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 Online version:10.1073/pnas.0903846106
Keywords	Bicyclo Compounds, Heterocyclic; Chromatin Immunoprecipitation; DNA-Directed RNA Polymerases; Escherichia coli; Genes, Bacterial; Microarray Analysis; RNA; Transcription, Genetic; rho GTP-Binding Proteins
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Annotations

Gene product	Qualifier	GO ID	GO term name	Evidence Code	with/from	Aspect	Notes	Status
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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)	Replicates with and without BCM are shown as subtracks.	Gbrowse +BCM (19M gff) untreated (19M gff)
MG1655	ChIP-chip	RpoB RNAP beta	RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)	Replicates with and without BCM are shown as subtracks.	Gbrowse +BCM, (20M gff) untreated (20M gff)
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