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Long-term chromatin memory and environmental response

Planned Research

Project AreaIntegrative system of autonomous environmental signal recognition and memorization for plant plasticity
Project/Area Number 15H05963
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionThe University of Tokyo (2016-2019)
National Institute of Genetics (2015)

Principal Investigator

Kakutani Tetsuji  東京大学, 大学院理学系研究科(理学部), 教授 (20332174)

Project Period (FY) 2015-06-29 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥84,760,000 (Direct Cost: ¥65,200,000、Indirect Cost: ¥19,560,000)
Fiscal Year 2019: ¥20,800,000 (Direct Cost: ¥16,000,000、Indirect Cost: ¥4,800,000)
Fiscal Year 2018: ¥20,930,000 (Direct Cost: ¥16,100,000、Indirect Cost: ¥4,830,000)
Fiscal Year 2017: ¥18,590,000 (Direct Cost: ¥14,300,000、Indirect Cost: ¥4,290,000)
Fiscal Year 2016: ¥13,910,000 (Direct Cost: ¥10,700,000、Indirect Cost: ¥3,210,000)
Fiscal Year 2015: ¥10,530,000 (Direct Cost: ¥8,100,000、Indirect Cost: ¥2,430,000)
Keywordsヒストン修飾 / 環境応答 / ヒストンバリアント / DNAメチル化 / 非コードRNA / エピゲノム / エピジェネティクス / 維持メチル化 / ヒストン
Outline of Final Research Achievements

Reflecting environmental conditions, ON/OFF states of gene activity are memorized on chromatin in the forms of DNA and histone modifications. These modifications are found in both promoters in internal regions of genes (gene bodies), but role of gene body modifications remains largely unexplored. We examined factors controlling gene body modifications by genetic approaches. Arabidopsis mutations of the histone demethylase gene IBM1 induces accumulation of silent mark H3K9me (methylation of histone H3 lysine 9) in gene bodies as well as developmental abnormalities and defense responses. Genetic screening of suppressor of the ibm1 mutation identified another histone demethylase gene LDL2. LDL2 mediates developmental abnormalities through removal of H3K4me1. A related H3K4 demethylase FLD mediates memory of cold by removing H3K4me1 around transcription terminations sites; and this is co-opted from the global mechanism to control bidirectional transcription.

Academic Significance and Societal Importance of the Research Achievements

植物にとって、病原応答性の記憶や季節応答性の記憶は重要であるが、その機構は大部分が未開拓である。本研究では、良く研究されているプロモーター付近でなく、遺伝子内部の修飾と表現型とのつながりを遺伝学的に調べることにより、転写状態の長期記憶に関わるヒストン脱メチル化因子の役割と制御を明らかにした。

Report

(6 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • Research Products

    (46 results)

All 2019 2018 2017 2016 2015

All Journal Article (10 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 10 results,  Open Access: 7 results,  Acknowledgement Compliant: 1 results) Presentation (36 results) (of which Int'l Joint Research: 8 results,  Invited: 7 results)

  • [Journal Article] Histone acetylation orchestrates wound-induced transcriptional activation and cellular reprogramming in Arabidopsis2019

    • Author(s)
      Rymen Bart、Kawamura Ayako、Lambolez Alice、Inagaki Soichi、Takebayashi Arika、Iwase Akira、Sakamoto Yuki、Sako Kaori、Favero David S.、Ikeuchi Momoko、Suzuki Takamasa、Seki Motoaki、Kakutani Tetsuji、Roudier Fran?ois、Sugimoto Keiko
    • Journal Title

      Communications Biology

      Volume: 2 Issue: 1 Pages: 404-404

    • DOI

      10.1038/s42003-019-0646-5

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Seasonal Stability and Dynamics of DNA Methylation in Plants in a Natural Environment2019

    • Author(s)
      Ito、Nishio、Tarutani、Emura、Honjo、Toyoda、Fujiyama、Kakutani、Kudoh
    • Journal Title

      Genes

      Volume: 10 Issue: 7 Pages: 544-544

    • DOI

      10.3390/genes10070544

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genome defense against integrated organellar DNA fragments from plastids into plant nuclear genomes through DNA methylation2019

    • Author(s)
      Yoshida Takanori、Furihata Hazuka Y.、To Taiko Kim、Kakutani Tetsuji、Kawabe Akira
    • Journal Title

      Scientific Reports

      Volume: 9 Issue: 1 Pages: 2060-2060

    • DOI

      10.1038/s41598-019-38607-6

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Primed histone demethylation regulates shoot regenerative competency.2019

