Literature DB >> 23514152

DNA thermodynamics shape chromosome organization and topology.

Andrew A Travers1, Georgi Muskhelishvili.   

Abstract

How much information is encoded in the DNA sequence of an organism? We argue that the informational, mechanical and topological properties of DNA are interdependent and act together to specify the primary characteristics of genetic organization and chromatin structures. Superhelicity generated in vivo, in part by the action of DNA translocases, can be transmitted to topologically sensitive regions encoded by less stable DNA sequences.

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Year:  2013        PMID： 23514152      PMCID： PMC4085469          DOI： 10.1042/BST20120334

Source DB:  PubMed          Journal:  Biochem Soc Trans        ISSN： 0300-5127            Impact factor:   5.407


  45 in total

1.  DNA supercoiling contributes to disconnect sigmaS accumulation from sigmaS-dependent transcription in Escherichia coli.

Authors:  Patricia Bordes; Annie Conter; Violette Morales; Jean Bouvier; Annie Kolb; Claude Gutierrez
Journal:  Mol Microbiol       Date:  2003-04       Impact factor: 3.501

2.  Mechanism of transcriptional activation by FIS: role of core promoter structure and DNA topology.

Authors:  Helge Auner; Malcolm Buckle; Annette Deufel; Tamara Kutateladze; Linda Lazarus; Ramesh Mavathur; Georgi Muskhelishvili; Iain Pemberton; Robert Schneider; Andrew Travers
Journal:  J Mol Biol       Date:  2003-08-08       Impact factor: 5.469

Review 3.  Pervasive regulation of nucleoid structure and function by nucleoid-associated proteins.

Authors:  Sylvie Rimsky; Andrew Travers
Journal:  Curr Opin Microbiol       Date:  2011-01-31       Impact factor: 7.934

4.  Promoter selectivity of Escherichia coli RNA polymerase E sigma 70 and E sigma 38 holoenzymes. Effect of DNA supercoiling.

Authors:  S Kusano; Q Ding; N Fujita; A Ishihama
Journal:  J Biol Chem       Date:  1996-01-26       Impact factor: 5.157

5.  In vitro evolution of preferred topoisomerase II DNA cleavage sites.

Authors:  D A Burden; N Osheroff
Journal:  J Biol Chem       Date:  1999-02-19       Impact factor: 5.157

6.  A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern.

Authors:  Amanda L Hughes; Yi Jin; Oliver J Rando; Kevin Struhl
Journal:  Mol Cell       Date:  2012-08-09       Impact factor: 17.970

Review 7.  Poly(dA:dT) tracts: major determinants of nucleosome organization.

Authors:  Eran Segal; Jonathan Widom
Journal:  Curr Opin Struct Biol       Date:  2009-02-07       Impact factor: 6.809

8.  H-NS cooperative binding to high-affinity sites in a regulatory element results in transcriptional silencing.

Authors:  Emeline Bouffartigues; Malcolm Buckle; Cyril Badaut; Andrew Travers; Sylvie Rimsky
Journal:  Nat Struct Mol Biol       Date:  2007-04-15       Impact factor: 15.369

9.  RNA polymerase and an activator form discrete subcomplexes in a transcription initiation complex.

Authors:  Sebastian Maurer; Jürgen Fritz; Georgi Muskhelishvili; Andrew Travers
Journal:  EMBO J       Date:  2006-08-03       Impact factor: 11.598

10.  High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes.

Authors:  Benjamin Lang; Nicolas Blot; Emeline Bouffartigues; Malcolm Buckle; Marcel Geertz; Claudio O Gualerzi; Ramesh Mavathur; Georgi Muskhelishvili; Cynthia L Pon; Sylvie Rimsky; Stefano Stella; M Madan Babu; Andrew Travers
Journal:  Nucleic Acids Res       Date:  2007-09-18       Impact factor: 16.971
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  10 in total

Review 1.  Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information.

Authors:  Georgi Muskhelishvili; Andrew Travers
Journal:  Cell Mol Life Sci       Date:  2013-06-15       Impact factor: 9.261

2.  Dynamic DNA underpins chromosome dynamics.

Authors:  Andrew Travers
Journal:  Biophys J       Date:  2013-11-19       Impact factor: 4.033

Review 3.  Supercoiling biases the formation of loops involved in gene regulation.

Authors:  Laura Finzi; David Dunlap
Journal:  Biophys Rev       Date:  2016-07-05

Review 4.  Spatiotemporal Coupling of DNA Supercoiling and Genomic Sequence Organization-A Timing Chain for the Bacterial Growth Cycle?

Authors:  Georgi Muskhelishvili; Patrick Sobetzko; Andrew Travers
Journal:  Biomolecules       Date:  2022-06-15

5.  Chromosomal "stress-response" domains govern the spatiotemporal expression of the bacterial virulence program.

Authors:  Xuejiao Jiang; Patrick Sobetzko; William Nasser; Sylvie Reverchon; Georgi Muskhelishvili
Journal:  MBio       Date:  2015-04-28       Impact factor: 7.867

6.  Relationship between digital information and thermodynamic stability in bacterial genomes.

Authors:  Dawit Nigatu; Werner Henkel; Patrick Sobetzko; Georgi Muskhelishvili
Journal:  EURASIP J Bioinform Syst Biol       Date:  2016-02-02

7.  Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein.

Authors:  Aleksandre Japaridze; Sylvain Renevey; Patrick Sobetzko; Liubov Stoliar; William Nasser; Giovanni Dietler; Georgi Muskhelishvili
Journal:  J Biol Chem       Date:  2017-03-18       Impact factor: 5.157

8.  DNA sequence-directed cooperation between nucleoid-associated proteins.

Authors:  Aleksandre Japaridze; Wayne Yang; Cees Dekker; William Nasser; Georgi Muskhelishvili
Journal:  iScience       Date:  2021-04-20

Review 9.  Composition of Transcription Machinery and Its Crosstalk with Nucleoid-Associated Proteins and Global Transcription Factors.

Authors:  Georgi Muskhelishvili; Patrick Sobetzko; Sanja Mehandziska; Andrew Travers
Journal:  Biomolecules       Date:  2021-06-22

10.  Genes on a Wire: The Nucleoid-Associated Protein HU Insulates Transcription Units in Escherichia coli.

Authors:  Michael Berger; Veneta Gerganova; Petya Berger; Radu Rapiteanu; Viktoras Lisicovas; Ulrich Dobrindt
Journal:  Sci Rep       Date:  2016-08-22       Impact factor: 4.379
  10 in total

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