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:

Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans

Nature Biotechnology volume 25, pages 663–668 (2007)Cite this article

Abstract

Differential regulation of gene expression is essential for cell fate specification in metazoans. Characterizing the transcriptional activity of gene promoters, in time and in space, is therefore a critical step toward understanding complex biological systems. Here we present an in vivo spatiotemporal analysis for ∼900 predicted C. elegans promoters (∼5% of the predicted protein-coding genes), each driving the expression of green fluorescent protein (GFP). Using a flow-cytometer adapted for nematode profiling, we generated 'chronograms', two-dimensional representations of fluorescence intensity along the body axis and throughout development from early larvae to adults. Automated comparison and clustering of the obtained in vivo expression patterns show that genes coexpressed in space and time tend to belong to common functional categories. Moreover, integration of this data set with C. elegans protein-protein interactome data sets enables prediction of anatomical and temporal interaction territories between protein partners.

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: Generating post-embryonic developmental chronograms.
Figure 2: Visualization of tissue-specific expression.
Figure 3: Feature extraction from multiple images.
Figure 4: In vivo expression pattern clustering.
Figure 5: Localization of protein-protein interactions.

Similar content being viewed by others

References

  1. Davidson, E.H. et al. A genomic regulatory network for development. Science 295, 1669–1678 (2002).

    Article  CAS  Google Scholar 

  2. Inoue, T., Wang, M., Ririe, T.O., Fernandes, J.S. & Sternberg, P.W. Transcriptional network underlying Caenorhabditis elegans vulval development. Proc. Natl. Acad. Sci. USA 102, 4972–4977 (2005).

    Article  CAS  Google Scholar 

  3. Cooper, S.J., Trinklein, N.D., Anton, E.D., Nguyen, L. & Myers, R.M. Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res. 16, 1–10 (2006).

    Article  CAS  Google Scholar 

  4. Sulston, J.E., Schierenberg, E., White, J.G. & Thomson, J.N. The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol. 100, 64–119 (1983).

    Article  CAS  Google Scholar 

  5. Sulston, J.E. & Horvitz, H.R. Post-embryonic cell lineages of the nematode, Caenorhabditis elegans. Dev. Biol. 56, 110–156 (1977).

    Article  CAS  Google Scholar 

  6. Kimble, J. & Hirsh, D. The postembryonic cell lineages of the hermaphrodite and male gonads in Caenorhabditis elegans. Dev. Biol. 70, 396–417 (1979).

    Article  CAS  Google Scholar 

  7. Chalfie, M., Tu, Y., Euskirchen, G., Ward, W.W. & Prasher, D.C. Green fluorescent protein as a marker for gene expression. Science 263, 802–805 (1994).

    Article  CAS  Google Scholar 

  8. Bao, Z. et al. Automated cell lineage tracing in Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 103, 2707–2712 (2006).

    Article  CAS  Google Scholar 

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

  10. Vidal, M. A biological atlas of functional maps. Cell 104, 333–339 (2001).

    Article  CAS  Google Scholar 

  11. Dupuy, D. et al. A first version of the Caenorhabditis elegans Promoterome. Genome Res. 14, 2169–2175 (2004).

    Article  CAS  Google Scholar 

  12. Hobert, O. PCR fusion-based approach to create reporter gene constructs for expression analysis in transgenic C. elegans. Biotechniques 32, 728–730 (2002).

    Article  CAS  Google Scholar 

  13. McKay, S.J. et al. Gene expression profiling of cells, tissues, and developmental stages of the nematode C. elegans. Cold Spring Harb. Symp. Quant. Biol. 68, 159–169 (2003).

    Article  CAS  Google Scholar 

  14. Reece-Hoyes, J.S. et al. Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns. BMC Genomics 8, 27 (2007).

    Article  Google Scholar 

  15. 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 

  16. Toms, N., Cooper, J., Patchen, B. & Aamodt, E. High copy arrays containing a sequence upstream of mec-3 alter cell migration and axonal morphology in C. elegans. BMC Dev. Biol. 1, 2 (2001).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  18. Li, S. et al. A map of the interactome network of the metazoan C. elegans. Science 303, 540–543 (2004).

    Article  CAS  Google Scholar 

  19. Gunsalus, K.C. et al. Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature 436, 861–865 (2005).

    Article  CAS  Google Scholar 

  20. Ge, H., Liu, Z., Church, G.M. & Vidal, M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat. Genet. 29, 482–486 (2001).

    Article  CAS  Google Scholar 

  21. Rual, J.F. et al. Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res. 14, 2162–2168 (2004).

    Article  CAS  Google Scholar 

  22. Eisen, M.B., Spellman, P.T., Brown, P.O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14863–14868 (1998).

    Article  CAS  Google Scholar 

  23. Jiang, M. et al. 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. Kamath, R.S. et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421, 231–237 (2003).

