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Molecular dynamics of epigenomic transcriptional regulation by Klf4 in iPSC generation

Research Project

Project/Area Number 19H03203
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 43050:Genome biology-related
Research InstitutionUniversity of Tsukuba

Principal Investigator

Nishimura Ken  筑波大学, 医学医療系, 准教授 (80500610)

Co-Investigator(Kenkyū-buntansha) 福田 綾  筑波大学, 医学医療系, 准教授 (50436276)
久野 朗広  筑波大学, 医学医療系, 助教 (60830122)
林 洋平  国立研究開発法人理化学研究所, バイオリソース研究センター, チームリーダー (90780130)
Project Period (FY) 2019-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥17,290,000 (Direct Cost: ¥13,300,000、Indirect Cost: ¥3,990,000)
Fiscal Year 2021: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Fiscal Year 2020: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Fiscal Year 2019: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
KeywordsiPS細胞 / Klf4 / 転写制御 / エピジェネティクス / 転写因子 / 量依存性 / 多能性 / エピゲノム / 転写 / KLF4 / X染色体再活性化 / Nanog
Outline of Research at the Start

高い多能性を持つiPS細胞を誘導するためには、細胞をエピジェネティックに十分に初期化することが重要である。そこで本研究では、我々独自のPaused iPS細胞の持つ、Klf4量依存的にエピジェネティクス変化が停止した、iPS細胞誘導の中間体であるという特徴を活かし、それらに関わる分子の同定やメカニズム解析を行う。それによって、エピジェネティックな転写制御の分子機構を解明し、高い多能性を持つiPS細胞の誘導方法の確立に繋げる。

Outline of Final Research Achievements

Production of highly pluripotent iPS cells requires complete epigenetic reprogramming. So, we should understand molecular mechanism of whole genome epigenetic transcriptional regulation (epigenomic transcriptional regulation). Our paused iPSCs are epigenetic intermediates paused at different phase of iPSC generation according to Klf4 dose. We utilized these unique characteristics to mechanistic analyses of the Klf4-dose dependent epigenomic transcriptional regulation during reprogramming. We identified Kdm1a that negatively regulates the transcriptional regulation. Moreover, DNA binding capacity of Klf4 is important for chromatin structure changes, and an increase of these changes can enhance the epigenomic transcriptional regulation.

Academic Significance and Societal Importance of the Research Achievements

本研究成果は、高い多能性を獲得した高品質iPS細胞を効率良く誘導する方法の確立につながることが期待される。このような技術は、より安全なiPS細胞を用いた再生医療の実現に大きく貢献すると考えられる。またエピゲノム転写制御は、がん化や細胞分化といった他の生命現象にも深く関わり、それらを制御する方法の確立にもつながることから、大きな学術的、社会的意義があると思われる。

Report

(4 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • Research Products

    (21 results)

All 2022 2021 2020 2019 Other

All Journal Article (8 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 8 results,  Open Access: 6 results) Presentation (12 results) (of which Int'l Joint Research: 7 results,  Invited: 3 results) Remarks (1 results)

  • [Journal Article] Early reactivation of clustered genes on the inactive X chromosome during somatic cell reprogramming2022

    • Author(s)
      Aizawa Shiho、Nishimura Ken、Mondejar Gonzalo Seminario、Kumar Arun、Bui Phuong Linh、Tran Yen Thi Hai、Kuno Akihiro、Muratani Masafumi、Kobayashi Shin、Nabekura Tsukasa、Shibuya Akira、Sugihara Eiji、Sato Taka-Aki、Fukuda Aya、Hayashi Yohei、Hisatake Koji
    • Journal Title

      Stem Cell Reports

      Volume: 17 Issue: 1 Pages: 53-67

    • DOI

      10.1016/j.stemcr.2021.11.008

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structurally-discovered KLF4 variants accelerate and stabilize reprogramming to pluripotency2022

    • Author(s)
      Borisova Evgeniia、Nishimura Ken、An Yuri、Takami Miho、Li Jingyue、Song Dan、Matsuo-Takasaki Mami、Luijkx Dorian、Aizawa Shiho、Kuno Akihiro、Sugihara Eiji、Sato Taka-aki、Yumoto Fumiaki、Terada Tohru、Hisatake Koji、Hayashi Yohei
    • Journal Title

      iScience

      Volume: 25 Issue: 1 Pages: 103525-103525

    • DOI

      10.1016/j.isci.2021.103525

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Downregulation of Odd-Skipped Related 2, a Novel Regulator of Epithelial-Mesenchymal Transition, Enables Efficient Somatic Cell Reprogramming2022

    • Author(s)
      Anh Le Phuong Hoang、Nishimura Ken、Kuno Akihiro、Linh Nguyen Thuy、Kato Tetsuo、Ohtaka Manami、Nakanishi Mahito、Sugihara Eiji、Sato Taka-Aki、Hayashi Yohei、Fukuda Aya、Hisatake Koji
    • Journal Title

      Stem Cells

      Volume: 40 Issue: 4 Pages: 397-410

    • DOI

      10.1093/stmcls/sxac012

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Efficient Reprogramming of Canine Peripheral Blood Mononuclear Cells into Induced Pluripotent Stem Cells2021

    • Author(s)
      Kimura Kazuto、Tsukamoto Masaya、Tanaka Miyuu、Kuwamura Mitsuru、Ohtaka Manami、Nishimura Ken、Nakanishi Mahito、Sugiura Kikuya、Hatoya Shingo
    • Journal Title

