The DNA-binding network of Mycobacterium tuberculosis

Nat Commun. 2015 Jan 12:6:5829. doi: 10.1038/ncomms6829.

Abstract

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

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

Substances

  • Bacterial Proteins
  • DNA, Bacterial
  • DNA-Binding Proteins
  • Recombinant Proteins
  • Transcription Factors