Author
Listed:
- Kyle J. Minch
(Seattle Biomedical Research Institute
Interdisciplinary Program of Pathobiology, University of Washington)
- Tige R. Rustad
(Seattle Biomedical Research Institute)
- Eliza J. R. Peterson
(Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA)
- Jessica Winkler
(Seattle Biomedical Research Institute)
- David J. Reiss
(Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA)
- Shuyi Ma
(Seattle Biomedical Research Institute
Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA
University of Illinois Urbana-Champaign)
- Mark Hickey
(Seattle Biomedical Research Institute)
- William Brabant
(Seattle Biomedical Research Institute)
- Bob Morrison
(Seattle Biomedical Research Institute)
- Serdar Turkarslan
(Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA)
- Chris Mawhinney
(Boston University)
- James E. Galagan
(Boston University
Boston University
Bioinformatics Program, Boston University
The Eli and Edythe L. Broad Institute of Harvard and MIT)
- Nathan D. Price
(Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA)
- Nitin S. Baliga
(Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA)
- David R. Sherman
(Seattle Biomedical Research Institute
Interdisciplinary Program of Pathobiology, University of Washington)
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.
Suggested Citation
Kyle J. Minch & Tige R. Rustad & Eliza J. R. Peterson & Jessica Winkler & David J. Reiss & Shuyi Ma & Mark Hickey & William Brabant & Bob Morrison & Serdar Turkarslan & Chris Mawhinney & James E. Gala, 2015.
"The DNA-binding network of Mycobacterium tuberculosi s,"
Nature Communications, Nature, vol. 6(1), pages 1-10, May.
Handle:
RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms6829
DOI: 10.1038/ncomms6829
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