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| Status |
Public on Jun 23, 2009 |
| Title |
Rho directs widespread termination of intragenic and stable RNA transcription |
| Platform organisms |
Escherichia coli; 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 |
The transcription termination factor Rho is a global regulator of RNA polymerase (RNAP). Although individual Rho-dependent terminators have been studied extensively, less is known about the sites of RNAP regulation by Rho on a genome-wide scale. Using chromatin immunoprecipitation and microarrays (ChIP-chip), we examined changes in the distribution of Escherichia coli RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM). We found ~200 Rho-terminated loci that were divided evenly into two classes: intergenic (at the ends of genes) and intragenic (within genes). The intergenic class contained noncoding RNAs such as small RNAs (sRNAs) and transfer RNAs (tRNAs), establishing a previously unappreciated role of Rho in termination of stable RNA synthesis. The intragenic class of terminators included a novel set of short antisense transcripts, as judged by a shift in the distribution of RNAP in BCM-treated cells that was opposite to the direction of the corresponding gene. These Rho-terminated antisense transcripts point to a novel role of noncoding transcription in E. coli gene regulation that may resemble the ubiquitous noncoding transcription recently found to play myriad roles in eukaryotic gene regulation.
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| Overall design |
Chromatin immunoprecipitation (ChIP) experiments were performed using antibodies against RNA polymerase (Beta or Beta' subunit) in cells treated with 20ug/ml bicyclomycin or untreated cells. Differentially labeled ChIP DNA and genomic DNA were competitively hybridized to an E. coli K-12 MG1655 tiling array with overlapping probes at ~12bp spacing across the entire genome. The series contains 4 datasets.
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| Contributor(s) |
Peters JM, Mooney RA, Kuan PF, Rowland JL, Keles S, Landick RC |
| Citation(s) |
19706412 |
| Submission date |
Jun 11, 2009 |
| Last update date |
Apr 29, 2013 |
| Contact name |
Jason Matthew Peters |
| URL |
http://www.bact.wisc.edu:16080/landick/
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| Organization name |
UW-Madison
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| Department |
Biochemistry
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| Lab |
Landick Lab
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| Street address |
1550 Linden Drive
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706-1567 |
| Country |
USA |
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| Platforms (2) |
| GPL7790 |
Escherichia coli K-12 MG1655 tiling array (Nimblegen Design) |
| GPL8708 |
UW-Madison Escherichia coli K-12 MG1655 tiling array (YD Design) |
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| Samples (4)
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| GSM416594 |
RNA polymerase (Beta) ChIP-chip in E. coli K-12 MG1655 cells (Dataset 3427302) |
| GSM416595 |
RNA polymerase (Beta) ChIP-chip in E. coli K-12 MG1655 cells treated with 20ug/ml bicyclomycin (Dataset 3428302) |
| GSM424656 |
RNA polymerase (Beta') ChIP-chip in E. coli K-12 MG1655 cells treated with 20ug/ml bicyclomycin (Dataset 94828) |
| GSM424657 |
RNA polymerase (Beta') ChIP-chip in E. coli K-12 MG1655 cells (Dataset 100040) |
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| Relations |
| BioProject |
PRJNA116199 |
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