Literature DB >> 27115204

Transcription-induced DNA supercoiling: New roles of intranucleosomal DNA loops in DNA repair and transcription.

N S Gerasimova1, N A Pestov2, O I Kulaeva1,3, D J Clark4, V M Studitsky1,2,3.   

Abstract

RNA polymerase II (Pol II) transcription through chromatin is accompanied by formation of small intranucleosomal DNA loops. Pol II captured within a small loop drives accumulation of DNA supercoiling, facilitating further transcription. DNA breaks relieve supercoiling and induce Pol II arrest, allowing detection of DNA damage hidden in chromatin structure.

Entities:  

Keywords:  DNA repair; DNA supercoiling; RNA polymerase II; chromatin; elongation; intermediates; intranucleosomal DNA loops; mechanism; nucleosome; single strand DNA breaks; structure; transcription

Mesh：

Substances：

Year:  2016        PMID： 27115204      PMCID： PMC4984681          DOI： 10.1080/21541264.2016.1182240

Source DB:  PubMed          Journal:  Transcription        ISSN： 2154-1272


  23 in total

1.  Nucleosome assembly depends on the torsion in the DNA molecule: a magnetic tweezers study.

Authors:  Pooja Gupta; Jordanka Zlatanova; Miroslav Tomschik
Journal:  Biophys J       Date:  2009-12-16       Impact factor: 4.033

2.  Nucleosome structure and positioning modulate nucleotide excision repair in the non-transcribed strand of an active gene.

Authors:  R E Wellinger; F Thoma
Journal:  EMBO J       Date:  1997-08-15       Impact factor: 11.598

3.  Crystal structure of the nucleosome core particle at 2.8 A resolution.

Authors:  K Luger; A W Mäder; R K Richmond; D F Sargent; T J Richmond
Journal:  Nature       Date:  1997-09-18       Impact factor: 49.962

4.  Supercoiling of the DNA template during transcription.

Authors:  L F Liu; J C Wang
Journal:  Proc Natl Acad Sci U S A       Date:  1987-10       Impact factor: 11.205

5.  Supercoiling of intracellular DNA can occur in eukaryotic cells.

Authors:  G N Giaever; J C Wang
Journal:  Cell       Date:  1988-12-02       Impact factor: 41.582

6.  DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC.

Authors:  Yongli Zhang; Corey L Smith; Anjanabha Saha; Stephan W Grill; Shirley Mihardja; Steven B Smith; Bradley R Cairns; Craig L Peterson; Carlos Bustamante
Journal:  Mol Cell       Date:  2006-11-17       Impact factor: 17.970

7.  Topological domains in mammalian genomes identified by analysis of chromatin interactions.

Authors:  Jesse R Dixon; Siddarth Selvaraj; Feng Yue; Audrey Kim; Yan Li; Yin Shen; Ming Hu; Jun S Liu; Bing Ren
Journal:  Nature       Date:  2012-04-11       Impact factor: 49.962

8.  Heavy transcription of yeast genes correlates with differential loss of histone H2B relative to H4 and queued RNA polymerases.

Authors:  Hope A Cole; Josefina Ocampo; James R Iben; Răzvan V Chereji; David J Clark
Journal:  Nucleic Acids Res       Date:  2014-10-27       Impact factor: 16.971

9.  Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II.

Authors:  Olga I Kulaeva; Daria A Gaykalova; Nikolai A Pestov; Viktor V Golovastov; Dmitry G Vassylyev; Irina Artsimovitch; Vasily M Studitsky
Journal:  Nat Struct Mol Biol       Date:  2009-11-22       Impact factor: 15.369

10.  Structural Basis of Detection and Signaling of DNA Single-Strand Breaks by Human PARP-1.

Authors:  Sebastian Eustermann; Wing-Fung Wu; Marie-France Langelier; Ji-Chun Yang; Laura E Easton; Amanda A Riccio; John M Pascal; David Neuhaus
Journal:  Mol Cell       Date:  2015-11-25       Impact factor: 17.970
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  5 in total

1.  Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro.

Authors:  Soumitra Pal; Jan Hoinka; Teresa M Przytycka
Journal:  Nucleic Acids Res       Date:  2019-07-26       Impact factor: 16.971

2.  Histone Modifications, Internucleosome Dynamics, and DNA Stresses: How They Cooperate to "Functionalize" Nucleosomes.

Authors:  Wladyslaw A Krajewski
Journal:  Front Genet       Date:  2022-04-28       Impact factor: 4.772

3.  Structure of an Intranucleosomal DNA Loop That Senses DNA Damage during Transcription.

Authors:  Nadezhda S Gerasimova; Olesya I Volokh; Nikolay A Pestov; Grigory A Armeev; Mikhail P Kirpichnikov; Alexey K Shaytan; Olga S Sokolova; Vasily M Studitsky
Journal:  Cells       Date:  2022-08-28       Impact factor: 7.666

4.  DNA Damage and Chromatin Conformation Changes Confer Nonhost Resistance: A Hypothesis Based on Effects of Anti-cancer Agents on Plant Defense Responses.

Authors:  Lee A Hadwiger; Kiwamu Tanaka
Journal:  Front Plant Sci       Date:  2018-07-24       Impact factor: 5.753

5.  Effects of histone H2B ubiquitylation on the nucleosome structure and dynamics.

Authors:  Wladyslaw A Krajewski; Jiabin Li; Yali Dou
Journal:  Nucleic Acids Res       Date:  2018-09-06       Impact factor: 16.971
  5 in total

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