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Analysis of Epigenome Marks and Transcriptome in the Germ Line by the Next Generation Sequencer

Research Project

Project/Area Number 22228004
Research Category

Grant-in-Aid for Scientific Research (S)

Allocation TypeSingle-year Grants
Research Field Applied animal science
Research InstitutionTokyo University of Agriculture

Principal Investigator

KONO Tomohiro  東京農業大学, 応用生物科学部, 教授 (80153485)

Co-Investigator(Kenkyū-buntansha) SOTOMARU Yusuke  広島大学, 自然科学研究支援センター, 教授 (90309352)
SUZUKI Yutaka  東京大学, 新領域形成研究科, 教授 (40323646)
Research Collaborator KOBAYASHI Hisato  東京農業大学, 応用生物科学部・生物資源ゲノム解析センター, 准教授 (70632727)
Project Period (FY) 2010-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥217,620,000 (Direct Cost: ¥167,400,000、Indirect Cost: ¥50,220,000)
Fiscal Year 2014: ¥43,680,000 (Direct Cost: ¥33,600,000、Indirect Cost: ¥10,080,000)
Fiscal Year 2013: ¥43,680,000 (Direct Cost: ¥33,600,000、Indirect Cost: ¥10,080,000)
Fiscal Year 2012: ¥43,680,000 (Direct Cost: ¥33,600,000、Indirect Cost: ¥10,080,000)
Fiscal Year 2011: ¥42,380,000 (Direct Cost: ¥32,600,000、Indirect Cost: ¥9,780,000)
Fiscal Year 2010: ¥44,200,000 (Direct Cost: ¥34,000,000、Indirect Cost: ¥10,200,000)
KeywordsDNA メチローム / 生殖系列 / 次世代シークエンサー / トランスクリプトーム / 始原生殖細胞 / 生殖細胞 / リプログラミング / DNAメチローム / 脱メチル化 / エピゲノム / DNAメチル化 / メチローム / イピゲノム
Outline of Final Research Achievements

To clarify DNA methylation reprogramming and transcriptome in the whole female and male germline lineage in mice, a comprehensive DNA methylation analysis for all cytosine was conducted using a next-generation sequencer. DNA methylation was 30% and 80% in the oocytes and sperm, respectively. After fertilization the level decreased and reached to 18% at the blastocysts, however, in the E7.5 epiblast, the DNA methylation was quickly increased to 73%. In the primordial germ cells, which are differentiated at this stage, demethylation occurred rapidly, and the methylation level deceased to less than 5% in both sexes at E13.5. Subsequently, female- and male-specific DNA methylomes were established independently in the sparmatogonium before birth and during oocyte growth period, respectively. Transcriptome analysis revealed that DNA methylation is a critical regulator of gene expression in germline cells. This is the first report of a complete DNA methylome map of the whole germline in mice.

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

(9 results)
  • 2015 Research Progress Assessment (Verification Result) ( PDF )
  • 2014 Annual Research Report   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

    (57 results)

All 2015 2014 2013 2012 2011 2010 Other

All Journal Article (12 results) (of which Peer Reviewed: 10 results,  Open Access: 2 results,  Acknowledgement Compliant: 1 results) Presentation (39 results) (of which Invited: 7 results) Book (2 results) Remarks (4 results)

  • [Journal Article] Dynamics of genomic 5-hydroxymethylcytosine during mouse oocyte growth2014

    • Author(s)
      Akihito Sakashita, Hisato Kobayashi, Takuya Wakai, Yuusuke Sotomaru, Kenichiro Hata, Tomohiro Kono
    • Journal Title

      Genes Cells

      Volume: 19 Issue: 8 Pages: 629-636

    • DOI

      10.1111/gtc.12164

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] DNAメチル化情報として生殖細胞に記憶される性差2014

    • Author(s)
      河野友宏
    • Journal Title

      岩波科学

      Volume: 84 Pages: 773-778

    • Related Report
      2014 Annual Research Report
  • [Journal Article] Forced expression of DNA methyltransferases during oocyte growth accelerates the establishment of methylation imprints but not functional genomic imprinting2014

    • Author(s)
      Hara S, Takano T, Fujikawa T, Yamada M, Wakai T, Kono T, Obata Y
    • Journal Title

      Hum Mol Genet

      Volume: 23(10) Issue: 14 Pages: 1-12

    • DOI

      10.1093/hmg/ddu100

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Epigenetic and transcriptional features of the novel human imprinted lncRNA GPR1AS suggest it is a functional ortholog to mouse Zdbf2linc.2013

    • Author(s)
      Kobayashi H, Yanagisawa E, Sakashita A, Sugawara N, Kumakura S, Ogawa H, Akutsu H, Hata K, Nakabayashi K, Kono T.
    • Journal Title