    Article  CAS  Google Scholar 

  25. Simmer, F. et al. Genome-wide RNAi of C. elegans using the hypersensitive rrf-3 strain reveals novel gene functions. PLoS Biol. 1, E12 (2003).

    Article  Google Scholar 

  26. Fernandez, A.G. et al. New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones. Genome Res. 15, 250–259 (2005).

    Article  CAS  Google Scholar 

  27. Lundquist, E.A. et al. The mec-8 gene of C. elegans encodes a protein with two RNA recognition motifs and regulates alternative splicing of unc-52 transcripts. Development 122, 1601–1610 (1996).

    CAS  PubMed  Google Scholar 

  28. Spike, C.A., Davies, A.G., Shaw, J.E. & Herman, R.K. MEC-8 regulates alternative splicing of unc-52 transcripts in C. elegans hypodermal cells. Development 129, 4999–5008 (2002).

    CAS  PubMed  Google Scholar 

  29. Anyanful, A. et al. The RNA-binding protein SUP-12 controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. J. Cell Biol. 167, 639–647 (2004).

    Article  CAS  Google Scholar 

  30. Loria, P.M., Duke, A., Rand, J.B. & Hobert, O. Two neuronal, nuclear-localized RNA binding proteins involved in synaptic transmission. Curr. Biol. 13, 1317–1323 (2003).

    Article  CAS  Google Scholar 

  31. Fujita, M. et al. The role of the ELAV homologue EXC-7 in the development of the Caenorhabditis elegans excretory canals. Dev. Biol. 256, 290–301 (2003).

    Article  CAS  Google Scholar 

  32. Han, J.D. et al. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430, 88–93 (2004).

    Article  CAS  Google Scholar 

  33. Chevenet, F., Brun, C., Banuls, A.L., Jacq, B. & Christen, R. TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics 7, 439 (2006).

    Article  Google Scholar 

  34. Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R.J. & Church, G.M. Systematic determination of genetic network architecture. Nat. Genet. 22, 281–285 (1999).

    Article  CAS  Google Scholar 

  35. Thacker, C., Sheps, J.A. & Rose, A.M. Caenorhabditis elegans dpy-5 is a cuticle procollagen processed by a proprotein convertase. Cell. Mol. Life Sci. 63, 1193–1204 (2006).

    Article  CAS  Google Scholar 

  36. Kim, S. & Wadsworth, W.G. Positioning of longitudinal nerves in C. elegans by nidogen. Science 288, 150–154 (2000).

    Article  CAS  Google Scholar 

  37. Sagasti, A., Hobert, O., Troemel, E.R., Ruvkun, G. & Bargmann, C.I. Alternative olfactory neuron fates are specified by the LIM homeobox gene lim-4. Genes Dev. 13, 1794–1806 (1999).

    Article  CAS  Google Scholar 

  38. Kostic, I. & Roy, R. Organ-specific cell division abnormalities caused by mutation in a general cell cycle regulator in C. elegans. Development 129, 2155–2165 (2002).

    CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  40. Harfe, B.D. et al. Analysis of a Caenorhabditis elegans Twist homolog identifies conserved and divergent aspects of mesodermal patterning. Genes Dev. 12, 2623–2635 (1998).

    Article  CAS  Google Scholar 

  41. Hall, D.H. et al. Ultrastructural features of the adult hermaphrodite gonad of Caenorhabditis elegans: relations between the germ line and soma. Dev. Biol. 212, 101–123 (1999).

    Article  CAS  Google Scholar 

  42. Bulow, H.E. & Hobert, O. Differential sulfations and epimerization define heparan sulfate specificity in nervous system development. Neuron 41, 723–736 (2004).

    Article  Google Scholar 

Download references

Acknowledgements

This work was funded by the National Cancer Institute (NCI 4 R33 CA097516-02)(M.V.), Genome British Columbia, the Canadian Institute of Health Research and Genome Canada (D.B. and D.G.M.), the NetWork Bench National Science Foundation (IIS-0513650), the Muscular Dystrophy Association, the National Institutes of Health (NIH) (1 P20 CA11300-01, A.L.B. and HD43156, W.A.M.) and the Helen Kellogg Institute for International Studies (C.A.H.R.). F.P.R. was supported in part by NIH grant HG003224. M.T. was supported by NIH NRSA Fellowship HG004098. Some nematode strains used in this work were provided by the Caenorhabditis Genetics Center, which is funded by the NIH National Center for Research Resources. Thanks to Tracey Clingingsmith and Abigail Bird for their indispensable assistance and to Michael Cusick and Mike Boxem for careful proofreading of the manuscript.

