PMID:19706412

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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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)		Gbrowse +BCM (19M gff)
MG1655	ChIP-chip	RpoB RNAP beta	RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)		Gbrowse +BCM, (20M gff)
MG1655	ChIP-chip	RpoB RNAP beta	Untreated		Gbrowse untreated (20M gff)
MG1655	ChIP-chip	RpoC RNAP beta prime	Untreated		Gbrowse untreated (19M gff)
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