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PMID:19706412

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Contents

Citation

Peters, JM, Mooney, RA, Kuan, PF, Rowland, JL, Keles, S and Landick, R (2009) Rho directs widespread termination of intragenic and stable RNA transcription. Proc. Natl. Acad. Sci. U.S.A. 106:15406-11

Abstract

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 approximately 200 Rho-terminated loci that were divided evenly into 2 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 previously uncharacterized 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 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.

Links

PubMed PMC2741264 Online version:10.1073/pnas.0903846106

Keywords

Bicyclo Compounds, Heterocyclic; Chromatin Immunoprecipitation; DNA-Directed RNA Polymerases/metabolism; Escherichia coli/metabolism; Genes, Bacterial/genetics; Microarray Analysis; RNA/biosynthesis; Transcription, Genetic/physiology; rho GTP-Binding Proteins/antagonists & inhibitors; rho GTP-Binding Proteins/metabolism

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Useful Materials and Methods

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Annotations

Gene product Qualifier GO ID GO term name Evidence Code with/from Aspect Notes Status

Data

Strain/Organism Assay Analyte Variable Conditions Notes Links

MG1655

ChIP-chip

RpoC RNAP beta prime

RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)

MG1655

ChIP-chip

RpoB RNAP beta

RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)

MG1655

ChIP-chip

RpoB RNAP beta

Untreated

MG1655

ChIP-chip

RpoC RNAP beta prime

Untreated

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See also

References

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