Gene Regulatory Networks pp 21-50

Part of the Methods in Molecular Biology book series (MIMB, volume 786) | Cite as

Expression Pattern Analysis of Regulatory Transcription Factors in Caenorhabditis elegans



Expression pattern data are fundamental to understanding transcriptional regulatory networks and the biological significance of such networks. For Caenorhabditis elegans, expression pattern analysis of transcription factor genes, with cellular resolution, typically involves generation of transcription factor gene/reporter gene fusions. This is followed by the creation of C. elegans strains transgenic for, and determination of expression patterns driven by, these fusions. Physiologically relevant regulatory relationships between transcription factors are both inferred from their expression patterns, in combination with protein–DNA interaction data, and evidenced from alterations of expression patterns when networks are disturbed.

Key words

Transcription factor Gateway Recombineering Reporters Caenorhabditis elegans 


  1. 1.
    Hobert, O. (2008) Gene regulation by transcription factors and microRNAs. Science 319, 1785–1786.PubMedCrossRefGoogle Scholar
  2. 2.
    Wenick, A. S. and Hobert, O. (2004) Genomic cis-regulatory architecture and trans-acting regulators of a single interneuron-specific gene battery in C. elegans. Dev. Cell 6, 757–770.Google Scholar
  3. 3.
    Sulston, J. E., Schierenberg, E., White, J. G., and Thomson, J. N. (1983) The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol. 100, 64–119.PubMedCrossRefGoogle Scholar
  4. 4.
    Sulston, J. E. (1977) Postembryonic cell lineages of the nematode Caenorhabditis elegans. Dev. Biol. 56, 110–156.PubMedCrossRefGoogle Scholar
  5. 5.
    The C. elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282, 2012–2018.Google Scholar
  6. 6.
    Dupuy, D., Li, Q.-R., Deplancke, B., Boxem, M., Hao, T., Lamesch, P., et al. (2004) A first version of the Caenorhabditis elegans promoterome. Genome Res. 14(10b), 2169–2175.Google Scholar
  7. 7.
    Lamesch, P., Milstein, S., Hao, T., Rosenberg, J., Li, N., Sequerra, R., et al. (2004) C. elegans ORFeome Version 3.1: increasing the coverage of ORFeome resources with improved gene predictions. Genome Res. 14(10b), 2064–2069.Google Scholar
  8. 8.
    Luan, C.-H., Qiu, S., Finley, J. B., Carson, M., Gray, R. J., Huang, W., et al. (2004) High-Throughput Expression of C. elegans Proteins. Genome Res. 14(10b), 2102–2110.Google Scholar
  9. 9.
    Invitrogen Life Technologies. MultiSite Gateway three-fragment vector construction kit – using Gateway technology to simultaneously clone multiple DNA fragments. Available from:
  10. 10.
    Hartley, J. L., Temple, G. F. and Brasch, M. A. (2000) DNA cloning using in vitro site-specific recombination. Genome Res. 10(11), 1788–1795.PubMedCrossRefGoogle Scholar
  11. 11.
    Reece-Hoyes, J. S., Deplancke, B., Shingles, J., Grove, C. A., Hope, I. A., and Walhout, A. J. M. (2005) A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. Genome Biol. 6, R110.PubMedCrossRefGoogle Scholar
  12. 12.
    Reece-Hoyes, J. S., Shingles, J., Dupuy, D., Grove, C. A., Walhout, A. J., Vidal, M., et al. (2007) Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns. BMC Genomics 8, 27.PubMedCrossRefGoogle Scholar
  13. 13.
    Dolphin, C. T. and Hope, I. A. (2006) Caenor-habditis elegans reporter fusion genes generated by seamless modification of large genomic DNA clones. Nucleic Acids Res. 34(9), e72.PubMedCrossRefGoogle Scholar
  14. 14.
    Bamps, S., Wirtz, J., Savory, F. R., Lake, D., and Hope, I. A. (2009) The Caenorhabditis elegans sirtuin gene, sir-2.1, is widely expressed and induced upon caloric restriction. Mech. Ageing & Dev. 130, 762–770.CrossRefGoogle Scholar
  15. 15.
    Stavropoulos, T. A. and Strathdee, C. A. (2001) Synergy between tetA and rpsL provides high-stringency positive and negative selection in bacterial artificial chromosome vectors. Genomics 72(1), 99–104.PubMedCrossRefGoogle Scholar
  16. 16.
    Epicenter Biotechnologies. CopyControl™ Fosmid Library Production Kit. Available from:
  17. 17.
    Westenberg, M., Bamps, S., Soedling, H., Hope, I. A., and Dolphin, C. T. (2010) Escherichia coli MW005: lambda Red-mediated recombineering and copy-number induction of oriV-equipped constructs in a single host. BMC Biotechnology 10, 27.PubMedCrossRefGoogle Scholar
  18. 18.
    Mello, C. C., Kramer, J. M., Dan, S., and Ambros, V. (1991) Efficient gene transfer in C. elegans: extrachromosomal maintenance and integration of transforming sequences. The EMBO Journal 10(12), 3959–3970.PubMedGoogle Scholar
  19. 19.
    Praitis, V., Casey, E., Collar, D., and Austin, J. (2001) Creation of low-copy integrated transgenic lines in Caenorhabditis elegans. Genetics 157(3), 1217–1226.PubMedGoogle Scholar
  20. 20.
    Hunt-Newbury, R., Viveiros, R., Johnsen, R., Mah, A., Anastas, D., Fang, L., et al. (2007) High-throughput in vivo analysis of gene expression in Caenorhabditis elegans. PLoS Biology 5(9), e237.PubMedCrossRefGoogle Scholar
  21. 21.
    Berezikov, E., Bargmann, C. I. and Plasterk, R. H. A. (2004) Homologous gene targeting in Caenorhabditis elegans by biolistic transformation. Nucleic Acids Res. 32(4), e40.PubMedCrossRefGoogle Scholar
  22. 22.
    Wilm, T., Demel, P., Koop H.-U., Schnabel H., and Schnabel, R. (1999) Ballistic transformation of Caenorhabditis elegans. Gene 229, 31–35.PubMedCrossRefGoogle Scholar
  23. 23.
    Jackstadt, P., Wilm, T. P., Horst, Z., and Gerd, H. (1999) Transformation of nematodes via ballistic DNA transfer Mol. Biochem. Parasitology 103(2), 261–266.CrossRefGoogle Scholar
  24. 24.
    Yochem, J., Nomarski images for learning the anatomy, with tips for mosaic analysis, in WormBook, The C. elegans research community, Editor. 2006. (
  25. 25.
    Bao, Z., John I. Murray, Thomas Boyle, Siew Loon Ooi, Matthew J. Sandel, and Waterston, R. H. (2006) Automated cell lineage tracing in Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA. 103, 2707–2712.PubMedCrossRefGoogle Scholar
  26. 26.
    Murray, J. I., Bao, Z., Boyle, T., and Waterston, R. H. (2006) The lineaging of fluorescently labeled Caenorhabditis elegans embryos with StarryNite and AceTree. Nat. Protoc. 1, 1468–1476.PubMedCrossRefGoogle Scholar
  27. 27.
    Boyle, T. J., Bao, Z., Murray, J. I., Araya, C. L., Waterston, R. H., and (2006). (2006) AceTree: a tool for visual analysis of Caenorhabditis ­elegans embryogenesis. BMC Bioinformatics 7, 275.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Faculty of Biological Sciences, Institute of Integrative and Comparative BiologyThe University of LeedsLeedsUK

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