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

Research paper by Bart B Deplancke, Arnab A Mukhopadhyay, Wanyuan W Ao, Ahmed M AM Elewa, Christian A CA Grove, Natalia J NJ Martinez, Reynaldo R Sequerra, Lynn L Doucette-Stamm, John S JS Reece-Hoyes, Ian A IA Hope, Heidi A HA Tissenbaum, Susan E SE Mango, Albertha J M AJ Walhout

Indexed on: 17 Jun '06Published on: 17 Jun '06Published in: Cell



Abstract

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.