Literature DB >> 21567156

The torsional state of DNA within the chromosome.

Joaquim Roca1.   

Abstract

Virtually all processes of the genome biology affect or are affected by the torsional state of DNA. Torsional energy associated with an altered twist facilitates or hinders the melting of the double helix, its molecular interactions, and its spatial folding in the form of supercoils. Yet, understanding how the torsional state of DNA is modulated remains a challenging task due to the multiplicity of cellular factors involved in the generation, transmission, and dissipation of DNA twisting forces. Here, an overview of the implication of DNA topoisomerases, DNA revolving motors, and other DNA interactions that determine local levels of torsional stress in bacterial and eukaryotic chromosomes is provided. Particular emphasis is made on the experimental approaches being developed to assess the torsional state of intracellular DNA and its organization into topological domains.

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Year:  2011        PMID: 21567156     DOI: 10.1007/s00412-011-0324-y

Source DB:  PubMed          Journal:  Chromosoma        ISSN: 0009-5915            Impact factor:   4.316


  103 in total

1.  Transport of torsional stress in DNA.

Authors:  P Nelson
Journal:  Proc Natl Acad Sci U S A       Date:  1999-12-07       Impact factor: 11.205

Review 2.  Mechanisms of separation of the complementary strands of DNA during replication.

Authors:  A I Alexandrov; N R Cozzarelli; V F Holmes; A B Khodursky; B J Peter; L Postow; V Rybenkov; A V Vologodskii
Journal:  Genetica       Date:  1999       Impact factor: 1.082

3.  Unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers.

Authors:  M L Bennink; S H Leuba; G H Leno; J Zlatanova; B G de Grooth; J Greve
Journal:  Nat Struct Biol       Date:  2001-07

4.  Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination.

Authors:  Pablo Huertas; Andrés Aguilera
Journal:  Mol Cell       Date:  2003-09       Impact factor: 17.970

5.  Spiral structure of Escherichia coli HUalphabeta provides foundation for DNA supercoiling.

Authors:  Fusheng Guo; Sankar Adhya
Journal:  Proc Natl Acad Sci U S A       Date:  2007-03-05       Impact factor: 11.205

6.  Histone acetylation reduces nucleosome core particle linking number change.

Authors:  V G Norton; B S Imai; P Yau; E M Bradbury
Journal:  Cell       Date:  1989-05-05       Impact factor: 41.582

7.  Localized chemical hyperreactivity in supercoiled DNA: evidence for base unpairing in sequences that induce low-salt cruciform extrusion.

Authors:  J C Furlong; K M Sullivan; A I Murchie; G W Gough; D M Lilley
Journal:  Biochemistry       Date:  1989-03-07       Impact factor: 3.162

8.  Letter: Electron microscopic visualization of the folded chromosome of Escherichia coli.

Authors:  H Delius; A Worcel
Journal:  J Mol Biol       Date:  1974-01-05       Impact factor: 5.469

9.  Specialized chromatin structure domain boundary elements flanking a Drosophila heat shock gene locus are under torsional strain in vivo.

Authors:  E R Jupe; R R Sinden; I L Cartwright
Journal:  Biochemistry       Date:  1995-02-28       Impact factor: 3.162

10.  Positional dependence of transcriptional inhibition by DNA torsional stress in yeast chromosomes.

Authors:  Ricky S Joshi; Benjamin Piña; Joaquim Roca
Journal:  EMBO J       Date:  2010-01-07       Impact factor: 11.598

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  14 in total

Review 1.  Controlling gene expression by DNA mechanics: emerging insights and challenges.

Authors:  David Levens; Laura Baranello; Fedor Kouzine
Journal:  Biophys Rev       Date:  2016-11-14

Review 2.  Controlling gene expression by DNA mechanics: emerging insights and challenges.

Authors:  David Levens; Laura Baranello; Fedor Kouzine
Journal:  Biophys Rev       Date:  2016-08-20

3.  Chromatin regulates DNA torsional energy via topoisomerase II-mediated relaxation of positive supercoils.

Authors:  Xavier Fernández; Ofelia Díaz-Ingelmo; Belén Martínez-García; Joaquim Roca
Journal:  EMBO J       Date:  2014-05-23       Impact factor: 11.598

Review 4.  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

5.  Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers.

Authors:  Franziska Kriegel; Niklas Ermann; Ruaridh Forbes; David Dulin; Nynke H Dekker; Jan Lipfert
Journal:  Nucleic Acids Res       Date:  2017-06-02       Impact factor: 16.971

6.  Chiral discrimination and writhe-dependent relaxation mechanism of human topoisomerase IIα.

Authors:  Yeonee Seol; Amanda C Gentry; Neil Osheroff; Keir C Neuman
Journal:  J Biol Chem       Date:  2013-03-18       Impact factor: 5.157

Review 7.  Torque measurement at the single-molecule level.

Authors:  Scott Forth; Maxim Y Sheinin; James Inman; Michelle D Wang
Journal:  Annu Rev Biophys       Date:  2013       Impact factor: 12.981

8.  Topoisomerase II is required for the production of long Pol II gene transcripts in yeast.

Authors:  Ricky S Joshi; Benjamin Piña; Joaquim Roca
Journal:  Nucleic Acids Res       Date:  2012-06-19       Impact factor: 16.971

9.  Transcription-dependent dynamic supercoiling is a short-range genomic force.

Authors:  Fedor Kouzine; Ashutosh Gupta; Laura Baranello; Damian Wojtowicz; Khadija Ben-Aissa; Juhong Liu; Teresa M Przytycka; David Levens
Journal:  Nat Struct Mol Biol       Date:  2013-02-17       Impact factor: 15.369

Review 10.  DNA-Topology Simplification by Topoisomerases.

Authors:  Andreas Hanke; Riccardo Ziraldo; Stephen D Levene
Journal:  Molecules       Date:  2021-06-03       Impact factor: 4.411

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