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Prediction of the nuclear compartment dynamics during embryonic development by single-cell replication sequencing

Research Project

Project/Area Number 18K14681
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 43050:Genome biology-related
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Takahashi Saori  国立研究開発法人理化学研究所, 生命機能科学研究センター, 研究員 (80748856)

Project Period (FY) 2018-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2020: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2019: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2018: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
KeywordsDNA複製タイミング / 核内コンパートメント / 初期胚発生 / 1細胞解析 / ES細胞分化 / マウス初期胚発生 / scRepli-seq / 細胞分化 / 核内構造 / エピゲノム / 複製タイミング / シングルセル
Outline of Final Research Achievements

In this study, we predicted the nuclear compartment (3D genome organization) dynamics during mouse ES cell differentiation and early pre-implantation embryogenesis by single-cell DNA replication sequencing (scRepli-seq) analysis in a genome-wide manner. The results suggested that the nuclear compartment profiles changed gradually but uniformly within a differentiating population. The scRepli-seq analysis in early mouse embryos is still ongoing, but we have successfully established haplotype-resolved scRepli-seq analysis. We have also acquired scRepli-seq and scRNA-seq from the same single cell.

Academic Significance and Societal Importance of the Research Achievements

近年、ゲノム三次元構造の時系列変化の包括的な理解を目指す「4Dヌクレオーム」研究が国内外で注目されている。本研究では、我々が開発した1細胞全ゲノムDNA複製タイミング解析法(scRepli-seq法)を用いることで、1細胞レベルでマウスES細胞分化過程における核内コンパートメント変化の予測に成功した。また、初期胚発生過程での変化の様式も明らかに出来つつある。ゆえに、本研究は、生体外(in vitro)での細胞分化実験と生体(in vivo)の発生過程における4Dヌクレオームの共通点と差異を解明できるだけでなく、ゲノム三次元構造が規定する新たな生命現象を見出す可能性がある。

Report

(4 results)
  • 2020 Annual Research Report   Final Research Report ( PDF )
  • 2019 Research-status Report
  • 2018 Research-status Report
  • Research Products

    (14 results)

All 2021 2020 2019 2018

All Journal Article (8 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 7 results,  Open Access: 8 results) Presentation (5 results) (of which Int'l Joint Research: 1 results,  Invited: 2 results) Book (1 results)

  • [Journal Article] The Temporal Order of DNA Replication Shaped by Mammalian DNA Methyltransferases2021

    • Author(s)
      Takebayashi Shin-ichiro、Ryba Tyrone、Wimbish Kelsey、Hayakawa Takuya、Sakaue Morito、Kuriya Kenji、Takahashi Saori、Ogata Shin、Hiratani Ichiro、Okumura Katsuzumi、Okano Masaki、Ogata Masato
    • Journal Title

      Cells

      Volume: 10 Issue: 2 Pages: 266-266

    • DOI

      10.3390/cells10020266

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Dynamics of transcription-mediated conversion from euchromatin to facultative heterochromatin at the Xist promoter by Tsix2021

    • Author(s)
      Ohhata Tatsuya、Yamazawa Kazuki、Miura-Kamio Asuka、Takahashi Saori、Sakai Satoshi、Tamura Yuka、Uchida Chiharu、Kitagawa Kyoko、Niida Hiroyuki、Hiratani Ichiro、Kobayashi Hisato、Kimura Hiroshi、Wutz Anton、Kitagawa Masatoshi
    • Journal Title

      Cell Reports

      Volume: 34 Issue: 13 Pages: 108912-108912

    • DOI

      10.1016/j.celrep.2021.108912

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Mapping replication timing domains genome wide in single mammalian cells with single-cell DNA replication sequencing2020

    • Author(s)
      Miura Hisashi、Takahashi Saori、Shibata Takahiro、Nagao Koji、Obuse Chikashi、Okumura Katsuzumi、Ogata Masato、Hiratani Ichiro、Takebayashi Shin-ichiro
    • Journal Title

      Nature Protocols

      Volume: 15 Issue: 12 Pages: 4058-4100

    • DOI

      10.1038/s41596-020-0378-5

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Enhanced processivity of Dnmt1 by monoubiquitinated histone H32020

