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.

  • Article
  • Published:

Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III

Abstract

Genome sequencing projects generate a wealth of information; however, the ultimate goal of such projects is to accelerate the identification of the biological function of genes. This creates a need for comprehensive studies to fill the gap between sequence and function. Here we report the results of a functional genomic screen to identify genes required for cell division in Caenorhabditis elegans. We inhibited the expression of 96% of the 2,300 predicted open reading frames on chromosome III using RNA-mediated interference (RNAi). By using an in vivo time-lapse differential interference contrast microscopy assay, we identified 133 genes (6%) necessary for distinct cellular processes in early embryos. Our results indicate that these genes represent most of the genes on chromosome III that are required for proper cell division in C. elegans embryos. The complete data set, including sample time-lapse recordings, has been deposited in an open access database. We found that 47% of the genes associated with a differential interference contrast phenotype have clear orthologues in other eukaryotes, indicating that this screen provides putative gene functions for other species as well.

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

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

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

Figure 1: Single images taken from time-lapse DIC recordings of wild-type (left) and embryos representative of six distinct phenotypic classes (right).
Figure 2: Distribution of predicted proteins according to homology and orthology relationships.

Similar content being viewed by others

References

  1. Ross-Macdonald, P. et al. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402, 413– 418 (1999).

    Article  ADS  CAS  Google Scholar 

  2. 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 

  3. Gönczy, P. et al. Dissection of cell division processes in the one cell stage Caenorhabditis elegans embryo by mutational analysis. J. Cell Biol. 144, 927–946 ( 1999).

    Article  Google Scholar 

  4. 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 

  5. Shelton, C. A., Carter, J. C., Ellis, G. C. & Bowerman, B. The nonmuscle myosin regulatory light chain gene mlc-4 is required for cytokinesis, anterior-posterior polarity, and body morphology during Caenorhabditis elegans embryogenesis. J. Cell Biol. 146, 439–451 (1999).

    Article  CAS  Google Scholar 

  6. Zhang, B. et al. A conserved RNA-binding protein that regulates sexual fates in the C. elegans hermaphrodite germ line. Nature 390, 477–484 (1997).

    Article  ADS  CAS  Google Scholar 

  7. Cox, D. N. et al. A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal. Genes Dev. 12, 3715–3727 (1998).

    Article  CAS  Google Scholar 

  8. Skop, A. R. & White, J. G. The dynactin complex is required for cleavage plane specification in early Caenorhabditis elegans embryos. Curr. Biol. 8, 1110–1116 (1998).

    Article  CAS  Google Scholar 

  9. Gönczy, P., Pichler, S., Kirkham, M. & Hyman, A. A. Cytoplasmic dynein is required for distinct aspects of MTOC positioning, including centrosome separation, in the one cell stage Caenorhabditis elegans embryo. J. Cell Biol. 147, 135–150 (1999).

    Article  Google Scholar 

  10. Chase, D. et al. The polo-like kinase PLK-1 is required for nuclear envelope breakdown and the completion of meiosis in Caenorhabditis elegans. Genesis 26, 26–41 ( 2000).

    Article  CAS  Google Scholar 

  11. Boxem, M., Srinivasan, D. G. & van den Heuvel, S. The Caenorhabditis elegans gene ncc-1 encodes a cdc2-related kinase required for M phase in meiotic and mitotic cell divisions, but not for S phase. Development 126, 2227–2239 (1999).

    CAS  PubMed  Google Scholar 

  12. Feng, H. et al. CUL-2 is required for the G1-to-S-phase transition and mitotic chromosome condensation in Caenorhabditis elegans. Nature Cell Biol. 1, 486–492 ( 1999).

    Article  CAS  Google Scholar 

  13. Rappleye, C. A., Paredez, A. R., Smith, C. W., McDonald, K. L. & Aroian, R. V. The coronin-like protein POD-1 is required for anterior-posterior axis formation and cellular architecture in the nematode Caenorhabditis elegans. Genes Dev. 13, 2838–2851 (1999).

