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Characterization of repetitive sequences by epigenetic and epigenomic approaches

Research Project

Project/Area Number 22227001
Research Category

Grant-in-Aid for Scientific Research (S)

Allocation TypeSingle-year Grants
Research Field Genetics/Genome dynamics
Research InstitutionNational Institute of Genetics

Principal Investigator

KAKUTANI Tetsuji  国立遺伝学研究所, 総合遺伝研究系, 教授 (20332174)

Project Period (FY) 2010-05-31 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥138,710,000 (Direct Cost: ¥106,700,000、Indirect Cost: ¥32,010,000)
Fiscal Year 2014: ¥21,320,000 (Direct Cost: ¥16,400,000、Indirect Cost: ¥4,920,000)
Fiscal Year 2013: ¥32,500,000 (Direct Cost: ¥25,000,000、Indirect Cost: ¥7,500,000)
Fiscal Year 2012: ¥32,500,000 (Direct Cost: ¥25,000,000、Indirect Cost: ¥7,500,000)
Fiscal Year 2011: ¥31,460,000 (Direct Cost: ¥24,200,000、Indirect Cost: ¥7,260,000)
Fiscal Year 2010: ¥20,930,000 (Direct Cost: ¥16,100,000、Indirect Cost: ¥4,830,000)
Keywordsトランスポゾン / DNAメチル化 / クロマチン / 進化
Outline of Final Research Achievements

By epigenomics approach using various mutants of Arabidopsis thaliana, we analyzed effects of mutation in the IBM1 gene, which encodes a protein removing H3K9 methylation, a mark of silent chromatin. The results showed that this enzyme removes H3K9 methylation from transcribed sequences, contributing to differentiation of active and inactive sequences. We also identified a transposon which targets to centromere, through analysis of a transposon of Arabidopsis lyrata, which shows sequence similarity to a mobile transposon of Arabidopsis thaliana. I addition, by characterizing another mobile transposon, we identified a novel anti-silencing factor encoded by the transposon.

Assessment Rating
Verification Result (Rating)

A+

Assessment Rating
Result (Rating)

A+: Progress in the research exceeds the initial goal. More than expected research results are expected.

Report

(8 results)
  • 2015 Research Progress Assessment (Verification Result) ( PDF )
  • 2014 Final Research Report ( PDF )
  • 2013 Annual Research Report   Abstract(Research Progress Assessment) ( PDF )   Research Progress Assessment (Result) ( PDF )
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (53 results)

All 2013 2012 2011 2010 Other

All Journal Article (14 results) (of which Peer Reviewed: 12 results) Presentation (38 results) (of which Invited: 11 results) Remarks (1 results)

  • [Journal Article] Mobilization of a plant transposon by expression of the transposon-encoded anti-silencing factor.2013

    • Author(s)
      Fu Y, Kawabe A, Etcheverry M, Ito T, Toyoda A, Fujiyama A, Colot V, Tarutani Y, Kakutani T
    • Journal Title

      EMBO Journal

      Volume: 32 Issue: 17 Pages: 2407-2417

    • DOI

      10.1038/emboj.2013.169

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mechanism for full-length RNA processing of Arabidopsis genes containing intragenic heterochromatin.2013

    • Author(s)
      Saze H, Kitayama J, Takashima K, Miura S, Harukawa Y, Ito T, Kakutani T
    • Journal Title

      Nat Commun

      Volume: 4 Issue: 1 Pages: 2301-2301

    • DOI

      10.1038/ncomms3301

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] What triggers DNA methylation in genes and TEs: contribution of body methylation?2013

    • Author(s)
      Inagaki S, Kakutani T
    • Journal Title

      Cold Spring Harbor Symp Quant Biol

      Volume: published online

    • Related Report
      2012 Annual Research Report
  • [Journal Article] Centromere-targeted de novo integrations of an LTR retrotransposon in Arabidopsis lyrata2012

    • Author(s)
      Tsukahara, et al
    • Journal Title

      Genes & Development

      Volume: 26 Issue: 7 Pages: 705-713

    • DOI

      10.1101/gad.183871.111

    • Related Report
      2012 Annual Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] RNAi-independent de novo DNA methylation in Arabidopsis mutants of a chromatin remodeling gene DDM12012

    • Author(s)
      Sasaki T, Kobaysshi A, Saze H, Kakutani T
    • Journal Title

      Plant Journal

      Volume: (on line) Issue: 5 Pages: 750-758

    • DOI

      10.1111/j.1365-313x.2012.04911.x

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] HMG domain containing SSRP1 is required for DNA demethylation and genomic imprinting in Arabidopsis2011

    • Author(s)
      池田陽子, 他8名
    • Journal Title

      Developmental Cell

      Volume: 21 Issue: 3 Pages: 589-596

    • DOI

      10.1016/j.devcel.2011.08.013

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Arabidopsis HDA6 regulates locus-directed heterochromatin silencing in cooperation with MET12011

