3D analysis of chromatin structure in cell nucleus with electron microscopy and mathematical modeling

• Project/Area Number: 21K18234
• Research Category: Grant-in-Aid for Challenging Research (Pioneering)
• Allocation Type: Multi-year Fund
• Review Section: Medium-sized Section 43:Biology at molecular to cellular levels, and related fields
• Research Institution: Hiroshima University
• Principal Investigator: 楯 真一 広島大学, 統合生命科学研究科(理), 教授 (20216998)
• Co-Investigator(Kenkyū-buntansha): 粟津 暁紀 広島大学, 統合生命科学研究科(理), 准教授 (00448234)
• Project Period (FY): 2021-07-09 – 2025-03-31
• Project Status: Granted (Fiscal Year 2023)
• Budget Amount: ¥26,000,000 (Direct Cost: ¥20,000,000、Indirect Cost: ¥6,000,000); Fiscal Year 2024: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000); Fiscal Year 2023: ¥7,280,000 (Direct Cost: ¥5,600,000、Indirect Cost: ¥1,680,000); Fiscal Year 2022: ¥6,760,000 (Direct Cost: ¥5,200,000、Indirect Cost: ¥1,560,000); Fiscal Year 2021: ¥6,760,000 (Direct Cost: ¥5,200,000、Indirect Cost: ¥1,560,000)
• Keywords: 核内クロマチン構造 / 電子顕微鏡 / 数理モデル / 分裂酵母

Outline of Research at the Start

FIB-SEMを用いた核内クロマチン構造の3次元電子顕微鏡像観測，基準点となるスピンドル極体(SPB)と標的とする遺伝子座に蛍光タンパク質で標識導入した分裂酵母を対象に，核内での遺伝子座の動態計測を共焦点顕微鏡で行う．2つの計測データをもとに，粗視化モデルとして核内クロマチン構造・動態を表現する数理モデルを構築する．構築する数理モデルを用いて，核内クロマチン構造・動態をシミュレートすることにより，核内クロマチン高次構造の遺伝情報制御における役割を解明する．

Outline of Annual Research Achievements

133箇所の遺伝子座に蛍光標識を導入して観測した時分割クロマチン構造動態データにHi-Cのデータを加えて分裂酵母核内クロマチンの動的構造モデルを完成した．当初のボトムアップモデルのみでは限界があるために，Hi-Cデータとの併用を導入した．導入には，理研・新海博士が開発したPHi-C法を用いた．
PHi-C法では，Hi-Cデータ（データはパブリックデータを利用）からは，遺伝子座間のコンタクト確率を基にして，SPBから蛍光標識した各遺伝子座の距離の揺らぎをの振幅に対応するパラメータを計算できる．PHi-Cから計算で得られたた遺伝子座のSPBからの距離の平均値およびその揺らぎ幅を時分割蛍光顕微鏡像から得られたデータと比較したところ，3つの染色体術全てに対して実験データを極めて良好に再現できること分かった．このことは，PHi-Cで構築したクロマチン構造・動態モデルが，核内クロマチン構造を記述する上で十分に実験情報を再現する有効なモデルになることを示している．
さらに，PHi-C法からは，各遺伝子座周辺のクロマチン構造の構造柔軟性に相当するパラメーターを抽出することができる．このパラメーターは，標識した遺伝子座のSPBからのmean-square-deviation(MSD)の時間発展を再現することができる．現時点では，観測データに残るノイズのために，完全にはMSDを再現することができていないが，観測データに残るノイズの原因（主としてSPBの揺動に由来することは分かっている）を除くことで，PHi-C解析により各遺伝子座のMSDも正確に再現できることを実証する．
残る期間では，各遺伝子座のMSDをより精密に再現することにより核内クロマチン構造・動態モデルの完成度を高めてゆく．

Current Status of Research Progress

1: Research has progressed more than it was originally planned.

