Condensed but liquid-like domain organization of active chromatin regions in living human cells
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- Tadasu Nozaki
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
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- Soya Shinkai
- Laboratory for Developmental Dynamics, Center for Biosystems Dynamics Research (BDR), RIKEN, Kobe, Hyogo 650-0047, Japan.
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- Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
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- Koichi Higashi
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan.
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- Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
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- Masa A. Shimazoe
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
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- Masaki Nakagawa
- Department of Computer Science and Engineering, Fukuoka Institute of Technology, Fukuoka, Fukuoka 811-0295, Japan.
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- Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, University of Tokyo, 5-1-5 Kashiwanoha Kashiwa, Chiba 277-8562, Japan.
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- Yasushi Okada
- Laboratory for Cell Polarity Regulation, Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka 565-0874, Japan.
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- Masaki Sasai
- Department of Complex Systems Science, Nagoya University, Nagoya 464-8601, Japan.
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- Shuichi Onami
- Laboratory for Developmental Dynamics, Center for Biosystems Dynamics Research (BDR), RIKEN, Kobe, Hyogo 650-0047, Japan.
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- Ken Kurokawa
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan.
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- Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
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- Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
抄録
<jats:p>In eukaryotes, higher-order chromatin organization is spatiotemporally regulated as domains, for various cellular functions. However, their physical nature in living cells remains unclear (e.g., condensed domains or extended fiber loops; liquid-like or solid-like). Using novel approaches combining genomics, single-nucleosome imaging, and computational modeling, we investigated the physical organization and behavior of early DNA replicated regions in human cells, which correspond to Hi-C contact domains with active chromatin marks. Motion correlation analysis of two neighbor nucleosomes shows that nucleosomes form physically condensed domains with ~150-nm diameters, even in active chromatin regions. The mean-square displacement analysis between two neighbor nucleosomes demonstrates that nucleosomes behave like a liquid in the condensed domain on the ~150 nm/~0.5 s spatiotemporal scale, which facilitates chromatin accessibility. Beyond the micrometers/minutes scale, chromatin seems solid-like, which may contribute to maintaining genome integrity. Our study reveals the viscoelastic principle of the chromatin polymer; chromatin is locally dynamic and reactive but globally stable.</jats:p>
収録刊行物
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- Science Advances
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Science Advances 9 (14), 2023-04-07
American Association for the Advancement of Science (AAAS)