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Development of a translational correction method for resolutional improvement of nucleosome maps

Research Project

Project/Area Number 21K05505
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 38060:Applied molecular and cellular biology-related
Research InstitutionShimane University

Principal Investigator

Kato Hiroaki  島根大学, 学術研究院医学・看護学系, 准教授 (40548418)

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: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2022: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2021: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywordsヌクレオソーム / ヒストン / 転写 / エピジェネティクス / DNA / 転写開始点 / 並進補正 / マイクロコッカルヌクレアーゼ / ソフトウェア
Outline of Research at the Start

ヒストンタンパク質にDNAが巻きついたヌクレオソームコア粒子(NCP)は、エピジェネティクスの制御基盤として重要な役割を果たします。NCPはトランス因子と特定の空間的位置関係で相互作用すると考えられますが、細胞内の文脈でそれを理解するためには、ゲノム座標上でのNCP配置を厳密に把握する必要があります。本研究は、実験的に得られたNCPの位置情報をソフトウェアレベルで補正する手法の確立を目指します。

Outline of Final Research Achievements

By analyzing the digestion preference of micrococcal nuclease (MNase), we successfully extracted nucleosome positions of high accuracy from MNase-seq data sets. These nucleosomes exhibited a fine pattern of WW/SS dinucleotides, which is comparable to those determined by chemical mapping methods. Comparison of MNase-seq-based and chemical mapping-based nucleosomes revealed that even chemical mapping methods have histone mutant-specific cleavage biases. Analysis of genes with a hybrid chemical model suggested that +1 nucleosome DNA has a high affinity to histones especially in the promoter-proximal half. Transcription start sites determined by CAGE-seq were located in the promoter-proximal side of +1 nucleosome. Analysis of promoter sequences identified two types of TSS in yeast: one has adenine at -8 nucleotide position, and the other one that are related to the rotational setting of +1 nucleosomes.

Academic Significance and Societal Importance of the Research Achievements

今日、様々な生体分子の振る舞いは構造生物学によって高解像度に明らかにされつつある。ただし、その多くは人工的に再構成された複合体を対象としており、自然条件における実際の分子の振る舞いまで網羅することが難しい。例えばヌクレオソームの関わる再構成系では特別なDNA配列が使用される傾向があり、自然配列を網羅的に評価できないので、タンパク質複合体と自然DNA配列との関係性については謎に包まれている。
塩基対解像度でヌクレオソーム配置に関わるDNA配列の特徴を明らかにしようとする本研究は、自然配列を対象とする点で特徴的であり、構造生物学の不足を補う視点を提供できる。このため、今後の進展が期待される。

Report

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

    (14 results)

All 2024 2023 2022 2021 Other

All Int'l Joint Research (2 results) Journal Article (4 results) (of which Peer Reviewed: 4 results,  Open Access: 4 results) Presentation (5 results) (of which Invited: 1 results) Remarks (3 results)

  • [Int'l Joint Research] カンザス州立大学(米国)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] カンザス州立大学(米国)

    • Related Report
      2021 Research-status Report
  • [Journal Article] A budding yeast CAGE dataset comprising two cell types2024

    • Author(s)
      Kawakami Kei、Maeda Shin-ichi、Tanimoto Yoshiko、Shimizu Mitsuhiro、Kato Hiroaki
    • Journal Title

      Genes & Genetic Systems

      Volume: 99 Issue: 0 Pages: n/a

    • DOI

      10.1266/ggs.24-00020

    • ISSN
      1341-7568, 1880-5779
    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Kinetics of Anti-SARS-CoV-2 Antibody Response Following Two Doses of the BNT162b2 mRNA Vaccine: A Japanese Single-Center Primary Care Clinic Report Involving Volunteers and Patients with Autoimmune Disease2022

    • Author(s)
      Sugiura Tomoko、Sugiura Hiroaki、Kato Hiroaki、Nariai Yuko、Mizumoto Yuuki、Hanada Kozue、Takahashi Rieko、Hinotubo Yukari、Tanaka Naoko、Sasaki Mutsumi、Eguchi Haruki、Kamino Hiroki、Urano Takeshi
    • Journal Title

      Infectious Disease Reports

      Volume: 15 Issue: 1 Pages: 24-33

    • DOI

      10.3390/idr15010003

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Chemical map-based prediction of nucleosome positioning using the Bioconductor package nuCpos2021

    • Author(s)
      Kato Hiroaki、Shimizu Mitsuhiro、Urano Takeshi
    • Journal Title

      BMC Bioinformatics

      Volume: 22 Issue: 1 Pages: 322-322

    • DOI

      10.1186/s12859-021-04240-2

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Sequence-dependent nucleosome formation in trinucleotide repeats evaluated by in vivo chemical mapping2021

    • Author(s)
      Koji Katsumata, Yuichi Ichikawa, Tomohiro Fuse, Hitoshi Kurumizaka, Akio Yanagida , Takeshi Urano, Hiroaki Kato, Mitsuhiro Shimizu
    • Journal Title

      Biochem. Biophys. Res. Commun.

      Volume: 556 Pages: 179-184

    • DOI

      10.1016/j.bbrc.2021.03.155

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] タンパク質コード領域におけるヌクレオソーム配置とDNA配列の関係について2023

    • Author(s)
      加藤 太陽、清水 光弘、浦野 健
    • Organizer
      日本遺伝学会 第95回大会
    • Related Report
      2023 Annual Research Report
  • [Presentation] 転写と共役したエピゲノム維持に関する研究2023

    • Author(s)
      加藤太陽
    • Organizer
      日本遺伝学会 第95回大会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 自分でデータを解析したい2022

    • Author(s)
      加藤太陽
    • Organizer
      第94回日本遺伝学会大会
    • Related Report
      2022 Research-status Report
  • [Presentation] A chimeric chemical model revealed asymmetric DNA pattern in transcribed nucleosomes2022

    • Author(s)
      Kato H, Shimizu M, Urano T
    • Organizer
      The 30th Hot Spring Harbor International Symposium
    • Related Report
      2021 Research-status Report
  • [Presentation] ケミカルハイブリッドモデルによるヌクレオソーム配置予測2021

    • Author(s)
      加藤太陽、清水光弘、浦野健
    • Organizer
      第93回日本遺伝学会大会
    • Related Report
      2021 Research-status Report
  • [Remarks] researchmap

    • URL

      https://researchmap.jp/hrk_kato/

    • Related Report
      2023 Annual Research Report
  • [Remarks] 島根大学医学部病態生化学

    • URL

      http://www.shimane-med.ac.jp/biochem2/index.html

    • Related Report
      2021 Research-status Report
  • [Remarks] Researchmap

    • URL

      https://researchmap.jp/hrk_kato/

    • Related Report
      2021 Research-status Report

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

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