    • Author(s)
      To TK, Kim JM, Matsui A, Kurihara Y, Morosawa T, Ishida J, Tanaka M, Endo T, Kakutani T, Toyoda T, Kimura H, Yokoyama S, Shinozaki K, Seki M
    • Journal Title

      PLoS Genetics

      Volume: 7 Issue: 4 Pages: e1002055-e1002055

    • DOI

      10.1371/journal.pgen.1002055

    • NAID

      130006996644

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Coexistence of trichome variation in a natural plant population : a combined study using ecological and candidate gene approaches2011

    • Author(s)
      Kawagoe T, Shimizu KK, Kakutani T, Kudoh H
    • Journal Title

      PLoS One

      Volume: 6 Issue: 7 Pages: e22184-e22184

    • DOI

      10.1371/journal.pone.0022184

    • NAID

      120006653905

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Epigenetic variation in the FWA gene within the genus Arabidopsis2011

    • Author(s)
      Fujimoto R, Sasaki T, Kudoh H, Taylor JM, Kakutani T, Dennis ES
    • Journal Title

      Plant Journal

      Volume: 66 Issue: 5 Pages: 831-843

    • DOI

      10.1111/j.1365-313x.2011.04549.x

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Epigenetic variation in the FWA gene within the genus Arabidopsis2011

    • Author(s)
      Fujimoto R., et al
    • Journal Title

      Plant J

      Volume: (in press)

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Developmental changees in crossover frequency in Arabidopsis2011

    • Author(s)
      Toyama M., et al
    • Journal Title

      Plant J

      Volume: 14 Pages: 81-87

    • Related Report
      2010 Annual Research Report
  • [Journal Article] Deferentiation of epigenetic modifications between transposons and genes2011

    • Author(s)
      Saze H., et al
    • Journal Title

      Curr Opin Plant Biol

      Volume: 65 Pages: 589-599

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Control of genic DNA methylation in Arabidopsis2011

    • Author(s)
      Inagaki S., et al
    • Journal Title

      J Plant Research

      Volume: 123 Pages: 299-302

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Autocatalytic differentiation of epigenetic modifications in Arabidopsis genome2010

    • Author(s)
      Inagaki S., et al
    • Journal Title

      EMBO J

      Volume: 29 Pages: 3496-3506

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] Genetics of DNA Methylation in Genes and Transposons in Arabidopsis2013

    • Author(s)
      Kakutani T.
    • Organizer
      21st International Congress of Genetics
    • Place of Presentation
      Singapore
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] シロイヌナズナのエピ遺伝学2013

    • Author(s)
      角谷徹仁
    • Organizer
      エピゲノム・エピジェネティックスJST・NEDO公開シンポジウム
    • Place of Presentation
      東京都・秋葉原
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] シロイヌナズナTEの抑制解除活性2013

    • Author(s)
      付煜、河邊昭、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85回大会
    • Place of Presentation
      神奈川県・横浜市
    • Related Report
      2013 Annual Research Report
  • [Presentation] シロイヌナズナのibm1(INCREASE IN BONSAI METHYLATION1)変異は世代を越えて漸進的なゲノムDNA高メチル化を誘発する2013

    • Author(s)
      伊藤佑、樽谷芳明、豊田敦、藤山秋佐夫、佐瀬英俊、角谷徹仁
    • Organizer
      日本遺伝学会第85回大会
    • Place of Presentation
      神奈川県・横浜市
    • Related Report
      2013 Annual Research Report
  • [Presentation] DNAメチル化と植物トランスポゾンの動態2013

    • Author(s)
      角谷徹仁
    • Organizer
      日本遺伝学会第85回大会
    • Place of Presentation
      神奈川県・横浜市
    • Related Report
      2013 Annual Research Report
  • [Presentation] Epigenetic regulation in plant environmental responses2013

    • Author(s)
      藤泰子
    • Organizer
      日本遺伝学会第85回大会・若手企画公開国際シンポジウム
    • Place of Presentation
      神奈川県・横浜市
    • Related Report
      2013 Annual Research Report
  • [Presentation] 植物トランスポゾンの抗サイレンシング機構2013

    • Author(s)
      付煜
    • Organizer
      2013年度国立遺伝学研究所研究集会「転移因子と宿主の相互作用による生命機能
    • Place of Presentation
      静岡県・三島市
    • Related Report
      2013 Annual Research Report
  • [Presentation] 動原体をターゲットとするLTR型トランスポゾン2013

    • Author(s)
      河邊昭,角谷徹仁
    • Organizer
      2013年度国立遺伝学研究所研究集会「転移因子と宿主の相互作用による生命機能
    • Place of Presentation
      静岡県・三島市
    • Related Report
      2013 Annual Research Report
  • [Presentation] シロイヌナズナのDNAメチル化とトランスポゾン動態2013

