Back to Search Start Over

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

Authors :
Juan I Fuxman Bass
Carles Pons
Lucie Kozlowski
John S Reece‐Hoyes
Shaleen Shrestha
Amy D Holdorf
Akihiro Mori
Chad L Myers
Albertha JM Walhout
Source :
Molecular Systems Biology, Vol 12, Iss 10, Pp 1-19 (2016)
Publication Year :
2016
Publisher :
Springer Nature, 2016.

Abstract

Abstract 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.

Details

Language :
English
ISSN :
17444292
Volume :
12
Issue :
10
Database :
Directory of Open Access Journals
Journal :
Molecular Systems Biology
Publication Type :
Academic Journal
Accession number :
edsdoj.6b21d56d5cf41ec85dc315ca42fac2b
Document Type :
article
Full Text :
https://doi.org/10.15252/msb.20167131