Literature DB >> 34415541

Predictive Polymer Models for 3D Chromosome Organization.

Michael Chiang1, Giada Forte1,2, Nick Gilbert2, Davide Marenduzzo3, Chris A Brackley1.   

Abstract

Polymer simulations and predictive mechanistic modelling are increasingly used in conjunction with experiments to study the organization of eukaryotic chromosomes. Here we review some of the most prevalent models for mechanisms which drive different aspects of chromosome organization, as well as a recent simulation scheme which combines several of these mechanisms into a single predictive model. We give some practical details of the modelling approach, as well as review some of the key results obtained by these and similar models in the last few years.
© 2022. Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Bridging-induced attraction; Chromosome organization; HiP-HoP model; Polymer simulation

Mesh:

Substances:

Year:  2022        PMID: 34415541     DOI: 10.1007/978-1-0716-1390-0_14

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  52 in total

Review 1.  Disseminating the genome: joining, resolving, and separating sister chromatids during mitosis and meiosis.

Authors:  K Nasmyth
Journal:  Annu Rev Genet       Date:  2001       Impact factor: 16.830

Review 2.  Chromosome conformation capture technologies and their impact in understanding genome function.

Authors:  Satish Sati; Giacomo Cavalli
Journal:  Chromosoma       Date:  2016-04-30       Impact factor: 4.316

3.  Virulence of Bordetella bronchiseptica in the porcine respiratory tract.

Authors:  L A Collings; J M Rutter
Journal:  J Med Microbiol       Date:  1985-04       Impact factor: 2.472

4.  High-resolution mapping of the spatial organization of a bacterial chromosome.

Authors:  Tung B K Le; Maxim V Imakaev; Leonid A Mirny; Michael T Laub
Journal:  Science       Date:  2013-10-24       Impact factor: 47.728

5.  A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

Authors:  Suhas S P Rao; Miriam H Huntley; Neva C Durand; Elena K Stamenova; Ivan D Bochkov; James T Robinson; Adrian L Sanborn; Ido Machol; Arina D Omer; Eric S Lander; Erez Lieberman Aiden
Journal:  Cell       Date:  2014-12-11       Impact factor: 41.582

Review 6.  Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations.

Authors:  Peter R Cook; Davide Marenduzzo
Journal:  Nucleic Acids Res       Date:  2018-11-02       Impact factor: 16.971

7.  Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C.

Authors:  Tsung-Han S Hsieh; Assaf Weiner; Bryan Lajoie; Job Dekker; Nir Friedman; Oliver J Rando
Journal:  Cell       Date:  2015-06-25       Impact factor: 41.582

8.  Topological domains in mammalian genomes identified by analysis of chromatin interactions.

Authors:  Jesse R Dixon; Siddarth Selvaraj; Feng Yue; Audrey Kim; Yan Li; Yin Shen; Ming Hu; Jun S Liu; Bing Ren
Journal:  Nature       Date:  2012-04-11       Impact factor: 49.962

9.  DNA Entry into and Exit out of the Cohesin Ring by an Interlocking Gate Mechanism.

Authors:  Yasuto Murayama; Frank Uhlmann
Journal:  Cell       Date:  2015-12-17       Impact factor: 41.582

Review 10.  Functional implications of genome topology.

Authors:  Giacomo Cavalli; Tom Misteli
Journal:  Nat Struct Mol Biol       Date:  2013-03       Impact factor: 15.369

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  1 in total

Review 1.  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
  1 in total

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