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Timing RNA polymerase pausing with TV-PRO-seq

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Zhang, Jie, Cavallaro, Massimo and Hebenstreit, Daniel (2021) Timing RNA polymerase pausing with TV-PRO-seq. Cell Reports Methods, 1 (6). 100083. doi:10.1016/j.crmeth.2021.100083

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Official URL: https://doi.org/10.1016/j.crmeth.2021.100083

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Abstract

Various next-generation sequencing-based methods, including Pol II ChIP-seq, GRO-seq, NET-seq, and PRO-seq, have been able to reveal the presence of polymerase pausing. However, these methods are mainly based on detection of polymerase occupancy, which is affected by factors other than the pausing. As an example, recent research revealed that polymerase has a high abortive transcription rate, especially at genes featuring strong pausing, which also contributes to high polymerase occupancy in the promoter-proximal regions. Further, the accuracy of the most widely used method to measure pausing—treating cells with triptolide (Trp)—is challenged by the latter's slow uptake. A method that outputs the actual pausing time is still required to dissect the pausing profile. We have developed TV-PRO-seq, which reveals polymerase pausing times at single-base resolution genome-wide and is not influenced by the polymerase turnover and other confounding factors.

Item Type: Journal Article
Subjects: Q Science > QH Natural history > QH426 Genetics
Divisions: Faculty of Science > Life Sciences (2010- )
Faculty of Science > Mathematics
Library of Congress Subject Headings (LCSH): RNA polymerases, Genetic transcription
Journal or Publication Title: Cell Reports Methods
Publisher: Cell Press
ISSN: 2667-2375
Official Date: 25 October 2021
Dates:
DateEvent
25 October 2021Published
27 September 2021Available
18 August 2021Accepted
Volume: 1
Number: 6
Article Number: 100083
DOI: 10.1016/j.crmeth.2021.100083
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
BB/L006340/1[BBSRC] Biotechnology and Biological Sciences Research Councilhttp://dx.doi.org/10.13039/501100000268
BB/M017982/1[BBSRC] Biotechnology and Biological Sciences Research Councilhttp://dx.doi.org/10.13039/501100000268
EP/T002794/1[EPSRC] Engineering and Physical Sciences Research Councilhttp://dx.doi.org/10.13039/501100000266
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