About the Research
Research Theme
Physics of gene regulation
Keyword
Gene regulation, transcription, phase separation, DNA(chromatin), interface, cell differentiation and reprogramming
Research Outline
Multicelluar organism is composed of many different types of cells although these cells have the same DNA. The specificity of cells is determined by which genes are actively expressed and which genes are repressed. We are theoretically analyzing how the dynamics of gene expression is regulated by the structure and dynamics of DNA (chromatin), RNA, and associating proteins. We are also extending our research to the physics involved in DNA replication, mitosis, and RNA splicing.
Representative Research Achievements
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Elasticity control of entangled chromosomes: Crosstalk between condensin complexes and nucleosomes
, K. Kinoshita, T. Hirano, Biophysical Journal, 2023, 122, 19, 3869-3881
DOI: 10.1016/j.bpj.2023.08.006 -
Polymeric Nature of Tandemly Repeated Genes Enhances Assembly of Constitutive Heterochromatin in Fission Yeast
, T. Asanuma, Y. Murakami, Communications Biology, 2023, 6, Article number: 796
DOI: 10.1038/s42003-023-05154-w - Slow chromatin dynamics enhances promoter accessibility to transcriptional condensates
Tetsuya Yamamoto, Takahiro Sakaue, Helmut Schiessel, Nucleic Acids Research, 2021, 49, 5017-5027
DOI: 10.1093/nar/gkab275 - Paraspeckles are constructed as block copolymer micelles
Tomohiro Yamazaki, Tetsuya Yamamoto, Hyura Yoshino, Sylvie Souquere, Shinichi Nakagawa, Gerard Pierron, Tetsuro Hirose, EMBO J, 2021, e107270
DOI: 10.15252/embj.2020107270 - Phase separation driven by production of architectural RNA transcripts
Tetsuya Yamamoto, Tomohiro Yamazaki, Tetsuro Hirose, Soft Matter, 2020, 16, 4692-4698
DOI: 10.1039/C9SM02458A - Osmotic mechanism of the loop extrusion process
Tetsuya Yamamoto, Helmut Schiessel, PHYSICAL REVIEW E, 2017, 96, 030402(R)
DOI: 10.1103/PhysRevE.96.030402 -
Transcription rates in DNA brushes
Tetsuya Yamamoto, S. A. Safran, Soft Matter, 2015, 11, 3017-3021
DOI: 10.1039/C4SM02871F
Related Research
Publications
2025
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Biophysical Aspect of Assembly and Regulation of Nuclear Bodies Scaffolded by Architectural RNA
, T. Yamazaki, K. Ninomiya, S. Nakagawa, T. Hirose, JOURNAL OF MOLECULAR BIOLOGY, 2025, 437(9), 169016
DOI: 10.1016/j.jmb.2025.169016
2024
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Dissolution-Limited Reactions in Solid-State Synthesis
, K. Kubota, H. Ito, NIHON REOROJI GAKKAISHI, 2024, 52(2), 161-170
DOI: 10.1678/rheology.52.161
2023
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Nascent Ribosomal RNA Act as Surfactant that Suppresses Growth of Fibrillar Centers in Nucleolus
, Yamazaki, T., Ninomiya, K., Hirose, T., Communications Biology, 2023, 6, 1129
DOI: 10.1038/s42003-023-05519-1
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Elasticity control of entangled chromosomes: Crosstalk between condensin complexes and nucleosomes
, K. Kinoshita, T. Hirano, Biophysical Journal, 2023, 122, 19, 3869-3881
DOI: 10.1016/j.bpj.2023.08.006
-
Polymeric Nature of Tandemly Repeated Genes Enhances Assembly of Constitutive Heterochromatin in Fission Yeast
, T. Asanuma, Y. Murakami, Communications Biology, 2023, 6, Article number: 796
DOI: 10.1038/s42003-023-05154-w
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Polymer Brush Inspired by Ribosomal RNA Transcription
, W. Li, European Physical Journal E, 2023, 46, 61
DOI: 10.1140/epje/s10189-023-00323-5
2022
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Triblock Copolymer Micelle Model of Spherical Paraspeckles
, T. Yamazaki, T. Hirose, Frontiers in Molecular Biosciences, 2022, 9,
DOI: 10.3389/fmolb.2022.925058
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Micellization: A New Principle in the Formation of Biomolecular Condensates
, T. Yamamoto, T. Hirose, Frontiers in Molecular Biosciences, 2022, 9,
DOI: 10.3389/fmolb.2022.974772
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Loop Extrusion Driven Volume Phase Transition of Entangled Chromosomes
, H. Schiessel, Biophysical Journal, 2022, 121, 2742-2750
DOI: 10.1016/j.bpj.2022.06.014
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Scaling Theory of Swelling and Deswelling of Polymer Networks
, J. A. Campbell, S. Panyukov, M. Rubinstein, Macromolecules, 2022, 55, 3588-3601
DOI: 10.1021/acs.macromol.1c02553
2021
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Slow Chromatin Dynamics Enhances Promoter Accessibility to Transcriptional Condensates
, T. Sakaue, H. Schiessel, Nucleic Acids Research, 2021, 49, 5017-5027
DOI: 10.1093/nar/gkab275
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Paraspeckles Are Constructed as Block Copolymer Micelles
, T. Yamamoto, H. Yoshino, S. Souquere, S. Nakagawa, G. Pierron, T. Hirose, Embo Journal, 2021, , 19
DOI: 10.15252/embj.2020107270
2020
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Fracture Strain of Composite with Nonuniformly Distributed Reinforcing Fibers
, Y. Masubuchi, M. Doi, Journal of Rheology, 2020, 64, 933-939
DOI: 10.1122/8.0000046
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Phase Separation Driven by Production of Architectural RNA Transcripts
, T. Yamazaki, T. Hirose, Soft Matter, 2020, 16, 4692-4698
DOI: 10.1039/c9sm02458a