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A gene-centered C. elegans protein-DNA interaction network.

Transcription regulatory networks consist of physical and functional interactions between transcription factors (TFs) and their target genes. The systematic mapping of TF-target gene interactions has been pioneered in unicellular systems, using "TF-centered" methods (e.g., chromatin immunoprecipitation). However, metazoan systems are less amenable to such methods. Here, we used "gene-centered" high-throughput yeast one-hybrid (Y1H) assays to identify 283 interactions between 72 C. elegans digestive tract gene promoters and 117 proteins. The resulting protein-DNA interaction (PDI) network is highly connected and enriched for TFs that are expressed in the digestive tract. We provide functional annotations for approximately 10% of all worm TFs, many of which were previously uncharacterized, and find ten novel putative TFs, illustrating the power of a gene-centered approach. We provide additional in vivo evidence for multiple PDIs and illustrate how the PDI network provides insights into metazoan differential gene expression at a systems level.

Pubmed ID: 16777607


  • Deplancke B
  • Mukhopadhyay A
  • Ao W
  • Elewa AM
  • Grove CA
  • Martinez NJ
  • Sequerra R
  • Doucette-Stamm L
  • Reece-Hoyes JS
  • Hope IA
  • Tissenbaum HA
  • Mango SE
  • Walhout AJ



Publication Data

June 16, 2006

Associated Grants

  • Agency: NIA NIH HHS, Id: AG025891
  • Agency: NIDDK NIH HHS, Id: DK068429
  • Agency: NIGMS NIH HHS, Id: GM056246
  • Agency: NIGMS NIH HHS, Id: R01 GM056264
  • Agency: NIGMS NIH HHS, Id: R01 GM056264-08
  • Agency: NIGMS NIH HHS, Id: R01 GM056264-08S1
  • Agency: NIGMS NIH HHS, Id: R01 GM056264-09
  • Agency: NIGMS NIH HHS, Id: R01 GM056264-10

Mesh Terms

  • Animals
  • Caenorhabditis elegans
  • Caenorhabditis elegans Proteins
  • Computational Biology
  • DNA, Helminth
  • DNA-Binding Proteins
  • Digestive System
  • Promoter Regions, Genetic
  • Regulatory Elements, Transcriptional
  • Saccharomyces cerevisiae
  • Transcription Factors
  • Transcription, Genetic
  • Two-Hybrid System Techniques