Transcriptomics

Dataset Information

2

Genome-wide characterization of PhoB binding profile in Escherichia coli (ChIP-chip data)


ABSTRACT: Chromatin immunoprecipitation was combined with high-density tiling array (ChIP-chip) and gene expression microarray to reveal the adaptive responses of Escherichia coli to phosphate starvation. The first sketch of the genome-wide distribution of PhoB binding profile was unveiled and 43 regions were identified as the PhoB binding regions. The presence of a significant common motif in these binding regions allowed us to reconstruct the PhoB binding pattern. By comparing the ChIP-chip and microarray datasets, we were also able to identify genes directly or indirectly affected through PhoB regulation. Nineteen out of the 287 differentially expressed genes in the presence and absence of PhoB activity were considered as the genes directly regulated by PhoB. The adaptive responses affected through PhoB regulation are discussed and these responses involve in several important biological functions including transcriptional regulation, transportation, membrane component arrangement, sigma factor modulation and DNA replication inhibition. Comparison of the E. coli K12 MG1655 wild type and a PhoB-FLAG fusion expressing strain (MG1655_PhoB_FLAG). The anti-FLAG antibody was used to recognize PhoB-FLAG fusion protein. Therefore, ChIPed DNA from the wild type strain was used as the control group. Three biological replicates were performed.

ORGANISM(S): Escherichia coli  

SUBMITTER: Whei-Fen Wu   Shiau-Yi Wen  Chun-Yang Chang  Tzu-Wen Huang  Chi Yang  Shih-Feng Tsai  Chuan-Hsiung Chang 

PROVIDER: E-GEOD-21856 | ArrayExpress | 2012-10-21

SECONDARY ACCESSION(S): GSE21856PRJNA129323

REPOSITORIES: GEO, ArrayExpress

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Publications

Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli.

Yang Chi C   Huang Tzu-Wen TW   Wen Shiau-Yi SY   Chang Chun-Yang CY   Tsai Shih-Feng SF   Wu Whei-Fen WF   Chang Chuan-Hsiung CH  

PloS one 20121005 10


The phosphate starvation response in bacteria has been studied extensively for the past few decades and the phosphate-limiting signal is known to be mediated via the PhoBR two-component system. However, the global DNA binding profile of the response regulator PhoB and the PhoB downstream responses are currently unclear. In this study, chromatin immunoprecipitation for PhoB was combined with high-density tiling array (ChIP-chip) as well as gene expression microarray to reveal the first global dow  ...[more]

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