Open AccessA gene‐centered C. elegans protein– DNA interaction network provides a framework for functional predictions
Author(s) -
Fuxman Bass Juan I,
Pons Carles,
Kozlowski Lucie,
ReeceHoyes John S,
Shrestha Shaleen,
Holdorf Amy D,
Mori Akihiro,
Myers Chad L,
Walhout Albertha JM
Publication year - 2016
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.15252/msb.20167131
Subject(s) - biology , caenorhabditis elegans , computational biology , gene , gene regulatory network , genetics , dna , systems biology , gene expression
Abstract Transcription factors ( TF s) 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 ( PDI s) with TF regulatory activity, expression patterns, and phenotypic data. Although great progress has been made in mapping PDI s using chromatin immunoprecipitation, these studies have only characterized ~10% of TF s 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 TF s and 15% of gene promoters. We used this network as a backbone to predict TF binding sites for 77 TF s, 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 TF s.