      Epigenetics

      Volume: 8 (6) Issue: 6 Pages: 635-645

    • DOI

      10.4161/epi.24887

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Long exposure to mature ooplasm can alter DNA methylation at imprinted loci in non-growing oocytes but not in prospermatogonia.2013

    • Author(s)
      Obata Y, Wakai T, Hara S, Kono T.
    • Journal Title

      Reproduction

      Volume: 147(1) Pages: 1-6

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mouse oocyte methylomes at base resolution reveal genome- wide accumulation of non-CpG methylation and role of DNA methyltransferases2013

    • Author(s)
      Shirane K, Toh H, Kobayashi H, Miura F, Chiba H, Ito T, Kono T, Sasaki H
    • Journal Title

      PLoS Genet

      Volume: 9(4) Issue: 4 Pages: 303-306

    • DOI

      10.1371/journal.pgen.1003439

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency2012

    • Author(s)
      Wang L, Aburatani H, et al.
    • Journal Title

      Genome Research

      Volume: 22 Issue: 3 Pages: 208-219

    • DOI

      10.1101/gr

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Imprinted DNA methylation reprogramming during early mouse embryogenesis at the Gprl-Zdbf2 locus is linked to long cis-intergenic transcription2012

    • Author(s)
      Kobayashi, Hisato.
    • Journal Title

      FEBS Letters

      Volume: 586 Pages: 827-833

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] DNA methylation analysis of germ cells by using bisulfite-based sequencing methods2012

    • Author(s)
      Kobayashi, Hisato.
    • Journal Title

      Methods in Molecular Biology

      Volume: 825 Pages: 223-235

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks2012

    • Author(s)
      Kobayashi, Hisato.
    • Journal Title

      PLoS GENETICS

      Volume: 8

    • NAID

      120005300482

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A tripartite paternally methylated region within the Gprl-Zdbf2 imprinted domain on mouse chromosome 1 identified by meDIP-on-chip.2010

    • Author(s)
      Hiura, Hitoshi.
    • Journal Title

      Nucleic Acids Research

      Volume: 38 Pages: 4929-4945

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 卵子形成とエピジェネティクス2010

    • Author(s)
      河野友宏
    • Journal Title

      HORMONE FRONTIER IN GYNECOLOGY

      Volume: 5 Pages: 335-340

    • Related Report
      2010 Annual Research Report
  • [Presentation] これからの生殖医療技術とその安全・安心 -遺伝子解析技術の進歩2015

    • Author(s)
      河野友宏
    • Organizer
      岡大ARTセンターシンポジウム
    • Place of Presentation
      岡山大学
    • Year and Date
      2015-01-25
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] マウス生殖細胞・初期胚のDNAメチローム解析2014

    • Author(s)
      小林久人、坂下陽彦、若井拓哉、小池佐、佐野賢、河野友宏
    • Organizer
      日本分子生物学会大会
    • Place of Presentation
      横浜国際展示場
    • Year and Date
      2014-11-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] 体細胞クローンマウス精子のDNAメチル化リプログラミング2014

    • Author(s)
      若井 拓哉、水谷英二、小林久人、若山 清香、坂下 陽彦、伊藤 隆司、 三浦 史仁、河野 友
    • Organizer
      日本分子生物学会
    • Place of Presentation
      横浜国際展示場
    • Year and Date
      2014-11-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] 体細胞クローンマウス精子のDNAメチレーションエラー2014

    • Author(s)
      河野友宏, 若井拓也, 水谷英二, 小林久人, 若山清香, 坂下陽彦, 三浦史仁, 伊藤隆司
    • Organizer
      日本繁殖生物学会
    • Place of Presentation
      帯広畜産大学
    • Year and Date
      2014-09-22
    • Related Report
      2014 Annual Research Report
  • [Presentation] Genome-wide reprogramming by DNA demethylation during mouse oocyte growth and early development2014

    • Author(s)
      Akihiko SAKASHITA, Yosuke ISEKI, Mei NAKAJIMA, Takuya WAKAI, Hisato KOBAYASHI, Tomohiro KONO
    • Organizer
      World Congress of Reproductive Biology
    • Place of Presentation
      Edinburgh (UK)
    • Year and Date
      2014-09-03
    • Related Report
      2014 Annual Research Report
  • [Presentation] High-resolution DNA methylome analysis of mouse germ cells2014

    • Author(s)
      Hisato Kobayash
    • Organizer
      World Congress of Reproductive Biology
    • Place of Presentation
      Edinburgh (UK)
    • Year and Date
      2014-09-02
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] マウス初期胚における5hmCおよびH3K9me2の挙動とDNA脱メチル化制御機構2014

