Possible roles of σ-dependent RNA polymerase pausing in transcription regulation

Petushkov, Ivan; Esyunina, Daria; Kulbachinskiy, Andrey

doi:10.1080/15476286.2017.1356568

Cited by 16 publications

(12 citation statements)

References 45 publications

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“…This notion is consistent with a negative correlation between the binding pattern of σ 70 and the binding patterns of NusA and NusG observed by ChIP-seq analysis of promoter-proximal regions 52 . The G1 pausing may also stabilize binding of σ 70 to RNAP and make transcription of the target genes, such as ncRNA and antisense RNA genes, independent of regulation by Nus and Rho factors 18 , 53 . In addition, the G1 pausing could increase retention of σ 70 in the elongation complexes at a large distance from the original promoter to additionally reinforce pausing caused by σ 70 -mediated recognition of the −10-like sequences 18 .…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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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.

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Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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“…This notion is consistent with a negative correlation between binding pattern of σ 70 and binding patterns of NusA and NusG observed by ChIP-seq analysis of promoter-proximal regions 48 . The G1 pausing may also stabilize binding of σ 70 to RNAP and make transcription of the target genes, such as ncRNA and antisense RNA genes, independent of regulation by Nus and Rho factors 18,49 .…”

Section: Discussionmentioning

confidence: 99%

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

Sun

Yakhnin

Fitzgerald

et al. 2020

Preprint

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Promoter-proximal pausing regulates expression of many eukaryotic genes and serves as checkpoints for assembly of elongation/splicing machinery. Little is known how broadly the pausing is employed in transcriptional regulation in bacteria. We applied NET-seq combined with RNase I footprinting for genome-wide analysis of σ70-dependent transcription pauses in Escherichia coli. Many E. coli genes appear to contain clusters of strong backtracked pauses at 10-20-bp distance from the transcription start site caused by retention of σ70 subunit in RNA polymerase. The pauses in 10-15-bp register of the promoter are dictated by binding of σ70 to canonical -10 element, 6-7 nt spacer and ″YR+1Y″ motif centered at transcription start site all characteristic for strong E. coli promoters. The promoters for the pauses in 16-20-bp register contain an additional -10-like sequence positioned on the same face of the DNA duplex as the original -10 element suggesting that σ70 hopping was responsible for these pauses. Our in vitro analysis reveals that RNA polymerase backtracking and DNA scrunching are involved in these pauses that are relieved by Gre transcript 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.

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“…The fact that a sigma factor is able to bind a promoter region in vivo does not always mean that the gene expression is actually switched on. Thus the σ 70 subunit of E. coli may induce transcriptional pausing at promoter motifs (44,45). Also, our binding analysis was performed at one specific point, other conditions, or a different developmental stage, may involve other transcriptional regulators that might influence the HrdB-promoter affinities.…”

Section: Discussionmentioning

confidence: 99%

DNA mapping and kinetic modeling of the HrdB regulon inStreptomyces coelicolor

Šmídová

Ziková

Pospíšil

et al. 2018

Nucleic Acids Research

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HrdB in streptomycetes is a principal sigma factor whose deletion is lethal. This is also the reason why its regulon has not been investigated so far. To overcome experimental obstacles, for investigating the HrdB regulon, we constructed a strain whose HrdB protein was tagged by an HA epitope. ChIP-seq experiment, done in 3 repeats, identified 2137 protein-coding genes organized in 337 operons, 75 small RNAs, 62 tRNAs, 6 rRNAs and 3 miscellaneous RNAs. Subsequent kinetic modeling of regulation of protein-coding genes with HrdB alone and with a complex of HrdB and a transcriptional cofactor RbpA, using gene expression time series, identified 1694 genes that were under their direct control. When using the HrdB–RbpA complex in the model, an increase of the model fidelity was found for 322 genes. Functional analysis revealed that HrdB controls the majority of gene groups essential for the primary metabolism and the vegetative growth. Particularly, almost all ribosomal protein-coding genes were found in the HrdB regulon. Analysis of promoter binding sites revealed binding motif at the −10 region and suggested the possible role of mono- or di-nucleotides upstream of the −10 element.

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Possible roles of σ-dependent RNA polymerase pausing in transcription regulation

Cited by 16 publications

References 45 publications

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

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

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

DNA mapping and kinetic modeling of the HrdB regulon inStreptomyces coelicolor

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