Reason

133箇所の遺伝子座の動態データからボトムアップ的にクロマチン構造を構築するには，情報が不十分であり，電子顕微鏡像を解析するに十分な精度のクロマチン構造・動態モデルを構築することが困難であった．理研・新海博士のPHi-C法の用いてHi-Cデータの導入に成功することで，これまでの問題点を解決して，高精度のクロマチン構造・動態モデルをほぼ完成させることができた．
遺伝子座間の距離の変動データ等，補足となるデータも集積しているために，PHi-C法をもとに作り揚げた構造動態モデルに対して，遺伝子座間の動態データをも情報として加えることでよりモデルの精度を上げることができる．

Strategy for Future Research Activity

遺伝子座間の距離の時間変動データなど，SPBからの距離変動以外のデータも取り入れてPHi-c法によるクロマチン構造動態モデルの精度を向上させ，より完成度の高いクロマチン構造動態モデルを完成させる．
構築したクロマチン構造動態モデルをもとに，3Ｄ電子顕微鏡の解析を行い，クロマチン構造の3次元像の解明を実現する．

Research Products

• [Int'l Joint Research] ＮＩＨ(米国)
• [Int'l Joint Research] Seoul National University/UNIST Central Research Facilities(韓国)
• [Int'l Joint Research] University of Padova(イタリア)
• [Int'l Joint Research] National Institute of Health (NIH)(米国)
• [Int'l Joint Research] Seoul National University/UNIST Central Research Facilities(韓国)
• [Int'l Joint Research] University of Padova(イタリア)
• [Int'l Joint Research] National Institute of Health (NIH)(米国)
• [Journal Article] Quantitative prediction of rice starch digestibility using Raman spectroscopy and multivariate calibration analysis (2024)
  • Author(s): Ichinose Junya、Oba Kenji、Arase Yuya、Kaneshiro Junichi、Tate Shin-ichi、Watanabe Tomonobu M
  • Journal Title: Food Chemistry Volume: 435 Pages: 137505-137505
  • DOI: 10.1016/j.foodchem.2023.137505
  • Peer Reviewed
• [Journal Article] Possibilities of skin coat color‐dependent risks and risk factors of squamous cell carcinoma and deafness of domestic cats inferred via RNA‐seq data (2023)
  • Author(s): Awazu Akinori、Takemoto Daigo、Watanabe Kaichi、Sakamoto Naoaki
  • Journal Title: Genes to Cells Volume: 28 Issue: 12 Pages: 893-905
  • DOI: 10.1111/gtc.13076
  • Peer Reviewed / Open Access
• [Journal Article] The crucial role of CTCF in mitotic progression during early development of sea urchin (2023)
  • Author(s): Watanabe Kaichi、Fujita Megumi、Okamoto Kazuko、Yoshioka Hajime、Moriwaki Miki、Tagashira Hideki、Awazu Akinori、Yamamoto Takashi、Sakamoto Naoaki
  • Journal Title: Development, Growth and Differentiation Volume: 65 Issue: 7 Pages: 395-407
  • DOI: 10.1111/dgd.12875
  • Peer Reviewed
• [Journal Article] Mathematical model of structural changes in nuclear speckle (2023)
  • Author(s): Wakao, S., Saitoh, N., Awazu, A.
  • Journal Title: Biophysics and Physicobiology Volume: 20 Issue: 2 Pages: n/a
  • DOI: 10.2142/biophysico.bppb-v20.0020
  • ISSN: 2189-4779
  • Peer Reviewed / Open Access
• [Journal Article] Formation of Small-World Network Containing Module Networks in Globally and Locally Coupled Map System with Changes in Global Connection with Time Delay Effects (2023)
  • Author(s): Nakanishi Taito、Awazu Akinori
  • Journal Title: Journal of the Physical Society of Japan Volume: 92 Issue: 3 Pages: 034801-034801
  • DOI: 10.7566/jpsj.92.034801
  • Peer Reviewed / Open Access
• [Journal Article] Identification of aberrant transcription termination at specific gene loci with DNA hypomethylated transcription termination sites caused by DNA methyltransferase deficiency (2022)
  • Author(s): Masaki Shirai, Takuya Nara, Haruko Takahashi, Kazuya Takayama, Yuan Chen, Yudai Hirose, Masashi Fujii, Akinori Awazu, Nobuyoshi Shimoda, and Yutaka Kikuchi
  • Journal Title: Genes & Genetic Systems Volume: 97 Issue: 3 Pages: 139-152
