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 RNAP(B)_+BCM(3428302)_normalized.gff3 20M RNAP(B')_+BCM(94828)_normalized.gff3 19M RNAP(B')_untreated(100040)_normalized.gff3 19M RNAP(B)_untreated(3427302)_normalized.gff3 20M
Keywords	Bicyclo Compounds, Heterocyclic; Chromatin Immunoprecipitation; DNA-Directed RNA Polymerases; Escherichia coli; Genes, Bacterial; Microarray Analysis; RNA; Transcription, Genetic; rho GTP-Binding Proteins
edit table

Significance

You can help EcoliWiki by summarizing why this paper is useful

Useful Materials and Methods

You can help Ecoliwiki by describing the useful materials (strains, plasmids, antibodies, etc) described in this paper.

Annotations

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

EcoliWiki Links

Add links to pages that link here (e.g. gene, product, method pages)

References

See Help:References for how to manage references in EcoliWiki.

Strain/Organism	Assay	Analyte	Variable Conditions	Notes	Browser Link
MG1655	ChIP-chip	RNAP	RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)	Replicates with and w/o BCM are shown as subtracks.
edit table