    • Author(s)
      Ishihara H, Sugimoto K, Tarr PT, Temman H, Kadokura S, Inui Y, Sakamoto T, Sasaki T, Aida M, Suzuki T, Inagaki S, Morohashi K, Seki M, Kakutani T, Meyerowitz EM, Matsunaga S.
    • Journal Title

      Nat Commun

      Volume: 16 Issue: 1 Pages: 1786-1786

    • DOI

      10.1038/s41467-019-09386-5

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] DNA Methylation Diversification at the Integrated Organellar DNA-Like Sequence2018

    • Author(s)
      Yoshida Takanori、Tarutani Yoshiaki、Kakutani Tetsuji、Kawabe Akira
    • Journal Title

      Genes

      Volume: 9 Issue: 12 Pages: 602-602

    • DOI

      10.3390/genes9120602

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Transposable elements, genome evolution and transgenerational epigenetic variation.2018

    • Author(s)
      Hosaka, A., and Kakutani, T.
    • Journal Title

      Curr Opin Genet Dev.

      Volume: 49 Pages: 43-48

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Transposable elements, genome evolution and transgenerational epigenetic variation2018

    • Author(s)
      Hosaka, A., Kakutani, T.
    • Journal Title

      Current Opinion in Genetics & Development

      Volume: 49 Pages: 43-48

    • DOI

      10.1016/j.gde.2018.02.012

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Gene-body chromatin modification dynamics mediate epigenome differentiation in Arabidopsis.2017

    • Author(s)
      Inagaki S., Takahashi M., Hosaka A., Ito T., Toyoda A., Fujiyama A., Tarutani Y., and Kakutani T.
    • Journal Title

      EMBO J

      Volume: 36 Issue: 8 Pages: 970-980

    • DOI

      10.15252/embj.201694983

    • Related Report
      2017 Annual Research Report 2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Evolution of sequence-specific anti-silencing systems in Arabidopsis2017

    • Author(s)
      Hosaka Aoi、Saito Raku、Takashima Kazuya、Sasaki Taku、Fu Yu、Kawabe Akira、Ito Tasuku、Toyoda Atsushi、Fujiyama Asao、Tarutani Yoshiaki、Kakutani Tetsuji
    • Journal Title

      Nature Communications

      Volume: 8 Issue: 1 Pages: 2161-2161

    • DOI

      10.1038/s41467-017-02150-7

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A stress-Activated Transposon in Arabidopsis Induces transgenerational Abscisic Acid Insensitivity. Scientific Reports.2016

    • Author(s)
      Ito H, Kim JM, Matsunaga W, Saze H, Matsui A, Endo TA, Harukawa Y, Takagi H, Yaegashi H, Masuta Y, Masuda S, Ishida J, Tanaka M, Takahashi S, Morosawa T, Toyoda T, Kakutani T, Kato A, Seki M.
    • Journal Title

      Scientific Reports

      Volume: 6, Article number: 23181 Issue: 1 Pages: 1-12

    • DOI

      10.1038/srep23181

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] 遺伝子内ヒストン修飾によるエピゲノム分化制御2019

    • Author(s)
      角谷徹仁
    • Organizer
      日本細胞生物学会第71回大会ワークショップ「染色体のホメオスタティック制御システム」
    • Related Report
      2019 Annual Research Report
  • [Presentation] Control of convergently transcribed genes through modulating gene-body chromatin modification2019

    • Author(s)
      稲垣宗一
    • Organizer
      "Epigenetics"Gordon Research Conference
    • Related Report
      2019 Annual Research Report
  • [Presentation] セントロメア特異的に転移するレトロトランスポゾンTal1の挿入領域のロングリードシーケンスによる解析2019

    • Author(s)
      塚原小百合、加藤夏恵、河邊昭、豊田敦、角谷徹仁
    • Organizer
      日本遺伝学会第91回大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] トランスポゾンの遺伝子コード領域および非コード領域におけるヘテロクロマチンの消失とその継世代的回復2019

    • Author(s)
      藤泰子、西澤優一郎、稲垣宗一、樽谷芳明、富永さとみ、加藤夏恵、高橋まゆみ、高嶋和哉、豊田敦、藤山秋佐夫、角谷徹仁
    • Organizer
      日本遺伝学会第91回大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 遺伝子内クロマチン修飾によるコンバージェント遺伝子の転写制御2019