  • DOI: 10.1266/ggs.21-00092
  • ISSN: 1341-7568, 1880-5779
  • Year and Date: 2022-06-01
  • Peer Reviewed / Open Access
• [Journal Article] Valosin‐containing protein (VCP) regulates the stability of fused in sarcoma (FUS) granules in cells by changing ATP concentrations (2022)
  • Author(s): Yasuda Kyota、Watanabe Tomonobu M.、Kang Myeong‐Gyun、Seo Jeong Kon、Rhee Hyun‐Woo、Tate Shin‐ichi
  • Journal Title: FEBS Letters Volume: - Issue: 11 Pages: 1412-1423
  • DOI: 10.1002/1873-3468.14353
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Identification of embryonic RNA granules that act as sites of mRNA translation after changing their physical properties (2022)
  • Author(s): Sato Keisuke、Sakai Moeko、Ishii Anna、Maehata Kaori、Takada Yuki、Yasuda Kyota、Kotani Tomoya
  • Journal Title: iScience Volume: 25 Issue: 6 Pages: 104344-104344
  • DOI: 10.1016/j.isci.2022.104344
  • Peer Reviewed / Open Access
• [Journal Article] FUS液液相分離の機能と細胞内相分離制御機構 (2022)
  • Author(s): 安田恭大，楯 真一
  • Journal Title: 細胞 Volume: 54 Pages: 448-451
• [Journal Article] Epigenetic-structural changes in X chromosomes promote Xic pairing during early differentiation of mouse embryonic stem cells (2022)
  • Author(s): Komoto Tetsushi、Fujii Masashi、Awazu Akinori
  • Journal Title: Biophysics and Physicobiology Volume: 19 Issue: 0 Pages: n/a
  • DOI: 10.2142/biophysico.bppb-v19.0018
  • ISSN: 2189-4779
  • Peer Reviewed / Open Access
• [Journal Article] Molecular dynamics analysis of biomolecular systems including nucleic acids (2022)
  • Author(s): Kameda Takeru、Awazu Akinori、Togashi Yuichi
  • Journal Title: Biophysics and Physicobiology Volume: 19 Issue: 0 Pages: n/a
  • DOI: 10.2142/biophysico.bppb-v19.0027
  • ISSN: 2189-4779
  • Peer Reviewed / Open Access
• [Journal Article] Mathematical model of chromosomal dynamics during DNA double strand break repair in budding yeast (2022)
  • Author(s): Nakahata Shinjiro、Komoto Tetsushi、Fujii Masashi、Awazu Akinori
  • Journal Title: Biophysics and Physicobiology Volume: 19 Issue: 0 Pages: n/a
  • DOI: 10.2142/biophysico.bppb-v19.0012
  • ISSN: 2189-4779
  • Peer Reviewed / Open Access
• [Journal Article] Partial exogastrulation due to apical-basal polarity of F‐actin distribution disruption in sea urchin embryo by omeprazole (2022)
  • Author(s): Watanabe Kaichi、Yasui Yuhei、Kurose Yuta、Fujii Masashi、Yamamoto Takashi、Sakamoto Naoaki、Awazu Akinori
  • Journal Title: Genes to Cells Volume: - Issue: 6 Pages: 1-17
  • DOI: 10.1111/gtc.12934
  • Peer Reviewed / Open Access
• [Journal Article] Ribosomal protein L5 facilitates rDNA-bundled condensate and nucleolar assembly (2022)
  • Author(s): Matsumori Haruka、Watanabe Kenji、Tachiwana Hiroaki、Fujita Tomoko、Ito Yuma、Tokunaga Makio、Sakata-Sogawa Kumiko、Osakada Hiroko、Haraguchi Tokuko、Awazu Akinori、Ochiai Hiroshi、Sakata Yuka、Ochiai Koji、Toki Tsutomu、Ito Etsuro、Goldberg Ilya G、Tokunaga Kazuaki、Nakao Mitsuyoshi、Saitoh Noriko
  • Journal Title: Life Science Alliance Volume: 5 Issue: 7 Pages: 1-18
  • DOI: 10.26508/lsa.202101045
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Self-Organization of Diverse Directional Hierarchical Networks in Simple Coupled Maps with Connection Changes (2022)
  • Author(s): Nakanishi Taito、Fujii Masashi、Awazu Akinori
