Literature DB >> 20232928

The DNA sequence-dependence of nucleosome positioning in vivo and in vitro.

Andrew Travers1, Edwige Hiriart, Mark Churcher, Micaela Caserta, Ernesto Di Mauro.   

Abstract

The contribution of histone-DNA interactions to nucleosome positioning in vivo is currently a matter of debate. We argue here that certain nucleosome positions, often in promoter regions, in yeast may be, at least in part, specified by the DNA sequence. In contrast other positions may be poorly specified. Positioning thus has both statistical and DNA-determined components. We further argue that the relative affinity of the octamer for different DNA sequences can vary and therefore the interaction of histones with the DNA is a 'tunable' property.

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Year:  2010        PMID: 20232928      PMCID: PMC2864905          DOI: 10.1080/073911010010524942

Source DB:  PubMed          Journal:  J Biomol Struct Dyn        ISSN: 0739-1102


  116 in total

1.  Persistence length and bending dynamics of DNA from electrooptical measurements at high salt concentrations.

Authors:  D Porschke
Journal:  Biophys Chem       Date:  1991-05       Impact factor: 2.352

2.  Nucleosome loss activates yeast downstream promoters in vivo.

Authors:  M Han; M Grunstein
Journal:  Cell       Date:  1988-12-23       Impact factor: 41.582

3.  Initiation of transcription on nucleosomal templates.

Authors:  A P Wolffe; H R Drew
Journal:  Proc Natl Acad Sci U S A       Date:  1989-12       Impact factor: 11.205

4.  Artificial nucleosome positioning sequences.

Authors:  T E Shrader; D M Crothers
Journal:  Proc Natl Acad Sci U S A       Date:  1989-10       Impact factor: 11.205

5.  Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism.

Authors:  R D Kornberg; L Stryer
Journal:  Nucleic Acids Res       Date:  1988-07-25       Impact factor: 16.971

6.  Helical repeat and linking number of surface-wrapped DNA.

Authors:  J H White; N R Cozzarelli; W R Bauer
Journal:  Science       Date:  1988-07-15       Impact factor: 47.728

Review 7.  The bending of DNA in nucleosomes and its wider implications.

Authors:  A A Travers; A Klug
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  1987-12-15       Impact factor: 6.237

8.  Nucleosome positioning modulates accessibility of regulatory proteins to the mouse mammary tumor virus promoter.

Authors:  B Piña; U Brüggemeier; M Beato
Journal:  Cell       Date:  1990-03-09       Impact factor: 41.582

9.  Asymmetry and polarity of nucleosomes in chicken erythrocyte chromatin.

Authors:  S C Satchwell; A A Travers
Journal:  EMBO J       Date:  1989-01       Impact factor: 11.598

10.  Nucleosomes are positioned with base pair precision adjacent to the alpha 2 operator in Saccharomyces cerevisiae.

Authors:  M Shimizu; S Y Roth; C Szent-Gyorgyi; R T Simpson
Journal:  EMBO J       Date:  1991-10       Impact factor: 11.598

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  15 in total

1.  Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner.

Authors:  Yuri M Moshkin; Gillian E Chalkley; Tsung Wai Kan; B Ashok Reddy; Zeliha Ozgur; Wilfred F J van Ijcken; Dick H W Dekkers; Jeroen A Demmers; Andrew A Travers; C Peter Verrijzer
Journal:  Mol Cell Biol       Date:  2011-11-28       Impact factor: 4.272

2.  Snf1/AMPK regulates Gcn5 occupancy, H3 acetylation and chromatin remodelling at S. cerevisiae ADY2 promoter.

Authors:  Georgia Abate; Emanuela Bastonini; Katherine A Braun; Loredana Verdone; Elton T Young; Micaela Caserta
Journal:  Biochim Biophys Acta       Date:  2012-01-28

3.  Variety of genomic DNA patterns for nucleosome positioning.

Authors:  Ilya Ioshikhes; Sergey Hosid; B Franklin Pugh
Journal:  Genome Res       Date:  2011-07-12       Impact factor: 9.043

4.  Impact of methylation on the physical properties of DNA.

Authors:  Alberto Pérez; Chiara Lara Castellazzi; Federica Battistini; Kathryn Collinet; Oscar Flores; Ozgen Deniz; Maria Luz Ruiz; David Torrents; Ramon Eritja; Montserrat Soler-López; Modesto Orozco
Journal:  Biophys J       Date:  2012-05-02       Impact factor: 4.033

5.  Atomistic insight into sequence-directed DNA bending and minicircle formation propensity in the absence and presence of phased A-tracts.

Authors:  Alberto Mills; Federico Gago
Journal:  J Comput Aided Mol Des       Date:  2020-01-16       Impact factor: 3.686

Review 6.  Nucleosome distribution and linker DNA: connecting nuclear function to dynamic chromatin structure.

Authors:  Heather J Szerlong; Jeffrey C Hansen
Journal:  Biochem Cell Biol       Date:  2011-02       Impact factor: 3.626

7.  ICM Web: the interactive chromatin modeling web server.

Authors:  Richard C Stolz; Thomas C Bishop
Journal:  Nucleic Acids Res       Date:  2010-06-11       Impact factor: 16.971

8.  Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae.

Authors:  Christoforos Nikolaou; Sonja Althammer; Miguel Beato; Roderic Guigó
Journal:  Epigenetics Chromatin       Date:  2010-11-12       Impact factor: 4.954

9.  A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization.

Authors:  Triantaffyllos Gkikopoulos; Pieta Schofield; Vijender Singh; Marina Pinskaya; Jane Mellor; Michaela Smolle; Jerry L Workman; Geoffrey J Barton; Tom Owen-Hughes
Journal:  Science       Date:  2011-09-23       Impact factor: 47.728

Review 10.  Single-Molecule Techniques to Study Chromatin.

Authors:  Anna Chanou; Stephan Hamperl
Journal:  Front Cell Dev Biol       Date:  2021-07-05
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