Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Systematic functional analysis of the Caenorhabditis elegans genome using RNAi


A principal challenge currently facing biologists is how to connect the complete DNA sequence of an organism to its development and behaviour. Large-scale targeted-deletions have been successful in defining gene functions in the single-celled yeast Saccharomyces cerevisiae, but comparable analyses have yet to be performed in an animal. Here we describe the use of RNA interference to inhibit the function of 86% of the 19,427 predicted genes of C. elegans. We identified mutant phenotypes for 1,722 genes, about two-thirds of which were not previously associated with a phenotype. We find that genes of similar functions are clustered in distinct, multi-megabase regions of individual chromosomes; genes in these regions tend to share transcriptional profiles. Our resulting data set and reusable RNAi library of 16,757 bacterial clones will facilitate systematic analyses of the connections among gene sequence, chromosomal location and gene function in C. elegans.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Summary of RNAi phenotypes.
Figure 2: Relative enrichment of Nonv, Vpep and X chromosome genes for different functional classes.
Figure 3: Conservation of domains in genes with different RNAi phenotypes.
Figure 4: Distribution of RNAi phenotypes across the C. elegans chromosomes.

Similar content being viewed by others


  1. Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806–811 (1998)

    Article  ADS  CAS  Google Scholar 

  2. Fraser, A. G. et al. Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408, 325–330 (2000)

    Article  ADS  CAS  Google Scholar 

  3. Maeda, I., Kohara, Y., Yamamoto, M. & Sugimoto, A. Large-scale analysis of gene function in Caenorhabditis elegans by high- throughput RNAi. Curr Biol 11, 171–176 (2001)

    Article  CAS  Google Scholar 

  4. Gonczy, P. et al. Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature 408, 331–336 (2000)

    Article  ADS  CAS  Google Scholar 

  5. Timmons, L. & Fire, A. Specific interference by ingested dsRNA. Nature 395, 854 (1998)

    Article  ADS  CAS  Google Scholar 

  6. Timmons, L., Court, D. L. & Fire, A. Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans. Gene 263, 103–112 (2001)

    Article  CAS  Google Scholar 

  7. Kamath, R. K., Martinez-Campos, M., Zipperlen, P., Fraser, A. G. & Ahringer, J. Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in C. elegans. Genome Biol. 2, 1–10 (2001)

    Google Scholar 

  8. Pryer, N. K., Salama, N. R., Schekman, R. & Kaiser, C. A. Cytosolic Sec13p complex is required for vesicle formation from the endoplasmic reticulum in vitro. J. Cell Biol. 120, 865–875 (1993)

    Article  CAS  Google Scholar 

  9. Tavernarakis, N., Wang, S. L., Dorovkov, M., Ryazanov, A. & Driscoll, M. Heritable and inducible genetic interference by double-stranded RNA encoded by transgenes. Nature Genet. 24, 180–183 (2000)

    Article  CAS  Google Scholar 

  10. Piano, F., Schetter, A. J., Mangone, M., Stein, L. & Kemphues, K. J. RNAi analysis of genes expressed in the ovary of Caenorhabditis elegans. Curr. Biol. 10, 1619–1622 (2000)

    Article  CAS  Google Scholar 

  11. Mewes, H. W. et al. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 28, 37–40 (2000)

    Article  ADS  CAS  Google Scholar 

  12. Apweiler, R. et al. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 29, 37–40 (2001)

    Article  CAS  Google Scholar 

  13. Adams, M. D. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185–2195 (2000)

    Article  Google Scholar 

  14. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001)

    Article  Google Scholar 

  15. Venter, J. C. et al. The sequence of the human genome. Science 291, 1304–1351 (2001)

    Article  ADS  CAS  Google Scholar 

  16. Goffeau, A. et al. Life with 6000 genes. Science 274, 563–567 (1996) 546

    Article  Google Scholar 

  17. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815 (2000)

  18. The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012–2018 (1998)

    Article  ADS  Google Scholar 

  19. Kuwabara, P. E. Developmental genetics of Caenorhabditis elegans sex determination. Curr. Top. Dev. Biol. 41, 99–132 (1999)

