Literature DB >> 29850895

Coupling of replisome movement with nucleosome dynamics can contribute to the parent-daughter information transfer.

Tripti Bameta1, Dibyendu Das2, Ranjith Padinhateeri3.   

Abstract

Positioning of nucleosomes along the genomic DNA is crucial for many cellular processes that include gene regulation and higher order packaging of chromatin. The question of how nucleosome-positioning information from a parent chromatin gets transferred to the daughter chromatin is highly intriguing. Accounting for experimentally known coupling between replisome movement and nucleosome dynamics, we propose a model that can obtain de novo nucleosome assembly similar to what is observed in recent experiments. Simulating nucleosome dynamics during replication, we argue that short pausing of the replication fork, associated with nucleosome disassembly, can be a event crucial for communicating nucleosome positioning information from parent to daughter. We show that the interplay of timescales between nucleosome disassembly (τp) at the replication fork and nucleosome sliding behind the fork (τs) can give rise to a rich 'phase diagram' having different inherited patterns of nucleosome organization. Our model predicts that only when τp ≥ τs the daughter chromatin can inherit nucleosome positioning of the parent.

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Year:  2018        PMID: 29850895      PMCID: PMC6007630          DOI: 10.1093/nar/gky207

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  58 in total

1.  Chromatin fiber polymorphism triggered by variations of DNA linker lengths.

Authors:  Rosana Collepardo-Guevara; Tamar Schlick
Journal:  Proc Natl Acad Sci U S A       Date:  2014-05-20       Impact factor: 11.205

2.  Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity.

Authors:  Eliza C Small; Liqun Xi; Ji-Ping Wang; Jonathan Widom; Jonathan D Licht
Journal:  Proc Natl Acad Sci U S A       Date:  2014-06-02       Impact factor: 11.205

3.  The DNA-encoded nucleosome organization of a eukaryotic genome.

Authors:  Noam Kaplan; Irene K Moore; Yvonne Fondufe-Mittendorf; Andrea J Gossett; Desiree Tillo; Yair Field; Emily M LeProust; Timothy R Hughes; Jason D Lieb; Jonathan Widom; Eran Segal
Journal:  Nature       Date:  2008-12-17       Impact factor: 49.962

4.  Ubiquitous nucleosome crowding in the yeast genome.

Authors:  Răzvan V Chereji; Alexandre V Morozov
Journal:  Proc Natl Acad Sci U S A       Date:  2014-03-24       Impact factor: 11.205

5.  Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics.

Authors:  Jyotsana J Parmar; Dibyendu Das; Ranjith Padinhateeri
Journal:  Nucleic Acids Res       Date:  2015-11-08       Impact factor: 16.971

Review 6.  Epigenetics in human disease and prospects for epigenetic therapy.

Authors:  Gerda Egger; Gangning Liang; Ana Aparicio; Peter A Jones
Journal:  Nature       Date:  2004-05-27       Impact factor: 49.962

7.  Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- and downstream of transcription start sites.

Authors:  Wolfram Möbius; Ulrich Gerland
Journal:  PLoS Comput Biol       Date:  2010-08-19       Impact factor: 4.475

8.  Selective removal of promoter nucleosomes by the RSC chromatin-remodeling complex.

Authors:  Yahli Lorch; Joachim Griesenbeck; Hinrich Boeger; Barbara Maier-Davis; Roger D Kornberg
Journal:  Nat Struct Mol Biol       Date:  2011-07-03       Impact factor: 15.369

9.  Two distinct modes for propagation of histone PTMs across the cell cycle.

Authors:  Constance Alabert; Teresa K Barth; Nazaret Reverón-Gómez; Simone Sidoli; Andreas Schmidt; Ole N Jensen; Axel Imhof; Anja Groth
Journal:  Genes Dev       Date:  2015-03-15       Impact factor: 11.361

10.  Establishment of a promoter-based chromatin architecture on recently replicated DNA can accommodate variable inter-nucleosome spacing.

Authors:  Ross T Fennessy; Tom Owen-Hughes
Journal:  Nucleic Acids Res       Date:  2016-04-22       Impact factor: 16.971

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  1 in total

1.  High fidelity epigenetic inheritance: Information theoretic model predicts threshold filling of histone modifications post replication.

Authors:  Nithya Ramakrishnan; Sibi Raj B Pillai; Ranjith Padinhateeri
Journal:  PLoS Comput Biol       Date:  2022-02-17       Impact factor: 4.475

  1 in total

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