    Article  CAS  Google Scholar 

  14. Swan, K. A. et al. cyk-1: a C. elegans FH gene required for a late step in embryonic cytokinesis. J. Cell Sci. 111, 2017–2027 (1998).

    CAS  PubMed  Google Scholar 

  15. Jantsch-Plunger, V. et al. CYK-4. A rho family gtpase activating protein (gap) required for central spindle formation and cytokinesis. J. Cell Biol. 149, 1391–1404 (2000).

    Article  CAS  Google Scholar 

  16. Furuta, T. et al. EMB-30: an APC4 homologue required for metaphase-to-anaphase transitions during meiosis and mitosis in Caenorhabditis elegans. Mol. Biol. Cell 11, 1401–1419 (2000).

    Article  CAS  Google Scholar 

  17. Etemad-Moghadam, B., Guo, S. & Kemphues, K. J. Asymmetrically distributed PAR-3 protein contributes to cell polarity and spindle alignement in early C. elegans embryos. Cell 83, 743–752 (1995).

    Article  CAS  Google Scholar 

  18. Levitan, D. J., Boyd, L., Mello, C. C., Kemphues, K. J. & Stinchcomb, D. T. par-2, a gene required for blastomere asymmetry in Caenorhabditis elegans, encodes zinc-finger and ATP-binding motifs. Proc. Natl Acad. Sci. USA 91, 6108– 6112 (1994).

    Article  ADS  CAS  Google Scholar 

  19. Nicolas, F. et al. Xenopus Ran-binding protein 1: molecular interactions and effects on nuclear assembly in Xenopus egg extracts. J. Cell Sci. 110, 3019–3030 (1997).

    CAS  PubMed  Google Scholar 

  20. Carazo-Salas, R. E. et al. Generation of GTP-bound Ran by RCC1 is required for chromatin-induced mitotic spindle formation. Nature 400, 178 –181 (1999).

    Article  ADS  CAS  Google Scholar 

  21. Kalab, P., Pu, R. T. & Dasso, M. The ran GTPase regulates mitotic spindle assembly. Curr. Biol. 9, 481–484 ( 1999).

    Article  CAS  Google Scholar 

  22. Wilde, A. & Zheng, Y. Stimulation of microtubule aster formation and spindle assembly by the small GTPase Ran. Science 284, 1359–1362 (1999).

    Article  ADS  CAS  Google Scholar 

  23. Hetzer, M., Bilbao-Cortes, D., Walther, T. C., Gruss, O. J. & Mattaj, I. W. GTP hydrolysis by Ran is required for nuclear envelope assembly. Mol. Cell 5, 1013–1024 (2000).

    Article  CAS  Google Scholar 

  24. Zhang, C. & Clarke, P. R. Chromatin-independent nuclear envelope assembly induced by Ran GTPase in Xenopus egg extracts. Science 288, 1429–1432 ( 2000).

    Article  ADS  CAS  Google Scholar 

  25. Strome, S. & Wood, W. B. Generation of asymmetry and segregation of germ-line granules in early C. elegans embryos. Cell 35, 15–25 ( 1983).

    Article  CAS  Google Scholar 

  26. Swan, A., Nguyen, T. & Suter, B. Drosophila Lissencephaly-1 functions with Bic-D and dynein in oocyte determination and nuclear positioning. Nature Cell Biol. 1, 444–449 ( 1999).

    Article  CAS  Google Scholar 

  27. Willins, D. A., Liu, B., Xiang, X. & Morris, N. R. Mutations in the heavy chain of cytoplasmic dynein suppress the nudF nuclear migration mutation of Aspergillus nidulans. Mol. Gen. Genet. 255, 194–200 (1997).

    Article  CAS  Google Scholar 

  28. Tye, B. K. MCM proteins in DNA replication. Annu. Rev. Biochem. 68, 649–686 (1999).

    Article  CAS  Google Scholar 

  29. Mello, C. C., Kramer, J. M., Stinchcomb, D. & Ambros, V. Efficient gene transfer in C. elegans: extrachromosomal maintenance and integration of transforming sequences. EMBO J. 10, 3959–3970 (1991).

