Structural and biochemical analysis of DNA lesion-induced RNA polymerase II arrest.
DNA lesion
RNA polymerase II
Transcription
X-ray crystallography
Journal
Methods (San Diego, Calif.)
ISSN: 1095-9130
Titre abrégé: Methods
Pays: United States
ID NLM: 9426302
Informations de publication
Date de publication:
15 04 2019
15 04 2019
Historique:
received:
26
10
2018
revised:
30
01
2019
accepted:
19
02
2019
pubmed:
25
2
2019
medline:
24
6
2020
entrez:
25
2
2019
Statut:
ppublish
Résumé
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-arrested Pol II complex. These methods can provide a general platform for the structural and biochemical analysis of Pol II transcriptional pausing and bypass mechanisms.
Identifiants
pubmed: 30797902
pii: S1046-2023(18)30300-1
doi: 10.1016/j.ymeth.2019.02.019
pmc: PMC6589100
mid: NIHMS1522305
pii:
doi:
Substances chimiques
DNA
9007-49-2
RNA Polymerase II
EC 2.7.7.-
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
29-34Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM102362
Pays : United States
Informations de copyright
Published by Elsevier Inc.
Références
J Biol Chem. 2009 Nov 13;284(46):31658-63
pubmed: 19758983
Science. 2012 May 25;336(6084):1030-3
pubmed: 22628654
Mol Cell. 2009 Jun 26;34(6):710-21
pubmed: 19560423
Methods Enzymol. 2003;370:138-55
pubmed: 14712640
DNA Repair (Amst). 2014 Jul;19:71-83
pubmed: 24767259
Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501
pubmed: 20383002
J Am Chem Soc. 2013 Sep 4;135(35):13054-61
pubmed: 23927577
Nat Rev Mol Cell Biol. 2008 Dec;9(12):958-70
pubmed: 19023283
Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12426-12431
pubmed: 27791148
Transcription. 2016 May 26;7(3):57-62
pubmed: 27105138
Nature. 2009 Nov 19;462(7271):323-30
pubmed: 19820686
Mutagenesis. 2004 May;19(3):169-85
pubmed: 15123782
Cell. 2013 Jun 6;153(6):1194-217
pubmed: 23746838
Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):6969-73
pubmed: 12746498
Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):E410-9
pubmed: 25605892
Nat Rev Mol Cell Biol. 2015 Mar;16(3):167-77
pubmed: 25693130
Nature. 2016 Apr 27;533(7603):407-10
pubmed: 27120163
Nat Struct Mol Biol. 2007 Dec;14(12):1127-33
pubmed: 17994106
Science. 2007 Feb 9;315(5813):859-62
pubmed: 17290000
Biochim Biophys Acta. 2013 Jan;1829(1):151-7
pubmed: 22960598
Nat Struct Mol Biol. 2008 Aug;15(8):811-8
pubmed: 18552824
Mol Cell Biol. 2010 Jul;30(13):3206-15
pubmed: 20421413
Proc Natl Acad Sci U S A. 2010 May 25;107(21):9584-9
pubmed: 20448203
Proc Natl Acad Sci U S A. 2017 Aug 22;114(34):E7082-E7091
pubmed: 28784758
Science. 2009 May 29;324(5931):1203-6
pubmed: 19478184
Nature. 2015 Jul 30;523(7562):621-5
pubmed: 26123024
Nat Commun. 2016 Apr 19;7:11244
pubmed: 27091704
Proc Natl Acad Sci U S A. 2018 Mar 13;115(11):E2538-E2545
pubmed: 29487211
J Biol Chem. 2001 Jul 20;276(29):26733-6
pubmed: 11390411
Metallomics. 2009;1(4):280-91
pubmed: 20046924
Nature. 2011 Mar 10;471(7337):249-53
pubmed: 21346759
Nat Struct Mol Biol. 2012 Aug;19(8):831-3
pubmed: 22820989
Science. 2000 Apr 28;288(5466):640-9
pubmed: 10784442
EMBO J. 2004 Oct 13;23(20):4051-60
pubmed: 15372072
Mol Cell. 2012 Apr 13;46(1):18-29
pubmed: 22405652
Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
pubmed: 20124702
DNA Repair (Amst). 2004 Dec 2;3(12):1537-48
pubmed: 15474416
Nature. 2016 Jan 28;529(7587):551-4
pubmed: 26789250
Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):271-81
pubmed: 21460445
Proc Natl Acad Sci U S A. 2014 May 27;111(21):7665-70
pubmed: 24753580
Nature. 2017 Nov 30;551(7682):653-657
pubmed: 29168508
Mol Cell. 2008 Jun 6;30(5):547-56
pubmed: 18538653
Cell. 2006 Dec 1;127(5):941-54
pubmed: 17129781
Science. 2001 Jun 8;292(5523):1863-76
pubmed: 11313498
Nature. 2016 May 11;533(7603):353-8
pubmed: 27193681
Genes Dev. 2011 Apr 1;25(7):742-54
pubmed: 21460038
Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):6964-8
pubmed: 12746495