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Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria
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Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria
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Journal Article
Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria
2021
Overview
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 σ
70
-dependent transcription pauses in
Escherichia coli
. Retention of σ
70
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
+1
Y” 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 σ
70
. 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 σ
70
and Gre proteins regulate transcription in response to changing environmental cues.
Transcription by bacterial RNA polymerase is interrupted by pausing events that play diverse regulatory roles. Here, the authors find that a large number of
E. coli
sigma70-dependent pauses, clustered at a 10−20-bp distance from promoters, are regulated by Gre cleavage factors constituting a mechanism for rapid response to changing environmental cues.
Publisher
Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
Subject
/ 38/43
/ 38/77
/ 38/91
/ 49/22
/ Bacteria
/ Cleavage
/ DNA
/ DNA-Directed RNA Polymerases - genetics
/ DNA-Directed RNA Polymerases - metabolism
/ E coli
/ Escherichia coli - metabolism
/ Escherichia coli Proteins - genetics
/ Escherichia coli Proteins - metabolism
/ Gene Expression Regulation, Bacterial
/ Genomes
/ Humanities and Social Sciences
/ RNA
/ Science
/ Splicing
/ Transcription Factors - genetics
/ Transcription Factors - metabolism