    • Author(s)
      角谷徹仁
    • Organizer
      大阪大学蛋白質研究所セミナー「DNAメチル化の制御機構ーメチル化模様形成、維持と消去」
    • Place of Presentation
      大阪府・大阪市
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] DNA methylation and TE dynamics in Arabidopsis2013

    • Author(s)
      角谷徹仁
    • Organizer
      理研セミナー・エピジェネティクスセミナーシリーズ
    • Place of Presentation
      神奈川県・横浜市
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Genetics of DNA methylation in genes and transposons in Arabidopsis2011

    • Author(s)
      Kakutani T
    • Organizer
      CDB Symposium 2011 Epigenetic Landscape in Development and Disease
    • Place of Presentation
      神戸
    • Year and Date
      2011-03-14
    • Related Report
      2010 Annual Research Report
  • [Presentation] Genetics of DNA methylation in genes and transposons in Arabidopsis2011

    • Author(s)
      Kakutani T
    • Organizer
      Plant & Animal Genome XIX, EPIC : Plant Epigenome Project
    • Place of Presentation
      San Diego, USA
    • Year and Date
      2011-01-15
    • Related Report
      2010 Annual Research Report
  • [Presentation] シロイヌナズナにおけるDNAメチル化の遺伝学2010

    • Author(s)
      角谷徹仁
    • Organizer
      大阪大学蛋白質研究所セミナー「ゲノム記憶の成立機序とその制御」
    • Place of Presentation
      大阪
    • Year and Date
      2010-11-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] Genetics of DNA methylation in genes and transposons in Arabidopsis2010

    • Author(s)
      Kakutani T
    • Organizer
      Cold Spring Harbor Asia meeting "From Plant Biology to Crop Biotechnology"
    • Place of Presentation
      Suzhou, China
    • Year and Date
      2010-10-28
    • Related Report
      2010 Annual Research Report
  • [Presentation] Arabidopsis属におけるCOPIA93/COPIA20ファミリーの分布と挿入位置特異性2010

    • Author(s)
      河辺昭, 他
    • Organizer
      日本遺伝学会第82回大会
    • Place of Presentation
      札幌
    • Year and Date
      2010-09-21
    • Related Report
      2010 Annual Research Report
  • [Presentation] ArabidopsislyrataにおけるCOPIA93レトロトランスポゾンのセントロメア特異的分布の形成機構2010

    • Author(s)
      塚原小百合, 他
    • Organizer
      日本遺伝学会第82回大会
    • Place of Presentation
      札幌
    • Year and Date
      2010-09-21
    • Related Report
      2010 Annual Research Report
  • [Presentation] RNAi経路とクロマチン再構成による植物発生とDNAメチル化の制御2010

    • Author(s)
      佐々木卓, 他
    • Organizer
      日本遺伝学会第82回大会
    • Place of Presentation
      札幌
    • Year and Date
      2010-09-21
    • Related Report
      2010 Annual Research Report
  • [Presentation] シロイヌナズナの遺伝子領域におけるヘテロクロマチン修飾除去メカニズムの解析2010

    • Author(s)
      佐瀬英俊, 他
    • Organizer
      日本遺伝学会第82回大会
    • Place of Presentation
      札幌
    • Year and Date
      2010-09-21
    • Related Report
      2010 Annual Research Report
  • [Presentation] DNAメチル化とトランスポゾンとシロイヌナズナのエピ遺伝学2010

    • Author(s)
      角谷徹仁
    • Organizer
      日本遺伝学会第82回大会シンポジウム
    • Place of Presentation
      札幌
    • Year and Date
      2010-09-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] Genetics of DNA methylation in genes and transposons in Arabidopsis2010

    • Author(s)
      Kakutani T
    • Organizer
      International Conference of Arabidopsis Research
    • Place of Presentation
      横浜
    • Year and Date
      2010-06-08
    • Related Report
      2010 Annual Research Report
  • [Presentation] Genetics of DNA methylation in genes and transposons in Arabidopsis2010

    • Author(s)
      Kakutani T
    • Organizer
      ASM Conference "Mobile DNA"
    • Place of Presentation
      モントリオール・カナダ
    • Year and Date
      2010-04-27
    • Related Report
      2010 Annual Research Report
  • [Presentation] Genetics of DNA methylation in genes and transoposons in Arabidopsis

    • Author(s)
      Kakutani T.
    • Organizer
      The 77th Cold Spring Harbor Symposium on Quantitative Biology; Biology of Plants
    • Place of Presentation
      Cold Spring Harbor, NY, USA
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Genetics of DNA methylation in genes and transoposons in Arabidopsis