Author information

Author notes

  1. Denis Dupuy, Nicolas Bertin and César A Hidalgo: These authors contributed equally to this work.

Authors and Affiliations

  1. and Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Genetics, Center for Cancer Systems Biology (CCSB), Harvard Medical School, 44 Binney Street, Boston, 02115, Massachusetts, USA

    Denis Dupuy, Nicolas Bertin, César A Hidalgo, Kavitha Venkatesan, Jennifer Rosenberg, Nenad Svrzikapa, Aurélie Blanc, Alain Carnec, Anne-Ruxandra Carvunis, Albert-László Barabási & Marc Vidal

  2. Centre de Recherche en Biochimie Macromoléculaire, Centre National de la Recherche Scientifique FRE 2593, 1919 Route de Mende, Montpellier Cedex 5, 34293, France

    Nicolas Bertin & Christian Le Peuch

  3. Department of Physics, Center for Complex Network Research, University of Notre Dame, 225 Nieuwland Science Hall, Notre Dame, Indiana, 46556, USA

    César A Hidalgo & Albert-László Barabási

  4. Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, V5A 1S6, British Columbia, Canada

    Domena Tu, David Lee, Robert Johnsen & David Baillie

  5. Union Biometrica, 84 October Hill Road, Holliston, 01746, Massachusetts, USA

    Rock Pulak

  6. Institute of Integrative and Comparative Biology, University of Leeds, Clarendon Way, Leeds, LS2 9JT, West Yorkshire, UK

    Jane Shingles, John Reece-Hoyes & Ian A Hope

  7. Department of Zoology, The University of British Columbia, 6270 University Boulevard, Vancouver, V6T 1Z4, British Columbia, Canada

    Rebecca Hunt-Newbury, Ryan Viveiros & Donald G Moerman

  8. Department of Genetics and Developmental Biology and Center for Cell Analysis and Modeling, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, 06030, Connecticut, USA

    William A Mohler

  9. and Department of Biological Chemistry and Molecular Pharmacology, Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02115, Massachusetts, USA

    Murat Tasan & Frederick P Roth

Authors
  1. Denis Dupuy
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Nicolas Bertin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. César A Hidalgo
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kavitha Venkatesan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Domena Tu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. David Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Jennifer Rosenberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Nenad Svrzikapa
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Aurélie Blanc
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Alain Carnec
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Anne-Ruxandra Carvunis
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Rock Pulak
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Jane Shingles
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. John Reece-Hoyes
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Rebecca Hunt-Newbury
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Ryan Viveiros
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. William A Mohler
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Murat Tasan
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Frederick P Roth
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. Christian Le Peuch
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. Ian A Hope
    View author publications

    You can also search for this author in PubMed Google Scholar

  22. Robert Johnsen
    View author publications

    You can also search for this author in PubMed Google Scholar

  23. Donald G Moerman
    View author publications

    You can also search for this author in PubMed Google Scholar

  24. Albert-László Barabási
    View author publications

    You can also search for this author in PubMed Google Scholar

  25. David Baillie
    View author publications

    You can also search for this author in PubMed Google Scholar

  26. Marc Vidal
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Transgenic animals were generated by ballistic transformation by J.S. and J.R.-H. under the supervision of I.A.H., and by microinjection by D.T. and D.L. under the supervision of R.J. and D.B., anatomic annotations of the strains were performed by R.H.-N. and R.V. under the supervision of D.G.M. The chronogram concept was conceived by W.A.M. and implemented by D.D., N.B. and C.A.H. D.D. generated the Gateway promoter::GFP constructs with the help of J.R., and performed the profiling experiments with the technical support of R.P. Computational analyses were performed by N.B., C.A.H., K.V., A.-R.C., A.C. and M.T. under the supervision of D.D., F.P.R., C.L., A.-L.B. and M.V. Lab support was provided by J.R., N.S. and A.B. The manuscript was written by D.D., N.B., C.A.H., A.-L.B. and M.V. The project was conceived and codirected by D.B. and M.V.

Corresponding authors

Correspondence to Albert-László Barabási, David Baillie or Marc Vidal.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Repartition of the transgenic worm strains by origin, grouped by common locus. (PDF 242 kb)

Supplementary Fig. 2

High PCC value between the chronograms correlates with a strong visual resemblance between the fluorescent micrographs of the corresponding animals. (PDF 8567 kb)

Supplementary Fig. 3

Subtrees enrichments. s. (PDF 10891 kb)

Supplementary Fig. 4

Strains BC11521 and BC11545 showed clear expression in the vulval region and the spermatheca, respectively, that was not reported in the initial assessment. (PDF 3070 kb)

Supplementary Table 1

Average images of chronograms grouped in the neighbor joining tree branches that present enrichments in specific GO terms, microarray expression cluster and/or anatomical annotation. (PDF 21900 kb)

Supplementary Methods (PDF 429 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Dupuy, D., Bertin, N., Hidalgo, C. et al. Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans. Nat Biotechnol 25, 663–668 (2007). https://doi.org/10.1038/nbt1305

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt1305

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