  • Journal Title: Journal of the Physical Society of Japan Volume: 91 Issue: 2 Pages: 023801-023801
  • DOI: 10.7566/jpsj.91.023801
  • NAID: 210000159588
  • Peer Reviewed / Open Access
• [Journal Article] Path ensembles for Pin1-catalyzed cis-trans isomerization of a substrate calculated by weighted ensemble simulations (2021)
  • Author(s): Kei Moritsugu, Norifumi Yamamoto, Yasushige Yonezawa, Shin-ichi Tate, and Hiroshi Fujisaki
  • Journal Title: Journal of Chemical Theory and Computation Volume: 17 Issue: 4 Pages: 2522-2529
  • DOI: 10.1021/acs.jctc.0c01280
  • Peer Reviewed
• [Journal Article] Hepta-Histidine Inhibits Tau Aggregation (2021)
  • Author(s): Kondo Kanoh、Ikura Teikichi、Tanaka Hikari、Fujita Kyota、Takayama Sumire、Yoshioka Yuki、Tagawa Kazuhiko、Homma Hidenori、Liu Su、Kawasaki Ryosuke、Huang Yong、Ito Nobutoshi、Tate Shin-ichi、Okazawa Hitoshi
  • Journal Title: ACS Chemical Neuroscience Volume: 12 Issue: 16 Pages: 3015-3027
  • DOI: 10.1021/acschemneuro.1c00164
  • Peer Reviewed / Open Access
• [Journal Article] Ultrasensitive Nucleosome Binding Regulation Mediated by Intrinsically Disordered Regions (2021)
  • Author(s): TATE Shin-ichi
  • Journal Title: Seibutsu Butsuri Volume: 61 Issue: 5 Pages: 312-315
  • DOI: 10.2142/biophys.61.312
  • NAID: 130008093155
  • ISSN: 0582-4052, 1347-4219
  • Peer Reviewed / Open Access
• [Presentation] Spatio-temporal control of biomolecular condensation and the invovlment of amino acid chrality in it (2024)
  • Author(s): Kyota Yasuda, Rina Mihara, Hyun-woo Rhee, Shin-ichi Tate
  • Organizer: WPI-SKCM2 Spring Symposium
  • Invited
• [Presentation] Time-resolved proteomics of stress granules to identify key regulatory proteins to be expplored by NMR (2024)
  • Author(s): Miyu Murata, Kyota Yasuda, Hyun-woo Rhee, Shin-ichi Tate
  • Organizer: Taiwan-Japan NMR symposium
  • Int'l Joint Research
• [Presentation] Regulatory plays of intrinsically disordered regions (IDRs) in proteins revealed by NMR with multimodal approaches (2023)
  • Author(s): Shin-ichi Tate
  • Organizer: The 10th Asia-Pacific NMR Symposium 2023
  • Int'l Joint Research / Invited
• [Presentation] Spatio-temporal control of biomolecular condensation and its association to the human disease (2023)
  • Author(s): Kyota Yasuda, Rina Mihara, Hyun-woo Rhee, Shin-ichi Tate
  • Organizer: Mathematical and life science program symposium
  • Invited
• [Presentation] Structure biology on unstructured proteins - how the intrinsically disordered proteins (IDPs) work (2023)
  • Author(s): Shin-ichi Tate
  • Organizer: Mathematical and life science program symposium
  • Invited
• [Presentation] Protein condensates and their relevance to neurodegenerative disease as knotty social problems (2023)
  • Author(s): Shin-ichi Tate
  • Organizer: WPI-SKCM2 Poland Symposium
  • Int'l Joint Research / Invited
• [Presentation] Spatio-Temporal Control of Biomolecular Condensation and the Role of Amino Acid Chirality (2023)
  • Author(s): Kyota Yasuda, Rina Mihara, Hyun-woo Rhee, Shin-ichi Tate
  • Organizer: WPI-SKCM2 Winter School Lecture
  • Invited
• [Presentation] Identify and functional analysis of factors for stress granule-disassembly via Interactome analysis (2023)
  • Author(s): Miyu Murata, Kyota Yasuda, Hyun-woo Rhee, Shin-ichi Tate