    • Author(s)
      坂下 陽彦、中島 芽生、若井 拓哉、小林 久人、井関陽介、河野 友宏
    • Organizer
      本哺乳動物卵子学会
    • Place of Presentation
      神戸ポートピアホテル
    • Year and Date
      2014-05-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] 全ゲノムを対象としたメチローム解析が明らかにする雌雄差2014

    • Author(s)
      河野友宏
    • Organizer
      染色体研究会
    • Place of Presentation
      東京医科大学病院
    • Year and Date
      2014-04-19
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] マウス配偶子における全ゲノム包括的DNAメチローム解析2011

    • Author(s)
      小林久人
    • Organizer
      第34回日本分子生物学会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2011-12-16
    • Related Report
      2011 Annual Research Report
  • [Presentation] DNAメチローム解析による生殖系列のリプログラミング評価2011

    • Author(s)
      河野友宏
    • Organizer
      第56回日本生殖医学会学術講演会・総会
    • Place of Presentation
      パシフィコ横浜(招待講演)
    • Year and Date
      2011-12-08
    • Related Report
      2011 Annual Research Report
  • [Presentation] Mouse genomic DNA methylomes show the role of intergenic DNA methylation in the establishment of oocyte-specific heritable marks2011

    • Author(s)
      Kobayashi Hisato.
    • Organizer
      World Congress on Reproductive Biology & Society for Reproductive Biology
    • Place of Presentation
      オーストラリア・ケアンズ
    • Year and Date
      2011-10-12
    • Related Report
      2011 Annual Research Report
  • [Presentation] マウス配偶子における全ゲノム包括的DNAメチローム解析2011

    • Author(s)
      小林久人
    • Organizer
      第104回日本繁殖生物学会大会
    • Place of Presentation
      いわて県民情報交流センター・アイーナ(盛岡)
    • Year and Date
      2011-09-16
    • Related Report
      2011 Annual Research Report
  • [Presentation] マウス始原生殖細胞の包括的DNAメチル化解析2011

    • Author(s)
      櫻井隆順
    • Organizer
      第104回日本繁殖生物学会大会
    • Place of Presentation
      いわて県民情報交流センター・アイーナ(盛岡)
    • Year and Date
      2011-09-16
    • Related Report
      2011 Annual Research Report
  • [Presentation] エピゲノム解析(DNAメチローム解析)による卵子正常性の評価2011

    • Author(s)
      小林久人
    • Organizer
      第52回日本哺乳動物卵子学会
    • Place of Presentation
      国際医療福祉大学本校(栃木)(招待講演)
    • Year and Date
      2011-05-21
    • Related Report
      2011 Annual Research Report
  • [Presentation] Methylomes and transcriptomes in mouse germ cells2011

    • Author(s)
      Kono, Tomohiro.
    • Organizer
      Fertility 2011
    • Place of Presentation
      アイルランド・ダブリン
    • Year and Date
      2011-01-07
    • Related Report
      2010 Annual Research Report
  • [Presentation] Bisulphite Shotgun Sequencing法によるマウス生殖細胞の包括的DNAメチル化解析2010

    • Author(s)
      小林久人
    • Organizer
      第33回日本分子生物学会年会(BMB2010)
    • Place of Presentation
      神戸ポートアイランド(神戸市)
    • Year and Date
      2010-12-08
    • Related Report
      2010 Annual Research Report
  • [Presentation] 着床前マウスクローン胚におけるトランスクリプトーム解析2010

    • Author(s)
      曹峰
    • Organizer
      第33回日本分子生物学会年会(BMB2010)
    • Place of Presentation
      神戸ポートアイランド(神戸市)
    • Year and Date
      2010-12-07
    • Related Report
      2010 Annual Research Report
  • [Presentation] Methylomes and transcriptomes in mouse germ cell2010

    • Author(s)
      Kono, Tomohiro.
    • Organizer
      International Symposium on "Epigenome Network, Devel opment and Reprogramming of Germ Cells"
    • Place of Presentation
      九州大学医学部百年講堂(福岡市)
    • Year and Date
      2010-11-24
    • Related Report
      2010 Annual Research Report
  • [Presentation] Whole genome bisulphite shotgun sequencing in mouse germ cells2010

    • Author(s)
      Kobayashi, Hisato.
    • Organizer
      International Symposium on "Epigenome Network, Development and Reprogramming of Germ Cells"
    • Place of Presentation
      九州大学医学部百年講堂(福岡市)
    • Year and Date
      2010-11-22
    • Related Report
      2010 Annual Research Report
  • [Presentation] 新規インプリント遺伝子zdbf2発現制御機構の解明2010

    • Author(s)
      櫻井隆順
    • Organizer
      第103回日本繁殖生物学会大会
    • Place of Presentation
      北里大学獣医学部(十和田市)
    • Year and Date
      2010-09-02
    • Related Report
      2010 Annual Research Report
  • [Presentation] Amplification-free whole-genome shotgun bisulfite sequencing of mouse primordial germ cells

