The DNA-binding network of Mycobacterium tuberculosis.

Publication Type:

Journal Article

Authors:

Minch, Kyle J; Rustad, Tige R; Peterson, Eliza J R; Winkler, Jessica; Reiss, David J; Ma, Shuyi; Hickey, Mark; Brabant, William; Morrison, Bob; Turkarslan, Serdar; Mawhinney, Chris; Galagan, James E; Price, Nathan D; Baliga, Nitin S; Sherman, David R

Source:

Nat Commun, Volume 6, p.5829 (2015)

Keywords:

Amino Acid Motifs, Bacterial Proteins, Binding Sites, Chromatin Immunoprecipitation, Computational Biology, DNA, Bacterial, DNA-Binding Proteins, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Genetic Vectors, Genome-Wide Association Study, Mycobacterium tuberculosis, Nucleotide Motifs, Promoter Regions, Genetic, Protein Binding, Recombinant Proteins, ROC Curve, Transcription Factors, Transcription, Genetic

Abstract:

<p>Mycobacterium tuberculosis (MTB) infects 30% of all humans and kills someone every 20-30 s. Here we report genome-wide binding for ~80% of all predicted MTB transcription factors (TFs), and assayed global expression following induction of each TF. The MTB DNA-binding network consists of ~16,000 binding events from 154 TFs. We identify >50 TF-DNA consensus motifs and >1,150 promoter-binding events directly associated with proximal gene regulation. An additional ~4,200 binding events are in promoter windows and represent strong candidates for direct transcriptional regulation under appropriate environmental conditions. However, we also identify >10,000 'dormant' DNA-binding events that cannot be linked directly with proximal transcriptional control, suggesting that widespread DNA binding may be a common feature that should be considered when developing global models of coordinated gene expression.</p>