  • Organizer: The 46th Annual Meeting of the Molecular Biology Society of Japan
• [Presentation] Proximity labeling identified a protein essential for the proper formation and function of stress granule (2023)
  • Author(s): Kyota Yasuda, Rina Mihara, Hyun-woo Rhee, Shin-ichi Tate
  • Organizer: The 46th Annual Meeting of the Molecular Biology Society of Japan
• [Presentation] Proximity labeling identified a protein essential for the proper formation and function of stress granule (2023)
  • Author(s): Kyota Yasuda, Rina Mihara, Hyun-woo Rhee, Shin-ichi Tate
  • Organizer: The 61st Annual Meeting of the Biophysical Society of Japan
• [Presentation] Exploring the mechanism to explain the difference in protein liquid-liquid phase separation (LLPS) processes between in vitro and in cells (2023)
  • Author(s): Hitomi Kimura, Kyota Yasuda, Natsumi Tane, Shin-ichi Tate
  • Organizer: The 61st Annual Meeting of the Biophysical Society of Japan
• [Presentation] Structure dynamics of intrinsically disordered proteind (IDPs) and their biological roles (2022)
  • Author(s): Shin-ichi Tate
  • Organizer: The 7th International Symposium on Drug Discovery and Design by NMR
  • Int'l Joint Research / Invited
• [Presentation] NMRによる天然変性タンパク質の構造ダイナミクスと昨日との相関解析 (2022)
  • Author(s): 楯 真一
  • Organizer: 広島大学統合生命科学研究科シンポジウム「分子原子レベルの統合生命科学研究」
  • Invited
• [Presentation] Exogastrulation due to cytoskeletal polarity distribution in sea urchin embryo (2022)
  • Author(s): Kaichi Watanabe, Yuhei Yasui, Yuta Kurose, Naoaki Sakamoto, Akinori Awazu
  • Organizer: The 60th Annual Meeting of the Biophysical Society of Japan
• [Presentation] Epigenetic-structural changes in X chromosomes promote Xic pairing during early differentiation process from embryonic stem cell of mouse (2022)
  • Author(s): Tetsushi Komoto, Masashi Fujii, Akinori Awazu
  • Organizer: The 60th Annual Meeting of the Biophysical Society of Japan
• [Presentation] Simulations of structural dynamics of nuclear speckle (2022)
  • Author(s): Shingo Wakao, Masashi Fuji, Akinori Awazu
  • Organizer: The 60th Annual Meeting of the Biophysical Society of Japan
• [Presentation] Chirality Disruption in Protein Dynamics (2021)
  • Author(s): Shin-ichi Tate
  • Organizer: Molecular Chirality 2021
  • Invited
• [Presentation] ウニにおける H+/K+イオンポンプ活性は胚の細胞骨格分布極性を高めて原腸形成を促進させる (2021)
  • Author(s): 渡辺 開智, 安井 優平, 黒瀬 友太, 坂本 尚昭, 粟津 暁紀
  • Organizer: 第59回日本生物物理学会年会
• [Presentation] 核スペックルの構造形成・動態のシミュレーション (2021)
  • Author(s): 若尾 真吾, 藤井 雅史, 粟津 暁紀
  • Organizer: 第59回日本生物物理学会年会
• [Presentation] 空間的局所相互作用を伴う動的・可塑的ネットワーク系の自発的構造形成 (2021)
  • Author(s): 中西 大斗, 藤井 雅史, 粟津 暁紀
  • Organizer: 第59回日本生物物理学会年会
• [Presentation] 出芽酵母の DNA 二本鎖切断時における染色体動態の数理モデル (2021)
  • Author(s): 中畑 伸児郎, 藤井 雅史, 粟津 暁紀
  • Organizer: 第59回日本生物物理学会年会
• [Presentation] ES 細胞のクロマチンドメイン変化による染色体動態制御のモデル (2021)
  • Author(s): 小本 哲史, 藤井 雅史, 粟津 暁紀
  • Organizer: 第59回日本生物物理学会年会
• [Remarks] Shin-ichi Tate Lab.
  • URL: https://www.mls.sci.hiroshima-u.ac.jp/biophys/index.html
• [Remarks] Awazu Lab.
  • URL: http://www.math.sci.hiroshima-u.ac.jp/awa/
• [Remarks]
  • URL: https://www.mls.sci.hiroshima-u.ac.jp/biophys/index.html
• [Remarks] Molecular Biophysics Laboratory
• [Funded Workshop] Taiwan-Japan NMR Symposium (2024)