    • Author(s)
      稲垣宗一、高橋まゆみ、高嶋和哉、角谷徹仁
    • Organizer
      日本遺伝学会第91回大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] シロイヌナズナPaf1C変異体における遺伝子内クロマチン修飾の解析2019

    • Author(s)
      森秀世、大矢恵代、稲垣宗一、角谷徹仁
    • Organizer
      日本遺伝学会第91回大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Control of convergently transcribed genes through modulating gene-body chromatin modification2019

    • Author(s)
      稲垣宗一
    • Organizer
      新学術領域研究「環境記憶統合」第5回若手の会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Fantastic H3K4 methylases and where to find them2019

    • Author(s)
      大矢恵代
    • Organizer
      新学術領域研究「環境記憶統合」第5回若手の会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Analysis of the relaationship between ecquisition of environmental stress-induced memory and epigenetic changes in fission yeast.2019

    • Author(s)
      星野新
    • Organizer
      新学術領域研究「環境記憶統合」第5回若手の会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Analysis of repeats-targeted_de novo_integration of retrotransposons by PacBio sequencing2019

    • Author(s)
      塚原小百合、角谷徹仁
    • Organizer
      「先進ゲノム支援」2019年度拡大班会議
    • Related Report
      2019 Annual Research Report
  • [Presentation] The gene body H3K4mel dynamics mediate heterochromatin silencing2018

    • Author(s)
      Tetsuji Kakutani
    • Organizer
      CSHA meeting: Chromatin, Epigenetics & Transcription
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Evolution of sequence-specific anti-silencing DNA demethylation systems by transposon-encoded anti-silencing factor2018

    • Author(s)
      齋藤絡、角谷徹仁
    • Organizer
      CSHA meeting: Chromatin, Epigenetics & Transcription
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] トランスポゾンの抗抑制因子が備える標的特異性多様化機構2018

    • Author(s)
      斎藤絡
    • Organizer
      第12回日本エピジェネティクス研究会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Evolution of sequence-specific anti-silencing systems in Arabidopsis2018

    • Author(s)
      Tetsuji Kakutani
    • Organizer
      Annual meeting of Society for Molecular Biology and Evolution
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] シロイヌナズナにおけるヒストンバリアントH2A.ZとDNAメチル化の拮抗作用2018

    • Author(s)
      西澤優一郎、藤泰子、富永さやか、角谷徹仁
    • Organizer
      日本遺伝学会第90回大会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] シロイヌナズナのトランスポゾンVANDAL21の活性制御におけるRNAと抗抑制因子の拮抗的制御2018

    • Author(s)
      佐々木卓、加藤夏恵、樽谷芳明、角谷徹仁
    • Organizer
      日本遺伝学会第90回大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 分裂酵母を用いた遺伝子内クロマチン修飾動態制御の解析2018

    • Author(s)
      稲垣宗一、高畑信也、村上洋太、角谷徹仁
    • Organizer
      日本遺伝学会第90回大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] RNAi targets sequence-specific anti-silencing systems of DNA TE in Arabidopsis2018

    • Author(s)
      Tetsuji Kakutani
    • Organizer
      CSH meeting: Transposable Elements
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Evolution of sequence-specific anti-silencing systems in Arabidopsis2018

    • Author(s)
      Tetsuji Kakutani
    • Organizer
      International symposium of Plant Epi/Genetics
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 遺伝子内部のクロマチン修飾動態がシロイヌナズナのエピゲノム分化を仲介する2017

    • Author(s)
      稲垣宗一、高橋まゆみ、保坂碧、伊藤佑、豊田敦、藤山秋佐夫、樽谷芳明、角谷徹仁
    • Organizer
      第11回日本エピジェネティクス研究会
    • Related Report
      2017 Annual Research Report
  • [Presentation] シロイヌナズナの配列特異的抗抑制機構の早い進化2017

    • Author(s)
      保坂碧、斎藤絡、高嶋和哉、佐々木卓、樽谷芳明、角谷徹仁
    • Organizer
      第11回日本エピジェネティクス研究会
    • Related Report
      2017 Annual Research Report
  • [Presentation] トランスポゾンにコードされる抗抑制因子の特異性と多様性2017

    • Author(s)
      斎藤絡、佐々木卓、保坂碧、樽谷芳明、角谷徹仁
    • Organizer
      第11回日本エピジェネティクス研究会
    • Related Report
      2017 Annual Research Report
  • [Presentation] シロイヌナズナの配列特異的抗抑制系とその速い進化2017

