Structural and biochemical analysis of DNA lesion-induced RNA polymerase II arrest

Methods : a Companion to Methods in Enzymology
Juntaek OhDong Wang

Abstract

Transcription, catalyzed by RNA polymerase II (Pol II) in eukaryotes, is the first step in gene expression. RNA Pol II is a 12-subunit enzyme complex regulated by many different transcription factors during transcription initiation, elongation, and termination. During elongation, Pol II encounters various types of obstacles that can cause transcriptional pausing and arrest. Through decades of research on transcriptional pausing, it is widely known that Pol II can distinguish between different types of obstacles by its active site. A major class of obstacles is DNA lesions. While some DNA lesions can cause transient transcriptional pausing, which can be bypassed by Pol II itself or with the help from other elongation factors, bulky DNA damage can cause prolonged transcriptional pausing and arrest, which signals for transcription coupled repair. Using biochemical and structural biology approaches, the outcomes of many different types of DNA lesions, DNA modifications, and DNA binding molecules to transcription were studied. In this mini review, we will describe the in vitro transcription assays with Pol II to investigate the impacts of various DNA lesions on transcriptional outcomes and the crystallization method of lesion-arrest...Continue Reading

References

Jun 8, 2001·The Journal of Biological Chemistry·N Hernandez
May 15, 2003·Proceedings of the National Academy of Sciences of the United States of America·Karim-Jean ArmachePatrick Cramer
May 15, 2003·Proceedings of the National Academy of Sciences of the United States of America·David A Bushnell, Roger D Kornberg
May 5, 2004·Mutagenesis·Rinne De Bont, Nik van Larebeke
Sep 17, 2004·The EMBO Journal·Yoontae LeeV Narry Kim
Oct 12, 2004·DNA Repair·David A ScicchitanoAlexandra Dimitri
Feb 10, 2007·Science·Florian BruecknerPatrick Cramer
Nov 13, 2007·Nature Structural & Molecular Biology·Gerke E DamsmaPatrick Cramer
Jun 17, 2008·Nature Structural & Molecular Biology·Florian Brueckner, Patrick Cramer
Nov 22, 2008·Nature Reviews. Molecular Cell Biology·Philip C Hanawalt, Graciela Spivak
Sep 18, 2009·The Journal of Biological Chemistry·Gerke E Damsma, Patrick Cramer
Jan 5, 2010·Metallomics : Integrated Biometal Science·Ryan C Todd, Stephen J Lippard
Feb 4, 2010·Acta Crystallographica. Section D, Biological Crystallography·Paul D AdamsPeter H Zwart
Apr 13, 2010·Acta Crystallographica. Section D, Biological Crystallography·P EmsleyK Cowtan
May 8, 2010·Proceedings of the National Academy of Sciences of the United States of America·Dong WangStephen J Lippard
Feb 25, 2011·Nature·Alan C M Cheung, Patrick Cramer
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·T Geoff G BattyeAndrew G W Leslie
May 26, 2012·Science·P Andrew Karplus, Kay Diederichs
Jul 24, 2012·Nature Structural & Molecular Biology·Matthew W KellingerDong Wang
Sep 11, 2012·Biochimica Et Biophysica Acta·Marcus D WilsonJesper Q Svejstrup
Jun 12, 2013·Cell·Carlos López-OtínGuido Kroemer
Aug 10, 2013·Journal of the American Chemical Society·Matthew W KellingerDong Wang
Apr 23, 2014·Proceedings of the National Academy of Sciences of the United States of America·Daniel-Adriano SilvaXuhui Huang
Jan 22, 2015·Proceedings of the National Academy of Sciences of the United States of America·Celine WalmacqMikhail Kashlev
Feb 19, 2015·Nature Reviews. Molecular Cell Biology·Iris Jonkers, John T Lis
Jan 21, 2016·Nature·Carrie BerneckyPatrick Cramer
Nov 3, 2016·Proceedings of the National Academy of Sciences of the United States of America·Liang XuDong Wang
Aug 9, 2017·Proceedings of the National Academy of Sciences of the United States of America·Liang XuDong Wang
Mar 1, 2018·Proceedings of the National Academy of Sciences of the United States of America·Wei WangDong Wang

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Citations

Jun 19, 2021·Nature Chemical Biology·Juntaek OhDong Wang

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