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| Status |
Public on Oct 21, 2012 |
| Title |
Genome-wide characterization of PhoB binding profile in Escherichia coli (ChIP-chip data) |
| Platform organism |
Escherichia coli str. K-12 substr. MG1655 |
| Sample organism |
Escherichia coli |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
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| Summary |
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.
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| Overall design |
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.
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| Contributor(s) |
Yang C, Wen S, Huang T, Chang C, Tsai S, Wu W, Chang C |
| Citation(s) |
23071782 |
| |
| Submission date |
May 15, 2010 |
| Last update date |
Aug 08, 2013 |
| Contact name |
Chi Yang |
| E-mail(s) |
[email protected]
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| Organization name |
National Yang-Ming University
|
| Department |
Institute of BioMedical Informatics
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| Street address |
No.155, Sec.2, Linong Street
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| City |
Taipei |
| ZIP/Postal code |
112 |
| Country |
Taiwan |
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| Platforms (1) |
| GPL10416 |
NimbleGen E. coli K12 Mg1655 385K array |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE21857 |
Genome-wide characterization of PhoB binding profile in Escherichia coli |
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| Relations |
| BioProject |
PRJNA129323 |