    • Author(s)
      保坂碧, 斎藤絡、高嶋和哉、佐々木卓、樽谷芳明、角谷徹仁
    • Organizer
      日本遺伝学会第89回大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Evolution of sequence-specific anti-silencing system in Arabidopsis2017

    • Author(s)
      角谷徹仁
    • Organizer
      France・Japan Epigenetics workshop 2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] DNA methylation and trans-generational inheritance in plants2017

    • Author(s)
      角谷徹仁
    • Organizer
      Three Special Seminar
    • Related Report
      2017 Annual Research Report
  • [Presentation] 配列特異的抗抑制系の進化2017

    • Author(s)
      角谷徹仁
    • Organizer
      第40回日本分子生物学会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Rapid evolution of sequence-specific anti-silencing systems in Arabidopsis.2016

    • Author(s)
      T Kakitani
    • Organizer
      Cold Spring Harbor Meeting “Transposable Elements”
    • Place of Presentation
      Cold Spring Harbor, NY, USA
    • Year and Date
      2016-11-04
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] DNAメチル化消失の世代をこえた継承とその回復2016

    • Author(s)
      藤泰子、樽谷芳明、加藤夏絵、稲垣宗一、伊藤佑、高橋まゆみ、豊田敦、藤山秋佐夫、Vincent Colot、角谷徹仁
    • Organizer
      日本遺伝学会第88回大会
    • Place of Presentation
      日本大学国際関係学部(静岡県三島市)
    • Year and Date
      2016-09-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] 遺伝子内部のヒストン修飾動態がシロイヌナズナの遺伝子サイレンシングに関わる2016

    • Author(s)
      稲垣宗一、高橋まゆみ、角谷徹仁
    • Organizer
      日本遺伝学会第88回大会
    • Place of Presentation
      日本大学国際関係学部(静岡県三島市)
    • Year and Date
      2016-09-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] シロイヌナズナの配列特異的抗抑制系とその速い進化2016

    • Author(s)
      保坂碧、斎藤絡、高島和哉、佐々木卓、河辺昭、伊藤佑、豊田敦、藤山秋佐夫、樽谷芳明、角谷徹仁
    • Organizer
      日本遺伝学会第88回大会
    • Place of Presentation
      日本大学国際関係学部(静岡県三島市)
    • Year and Date
      2016-09-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] VANDAL属トランスポゾンがコードする抗抑制因子の特異性と多様性2016

    • Author(s)
      斎藤絡、高島和哉、樽谷芳明、角谷徹仁
    • Organizer
      日本遺伝学会第88回大会
    • Place of Presentation
      日本大学国際関係学部(静岡県三島市)
    • Year and Date
      2016-09-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] シロイヌナズナの転移因子VANDAL21の不活性化機構2016

    • Author(s)
      佐々木卓、樽谷芳明、角谷徹仁
    • Organizer
      日本遺伝学会第88回大会
    • Place of Presentation
      日本大学国際関係学部(静岡県三島市)
    • Year and Date
      2016-09-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] トランスポゾンによる配列特異的な抗抑制の進化2016

    • Author(s)
      斎藤絡
    • Organizer
      第57回植物生理学会
    • Place of Presentation
      岩手大学上田キャンパス(岩手県)
    • Year and Date
      2016-03-18
    • Related Report
      2015 Annual Research Report
  • [Presentation] Evolution of sequence-specific anti-silencing by transposable elements in Arabidopsis2016

    • Author(s)
      角谷徹仁
    • Organizer
      染色体OS-国際シンポジウム
    • Place of Presentation
      淡路夢舞台国際会議場(兵庫県)
    • Year and Date
      2016-03-02
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] シロイヌナズナのDNAメチル化とエピジェネティックな遺伝2015

    • Author(s)
      角谷徹仁
    • Organizer
      第38回日本分子生物学会
    • Place of Presentation
      神戸ポートアイランド(兵庫県)
    • Year and Date
      2015-12-01
    • Related Report
      2015 Annual Research Report
  • [Presentation] Genome-wide negative feedback system for transgenerational DNA methylation dynamics in Arabidopsis2015

    • Author(s)
      Tasuku Ito, Yoshiaki Tarutani, Taiko K.To, Kazuya Takashima, Hidetoshi Saze, Atsushi Toyoda, Asao Fujiyama, Tetsuji Kakutani
    • Organizer
      内藤コンファレンス2015
    • Place of Presentation
      シャトレーゼ ガトーキングダム 札幌(北海道)
    • Year and Date
      2015-09-16
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research

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Published: 2015-07-02   Modified: 2022-11-04  

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