Literature DB >> 32045823

Computational approaches from polymer physics to investigate chromatin folding.

Simona Bianco1, Andrea M Chiariello2, Mattia Conte2, Andrea Esposito2, Luca Fiorillo2, Francesco Musella2, Mario Nicodemi3.   

Abstract

Microscopy and sequencing-based technologies are providing increasing insights into chromatin architecture. Nevertheless, a full comprehension of chromosome folding and its link with vital cell functions is far from accomplished at the molecular level. Recent theoretical and computational approaches are providing important support to experiments to dissect the three-dimensional structure of chromosomes and its organizational mechanisms. Here, we review, in particular, the String&Binders polymer model of chromatin that describes the textbook scenario where contacts between distal DNA sites are established by cognate binders. It has been shown to recapitulate key features of chromosome folding and to be able at predicting how phenotypes causing structural variants rewire the interactions between genes and regulators.
Copyright © 2020 Elsevier Ltd. All rights reserved.

Keywords:  Chromatin organization; EPHA4; Loop extrusion model; Pitx1; Polymer models; SBS model; Statistical mechanics; Structural variants

Mesh:

Substances:

Year:  2020        PMID: 32045823     DOI: 10.1016/j.ceb.2020.01.002

Source DB:  PubMed          Journal:  Curr Opin Cell Biol        ISSN: 0955-0674            Impact factor:   8.382


  12 in total

1.  Chromosomes Phase Transition to Function.

Authors:  Mario Nicodemi; Simona Bianco
Journal:  Biophys J       Date:  2020-07-18       Impact factor: 4.033

Review 2.  Integrative approaches in genome structure analysis.

Authors:  Lorenzo Boninsegna; Asli Yildirim; Yuxiang Zhan; Frank Alber
Journal:  Structure       Date:  2021-12-27       Impact factor: 5.006

3.  Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations.

Authors:  Lorenzo Boninsegna; Asli Yildirim; Guido Polles; Yuxiang Zhan; Sofia A Quinodoz; Elizabeth H Finn; Mitchell Guttman; Xianghong Jasmine Zhou; Frank Alber
Journal:  Nat Methods       Date:  2022-07-11       Impact factor: 47.990

4.  3DGenBench: a web-server to benchmark computational models for 3D Genomics.

Authors: 
Journal:  Nucleic Acids Res       Date:  2022-05-25       Impact factor: 19.160

Review 5.  The Physics of DNA Folding: Polymer Models and Phase-Separation.

Authors:  Andrea Esposito; Alex Abraham; Mattia Conte; Francesca Vercellone; Antonella Prisco; Simona Bianco; Andrea M Chiariello
Journal:  Polymers (Basel)       Date:  2022-05-09       Impact factor: 4.967

6.  BRD2 compartmentalizes the accessible genome.

Authors:  Liangqi Xie; Peng Dong; Yifeng Qi; Tsung-Han S Hsieh; Brian P English; SeolKyoung Jung; Xingqi Chen; Margherita De Marzio; Rafael Casellas; Howard Y Chang; Bin Zhang; Robert Tjian; Zhe Liu
Journal:  Nat Genet       Date:  2022-04-11       Impact factor: 41.307

Review 7.  The Self-Organizing Genome: Principles of Genome Architecture and Function.

Authors:  Tom Misteli
Journal:  Cell       Date:  2020-09-24       Impact factor: 41.582

8.  The Interplay between Phase Separation and Gene-Enhancer Communication: A Theoretical Study.

Authors:  Andrea M Chiariello; Federico Corberi; Mario Salerno
Journal:  Biophys J       Date:  2020-07-18       Impact factor: 4.033

Review 9.  Genome-in-a-Box: Building a Chromosome from the Bottom Up.

Authors:  Anthony Birnie; Cees Dekker
Journal:  ACS Nano       Date:  2020-12-21       Impact factor: 15.881

Review 10.  A Liquid State Perspective on Dynamics of Chromatin Compartments.

Authors:  Rabia Laghmach; Michele Di Pierro; Davit Potoyan
Journal:  Front Mol Biosci       Date:  2022-01-13
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