A gene-centered C.elegans protein-DNA interaction network provides a framework for functional predictions

作者：Bass Juan I Fuxman; Pons Carles; Kozlowski Lucie; Reece Hoyes John S; Shrestha Shaleen; Holdorf Amy D; Mori Akihiro; Myers Chad L; Walhout Albertha J M^*

来源：Molecular Systems Biology, 2016, 12(10): 884.

DOI：10.15252/msb.20167131

• C
• elegans
• gene regulation
• protein-DNA interaction network
• transcription factors
• yeast one-hybrid assays

Transcription factors (TFs) play a central role in controlling spatiotemporal gene expression and the response to environmental cues. A comprehensive understanding of gene regulation requires integrating physical protein-DNA interactions (PDIs) with TF regulatory activity, expression patterns, and phenotypic data. Although great progress has been made in mapping PDIs using chromatin immunoprecipitation, these studies have only characterized 10% of TFs in any metazoan species. The nematode C.elegans has been widely used to study gene regulation due to its compact genome with short regulatory sequences. Here, we delineated the largest gene-centered metazoan PDI network to date by examining interactions between 90% of C. elegans TFs and 15% of gene promoters. We used this network as a backbone to predict TF binding sites for 77 TFs, two-thirds of which are novel, as well as integrate gene expression, protein-protein interaction, and phenotypic data to predict regulatory and biological functions for multiple genes and TFs.

• 出版日期2016-10