-protein interaction map of the Caenorhabditis elegans 26S proteasome. EMBO Rep. 2001 Sep;2(9):821–828. doi: 10.1093/embo-reports/kve184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Dorris M., De Ley P., Blaxter M. L. Molecular analysis of nematode diversity and the evolution of parasitism. Parasitol Today. 1999 May;15(5):188–193. doi: 10.1016/s0169-4758(99)01439-8. [DOI] [PubMed] [Google Scholar]
  15. Evans D., Zorio D., MacMorris M., Winter C. E., Lea K., Blumenthal T. Operons and SL2 trans-splicing exist in nematodes outside the genus Caenorhabditis. Proc Natl Acad Sci U S A. 1997 Sep 2;94(18):9751–9756. doi: 10.1073/pnas.94.18.9751. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. 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 Feb 19;391(6669):806–811. doi: 10.1038/35888. [DOI] [PubMed] [Google Scholar]
  17. Ge H., Liu Z., Church G. M., Vidal M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet. 2001 Dec;29(4):482–486. doi: 10.1038/ng776. [DOI] [PubMed] [Google Scholar]
  18. Gomez-Escobar Natalia, Gregory William F., Britton Collette, Murray Linda, Corton Craig, Hall Neil, Daub Jen, Blaxter Mark L., Maizels Rick M. Abundant larval transcript-1 and -2 genes from Brugia malayi: diversity of genomic environments but conservation of 5' promoter sequences functional in Caenorhabditis elegans. Mol Biochem Parasitol. 2002 Nov-Dec;125(1-2):59–71. doi: 10.1016/s0166-6851(02)00219-0. [DOI] [PubMed] [Google Scholar]
  19. Grishok A., Tabara H., Mello C. C. Genetic requirements for inheritance of RNAi in C. elegans. Science. 2000 Mar 31;287(5462):2494–2497. doi: 10.1126/science.287.5462.2494. [DOI] [PubMed] [Google Scholar]
  20. Harris Todd W., Lee Raymond, Schwarz Erich, Bradnam Keith, Lawson Daniel, Chen Wen, Blasier Darin, Kenny Eimear, Cunningham Fiona, Kishore Ranjana. WormBase: a cross-species database for comparative genomics. Nucleic Acids Res. 2003 Jan 1;31(1):133–137. doi: 10.1093/nar/gkg053. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Hashmi S., Hashmi G., Gaugler R. Genetic transformation of an entomopathogenic nematode by microinjection. J Invertebr Pathol. 1995 Nov;66(3):293–296. doi: 10.1006/jipa.1995.1103. [DOI] [PubMed] [Google Scholar]
  22. Hashmi S., Tawe W., Lustigman S. Caenorhabditis elegans and the study of gene function in parasites. Trends Parasitol. 2001 Aug;17(8):387–393. doi: 10.1016/s1471-4922(01)01986-9. [DOI] [PubMed] [Google Scholar]
  23. Hope I. A., Arnold J. M., McCarroll D., Jun G., Krupa A. P., Herbert R. Promoter trapping identifies real genes in C. elegans. Mol Gen Genet. 1998 Nov;260(2-3):300–308. doi: 10.1007/s004380050899. [DOI] [PubMed] [Google Scholar]
  24. Hussein Ayman S., Kichenin Ketty, Selkirk Murray E. Suppression of secreted acetylcholinesterase expression in Nippostrongylus brasiliensis by RNA interference. Mol Biochem Parasitol. 2002 Jun;122(1):91–94. doi: 10.1016/s0166-6851(02)00068-3. [DOI] [PubMed] [Google Scholar]
  25. Jackstadt P., Wilm T. P., Zahner H., Hobom G. Transformation of nematodes via ballistic DNA transfer. Mol Biochem Parasitol. 1999 Oct 15;103(2):261–266. doi: 10.1016/s0166-6851(99)00089-4. [DOI] [PubMed] [Google Scholar]