    • Author(s)
      Y. Mishima, L. Brueckner, S. Takahashi, T. Kawakami, J. Otani, A. Shinohara, K. Takeshita, R. G. Garvilles, M. Watanabe, N. Sakai, H. Takeshima, C. Nachtegael, A. Nishiyama, M. Nakanishi, K. Arita, K. Nakashima, H. Hojo, I. Suetake
    • Journal Title

      Genes Cells

      Volume: 25 Issue: 1 Pages: 22-32

    • DOI

      10.1111/gtc.12732

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Single-cell DNA Replication Profiling Identifies Spatiotemporal Developmental Dynamics of Chromosome Organization.2019

    • Author(s)
      Miura H, Takahashi S, Poonperm R, Tanigawa A, Takebayashi S I, and Hiratani I.
    • Journal Title

      Nature Genetics

      Volume: 51 Issue: 9 Pages: 1356-1368

    • DOI

      10.1038/s41588-019-0474-z

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] DNA replication timing enters the single-cell era2019

    • Author(s)
      Ichiro Hiratani and Saori Takahashi
    • Journal Title

      Genes

      Volume: 10 Issue: 3 Pages: 221-221

    • DOI

      10.3390/genes10030221

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genome-wide stability of the DNA replication program in single mammalian cells2019

    • Author(s)
      Saori Takahashi, Hisashi Miura, Takahiro Shibata, Koji Nagao, Katsuzumi Okumura, Masato Ogata, Chikashi Obuse, Shin-ichiro Takebayashi and Ichiro Hiratani
    • Journal Title

      Nature Genetics

      Volume: 51 Issue: 3 Pages: 529-540

    • DOI

      10.1038/s41588-019-0347-5

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Practical Analysis of Hi-C Data: Generating A/B Compartment Profiles2018

    • Author(s)
      Hisashi Miura, Rawin Poonperm, Saori Takahashi and Ichiro Hiratani
    • Journal Title

      Methods in Molecular Biology

      Volume: 1861 Pages: 221-245

    • DOI

      10.1007/978-1-4939-8766-5_16

    • ISBN
      9781493987658, 9781493987665
    • Related Report
      2018 Research-status Report
    • Open Access
  • [Presentation] Single-cell DNA replication sequencing and its application to studies of early mouse embryonic development2019

    • Author(s)
      Saori Takahashi, Hisashi Miura, Takahiro Shibata, Koji Nagao, Chikashi Obuse, Shin-ichiro Takebayashi and Ichiro Hiratani
    • Organizer
      第13回日本エピジェネティクス研究会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] 1細胞解析で明らかにされたDNA複製ドメインの細胞間の安定性と不均一性2019

    • Author(s)
      高橋沙央里,三浦尚,柴田隆豊,長尾恒治,小布施力史,竹林慎一郎,平谷伊智朗
    • Organizer
      第19回日本蛋白質科学会年会・第71回日本細胞生物学会大会合同年次大会
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] マウスES細胞分化および初期胚発生過程における1細胞全ゲノムDNA複製タイミング解析2019

    • Author(s)
      高橋沙央里,三浦尚,柴田隆豊,長尾恒治,小布施力史,竹林慎一郎,平谷伊智朗
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] Genome-wide single-cell DNA replication sequencing reveals cell-type specific signatures that are conserved from cell to cell2018

    • Author(s)
      Saori Takahashi, Hisashi Miura, Takahiro Shibata, Koji Nagao, Chikashi Obuse, Shin-ichiro Takebayashi and Ichiro Hiratani
    • Organizer
      EMBL Symposium: Principles of Chromosome Structure and Function
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] 分化前後のES細胞における複製ドメインは細胞間で極めて均一なプロファイルを示す2018

    • Author(s)
      高橋沙央里、三浦尚、柴田隆豊、長尾恒治、小布施力史、竹林慎一郎、平谷伊智朗
    • Organizer
      第12回日本エピジェネティクス研究会年会
    • Related Report
      2018 Research-status Report
  • [Book] 実験医学別冊・クロマチン解析実践プロトコール2020

    • Author(s)
      高橋沙央里、三浦尚、平谷伊智朗
    • Total Pages
      270
    • Publisher
      羊土社
    • ISBN
      9784758122481
    • Related Report
      2020 Annual Research Report

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Published: 2018-04-23   Modified: 2022-01-27  

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