The DNA-binding network of Mycobacterium tuberculosi s

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. Galagan, Nathan D. Price, Nitin S. Baliga and David R. Sherman ()
Additional contact information
Kyle J. Minch: Seattle Biomedical Research Institute
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
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
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

Nature Communications, 2015, vol. 6, issue 1, 1-10

Abstract: 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.

Date: 2015
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DOI: 10.1038/ncomms6829

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