  26. Jiang M., Ryu J., Kiraly M., Duke K., Reinke V., Kim S. K. Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans. Proc Natl Acad Sci U S A. 2001 Jan 2;98(1):218–223. doi: 10.1073/pnas.011520898. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Kamath Ravi S., Fraser Andrew G., Dong Yan, Poulin Gino, Durbin Richard, Gotta Monica, Kanapin Alexander, Le Bot Nathalie, Moreno Sergio, Sohrmann Marc. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature. 2003 Jan 16;421(6920):231–237. doi: 10.1038/nature01278. [DOI] [PubMed] [Google Scholar]
  28. Ketting R. F., Haverkamp T. H., van Luenen H. G., Plasterk R. H. Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell. 1999 Oct 15;99(2):133–141. doi: 10.1016/s0092-8674(00)81645-1. [DOI] [PubMed] [Google Scholar]
  29. Krause S., Sommer A., Fischer P., Brophy P. M., Walter R. D., Liebau E. Gene structure of the extracellular glutathione S-transferase from Onchocerca volvulus and its overexpression and promoter analysis in transgenic Caenorhabditis elegans. Mol Biochem Parasitol. 2001 Oct;117(2):145–154. doi: 10.1016/s0166-6851(01)00342-5. [DOI] [PubMed] [Google Scholar]
  30. Lee R. C., Ambros V. An extensive class of small RNAs in Caenorhabditis elegans. Science. 2001 Oct 26;294(5543):862–864. doi: 10.1126/science.1065329. [DOI] [PubMed] [Google Scholar]
  31. Lee Siu Sylvia, Lee Raymond Y. N., Fraser Andrew G., Kamath Ravi S., Ahringer Julie, Ruvkun Gary. A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity. Nat Genet. 2002 Nov 25;33(1):40–48. doi: 10.1038/ng1056. [DOI] [PubMed] [Google Scholar]
  32. Liu Ying, Dodds Phillippa, Emilion Gracy, Mungall Andrew J., Dunham Ian, Beck Stephan, Wells R. Spencer, Charnock F. Mark L., Ganesan Trivadi S. The human homologue of unc-93 maps to chromosome 6q27 - characterisation and analysis in sporadic epithelial ovarian cancer. BMC Genet. 2002 Oct 15;3:20–20. doi: 10.1186/1471-2156-3-20. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Lok James B., Massey Holman C., Jr Transgene expression in Strongyloides stercoralis following gonadal microinjection of DNA constructs. Mol Biochem Parasitol. 2002 Feb;119(2):279–284. doi: 10.1016/s0166-6851(01)00414-5. [DOI] [PubMed] [Google Scholar]
  34. Mounsey Andrew, Bauer Petra, Hope Ian A. Evidence suggesting that a fifth of annotated Caenorhabditis elegans genes may be pseudogenes. Genome Res. 2002 May;12(5):770–775. doi: 10.1101/gr208802. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Parkinson John, Blaxter Mark. SimiTri--visualizing similarity relationships for groups of sequences. Bioinformatics. 2003 Feb 12;19(3):390–395. doi: 10.1093/bioinformatics/btf870. [DOI] [PubMed] [Google Scholar]
  36. Parkinson John, Whitton Claire, Guiliano David, Daub Jen, Blaxter Mark. 200000 nematode expressed sequence tags on the Net. Trends Parasitol. 2001 Aug 1;17(8):394–396. doi: 10.1016/s1471-4922(01)01954-7. [DOI] [PubMed] [Google Scholar]
  37. Partridge Linda, Gems David. Mechanisms of ageing: public or private? Nat Rev Genet. 2002 Mar;3(3):165–175. doi: 10.1038/nrg753. [DOI] [PubMed] [Google Scholar]
  38. Piano Fabio, Schetter Aaron J., Morton Diane G., Gunsalus Kristin C., Reinke Valerie, Kim Stuart K., Kemphues Kenneth J. Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. Curr Biol. 2002 Nov 19;12(22):1959–1964. doi: 10.1016/s0960-9822(02)01301-5. [DOI] [PubMed] [Google Scholar]
