Transcriptomics

Dataset Information

297

Rho and NusG suppress pervasive antisense transcription in Escherichia coli [RNA-seq].


ABSTRACT: Despite the prevalence of antisense transcripts in bacterial transcriptomes, little is known about how their synthesis is controlled. We report that a major function of the Escherichia coli termination factor Rho and its co-factor NusG is suppression of ubiquitous antisense transcription genome-wide. Rho binds C-rich unstructured nascent RNA (high C/G ratio) prior to its ATP-dependent dissociation of transcription complexes. NusG is required for efficient termination at minority subsets (~20%) of both antisense and sense Rho-dependent terminators with lower C/G ratio sequences. In contrast, a widely studied nusA deletion proposed to compromise Rho-dependent termination had no effect on antisense or sense Rho-dependent terminators in vivo. Global co-localization of the nucleoid-associated protein H-NS with Rho-dependent terminators and genetic interactions between hns and rho suggest that H-NS aids Rho in suppression of antisense transcription. The combined actions of Rho, NusG, and H-NS appear to be analogous to the Sen1-Nrd1-Nab3 and nucleosome systems that suppress antisense transcription in eukaryotes. RNA-seq experiments were performed on ribosome-depleted RNA from cells treated with 20 ug/ml bicyclomycin or untreated cells. The series contains 4 datasets.

ORGANISM(S): Escherichia coli K-12  

SUBMITTER: Robert Landick   Jason Matthew Peters  Jason M Peters 

PROVIDER: E-GEOD-41939 | ArrayExpress | 2012-11-01

SECONDARY ACCESSION(S): GSE41939SRP016892PRJNA178547

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Rho and NusG suppress pervasive antisense transcription in Escherichia coli.

Peters Jason M JM   Mooney Rachel A RA   Grass Jeffrey A JA   Jessen Erik D ED   Tran Frances F   Landick Robert R  

Genes & development 20121201 23


Despite the prevalence of antisense transcripts in bacterial transcriptomes, little is known about how their synthesis is controlled. We report that a major function of the Escherichia coli termination factor Rho and its cofactor, NusG, is suppression of ubiquitous antisense transcription genome-wide. Rho binds C-rich unstructured nascent RNA (high C/G ratio) prior to its ATP-dependent dissociation of transcription complexes. NusG is required for efficient termination at minority subsets (~20%)  ...[more]

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