Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria.

Sun, Zhe; Yakhnin, Alexander V; FitzGerald, Peter C; Mclntosh, Carl E; Kashlev, Mikhail

Sun, Zhe; Yakhnin, Alexander V; FitzGerald, Peter C; Mclntosh, Carl E; Kashlev, Mikhail.

Afiliación

Sun Z; RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
Yakhnin AV; RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
FitzGerald PC; Genome Analysis Unit, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
Mclntosh CE; Genome Analysis Unit, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
Kashlev M; RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA. kashlevm@mail.nih.gov.

Nat Commun ; 12(1): 906, 2021 02 10.

Article en En | MEDLINE | ID: mdl-33568644

RESUMEN

Promoter-proximal pausing regulates eukaryotic gene expression and serves as checkpoints to assemble elongation/splicing machinery. Little is known how broadly this type of pausing regulates transcription in bacteria. We apply nascent elongating transcript sequencing combined with RNase I footprinting for genome-wide analysis of σ70-dependent transcription pauses in Escherichia coli. Retention of σ70 induces strong backtracked pauses at a 10-20-bp distance from many promoters. The pauses in the 10-15-bp register of the promoter are dictated by the canonical -10 element, 6-7 nt spacer and "YR+1Y" motif centered at the transcription start site. The promoters for the pauses in the 16-20-bp register contain an additional -10-like sequence recognized by σ70. Our in vitro analysis reveals that DNA scrunching is involved in these pauses relieved by Gre cleavage factors. The genes coding for transcription factors are enriched in these pauses, suggesting that σ70 and Gre proteins regulate transcription in response to changing environmental cues.

Asunto(s)

ARN Polimerasas Dirigidas por ADN/genética; Proteínas de Escherichia coli/metabolismo; Escherichia coli/genética; Escherichia coli/metabolismo; ARN Bacteriano/genética; Factor sigma/genética; Factores de Transcripción/metabolismo; Transcripción Genética; Factores de Elongación Transcripcional/metabolismo; ARN Polimerasas Dirigidas por ADN/metabolismo; Proteínas de Escherichia coli/genética; Regulación Bacteriana de la Expresión Génica; Regiones Promotoras Genéticas; ARN Bacteriano/metabolismo; Análisis de Secuencia de ARN; Factor sigma/metabolismo; Factores de Transcripción/genética; Factores de Elongación Transcripcional/genética

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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Factor sigma / Factores de Transcripción / Transcripción Genética / ARN Polimerasas Dirigidas por ADN / ARN Bacteriano / Proteínas de Escherichia coli / Factores de Elongación Transcripcional / Escherichia coli Tipo de estudio: Prognostic_studies Idioma: En Revista: Nat Commun Asunto de la revista: BIOLOGIA / CIENCIA Año: 2021 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido

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