Literature DB >> 28275417

DNA supercoiling during transcription.

Jie Ma1, Michelle D Wang2.   

Abstract

The twin-supercoiled-domain model describes how transcription can drive DNA supercoiling, and how DNA supercoiling, in turn plays an important role in regulating gene transcription. In vivo and in vitro experiments have disclosed many details of the complex interactions in this relationship, and recently new insights have been gained with the help of genome-wide DNA supercoiling mapping techniques and single molecule methods. This review summarizes the general mechanisms of the interplay between DNA supercoiling and transcription, considers the biological implications, and focuses on recent important discoveries and technical advances in this field. We highlight the significant impact of DNA supercoiling in transcription, but also more broadly in all processes operating on DNA.

Entities:  

Keywords:  chromatin; gene regulation; mechanics; supercoiling; torque; transcription

Year:  2016        PMID: 28275417      PMCID: PMC5338639          DOI: 10.1007/s12551-016-0215-9

Source DB:  PubMed          Journal:  Biophys Rev        ISSN: 1867-2450


  83 in total

1.  Large-scale effects of transcriptional DNA supercoiling in vivo.

Authors:  A S Krasilnikov; A Podtelezhnikov; A Vologodskii; S M Mirkin
Journal:  J Mol Biol       Date:  1999-10-08       Impact factor: 5.469

2.  DNA supercoiling allows enhancer action over a large distance.

Authors:  Y Liu; V Bondarenko; A Ninfa; V M Studitsky
Journal:  Proc Natl Acad Sci U S A       Date:  2001-12-11       Impact factor: 11.205

3.  A single-molecule technique to study sequence-dependent transcription pausing.

Authors:  Alla Shundrovsky; Thomas J Santangelo; Jeffrey W Roberts; Michelle D Wang
Journal:  Biophys J       Date:  2004-10-01       Impact factor: 4.033

4.  How are nucleosomes disrupted during transcription elongation?

Authors:  Jordanka Zlatanova; Jean-Marc Victor
Journal:  HFSP J       Date:  2009-11-12

5.  Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB.

Authors:  Daniel A Koster; Vincent Croquette; Cees Dekker; Stewart Shuman; Nynke H Dekker
Journal:  Nature       Date:  2005-03-31       Impact factor: 49.962

6.  Magnetic tweezers measurement of single molecule torque.

Authors:  Alfredo Celedon; Ilana M Nodelman; Bridget Wildt; Rohit Dewan; Peter Searson; Denis Wirtz; Gregory D Bowman; Sean X Sun
Journal:  Nano Lett       Date:  2009-04       Impact factor: 11.189

7.  Cruciform structures in palindromic DNA are favored by DNA supercoiling.

Authors:  K Mizuuchi; M Mizuuchi; M Gellert
Journal:  J Mol Biol       Date:  1982-04-05       Impact factor: 5.469

8.  Mechanism of transcriptional bursting in bacteria.

Authors:  Shasha Chong; Chongyi Chen; Hao Ge; X Sunney Xie
Journal:  Cell       Date:  2014-07-17       Impact factor: 41.582

9.  Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque.

Authors:  Marcelo Nöllmann; Michael D Stone; Zev Bryant; Jeff Gore; Nancy J Crisona; Seok-Cheol Hong; Sylvain Mitelheiser; Anthony Maxwell; Carlos Bustamante; Nicholas R Cozzarelli
Journal:  Nat Struct Mol Biol       Date:  2007-03-04       Impact factor: 15.369

10.  Biochemistry. A DNA twist diffuses and hops.

Authors:  Maxim Y Sheinin; Michelle D Wang
Journal:  Science       Date:  2012-10-05       Impact factor: 47.728

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  33 in total

1.  A review and summary of the contents of biophysical reviews volume 8, 2016.

Authors:  Cris Dos Remedios
Journal:  Biophys Rev       Date:  2017-02-07

2.  Increase of positive supercoiling in a hyperthermophilic archaeon after UV irradiation.

Authors:  A Gorlas; R Catchpole; E Marguet; P Forterre
Journal:  Extremophiles       Date:  2018-11-22       Impact factor: 2.395

3.  Single-molecule visualization of the effects of ionic strength and crowding on structure-mediated interactions in supercoiled DNA molecules.

Authors:  Shane Scott; Cynthia Shaheen; Brendon McGuinness; Kimberly Metera; Fedor Kouzine; David Levens; Craig J Benham; Sabrina Leslie
Journal:  Nucleic Acids Res       Date:  2019-07-09       Impact factor: 16.971

Review 4.  The many lives of type IA topoisomerases.

Authors:  Anna H Bizard; Ian D Hickson
Journal:  J Biol Chem       Date:  2020-04-10       Impact factor: 5.157

5.  DNA-RNA interactions are critical for chromosome condensation in Escherichia coli.

Authors:  Zhong Qian; Victor B Zhurkin; Sankar Adhya
Journal:  Proc Natl Acad Sci U S A       Date:  2017-10-30       Impact factor: 11.205

Review 6.  Emerging roles for R-loop structures in the management of topological stress.

Authors:  Frederic Chedin; Craig J Benham
Journal:  J Biol Chem       Date:  2020-02-27       Impact factor: 5.157

7.  Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling.

Authors:  Ivan E Ivanov; Addison V Wright; Joshua C Cofsky; Kevin D Palacio Aris; Jennifer A Doudna; Zev Bryant
Journal:  Proc Natl Acad Sci U S A       Date:  2020-03-02       Impact factor: 11.205

8.  The interplay of supercoiling and thymine dimers in DNA.

Authors:  Wilber Lim; Ferdinando Randisi; Jonathan P K Doye; Ard A Louis
Journal:  Nucleic Acids Res       Date:  2022-03-21       Impact factor: 16.971

9.  Single-molecule insights into torsion and roadblocks in bacterial transcript elongation.

Authors:  Jin Qian; Wenxuan Xu; David Dunlap; Laura Finzi
Journal:  Transcription       Date:  2021-11-01

10.  Properties of gene expression and chromatin structure with mechanically regulated elongation.

Authors:  Stuart A Sevier; Herbert Levine
Journal:  Nucleic Acids Res       Date:  2018-07-06       Impact factor: 16.971

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