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Mathematical study of transcriptional control by nuclear structures with non-coding DNA

Research Project

Project/Area Number 21K06124
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 43050:Genome biology-related
Research InstitutionHiroshima University

Principal Investigator

Awazu Akinori  広島大学, 統合生命科学研究科(理), 准教授 (00448234)

Co-Investigator(Kenkyū-buntansha) 坂本 尚昭  広島大学, 統合生命科学研究科(理), 准教授 (00332338)
上野 勝  広島大学, 統合生命科学研究科(先), 准教授 (90293597)
Project Period (FY) 2021-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2023: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2022: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2021: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Keywordsゲノム構造・動態 / エピゲノム / 核内構造体 / 遺伝子制御 / ウニ / イエネコ / 核スペックル / CTCF / X染色体対合形成 / 核小体 / DNA二本鎖切断修復 / 染色体動態 / ライブ観察 / 数理モデル
Outline of Research at the Start

本研究では、機能性非コードDNAがコアとなり形成される核内構造体の未知の機能、特に「分裂酵母核のセントロメア集団と核小体の規則的な大振幅振動 」、「ウニ胚細胞核のセントロメアの核膜上偏在と核小体の核中央偏在」が転写活性領域形成へ及ぼす寄与を、蛍光ライブ観察とデータ駆動型物理モデルより考察し、「核機能におけるセントロメアや核小体の「局在・動態」の役割」、「多細胞生物の核内構造体の細胞分化に伴う「役割の変化」」
を明らかにする。分裂酵母とウニ胚両者の核内動態の研究は、核大域的な転写制御系の普遍的な時空間設計原理を浮き彫りにする。

Outline of Final Research Achievements

In this study, we considered the structural-dynamical features of intra-nuclear structure of eukaryotes and their mechanisms, and clarified the following. 1) Regulation mechanism of nucleolus structure maintenance and dynamics, 2) Mechanism of changes in yeast nuclear genome structure upon DNA double-strand break, 3) Mechanism of X chromosome pairing formation associated with initiation of cell differentiation in female mouse ES cells, 4) Mechanism of changes in nuclear speckle structure depending on intracellular environment, 5) Function of sea urchin CTCF and evolutionary aspects of CTCF function in animals, 6) Characteristics of unique genomic sequence of domestic cat with white coat and its potential involvement in disease.

Academic Significance and Societal Importance of the Research Achievements

上記は全体として、生物の活動の基盤となる転写翻訳の制御機序に関するさらなる研究の進展を促進する成果である。特に (1)(4) の解明は、近年注目されている細胞内液滴群の研究に対し、知見を提供する。 また (2)(3)の解明は、発癌とも関連するDNA損傷修復、及び遺伝子量補償による正常な発生に関連した成果であり、ゲノム構造動態に基づく医療研究を促進する将来がある。(5)の解明は、分子機能の進化のみならず、ウニという資源生物に対する深い知見を提供している。そして(6)の解明は、ネコの獣医学研究の進展を促すものである。

Report

(4 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Research-status Report
  • 2021 Research-status Report
  • Research Products

    (20 results)

All 2023 2022

All Journal Article (10 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 10 results,  Open Access: 9 results) Presentation (10 results) (of which Int'l Joint Research: 4 results)

  • [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 data2023

    • 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

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The crucial role of CTCF in mitotic progression during early development of sea urchin2023

    • 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

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mathematical model of structural changes in nuclear speckle2023

    • 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
    • Related Report
      2023 Annual Research Report
    • 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 Effects2023

    • 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

    • Related Report
      2022 Research-status Report
    • 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 deficiency2022

    • 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
    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Epigenetic-structural changes in X chromosomes promote Xic pairing during early differentiation of mouse embryonic stem cells2022

    • 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
    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Mathematical model of chromosomal dynamics during DNA double strand break repair in budding yeast2022

    • 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
    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Partial exogastrulation due to apical-basal polarity of F‐actin distribution disruption in sea urchin embryo by omeprazole2022

    • 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

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Ribosomal protein L5 facilitates rDNA-bundled condensate and nucleolar assembly2022

    • 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

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Self-Organization of Diverse Directional Hierarchical Networks in Simple Coupled Maps with Connection Changes2022

    • 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

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] 培養細胞を用いた白いネコ特有のゲノムと疾患の解析2023

    • Author(s)
      渡邊 開智, 竹本 大悟, 坂本 尚昭, 粟津 暁紀
    • Organizer
      日本分子生物学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] リピート DNA 配列から染色体内および染色体間の動態の法則を探る2023

    • Author(s)
      奈良 拓也, 高橋 治子, 粟津 暁紀, 菊池 裕
    • Organizer
      日本分子生物学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] 遅発性アルツハイマー病の状態の多様性とその関連遺伝子群の解析2023

    • Author(s)
      本田 晃誠, 粟津 暁紀
    • Organizer
      日本分子生物学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] ウニFLVCR遺伝子機能解析とFLVCR遺伝子ノックアウト胚の表現型観察2023

    • Author(s)
      竹本 大悟, 三澤 祐太朗, 渡辺 開智, 坂本 尚昭, 粟津 暁紀
    • Organizer
      日本分子生物学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] ウニのCTCFは初期発生において分裂期の進行に必須である2023

    • Author(s)
      坂本 尚昭, 渡辺 開智, 藤田 恵, 岡本 和子, 吉岡 一, 森脇 三貴, 田頭 英樹, 粟津 暁紀, 山本 卓,
    • Organizer
      日本分子生物学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] ヒト染色体の細胞種普遍的・特異的な3次元構造を制御するゲノム領域の特徴2023

    • Author(s)
      原岡 郁弥, 粟津 暁紀
    • Organizer
      日本分子生物学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] A model of communication between individual organisms using dynamic-plastic coupled dynamical systems2023

    • Author(s)
      Haruto Nakata, Akinori Awazu
    • Organizer
      The 61st Annual Meeting of the Biophysical Society of Japan
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Exogastrulation due to cytoskeletal polarity distribution in sea urchin embryo2022

    • Author(s)
      Kaichi Watanabe, Yuhei Yasui, Yuta Kurose, Naoaki Sakamoto, Akinori Awazu
    • Organizer
      The 60th Annual Meeting of the Biophysical Society of Japan
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] Epigenetic-structural changes in X chromosomes promote Xic pairing during early differentiation process from embryonic stem cell of mouse2022

    • Author(s)
      Tetsushi Komoto, Masashi Fujii, Akinori Awazu
    • Organizer
      The 60th Annual Meeting of the Biophysical Society of Japan
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] Simulations of structural dynamics of nuclear speckle2022

    • Author(s)
      Shingo Wakao, Masashi Fuji, Akinori Awazu
    • Organizer
      The 60th Annual Meeting of the Biophysical Society of Japan
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research

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Published: 2021-04-28   Modified: 2025-01-30  

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