Genome-Wide De Novo Prediction of Cis-Regulatory Binding Sites in Mycobacterium tuberculosis H37Rv.

The transcription regulatory system of Mycobacterium tuberculosis (M. tb) remains incompletely understood. In this study, we have applied the eGLECLUBS algorithm to a group of related prokaryotic genomes for de novo genome-wide prediction of cis-regulatory binding sites (CRBSs) in M. tb H37Rv. The t...

Full description

Bibliographic Details
Main Authors: Wei Wu, Xian Sun, Yun Gao, Jun Jiang, Zhenling Cui, Baoxue Ge, Hai Wu, Lu Zhang, Yao Li
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2016-01-01
Series:PLoS ONE
Online Access:http://europepmc.org/articles/PMC4757040?pdf=render
id doaj-6216a96a72964be8acfd1c0541516504
record_format Article
spelling doaj-6216a96a72964be8acfd1c05415165042020-11-25T02:28:58ZengPublic Library of Science (PLoS)PLoS ONE1932-62032016-01-01112e014896510.1371/journal.pone.0148965Genome-Wide De Novo Prediction of Cis-Regulatory Binding Sites in Mycobacterium tuberculosis H37Rv.Wei WuXian SunYun GaoJun JiangZhenling CuiBaoxue GeHai WuLu ZhangYao LiThe transcription regulatory system of Mycobacterium tuberculosis (M. tb) remains incompletely understood. In this study, we have applied the eGLECLUBS algorithm to a group of related prokaryotic genomes for de novo genome-wide prediction of cis-regulatory binding sites (CRBSs) in M. tb H37Rv. The top 250 clusters from our prediction recovered 83.3% (50/60) of all known CRBSs in extracted inter-operonic sequences of this strain. We further demonstrated that the integration of our prediction results with the ChIP-Seq datasets is very effective in identifying true binding sites of TFs. Using electrophoretic mobility shift assays and real-time RT-PCR, we experimentally verified our prediction of CRBSs for Rv0081, an important transcription factor thought to be involved in regulation of M. tb under hypoxia.http://europepmc.org/articles/PMC4757040?pdf=render
collection DOAJ
language English
format Article
sources DOAJ
author Wei Wu
Xian Sun
Yun Gao
Jun Jiang
Zhenling Cui
Baoxue Ge
Hai Wu
Lu Zhang
Yao Li
spellingShingle Wei Wu
Xian Sun
Yun Gao
Jun Jiang
Zhenling Cui
Baoxue Ge
Hai Wu
Lu Zhang
Yao Li
Genome-Wide De Novo Prediction of Cis-Regulatory Binding Sites in Mycobacterium tuberculosis H37Rv.
PLoS ONE
author_facet Wei Wu
Xian Sun
Yun Gao
Jun Jiang
Zhenling Cui
Baoxue Ge
Hai Wu
Lu Zhang
Yao Li
author_sort Wei Wu
title Genome-Wide De Novo Prediction of Cis-Regulatory Binding Sites in Mycobacterium tuberculosis H37Rv.
title_short Genome-Wide De Novo Prediction of Cis-Regulatory Binding Sites in Mycobacterium tuberculosis H37Rv.
title_full Genome-Wide De Novo Prediction of Cis-Regulatory Binding Sites in Mycobacterium tuberculosis H37Rv.
title_fullStr Genome-Wide De Novo Prediction of Cis-Regulatory Binding Sites in Mycobacterium tuberculosis H37Rv.
title_full_unstemmed Genome-Wide De Novo Prediction of Cis-Regulatory Binding Sites in Mycobacterium tuberculosis H37Rv.
title_sort genome-wide de novo prediction of cis-regulatory binding sites in mycobacterium tuberculosis h37rv.
publisher Public Library of Science (PLoS)
series PLoS ONE
issn 1932-6203
publishDate 2016-01-01
description The transcription regulatory system of Mycobacterium tuberculosis (M. tb) remains incompletely understood. In this study, we have applied the eGLECLUBS algorithm to a group of related prokaryotic genomes for de novo genome-wide prediction of cis-regulatory binding sites (CRBSs) in M. tb H37Rv. The top 250 clusters from our prediction recovered 83.3% (50/60) of all known CRBSs in extracted inter-operonic sequences of this strain. We further demonstrated that the integration of our prediction results with the ChIP-Seq datasets is very effective in identifying true binding sites of TFs. Using electrophoretic mobility shift assays and real-time RT-PCR, we experimentally verified our prediction of CRBSs for Rv0081, an important transcription factor thought to be involved in regulation of M. tb under hypoxia.
url http://europepmc.org/articles/PMC4757040?pdf=render
work_keys_str_mv AT weiwu genomewidedenovopredictionofcisregulatorybindingsitesinmycobacteriumtuberculosish37rv
AT xiansun genomewidedenovopredictionofcisregulatorybindingsitesinmycobacteriumtuberculosish37rv
AT yungao genomewidedenovopredictionofcisregulatorybindingsitesinmycobacteriumtuberculosish37rv
AT junjiang genomewidedenovopredictionofcisregulatorybindingsitesinmycobacteriumtuberculosish37rv
AT zhenlingcui genomewidedenovopredictionofcisregulatorybindingsitesinmycobacteriumtuberculosish37rv
AT baoxuege genomewidedenovopredictionofcisregulatorybindingsitesinmycobacteriumtuberculosish37rv
AT haiwu genomewidedenovopredictionofcisregulatorybindingsitesinmycobacteriumtuberculosish37rv
AT luzhang genomewidedenovopredictionofcisregulatorybindingsitesinmycobacteriumtuberculosish37rv
AT yaoli genomewidedenovopredictionofcisregulatorybindingsitesinmycobacteriumtuberculosish37rv
_version_ 1724835182201012224