      Stem Cells and Development

      Volume: 30 Issue: 2 Pages: 79-90

    • DOI

      10.1089/scd.2020.0084

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 4-Phenylbutyrate ameliorates apoptotic neural cell death in Down syndrome by reducing protein aggregates2020

    • Author(s)
      Hirata Katsuya、Nambara Toshihiko、Kawatani Keiji、Nawa Nobutoshi、Yoshimatsu Hidetaka、Kusakabe Haruna、Banno Kimihiko、Nishimura Ken、Ohtaka Manami、Nakanishi Mahito、Taniguchi Hidetoshi、Arahori Hitomi、Wada Kazuko、Ozono Keiichi、Kitabatake Yasuji
    • Journal Title

      Scientific Reports

      Volume: 10 Issue: 1 Pages: 14047-14047

    • DOI

      10.1038/s41598-020-70362-x

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Functional analysis of PTH1R variants found in primary failure of eruption.2020

    • Author(s)
      Izumida E, Suzawa T, Miyamoto Y, Yamada A, Takimoto R, Otsu M, Saito T, Yamaguchi T, Nishimura K, Ohtaka M, Nakanishi M, Yoshimura K, Sasa K, Takimoto R, Uyama R, Shirota T, Maki K, Kamijo R.
    • Journal Title

      Journal of Dental Research

      Volume: 99 Issue: 4 Pages: 429-436

    • DOI

      10.1177/0022034520901731

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Induction of Noonan syndrome-specific human-induced pluripotent stem cells under serum-, feeder-, and integration-free conditions2020

    • Author(s)
      Atsuko Hamada, Eri Akagi, Fumitaka Obayashi, Sachiko Yamasaki, Koichi Koizumi, Manami Ohtaka, Ken Nishimura, Mahito Nakanishi, Shigeaki Toratani & Tetsuji Okamoto
    • Journal Title

      In Vitro Cellular & Developmental Biology - Animal

      Volume: 56(10) Issue: 10 Pages: 888-895

    • DOI

      10.1007/s11626-020-00515-9

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Template Activating Factor-I α Regulates Retroviral Silencing during Reprogramming2019

    • Author(s)
      Bui Phuong Linh、Nishimura Ken、Seminario Mondejar Gonzalo、Kumar Arun、Aizawa Shiho、Murano Kensaku、Nagata Kyosuke、Hayashi Yohei、Fukuda Aya、Onuma Yasuko、Ito Yuzuru、Nakanishi Mahito、Hisatake Koji
    • Journal Title

      Cell Reports

      Volume: 29 Issue: 7 Pages: 1909-1922

    • DOI

      10.1016/j.celrep.2019.10.010

    • NAID

      120007127699

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] リプログラム因子のパイオニア因子としての機能と量依存性2022

    • Author(s)
      西村健、久野朗広、久武幸司
    • Organizer
      第21回日本再生医療学会総会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Application of iPS cells to regenerative medicine using novel gene transfer system2021

    • Author(s)
      Ken Nishimura
    • Organizer
      International Conference and Workshop on Global Trends in Health and Life Sciences
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Interleukin Enhancer Binding Factors 2 and 3 inhibit retrovirus expression2021

    • Author(s)
      Gonzalo SB, Bui PL, Nishimura K, Hisatake K
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Interleukin Enhancer Binding Factors 2 and 3 inhibit retrovirus expression2021

    • Author(s)
      Gonzalo SB, Nishimura K, Hisatake K
    • Organizer
      Tsukuba Conference 2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Mechanistic analysis of pluripotency acquisition by using paused iPSCs2021

    • Author(s)
      Hamzah M, Nishimura K, Hisatake K
    • Organizer
      Tsukuba Conference 2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Downregulation of Odd-Skipped Related 2, a Novel Regulator of Epithelial-Mesenchymal Transition, Enables Efficient Somatic Cell Reprogramming2021

    • Author(s)
      Nishimura K, Anh LPH, Linh NT, Kato T, Hisatake K
    • Organizer
      ISSCR2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] iPS細胞誘導におけるX染色体再活性化機構の解明2021

    • Author(s)
      相澤志穂、西村健、久武幸司
    • Organizer
      第20回日本再生医療学会総会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Paused iPS細胞を用いたKLF4量依存的エピジェネティクス制御機構の解析2021

    • Author(s)
      西村健、Arun Kumar、岸本拓実、久武幸司
    • Organizer
      第14回エピジェネティクス研究会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Reactivation of X chromosome might start from the identical region during mouse iPSC generation2020

    • Author(s)
      Aizawa S, Bui PL, Nishimura K, Hisatake K
    • Organizer
      ISSCR2020
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Analysis of KLF4 dose dependent iPSC generation in early stage of reprogramming2020

    • Author(s)
      Yamanaka T, Nishimura K, Hisatake K
    • Organizer
      TGSW2020
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Dose dependent transcriptional regulation of KLF42019

    • Author(s)
      Kumar BA, Nishimura K, Hisatake K
    • Organizer
      TC2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] PD imaging systemを用いて生きたまま幹細胞の多能性を定量的に解析する2019

    • Author(s)
      西村健、石渡裕、久武幸司
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Remarks] iPS細胞誘導時にレトロウイルスの遺伝子発現を抑制する新しい機構の発見

    • URL

      http://www.tsukuba.ac.jp/attention-research/p201911130100.html

    • Related Report
      2019 Annual Research Report

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Published: 2019-04-18   Modified: 2023-12-25  

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