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Rho Directs Widespread Termination of Intragenic and Stable RNA Transcription

Jason M. Peters, Rachel A. Mooney, Pei Fen Kuan, Jennifer L. Rowland, Sündüz Keleş, Robert Landick and Jeffrey W. Roberts
Proceedings of the National Academy of Sciences of the United States of America
Vol. 106, No. 36 (Sep. 8, 2009), pp. 15406-15411
Stable URL: http://www.jstor.org/stable/40484725
Page Count: 6
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Rho Directs Widespread Termination of Intragenic and Stable RNA Transcription
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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 ≈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.

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