A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis

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...

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Main Authors:	Turkarslan, Serdar, Peterson, Eliza J R, Rustad, Tige R, Minch, Kyle J, Reiss, David J, Morrison, Robert, Ma, Shuyi, Price, Nathan D, Sherman, David R, Baliga, Nitin S
Format:	Online
Language:	English
Published:	Nature Publishing Group 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4413241/

id	pubmed-4413241
recordtype	oai_dc
spelling	pubmed-44132412015-05-14 A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis Turkarslan, Serdar Peterson, Eliza J R Rustad, Tige R Minch, Kyle J Reiss, David J Morrison, Robert Ma, Shuyi Price, Nathan D Sherman, David R Baliga, Nitin S Data Descriptor 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. Nature Publishing Group 2015-03-31 /pmc/articles/PMC4413241/ /pubmed/25977815 http://dx.doi.org/10.1038/sdata.2015.10 Text en Copyright © 2015, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0 This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0 Metadata associated with this Data Descriptor is available at http://www.nature.com/sdata/ and is released under the CC0 waiver to maximize reuse.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Turkarslan, Serdar Peterson, Eliza J R Rustad, Tige R Minch, Kyle J Reiss, David J Morrison, Robert Ma, Shuyi Price, Nathan D Sherman, David R Baliga, Nitin S
spellingShingle	Turkarslan, Serdar Peterson, Eliza J R Rustad, Tige R Minch, Kyle J Reiss, David J Morrison, Robert Ma, Shuyi Price, Nathan D Sherman, David R Baliga, Nitin S A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis
author_facet	Turkarslan, Serdar Peterson, Eliza J R Rustad, Tige R Minch, Kyle J Reiss, David J Morrison, Robert Ma, Shuyi Price, Nathan D Sherman, David R Baliga, Nitin S
author_sort	Turkarslan, Serdar
title	A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis
title_short	A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis
title_full	A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis
title_fullStr	A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis
title_full_unstemmed	A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis
title_sort	comprehensive map of genome-wide gene regulation in mycobacterium tuberculosis
description	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.
publisher	Nature Publishing Group
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4413241/
_version_	1613216996754718720

A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis

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