Skip to main content

Thank you for visiting nature.com. 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.

  • Review Article
  • Published:

Functional exploration of the C. elegans genome using DNA microarrays

Nature Genetics volume 32, pages 541–546 (2002)Cite this article

Abstract

Global changes in gene expression underlie developmental processes such as organogenesis, embryogenesis and aging in Caenorhabditis elegans. Recently developed methods allow gene expression profiles to be determined selectively for individual tissues and cell types. Results from both whole-animal and tissue-specific expression profiling have provided an unprecedented view into genome organization and gene function. Integration of these results with other types of functional genomics data gathered from RNA-mediated interference and yeast two-hybrid analyses will allow rapid identification and exploration of the complex functional gene networks that govern C. elegans development.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Figure 1: Methods for measuring tissue-specific gene expression.

Bob Crimi

Figure 2: Genomic constraints on gene expression.

Bob Crimi

Similar content being viewed by others

References

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

  2. Costanzo, M.C. et al. The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information. Nucleic Acids Res. 28, 73–76 (2000).

    Article  CAS  Google Scholar 

  3. Gaudet, J. & Mango, S.E. Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4. Science 295, 821–825 (2001).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  5. Colaiácovo, M.P. et al. A targeted RNAi screen for genes involved in chromosome morphogenesis and nuclear organization in the C. elegans germ line. Genetics 162, 113–128 (2002).

    Google Scholar 

  6. MacQueen, A.J., Colaiacovo, M.P., McDonald, K. & Villeneuve, A.M. Synapsis-dependent and -independent mechanisms stabilize homolog pairing during meiotic prophase in C. elegans. Genes Dev. 16, 2428–2442 (2002).

    Article  CAS  Google Scholar 

  7. Horner, M.A. et al. pha-4, an HNF-3 homolog, specifies pharyngeal organ identity in Caenorhabditis elegans. Genes Dev. 12, 1947–1952 (1998).

    Article  CAS  Google Scholar 

  8. Roy, P.J., Stuart, J.M., Lund, J. & Kim, S.K. Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 418, 975–979 (2002).

    Article  CAS  Google Scholar 

  9. Gorlach, M., Burd, C.G. & Dreyfuss, G. The mRNA poly(A)-binding protein: localization, abundance, and RNA-binding specificity. Exp. Cell Res. 211, 400–407 (1994).

    Article  CAS  Google Scholar 

  10. Christensen, M. et al. A primary culture system for functional analysis of C. elegans neurons and muscle cells. Neuron 33, 503–514 (2002).

    Article  CAS  Google Scholar 

  11. Zhang, Y. et al. Identification of genes expressed in C. elegans touch receptor neurons. Nature 418, 331–335 (2002).

    Article  CAS  Google Scholar 

  12. Way, J.C. & Chalfie, M. mec-3, a homeobox-containing gene that specifies differentiation of the touch receptor neurons in C. elegans. Cell 54, 5–16 (1988).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    CAS  Google Scholar 

  15. Kelly, W.G. & Fire, A. Chromatin silencing and the maintenance of a functional germline in Caenorhabditis elegans. Development 125, 2451–2456 (1998).

    CAS  Google Scholar 

  16. Holdeman, R., Nehrt, S. & Strome, S. MES-2, a maternal protein essential for viability of the germline in Caenorhabditis elegans, is homologous to a Drosophila Polycomb group protein. Development 125, 2457–2467 (1998).

    CAS  Google Scholar 

  17. Korf, I., Fan, Y. & Strome, S. The Polycomb group in Caenorhabditis elegans and maternal control of germline development. Development 125, 2469–2478 (1998).

    CAS  Google Scholar 

  18. Fong, Y., Bender, L., Wang, W. & Strome, S. Regulation of the different chromatin states of autosomes and X chromosomes in the germ line of C. elegans. Science 296, 2235–2238 (2002).

