Literature DB >> 25764220

Physical mechanisms behind the large scale features of chromatin organization.

Ana Pombo1, Mario Nicodemi.   

Abstract

We review the picture emerging from recently published models of classical polymer physics of the general features of chromatin large scale spatial organization, as revealed by microscopy and Hi-C data.

Entities:  

Keywords:  computer simulations; contact matrices; genome organization; long-range chromatin interactions; polymer physics

Mesh：

Substances：

Year:  2014        PMID： 25764220      PMCID： PMC4214237          DOI： 10.4161/trns.28447

Source DB:  PubMed          Journal:  Transcription        ISSN： 2154-1272


  21 in total

1.  Creep of superconducting vortices in the limit of vanishing temperature: a fingerprint of off-equilibrium dynamics.

Authors:  M Nicodemi; H Jeldtoft Jensen
Journal:  Phys Rev Lett       Date:  2001-05-07       Impact factor: 9.161

2.  Critical clusters and efficient dynamics for frustrated spin models.

Authors: 
Journal:  Phys Rev Lett       Date:  1994-03-07       Impact factor: 9.161

Review 3.  Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions.

Authors:  Christian Lanctôt; Thierry Cheutin; Marion Cremer; Giacomo Cavalli; Thomas Cremer
Journal:  Nat Rev Genet       Date:  2007-02       Impact factor: 53.242

4.  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

5.  Chromatin folding--from biology to polymer models and back.

Authors:  Mariliis Tark-Dame; Roel van Driel; Dieter W Heermann
Journal:  J Cell Sci       Date:  2011-03-15       Impact factor: 5.285

Review 6.  Genome architecture: domain organization of interphase chromosomes.

Authors:  Wendy A Bickmore; Bas van Steensel
Journal:  Cell       Date:  2013-03-14       Impact factor: 41.582

7.  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

8.  Complexity of chromatin folding is captured by the strings and binders switch model.

Authors:  Mariano Barbieri; Mita Chotalia; James Fraser; Liron-Mark Lavitas; Josée Dostie; Ana Pombo; Mario Nicodemi
Journal:  Proc Natl Acad Sci U S A       Date:  2012-09-17       Impact factor: 11.205

9.  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

10.  Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes.

Authors:  Fabrizio Benedetti; Julien Dorier; Yannis Burnier; Andrzej Stasiak
Journal:  Nucleic Acids Res       Date:  2013-12-23       Impact factor: 16.971
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  3 in total

Review 1.  Topologically-associating domains: gene warehouses adapted to serve transcriptional regulation.

Authors:  Sergey V Razin; Alexey A Gavrilov; Yegor S Vassetzky; Sergey V Ulianov
Journal:  Transcription       Date:  2016-04-25

2.  Irregular Chromatin: Packing Density, Fiber Width, and Occurrence of Heterogeneous Clusters.

Authors:  Gaurav Bajpai; Ranjith Padinhateeri
Journal:  Biophys J       Date:  2019-11-14       Impact factor: 4.033

Review 3.  Gene functioning and storage within a folded genome.

Authors:  Sergey V Razin; Sergey V Ulianov
Journal:  Cell Mol Biol Lett       Date:  2017-08-29       Impact factor: 5.787
  3 in total

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