  39. Reboul J., Vaglio P., Tzellas N., Thierry-Mieg N., Moore T., Jackson C., Shin-i T., Kohara Y., Thierry-Mieg D., Thierry-Mieg J. Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans. Nat Genet. 2001 Mar;27(3):332–336. doi: 10.1038/85913. [DOI] [PubMed] [Google Scholar]
  40. Roy Peter J., Stuart Joshua M., Lund Jim, Kim Stuart K. Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature. 2002 Aug 29;418(6901):975–979. doi: 10.1038/nature01012. [DOI] [PubMed] [Google Scholar]
  41. Stein L., Sternberg P., Durbin R., Thierry-Mieg J., Spieth J. WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res. 2001 Jan 1;29(1):82–86. doi: 10.1093/nar/29.1.82. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Tabara H., Grishok A., Mello C. C. RNAi in C. elegans: soaking in the genome sequence. Science. 1998 Oct 16;282(5388):430–431. doi: 10.1126/science.282.5388.430. [DOI] [PubMed] [Google Scholar]
  43. Timmons L., Court D. L., Fire A. Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans. Gene. 2001 Jan 24;263(1-2):103–112. doi: 10.1016/s0378-1119(00)00579-5. [DOI] [PubMed] [Google Scholar]
  44. Urwin P. E., Lilley Catherine J., Atkinson Howard J. Ingestion of double-stranded RNA by preparasitic juvenile cyst nematodes leads to RNA interference. Mol Plant Microbe Interact. 2002 Aug;15(8):747–752. doi: 10.1094/MPMI.2002.15.8.747. [DOI] [PubMed] [Google Scholar]
  45. Vaglio Philippe, Lamesch Philippe, Reboul Jérôme, Rual Jean-François, Martinez Monica, Hill David, Vidal Marc. WorfDB: the Caenorhabditis elegans ORFeome Database. Nucleic Acids Res. 2003 Jan 1;31(1):237–240. doi: 10.1093/nar/gkg092. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Walhout A. J., Sordella R., Lu X., Hartley J. L., Temple G. F., Brasch M. A., Thierry-Mieg N., Vidal M. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science. 2000 Jan 7;287(5450):116–122. doi: 10.1126/science.287.5450.116. [DOI] [PubMed] [Google Scholar]
  47. Walhout Albertha J. M., Reboul Jérôme, Shtanko Olena, Bertin Nicolas, Vaglio Philippe, Ge Hui, Lee Hongmei, Doucette-Stamm Lynn, Gunsalus Kristin C., Schetter Aaron J. Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr Biol. 2002 Nov 19;12(22):1952–1958. doi: 10.1016/s0960-9822(02)01279-4. [DOI] [PubMed] [Google Scholar]
  48. Webb Colleen T., Shabalina Svetlana A., Ogurtsov Aleksey Yu, Kondrashov Alexey S. Analysis of similarity within 142 pairs of orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae. Nucleic Acids Res. 2002 Mar 1;30(5):1233–1239. doi: 10.1093/nar/30.5.1233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Wodarz Andreas. Establishing cell polarity in development. Nat Cell Biol. 2002 Feb;4(2):E39–E44. doi: 10.1038/ncb0202-e39. [DOI] [PubMed] [Google Scholar]
  50. de Bono Mario, Tobin David M., Davis M. Wayne, Avery Leon, Bargmann Cornelia I. Social feeding in Caenorhabditis elegans is induced by neurons that detect aversive stimuli. Nature. 2002 Oct 31;419(6910):899–903. doi: 10.1038/nature01169. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Comparative and Functional Genomics are provided here courtesy of Wiley

RESOURCES