    Article  CAS  Google Scholar 

  19. Blumenthal, T. Gene clusters and polycistronic transcription in eukaryotes. BioEssays 20, 480–487 (1998).

    Article  CAS  Google Scholar 

  20. Blumenthal, T. et al. A global analysis of Caenorhabditis elegans operons. Nature 417, 851–854 (2002).

    Article  CAS  Google Scholar 

  21. von Mering, C. & Bork, P. Teamed up for transcription. Nature 417, 797–798 (2002).

    Article  CAS  Google Scholar 

  22. Hill, A.A., Hunter, C.P., Tsung, B.T., Tucker-Kellogg, G. & Brown, E.L. Genomic analysis of gene expression in C. elegans. Science 290, 809–812 (2000).

    Article  CAS  Google Scholar 

  23. 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. USA 98, 218–223 (2001).

    Article  CAS  Google Scholar 

  24. Lund, J. et al. Transcriptional profile of aging in C. elegans. Curr. Biol. 12, 1566–1573 (2002).

    Article  CAS  Google Scholar 

  25. Lynch, A.S., Briggs, D. & Hope, I.A. Developmental expression pattern screen for genes predicted in the C. elegans genome sequencing project. Nature Genet. 11, 309–313 (1995).

    Article  CAS  Google Scholar 

  26. Jansen, G., Hazendonk, E., Thijssen, K.L. & Plasterk, R.H. Reverse genetics by chemical mutagenesis in Caenorhabditis elegans. Nat. Genet. 17, 119–121 (1997).

    Article  CAS  Google Scholar 

  27. Hunter, C.P. Gene silencing: shrinking the black box of RNAi. Curr. Biol. 9, R440–R442 (1999).

    Article  CAS  Google Scholar 

  28. 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  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  30. 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 

  31. 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 

  32. Reboul, J. et al. Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans. Nature Genet. 27, 332–336 (2001).

    Article  CAS  Google Scholar 

  33. Walhout, A.J. et al. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287, 116–122 (2000).

    Article  CAS  Google Scholar 

  34. Boulton, S.J. et al. Combined functional genomic maps of the C. elegans DNA damage response. Science 295, 127–131 (2002).

    Article  CAS  Google Scholar 

  35. Piano, F. et al. Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. Current Biol. (in press).

  36. Baugh, L.R., Hill, A.A., Brown, E.L. & Hunter, C.P. Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids. Res. 29, E29 (2001).

    Article  CAS  Google Scholar 

  37. Ge, H., Liu, Z., Church, G.M. & Vidal, M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nature Genet. 29, 482–486 (2002).

    Article  Google Scholar 

  38. Kemmeren, P. et al. Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol. Cell 9, 1133–1143 (2002).

    Article  CAS  Google Scholar 

  39. Qian, J., Dolled-Filhart, M., Lin, J., Yu, H., & Gerstein, M. Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions. J. Mol. Biol. 14, 1053–1066 (2001).

    Article  Google Scholar 

  40. Wells, J. & Farnham, P.J. Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation. Methods 26, 48–56 (2002).

    Article  CAS  Google Scholar 

  41. van Steensel, B., Delrow, J. & Henikoff, S. Chromatin profiling using targeted DNA adenine methyltransferase. Nature Genet. 27, 304–308 (2001).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

I thank K. White, S. West and W. Chi for critically reading the manuscript, and W.G. Kelly for the photograph in Fig. 2b.

Author information

Authors and Affiliations

  1. Department of Genetics, Yale University School of Medicine, New Haven, 06520, Connecticut, USA

    Valerie Reinke

Authors
  1. Valerie Reinke
    View author publications

    You can also search for this author in PubMed Google Scholar

Ethics declarations

Competing interests

The author declares no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Reinke, V. Functional exploration of the C. elegans genome using DNA microarrays. Nat Genet 32 (Suppl 4), 541–546 (2002). https://doi.org/10.1038/ng1039

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng1039

This article is cited by

Search

Advanced search

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