    Article  CAS  Google Scholar 

  30. Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, 45–48 ( 2000).

    Article  CAS  Google Scholar 

  31. 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 

  32. Tatusov, R. L., Koonin, E. V. & Lipman, D. J. A genomic perspective on protein families. Science 278, 631–637 ( 1997).

    Article  ADS  CAS  Google Scholar 

  33. Chervitz, S. A. et al. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science 282, 2022 –2028 (1998).

    Article  ADS  CAS  Google Scholar 

  34. Snel, B., Bork, P. & Huynen, M. A. Genome phylogeny based on gene content. Nature Genet. 21, 108–110 (1999).

    Article  CAS  Google Scholar 

  35. Rose, L. S. & Kemphues, K. The let-99 gene is required for proper spindle orientation during cleavage of the C. elegans embryo. Development 125, 1337– 1346 (1998).

    CAS  PubMed  Google Scholar 

  36. Clark-Maguire, S. & Mains, P. E. mei-1, a gene required for meiotic spindle formation in Caenorhabditis elegans , is a member of a family of ATPases. Genetics 136, 533–546 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Guo, S. & Kemphues, K. J. A non-muscle myosin required for embryonic polarity in Caenorhabditis elegans. Nature 382, 455–458 ( 1996).

    Article  ADS  CAS  Google Scholar 

  38. Pichler, S. et al. OOC-3, a novel putative transmembrane protein required for establishment of cortical domains and spindle orientation in the P1 blastomere of C. elegans embryos. Development 127, 2063–2073 (2000).

    CAS  PubMed  Google Scholar 

  39. Guo, S. & Kemphues, K. J. par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed. Cell 81, 611–620 (1995).

    Article  CAS  Google Scholar 

  40. Hung, T. J. & Kemphues, K. J. PAR-6 is a conserved PDZ domain-containing protein that colocalizes with PAR-3 in Caenorhabditis elegans embryos. Development 126, 127–135 (1999).

    CAS  PubMed  Google Scholar 

  41. Raich, W. B., Moran, A. N., Rothman, J. H. & Hardin, J. Cytokinesis and midzone microtubule organization in Caenorhabditis elegans require the kinesin-like protein ZEN-4. Mol. Biol. Cell 9, 2037–2049 (1998).

    Article  CAS  Google Scholar 

  42. Powers, J., Bossinger, O., Rose, D., Strome, S. & Saxton, W. A nematode kinesin required for cleavage furrow advancement. Curr. Biol. 8, 1133-1136 ( 1998).

    Article  Google Scholar 

  43. Matthews, L. R., Carter, P., Thierry, M. D. & Kemphues, K. ZYG-9, a Caenorhabditis elegans protein required for microtubule organization and function, is a component of meiotic and mitotic spindle poles. J. Cell Biol. 141, 1159-1168 ( 1998).

    Article  Google Scholar 

  44. Carter, P. W., Roos, J. M. & Kemphues, K. J. Molecular analysis of zyg-11, a maternal-effect gene required for early embryogenesis of Caenorhabditis elegans. Mol. Gen. Genet. 221, 72–80 (1990).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

For help in improving the manuscript, we thank A. Desai, A. Ephrussi, S. Grill, M. Labouesse, I. Mattaj and B. Sönnichsen. Work in the Hyman laboratory is supported by the EMBL (European Molecular Biology Laboratory) and the MPI (Max-Planck-Institute). P.G. was supported by a fellowship from the Swiss National Science Foundation. A.C. is supported by the UK Medical Research Council.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Anthony A. Hyman.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gönczy, P., Echeverri, C., Oegema, K. et al. Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature 408, 331–336 (2000). https://doi.org/10.1038/35042526

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/35042526

This article is cited by

Comments

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.

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