    Article  CAS  Google Scholar 

  20. Reinke, V. et al. A global profile of germline gene expression in C. elegans. Mol. Cell 6, 605–616 (2000)

    Article  CAS  Google Scholar 

  21. Kelly, W. G. et al. X-chromosome silencing in the germline of C. elegans. Development 129, 479–492 (2002)

    CAS  Google Scholar 

  22. Barnes, T. M., Kohara, Y., Coulson, A. & Hekimi, S. Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans. Genetics 141, 159–179 (1995)

    CAS  Google Scholar 

  23. Kim, S. K. et al. A gene expression map for Caenorhabditis elegans. Science 293, 2087–2092 (2001)

    Article  ADS  CAS  Google Scholar 

  24. Lercher, M. J., Urrutia, A. O. & Hurst, L. D. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nature Genet. 31, 180–183 (2002)

    Article  CAS  Google Scholar 

  25. Spellman, P. T. & Rubin, G. M. Evidence for large domains of similarly expressed genes in the Drosophila genome. J. Biol. 1(1), paper no. 5 〈〉 (2002)

  26. Cohen, B. A., Mitra, R. D., Hughes, J. D. & Church, G. M. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nature Genet. 26, 183–186 (2000)

    Article  CAS  Google Scholar 

  27. Roy, P. J., Stuart, J., Lund, J. & Kim, S. K. Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 418, 975–9 (2002)

    Article  ADS  CAS  Google Scholar 

  28. Kruglyak, S. & Tang, H. Regulation of adjacent yeast genes. Trends Genet. 16, 109–111 (2000)

    Article  CAS  Google Scholar 

  29. Paddison, P. J., Caudy, A. A., Bernstein, E., Hannon, G. J. & Conklin, D. S. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev. 16, 948–958 (2002)

    Article  CAS  Google Scholar 

  30. Donze, O. & Picard, D. RNA interference in mammalian cells using siRNAs synthesized with T7 RNA polymerase. Nucleic Acids Res. 30, e46 〈〉 (2002)

    Article  Google Scholar 

  31. Elbashir, S. M., Harborth, J., Weber, K. & Tuschl, T. Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods 26, 199–213 (2002)

    Article  CAS  Google Scholar 

  32. Paul, C. P., Good, P. D., Winer, I. & Engelke, D. R. Effective expression of small interfering RNA in human cells. Nature Biotechnol. 20, 505–8 (2002)

    Article  CAS  Google Scholar 

  33. Miyagishi, M. & Taira, K. U6 promoter driven siRNAs with four uridine 3′ overhangs efficiently suppress targeted gene expression in mammalian cells. Nature Biotechnol. 20, 497–500 (2002)

    Article  CAS  Google Scholar 

  34. Sui, G. et al. A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc. Natl Acad. Sci. USA 99, 5515–5520 (2002)

    Article  ADS  CAS  Google Scholar 

  35. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990)

    Article  CAS  Google Scholar 

  36. Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997)

    Article  CAS  Google Scholar 

  37. Schuler, G. D. Sequence mapping by electronic PCR. Genome Res. 7, 541–550 (1997)

    Article  CAS  Google Scholar 

  38. Rubin, G. M. et al. Comparative genomics of the eukaryotes. Science 287, 2204–2215 (2000)

    Article  CAS  Google Scholar 

  39. Wood, V. et al. The genome sequence of Schizosaccharomyces pombe. Nature 415, 871–880 (2002)

    Article  ADS  CAS  Google Scholar 

Download references


We thank T. Blumenthal, B. Kelly, S. Kim and V. Reinke for discussions and sharing data before publication; B. Shumacher for assistance early in the project; and G. Chalklin, J. Peacock, J. Abbott and K. Rossiter for preparing the media. R.S.K. was supported by a Howard Hughes Medical Institute Predoctoral Fellowship; A.G.F. by a US Army Breast Cancer Research Fellowship; Y.D., R.D., M.G., D.P.W. and P.Z. by the Wellcome Trust; G.P. by the Canadian Institute of Health Research and the Wellcome Trust; A.K. by the European Molecular Biology Laboratory; N.L.B. by the European Molecular Biology Organization; S.M. by the Centro de Investigacion del Cancer; M.S. by a Swiss National Science Foundation fellowship and J.A. by a Wellcome Trust Senior Research Fellowship.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Julie Ahringer.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kamath, R., Fraser, A., Dong, Y. et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421, 231–237 (2003).

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing