Literature DB >> 30566285

Models of polymer physics for the architecture of the cell nucleus.

Andrea Esposito1,2, Carlo Annunziatella1, Simona Bianco1, Andrea M Chiariello1, Luca Fiorillo1, Mario Nicodemi1,2,3.   

Abstract

The depth and complexity of data now available on chromosome 3D architecture, derived by new technologies such as Hi-C, have triggered the development of models based on polymer physics to explain the observed patterns and the underlying molecular folding mechanisms. Here, we give an overview of some of the ideas and models from physics introduced to date, along with their progresses and limitations in the description of experimental data. In particular, we focus on the Strings&Binders and the Loop Extrusion model of chromatin architecture. This article is categorized under: Analytical and Computational Methods > Computational Methods.
© 2018 Wiley Periodicals, Inc.

Entities:  

Keywords:  chromatin; computational biology; polymer physics

Mesh:

Substances:

Year:  2018        PMID: 30566285      PMCID: PMC6565494          DOI: 10.1002/wsbm.1444

Source DB:  PubMed          Journal:  Wiley Interdiscip Rev Syst Biol Med        ISSN: 1939-005X


  60 in total

1.  Radial arrangement of chromosome territories in human cell nuclei: a computer model approach based on gene density indicates a probabilistic global positioning code.

Authors:  G Kreth; J Finsterle; J von Hase; M Cremer; C Cremer
Journal:  Biophys J       Date:  2004-05       Impact factor: 4.033

2.  Thermodynamic pathways to genome spatial organization in the cell nucleus.

Authors:  Mario Nicodemi; Antonella Prisco
Journal:  Biophys J       Date:  2009-03-18       Impact factor: 4.033

3.  Genome architectures revealed by tethered chromosome conformation capture and population-based modeling.

Authors:  Reza Kalhor; Harianto Tjong; Nimanthi Jayathilaka; Frank Alber; Lin Chen
Journal:  Nat Biotechnol       Date:  2011-12-25       Impact factor: 54.908

4.  The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules.

Authors:  Davide Baù; Amartya Sanyal; Bryan R Lajoie; Emidio Capriotti; Meg Byron; Jeanne B Lawrence; Job Dekker; Marc A Marti-Renom
Journal:  Nat Struct Mol Biol       Date:  2010-12-05       Impact factor: 15.369

5.  Spatial partitioning of the regulatory landscape of the X-inactivation centre.

Authors:  Elphège P Nora; Bryan R Lajoie; Edda G Schulz; Luca Giorgetti; Ikuhiro Okamoto; Nicolas Servant; Tristan Piolot; Nynke L van Berkum; Johannes Meisig; John Sedat; Joost Gribnau; Emmanuel Barillot; Nils Blüthgen; Job Dekker; Edith Heard
Journal:  Nature       Date:  2012-04-11       Impact factor: 49.962

6.  A three-dimensional model of the yeast genome.

Authors:  Zhijun Duan; Mirela Andronescu; Kevin Schutz; Sean McIlwain; Yoo Jung Kim; Choli Lee; Jay Shendure; Stanley Fields; C Anthony Blau; William S Noble
Journal:  Nature       Date:  2010-05-02       Impact factor: 49.962

7.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Authors:  Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

8.  Diffusion-driven looping provides a consistent framework for chromatin organization.

Authors:  Manfred Bohn; Dieter W Heermann
Journal:  PLoS One       Date:  2010-08-25       Impact factor: 3.240

9.  Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling.

Authors:  Mathieu Rousseau; James Fraser; Maria A Ferraiuolo; Josée Dostie; Mathieu Blanchette
Journal:  BMC Bioinformatics       Date:  2011-10-25       Impact factor: 3.169

10.  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

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  3 in total

Review 1.  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

2.  Deciphering hierarchical organization of topologically associated domains through change-point testing.

Authors:  Haipeng Xing; Yingru Wu; Michael Q Zhang; Yong Chen
Journal:  BMC Bioinformatics       Date:  2021-04-10       Impact factor: 3.169

3.  CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells.

Authors:  Alan Perez-Rathke; Qiu Sun; Boshen Wang; Valentina Boeva; Zhifeng Shao; Jie Liang
Journal:  Genome Biol       Date:  2020-01-16       Impact factor: 13.583

  3 in total

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