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The DNA-binding network of Mycobacterium tuberculosi s

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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    Cited by:

    1. Cosme Claverie & Francesco Coppolino & Maria-Vittoria Mazzuoli & Cécile Guyonnet & Elise Jacquemet & Rachel Legendre & Odile Sismeiro & Giuseppe Valerio Gaetano & Giuseppe Teti & Patrick Trieu-Cuot & , 2024. "Constitutive activation of two-component systems reveals regulatory network interactions in Streptococcus agalactiae," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    2. Cheng Bei & Junhao Zhu & Peter H. Culviner & Mingyu Gan & Eric J. Rubin & Sarah M. Fortune & Qian Gao & Qingyun Liu, 2024. "Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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