    • Author(s)
      Kakutani T.
    • Organizer
      2012International Symposium on Epigenetic Regulation in Higher Plants
    • Place of Presentation
      北京、中国
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Genetics of DNA methylation in genes and transposos

    • Author(s)
      Kakutani T.
    • Organizer
      The 23rd International Conference on Arabidopsis Research
    • Place of Presentation
      ウイーン、オーストリア
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Genetics of DNA methylation in genes and transposos

    • Author(s)
      Kakutani T.
    • Organizer
      Cold Spring Harbor Asia Conferences:Plant Epigenetics, Stress and Evolution
    • Place of Presentation
      蘇州、中国
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] DNAメチル化の遺伝学

    • Author(s)
      角谷徹仁
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡
    • Related Report
      2012 Annual Research Report
  • [Presentation] Genetics of DNA methylation in genes and transoposons in Arabidopsis

    • Author(s)
      角谷徹仁
    • Organizer
      日本遺伝学会第84回大会
    • Place of Presentation
      福岡
    • Related Report
      2012 Annual Research Report
  • [Presentation] Terminal inverted repeat(TIR)を持たないシロイヌナズナMutator様因子の転移様式

    • Author(s)
      付煜
    • Organizer
      日本遺伝学会第84回大会
    • Place of Presentation
      福岡
    • Related Report
      2012 Annual Research Report
  • [Presentation] NAメチル化に作用するシロイヌナズナ変異体の一塩基解像度メチローム解析

    • Author(s)
      伊藤佑
    • Organizer
      日本遺伝学会第84回大会
    • Place of Presentation
      福岡
    • Related Report
      2012 Annual Research Report
  • [Presentation] rDNA-targeted intergration of a non-autonomous LTR retrotransposon

    • Author(s)
      程朝陽
    • Organizer
      Cold Spring Harbor Asia Conferences: Plant Epigenetics, Stress and Evolution
    • Place of Presentation
      蘇州、中国
    • Related Report
      2012 Annual Research Report
  • [Presentation] Genetics of DNA methylation in genes and transposons

    • Author(s)
      Tetsuji Kakutani
    • Organizer
      Gordon Research Conference, Epigenetics
    • Place of Presentation
      Stonehill College Easton, MA, USA
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] Genetics of DNA methylation in genes and transposons

    • Author(s)
      Tetsuji Kakutani
    • Organizer
      Keystone Symposium, Nuclear events in plant gene expression and signaling
    • Place of Presentation
      Taos, NM, USA
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] Genetics of DNA methylation in genes and transposons

    • Author(s)
      Tetsuji Kakutani
    • Organizer
      The 8th Okazaki Biology Conference, Speciation and Adaptation II
    • Place of Presentation
      岡崎
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] シロイヌナズナにおける遺伝子とトランスポゾンのDNAメチル化の遺伝学

    • Author(s)
      角谷徹仁
    • Organizer
      日本細胞生物学会年会シンポジウム「細胞、染色体機能を調節するヘテロクロマチンの動的制御」
    • Place of Presentation
      札幌
    • Related Report
      2011 Annual Research Report
  • [Presentation] A. lyrataにおけるLTRレトロトランスポゾンのセントロメア特異的分布の形成機構

    • Author(s)
      塚原小百合、河辺昭、小林啓恵、伊藤佑、会津智幸、新井理、豊田敦、藤山秋佐夫、角谷徹仁
    • Organizer
      日本遺伝学会第83回大会ワークショップ
    • Place of Presentation
      京都
    • Related Report
      2011 Annual Research Report
  • [Presentation] シロイヌナズナのDNAメチル化制御因子DDM1(decrease in DNA methylation)とIBM1(increase in BONSAI methylation)の遺伝的相互作用

    • Author(s)
      保坂碧、小林啓恵、佐瀬英俊、角谷徹仁
    • Organizer
      日本遺伝学会第83回大会
    • Place of Presentation
      京都
    • Related Report
      2011 Annual Research Report
  • [Presentation] Terminal Inverted Repeat(TIR)を持たないシロイヌナズナのMutator様因子の転移様式

    • Author(s)
      付ゆう、小林啓恵、角谷徹仁
    • Organizer
      日本遺伝学会第83回大会
    • Place of Presentation
      京都
    • Related Report
      2011 Annual Research Report
  • [Presentation] DNA methylation and transposon dynamics in Arabidopsis

    • Author(s)
      Tetsuji Kakutani
    • Organizer
      日本分子生物学会年会シンポジウム
    • Place of Presentation
      横浜
    • Related Report
      2011 Annual Research Report
  • [Remarks]

    • URL

      http://www.nig.ac.jp/labs/AgrGen/home-j.html

    • Related Report
      2010 Annual Research Report

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Published: 2010-08-23   Modified: 2019-07-29  

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