title: Rho directs widespread termination of intragenic and stable RNA transcription.
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.
authors.affiliation: Department of Biochemistry, University of Wisconsin, Madison, WI 5370, USA.
authors.forename: Jason M
authors.initials: JM
authors.lastname: Peters
authors.forename: Rachel A
authors.initials: RA
authors.lastname: Mooney
authors.forename: Pei Fen
authors.initials: PF
authors.lastname: Kuan
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Rowland
authors.forename: Sündüz
authors.initials: S
authors.lastname: Keles
authors.forename: Robert
authors.initials: R
authors.lastname: Landick
mesh_terms: D019086:Bridged Bicyclo Compounds, Heterocyclic; D047369:Chromatin Immunoprecipitation; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D004926:Escherichia coli / Q000378:metabolism*; D005798:Genes, Bacterial / Q000235:genetics; D046228:Microarray Analysis; D012313:RNA / Q000096:biosynthesis*; D014158:Transcription, Genetic / Q000502:physiology*; D020741:rho GTP-Binding Proteins / Q000037:antagonists & inhibitors / Q000378:metabolism*
chemical_list: D019086:Bridged Bicyclo Compounds, Heterocyclic; D012313:RNA; D012321:DNA-Directed RNA Polymerases; D020741:rho GTP-Binding Proteins; C024504:bicozamycin
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