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Bridging the dynamics and organization of chromatin domains by mathematical modeling

View ORCID ProfileSoya Shinkai, View ORCID ProfileTadasu Nozaki, View ORCID ProfileKazuhiro Maeshima, View ORCID ProfileYuichi Togashi
doi: https://doi.org/10.1101/151563
Soya Shinkai
1 Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima 739-8530, Japan.
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  • For correspondence: soya@rcmcd.hiroshima-u.ac.jp
Tadasu Nozaki
2 Structural Biology Center, National Institute of Genetics, Yata 1111, Mishima 411-8540, Japan.
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Kazuhiro Maeshima
2 Structural Biology Center, National Institute of Genetics, Yata 1111, Mishima 411-8540, Japan.
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Yuichi Togashi
1 Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima 739-8530, Japan.
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Abstract

The genome is three-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.

Extra View to Shinkai S, Nozaki T, Maeshima K, Togashi Y. Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells. PLoS Comput Biol. 2016;12(10):e1005136. doi: 10.1371/journal.pcbi.1005136. PubMed PMID: 27764097; PubMed Central PMCID: PMCPMC5072619.

Funding This work was supported by Platform Project for Supporting in Drug Discovery and Life Science Research (Platform for Dynamic Approaches to Living System) from MEXT and AMED; KAKENHI under Grant JP16H01408, JP23115007, JP23115005, JP16H04746; CREST grant (JPMJCR15G2) from JST; and Research Fellowship for Young Scientists under Grant JP13J04821, JP16J07205.

Disclosure No potential conflicts of interest were disclosed.

Acknowledgements We would like to thank Dr. Takashi Toda for comments regarding the manuscript.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 18, 2017.
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Bridging the dynamics and organization of chromatin domains by mathematical modeling
Soya Shinkai, Tadasu Nozaki, Kazuhiro Maeshima, Yuichi Togashi
bioRxiv 151563; doi: https://doi.org/10.1101/151563
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Bridging the dynamics and organization of chromatin domains by mathematical modeling
Soya Shinkai, Tadasu Nozaki, Kazuhiro Maeshima, Yuichi Togashi
bioRxiv 151563; doi: https://doi.org/10.1101/151563

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