Literature DB >> 18643465

Nucleosome switches.

David J Schwab1, Robijn F Bruinsma, Joseph Rudnick, Jonathan Widom.   

Abstract

We present a statistical-mechanical model for the positioning of nucleosomes along genomic DNA molecules as a function of the strength of the binding potential and the chemical potential of the nucleosomes. We show that a significant section of the DNA is composed of two-level nucleosome switching regions where the nucleosome distribution undergoes a localized, first-order transition. The location of the nucleosome switches shows a strong correlation with the location of gene-regulation regions.

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Year:  2008        PMID： 18643465      PMCID： PMC2711872          DOI： 10.1103/PhysRevLett.100.228105

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN： 0031-9007            Impact factor:   9.161


  3 in total

1.  A genomic code for nucleosome positioning.

Authors:  Eran Segal; Yvonne Fondufe-Mittendorf; Lingyi Chen; AnnChristine Thåström; Yair Field; Irene K Moore; Ji-Ping Z Wang; Jonathan Widom
Journal:  Nature       Date:  2006-07-19       Impact factor: 49.962

2.  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

3.  The chromatin repeat length of brain cortex and cerebellar neurons changes concomitant with terminal differentiation.

Authors:  A W Jaeger; C C Kuenzle
Journal:  EMBO J       Date:  1982       Impact factor: 11.598
  3 in total
  15 in total

1.  Statistical mechanics of integral membrane protein assembly.

Authors:  Karim Wahba; David Schwab; Robijn Bruinsma
Journal:  Biophys J       Date:  2010-10-06       Impact factor: 4.033

2.  A unified computational framework for modeling genome-wide nucleosome landscape.

Authors:  Hu Jin; Alex I Finnegan; Jun S Song
Journal:  Phys Biol       Date:  2018-09-12       Impact factor: 2.583

3.  Statistical mechanics of nucleosome ordering by chromatin-structure-induced two-body interactions.

Authors:  Răzvan V Chereji; Denis Tolkunov; George Locke; Alexandre V Morozov
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2011-05-13

4.  Calculation of nucleosomal DNA deformation energy: its implication for nucleosome positioning.

Authors:  Jian-Ying Wang; Jingyan Wang; Guoqing Liu
Journal:  Chromosome Res       Date:  2012-12-05       Impact factor: 5.239

5.  Statistical Mechanics of Transcription-Factor Binding Site Discovery Using Hidden Markov Models.

Authors:  Pankaj Mehta; David J Schwab; Anirvan M Sengupta
Journal:  J Stat Phys       Date:  2011-04       Impact factor: 1.548

Review 6.  Major Determinants of Nucleosome Positioning.

Authors:  Răzvan V Chereji; David J Clark
Journal:  Biophys J       Date:  2018-04-06       Impact factor: 4.033

Review 7.  The Latest Twists in Chromatin Remodeling.

Authors:  Ralf Blossey; Helmut Schiessel
Journal:  Biophys J       Date:  2018-01-06       Impact factor: 4.033

Review 8.  What does physics have to do with cancer?

Authors:  Franziska Michor; Jan Liphardt; Mauro Ferrari; Jonathan Widom
Journal:  Nat Rev Cancer       Date:  2011-08-18       Impact factor: 60.716

Review 9.  What controls nucleosome positions?

Authors:  Eran Segal; Jonathan Widom
Journal:  Trends Genet       Date:  2009-07-10       Impact factor: 11.639

10.  Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities.

Authors:  Vladimir B Teif; Karsten Rippe
Journal:  Nucleic Acids Res       Date:  2009-07-22       Impact factor: 16.971
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