Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue

Handle URI:
http://hdl.handle.net/10754/606053
Title:
Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue
Authors:
Da, Lin-Tai; Pardo-Avila, Fátima; Xu, Liang; Silva, Daniel-Adriano; Zhang, Lu; Gao, Xin ( 0000-0002-7108-3574 ) ; Wang, Dong; Huang, Xuhui
Abstract:
The dynamics of the RNA polymerase II (Pol II) backtracking process is poorly understood. We built a Markov State Model from extensive molecular dynamics simulations to identify metastable intermediate states and the dynamics of backtracking at atomistic detail. Our results reveal that Pol II backtracking occurs in a stepwise mode where two intermediate states are involved. We find that the continuous bending motion of the Bridge helix (BH) serves as a critical checkpoint, using the highly conserved BH residue T831 as a sensing probe for the 3′-terminal base paring of RNA:DNA hybrid. If the base pair is mismatched, BH bending can promote the RNA 3′-end nucleotide into a frayed state that further leads to the backtracked state. These computational observations are validated by site-directed mutagenesis and transcript cleavage assays, and provide insights into the key factors that regulate the preferences of the backward translocation.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue 2016, 7:11244 Nature Communications
Publisher:
Nature Publishing Group
Journal:
Nature Communications
Issue Date:
19-Apr-2016
DOI:
10.1038/ncomms11244
Type:
Article
ISSN:
2041-1723
Sponsors:
X.H. acknowledges the Hong Kong Research Grants Council (16302214, 609813, HKUST C6009-15G, AoE/M-09/12, T13-607/12R, and M-HKUST601/13) and National Science Foundation of China 21273188. D.W. acknowledges the NIH (GM102362), Kimmel Scholars award from the Sidney Kimmel Foundation for Cancer Research, start-up funds from Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD and Academic Senate Research Award from UCSD. X.G. was supported by funding from the King Abdullah University of Science and Technology. F.P. acknowledges the support from Hong Kong PhD Fellowship Scheme (2011/12) and the partial support for PhD studies from the CONACYT. This research made use of the resources of the Supercomputing Laboratory at King Abdullah University of Science and Technology. We thank Dr Jeffery Strathern (NCI) for providing yeast strain containing Pol II Rpb1 T831A mutant and Dr Mikhail Kashlev for providing purified Pol II Rpb1 T831A mutant.
Additional Links:
http://www.nature.com/doifinder/10.1038/ncomms11244
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorDa, Lin-Taien
dc.contributor.authorPardo-Avila, Fátimaen
dc.contributor.authorXu, Liangen
dc.contributor.authorSilva, Daniel-Adrianoen
dc.contributor.authorZhang, Luen
dc.contributor.authorGao, Xinen
dc.contributor.authorWang, Dongen
dc.contributor.authorHuang, Xuhuien
dc.date.accessioned2016-04-20T12:00:25Zen
dc.date.available2016-04-20T12:00:25Zen
dc.date.issued2016-04-19en
dc.identifier.citationBridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue 2016, 7:11244 Nature Communicationsen
dc.identifier.issn2041-1723en
dc.identifier.doi10.1038/ncomms11244en
dc.identifier.urihttp://hdl.handle.net/10754/606053en
dc.description.abstractThe dynamics of the RNA polymerase II (Pol II) backtracking process is poorly understood. We built a Markov State Model from extensive molecular dynamics simulations to identify metastable intermediate states and the dynamics of backtracking at atomistic detail. Our results reveal that Pol II backtracking occurs in a stepwise mode where two intermediate states are involved. We find that the continuous bending motion of the Bridge helix (BH) serves as a critical checkpoint, using the highly conserved BH residue T831 as a sensing probe for the 3′-terminal base paring of RNA:DNA hybrid. If the base pair is mismatched, BH bending can promote the RNA 3′-end nucleotide into a frayed state that further leads to the backtracked state. These computational observations are validated by site-directed mutagenesis and transcript cleavage assays, and provide insights into the key factors that regulate the preferences of the backward translocation.en
dc.description.sponsorshipX.H. acknowledges the Hong Kong Research Grants Council (16302214, 609813, HKUST C6009-15G, AoE/M-09/12, T13-607/12R, and M-HKUST601/13) and National Science Foundation of China 21273188. D.W. acknowledges the NIH (GM102362), Kimmel Scholars award from the Sidney Kimmel Foundation for Cancer Research, start-up funds from Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD and Academic Senate Research Award from UCSD. X.G. was supported by funding from the King Abdullah University of Science and Technology. F.P. acknowledges the support from Hong Kong PhD Fellowship Scheme (2011/12) and the partial support for PhD studies from the CONACYT. This research made use of the resources of the Supercomputing Laboratory at King Abdullah University of Science and Technology. We thank Dr Jeffery Strathern (NCI) for providing yeast strain containing Pol II Rpb1 T831A mutant and Dr Mikhail Kashlev for providing purified Pol II Rpb1 T831A mutant.en
dc.language.isoenen
dc.publisherNature Publishing Groupen
dc.relation.urlhttp://www.nature.com/doifinder/10.1038/ncomms11244en
dc.rightsThis work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/en
dc.titleBridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residueen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalNature Communicationsen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartment of Chemistry, School of Science and Institute for Advance Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kongen
dc.contributor.institutionDepartment of Cellular and Molecular Medicine, School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USAen
dc.contributor.institutionDepartment of Biochemistry, University of Washington, Seattle, Washington 98195, USAen
dc.contributor.institutionDivision of Biomedical Engineering, School of Science and Institute for Advance Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kongen
dc.contributor.institutionCenter of Systems Biology and Human Health, School of Science and Institute for Advance Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kongen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorGao, Xinen
All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.