title: A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis.
abstract: Mycobacterium tuberculosis (MTB) is a pathogenic bacterium responsible for 12 million active cases of tuberculosis (TB) worldwide. The complexity and critical regulatory components of MTB pathogenicity are still poorly understood despite extensive research efforts. In this study, we constructed the first systems-scale map of transcription factor (TF) binding sites and their regulatory target proteins in MTB. We constructed FLAG-tagged overexpression constructs for 206 TFs in MTB, used ChIP-seq to identify genome-wide binding events and surveyed global transcriptomic changes for each overexpressed TF. Here we present data for the most comprehensive map of MTB gene regulation to date. We also define elaborate quality control measures, extensive filtering steps, and the gene-level overlap between ChIP-seq and microarray datasets. Further, we describe the use of TF overexpression datasets to validate a global gene regulatory network model of MTB and describe an online source to explore the datasets.
authors.affiliation: Institute for Systems Biology , Seattle, Washington 98109, USA.
authors.forename: Serdar
authors.initials: S
authors.lastname: Turkarslan
authors.affiliation: Institute for Systems Biology , Seattle, Washington 98109, USA.
authors.forename: Eliza J R
authors.initials: EJ
authors.lastname: Peterson
authors.affiliation: Seattle Biomedical Research Institute , Seattle, Washington 98109, USA ; Interdisciplinary Program of Pathobiology, Department of Global Health, University of Washington , Seattle, Washington 98195, USA.
authors.forename: Tige R
authors.initials: TR
authors.lastname: Rustad
authors.affiliation: Seattle Biomedical Research Institute , Seattle, Washington 98109, USA.
authors.forename: Kyle J
authors.initials: KJ
authors.lastname: Minch
authors.affiliation: Institute for Systems Biology , Seattle, Washington 98109, USA.
authors.forename: David J
authors.initials: DJ
authors.lastname: Reiss
authors.affiliation: Seattle Biomedical Research Institute , Seattle, Washington 98109, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Morrison
authors.affiliation: Institute for Systems Biology , Seattle, Washington 98109, USA ; Seattle Biomedical Research Institute , Seattle, Washington 98109, USA ; Department of Chemical and Biomolecular Engineering, University of Illinois , Urbana, Illinois 61801, USA.
authors.forename: Shuyi
authors.initials: S
authors.lastname: Ma
authors.affiliation: Institute for Systems Biology , Seattle, Washington 98109, USA.
authors.forename: Nathan D
authors.initials: ND
authors.lastname: Price
authors.affiliation: Seattle Biomedical Research Institute , Seattle, Washington 98109, USA ; Interdisciplinary Program of Pathobiology, Department of Global Health, University of Washington , Seattle, Washington 98195, USA ; Molecular and Cellular Biology Program, University of Washington , Seattle, Washington 98195, USA.
authors.forename: David R
authors.initials: DR
authors.lastname: Sherman
authors.affiliation: Institute for Systems Biology , Seattle, Washington 98109, USA ; Molecular and Cellular Biology Program, University of Washington , Seattle, Washington 98195, USA ; Departments of Biology and Microbiology, University of Washington , Seattle, Washington 98195, USA ; Lawrence Berkeley National Lab , Berkeley, California 94720, USA.
authors.forename: Nitin S
authors.initials: NS
authors.lastname: Baliga
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D008957:Models, Genetic; D009169:Mycobacterium tuberculosis / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D014157:Transcription Factors