YAMAMOTO, Tetsuya

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YAMAMOTO, Tetsuya
Specially Appointed Associate Professor
Co-PI (Rubinstein Group)
Related Website
Contact

tyamamoto atmark icredd.hokudai.ac.jp

RUBINSTEIN, Michael Group
Principal Investigator
Faculty Members
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    YAMAMOTO, Tetsuya
Postdoctoral Fellows

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

  • Elasticity control of entangled chromosomes: Crosstalk between condensin complexes and nucleosomes
    T. Yamamoto, 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. Yamamoto, 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

Publications

2023

  • Nascent Ribosomal RNA Act as Surfactant that Suppresses Growth of Fibrillar Centers in Nucleolus
    Yamamoto, T., Yamazaki, T., Ninomiya, K., Hirose, T., Communications Biology, 2023, 6, 1129
    DOI: 10.1038/s42003-023-05519-1
  • Elasticity control of entangled chromosomes: Crosstalk between condensin complexes and nucleosomes
    T. Yamamoto, 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. Yamamoto, T. Asanuma, Y. Murakami, Communications Biology, 2023, 6, Article number: 796
    DOI: 10.1038/s42003-023-05154-w
  • Polymer Brush Inspired by Ribosomal RNA Transcription
    T. Yamamoto, W. Li, European Physical Journal E, 2023, 46, 61
    DOI: 10.1140/epje/s10189-023-00323-5

2022

  • Triblock Copolymer Micelle Model of Spherical Paraspeckles
    T. Yamamoto, T. Yamazaki, T. Hirose, Frontiers in Molecular Biosciences, 2022, 9,
    DOI: 10.3389/fmolb.2022.925058
  • Micellization: A New Principle in the Formation of Biomolecular Condensates
    T. Yamazaki, T. Yamamoto, T. Hirose, Frontiers in Molecular Biosciences, 2022, 9,
    DOI: 10.3389/fmolb.2022.974772
  • Loop Extrusion Driven Volume Phase Transition of Entangled Chromosomes
    T. Yamamoto, H. Schiessel, Biophysical Journal, 2022, 121, 2742-2750
    DOI: 10.1016/j.bpj.2022.06.014
  • Scaling Theory of Swelling and Deswelling of Polymer Networks
    T. Yamamoto, J. A. Campbell, S. Panyukov, M. Rubinstein, Macromolecules, 2022, 55, 3588-3601
    DOI: 10.1021/acs.macromol.1c02553

2021

  • Slow Chromatin Dynamics Enhances Promoter Accessibility to Transcriptional Condensates
    T. Yamamoto, T. Sakaue, H. Schiessel, Nucleic Acids Research, 2021, 49, 5017-5027
    DOI: 10.1093/nar/gkab275
  • Paraspeckles Are Constructed as Block Copolymer Micelles
    T. Yamazaki, T. Yamamoto, H. Yoshino, S. Souquere, S. Nakagawa, G. Pierron, T. Hirose, Embo Journal, 2021, , 19
    DOI: 10.15252/embj.2020107270

2020

  • Fracture Strain of Composite with Nonuniformly Distributed Reinforcing Fibers
    T. Yamamoto, Y. Masubuchi, M. Doi, Journal of Rheology, 2020, 64, 933-939
    DOI: 10.1122/8.0000046
  • Phase Separation Driven by Production of Architectural RNA Transcripts
    T. Yamamoto, T. Yamazaki, T. Hirose, Soft Matter, 2020, 16, 4692-4698
    DOI: 10.1039/c9sm02458a