Data Entry: Please note that the research database will be replaced by UNIverse by the end of October 2023. Please enter your data into the system https://universe-intern.unibas.ch. Thanks
A gene-centered C. elegans protein-DNA interaction network
JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift)
ID
4506897
Author(s)
Deplancke, Bart; Mukhopadhyay, Arnab; Ao, Wanyuan; Elewa, Ahmed M.; Grove, Christian A.; Martinez, Natalia J.; Sequerra, Reynaldo; Doucette-Stamm, Lynn; Reece-Hoyes, John S.; Hope, Ian A.; Tissenbaum, Heidi A.; Mango, Susan E.; Walhout, Albertha J. M.
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.
