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

The DNA-binding network of Mycobacterium tuberculosis.

Author information

1
1] Seattle Biomedical Research Institute, Seattle, Washington 98109, USA [2] Interdisciplinary Program of Pathobiology, Department of Global Health, University of Washington, Seattle, Washington 98195, USA.
2
Seattle Biomedical Research Institute, Seattle, Washington 98109, USA.
3
Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA.
4
1] Seattle Biomedical Research Institute, Seattle, Washington 98109, USA [2] Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA [3] Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA.
5
Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA.
6
1] Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA [2] Department of Microbiology, Boston University, Boston, Massachusetts 02215, USA [3] Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA [4] The Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.

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.

PMID:
25581030
PMCID:
PMC4301838
DOI:
10.1038/ncomms6829
[Indexed for MEDLINE]
Free PMC Article

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