Bridging the dynamics and organization of chromatin domains by mathematical modeling

Nucleus
Soya ShinkaiYuichi Togashi

Abstract

The genome is 3-dimensionally organized in the cell, and the mammalian genome DNA is partitioned into submegabase-sized chromatin domains. Genome functions are regulated within and across the domains according to their organization, whereas the chromatin itself is highly dynamic. However, the details of such dynamic organization of chromatin domains in living cells remain unclear. To unify chromatin dynamics and organization, we recently demonstrated that structural information of chromatin domains in living human cells can be extracted from analyses of the subdiffusive nucleosome movement using mathematical modeling. Our mathematical analysis suggested that as the chromatin domain becomes smaller and more compact, nucleosome movement becomes increasingly restricted. Here, we show the implication of these results for bridging the gap between chromatin dynamics and organization, and provide physical insight into chromatin domains as efficient units to conduct genome functions in the thermal noisy environment of the cell.

References

Aug 2, 2018·Biochemical Society Transactions·Maxime Woringer, Xavier Darzacq

Citations

Jan 1, 1988·Journal of Mathematical Biology·S Doi, S Sato
Jun 15, 1999·The Journal of Cell Biology·J A CroftWendy A Bickmore
Dec 12, 2001·Science·P HeunSusan M Gasser
Jan 8, 2008·Nature Methods·Makio TokunagaKumiko Sakata-Sogawa
Jan 27, 2009·Nature Methods·Fedor V SubachVladislav V Verkhusha
Dec 7, 2010·Nature Structural & Molecular Biology·Davide BaùMarc A Marti-Renom
Mar 31, 2012·Current Opinion in Cell Biology·Qian Bian, Andrew S Belmont
Jul 25, 2012·Nucleus·Yasumasa JotiKazuhiro Maeshima
Sep 19, 2012·EMBO Reports·Eden FussnerDavid P Bazett-Jones
Mar 19, 2013·Cell·Wendy A Bickmore, Bas van Steensel
Aug 16, 2013·Nucleus·Tadasu NozakiKazuhiro Maeshima
Sep 11, 2013·Proceedings of the National Academy of Sciences of the United States of America·Alexandra ZidovskaTimothy J Mitchison
Mar 15, 2015·Cell·Maria Aurelia RicciMaria Pia Cosma
May 20, 2015·FEBS Letters·François SerraMarc A Marti-Renom
Jun 21, 2015·Nucleic Acids Research·Hiroshi OchiaiTakashi Yamamoto
Jan 31, 2016·Current Opinion in Genetics & Development·Kazuhiro MaeshimaMasaki Sasai
Feb 9, 2016·Nucleus·Irena BronshteinYuval Garini
Apr 14, 2016·The EMBO Journal·Kazuhiro MaeshimaJeffrey C Hansen
Sep 9, 2016·Molecular Biology of the Cell·Chen ChenLu Gan

Related Concepts

In Silico
Nucleosomes
Genome
Environment
Nucleosome Location
Polynucleosomes
Human Cell Line
Gene Function
Diffusion
Structure

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