Timing RNA Polymerase Pausing with TV-PRO-seq

Overview

Journal Cell Rep Methods

Specialty Cell Biology

Date 2021 Nov 1

PMID 34723238

Citations 2

Authors

Jie Zhang

Massimo Cavallaro

Daniel Hebenstreit

Affiliations

Soon will be listed here.

Abstract

Transcription of many genes in metazoans is subject to polymerase pausing, which is the transient stop of transcriptionally engaged polymerases. This is known to mainly occur in promoter-proximal regions but it is not well understood. In particular, a genome-wide measurement of pausing times at high resolution has been lacking. We present here the time-variant precision nuclear run-on and sequencing (TV-PRO-seq) assay, an extension of the standard PRO-seq that allows us to estimate genome-wide pausing times at single-base resolution. Its application to human cells demonstrates that, proximal to promoters, polymerases pause more frequently but for shorter times than in other genomic regions. Comparison with single-cell gene expression data reveals that the polymerase pausing times are longer in highly expressed genes, while transcriptionally noisier genes have higher pausing frequencies and slightly longer pausing times. Analyses of histone modifications suggest that the marker H3K36me3 is related to the polymerase pausing.

Citing Articles

Bayesian inference of polymerase dynamics over the exclusion process.

Cavallaro M, Wang Y, Hebenstreit D, Dutta R R Soc Open Sci. 2023; 10(8):221469.

PMID: 37538742 PMC: 10394410. DOI: 10.1098/rsos.221469.

Reactivation of Epstein-Barr Virus from Latency Involves Increased RNA Polymerase Activity at CTCF Binding Sites on the Viral Genome.

Dunn L, Lu F, Su C, Lieberman P, Baines J J Virol. 2023; 97(2):e0189422.

PMID: 36744959 PMC: 9972995. DOI: 10.1128/jvi.01894-22.

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