    • Author(s)
      Kobayashi H, Sakurai T, Miura F, Imai M, Mochiduki K, Yanagisawa E,Sakashita A, Wakai T, Suzuki Y, Ito T, Matsui Y, Kono T.
    • Organizer
      Non-coding RNA, epigenetics and transgenerational inheritance 2013
    • Place of Presentation
      ケンブリッジ、イギリス
    • Related Report
      2013 Annual Research Report
  • [Presentation] マウス生殖細胞における全ゲノム包括的DNAメチローム解析

    • Author(s)
      小林久人
    • Organizer
      第7回 日本エピジェネティクス研究会
    • Place of Presentation
      奈良県新公会堂
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] マウス卵母細胞におけるゲノム刷り込みの分子機構

    • Author(s)
      原 聡史,川原玲香、尾畑やよい、河野友宏
    • Organizer
      第106回日本繁殖生物学会
    • Place of Presentation
      東京農工大学
    • Related Report
      2013 Annual Research Report
  • [Presentation] マウス12番染色体非コードインプリント遺伝子の過剰発現モデルにおける表現型解析

    • Author(s)
      藤原真,高橋望,平田裕,外丸祐介, 河野友宏
    • Organizer
      第106回日本繁殖生物学会
    • Place of Presentation
      東京農工大学
    • Related Report
      2013 Annual Research Report
  • [Presentation] マウス卵子形成過程における5ヒドロキシメチル化シトシンのダイナミクス

    • Author(s)
      坂下陽彦, 小林久人, 井関陽介、若井拓也、外丸祐介、 河野友宏
    • Organizer
      第106回日本繁殖生物学会
    • Place of Presentation
      東京農工大学
    • Related Report
      2013 Annual Research Report
  • [Presentation] DNAメチローム解析によって明らかにされたマウス生殖系列のリプログラミング

    • Author(s)
      河野友宏
    • Organizer
      日本遺伝学会第85回大会ワークショップ
    • Place of Presentation
      慶応義塾大学日吉キャンパス
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] マウス卵子形成過程における5-hydroxymethylcytosine のダイナミク ス

    • Author(s)
      坂下陽彦、小林久人, 井関陽介、若井拓也、外丸祐介、 河野友宏
    • Organizer
      第36回 日本分子生物学会
    • Place of Presentation
      神戸ポートアイランド国際会議場
    • Related Report
      2013 Annual Research Report
  • [Presentation] マウス12番染色体非コードインプリント遺伝子の過剰発現モデルに おける表現型解析

    • Author(s)
      藤原真、高橋望,平田裕,外丸祐介, 河野友宏
    • Organizer
      第36回 日本分子生物学会
    • Place of Presentation
      神戸ポートアイランド国際会議場
    • Related Report
      2013 Annual Research Report
  • [Presentation] ARTと生殖系列エピゲノムリプログラミング

    • Author(s)
      河野友宏
    • Organizer
      第10回 東海ARTカンファレンス
    • Place of Presentation
      名古屋市(名鉄ニューグランドホテル)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 1番染色体におけるインプリント発現する大型介在性ノンコーディングRNA:Zdbf2lincの同定

    • Author(s)
      小林久人
    • Organizer
      第6回エピジェネティクス研究会
    • Place of Presentation
      学術総合センター
    • Related Report
      2012 Annual Research Report
  • [Presentation] マウス卵子の減数分裂におけるH3K27me3の伝達機構

    • Author(s)
      若井拓哉
    • Organizer
      第53回日本哺乳動物卵子学会
    • Place of Presentation
      千里ライフサイエンスセンター
    • Related Report
      2012 Annual Research Report
  • [Presentation] マウスにおける新規父方特異的メチル化DNA領域の探索

    • Author(s)
      坂下陽彦
    • Organizer
      第53回日本哺乳動物卵子学会
    • Place of Presentation
      千里ライフサイエンスセンター
    • Related Report
      2012 Annual Research Report
  • [Presentation] マウス始原生殖細胞におけるDNAメチローム解析

    • Author(s)
      小林久人
    • Organizer
      第105回日本繁殖生物学会
    • Place of Presentation
      筑波大学大学会館
    • Related Report
      2012 Annual Research Report
  • [Presentation] Whole-genome profiling of cytosine methylation in mouse primordial germ cells

    • Author(s)
      小林久人
    • Organizer
      Next Generation Sequencing Asia Congress 2012,
    • Place of Presentation
      Singapore
    • Related Report
      2012 Annual Research Report
  • [Presentation] インプリント遺伝子クラスターGPR1-ZDBF2における転写調節・エピジェネティクス制御機構とヒト・マウスゲノム間の類似性

    • Author(s)
      河野友宏
    • Organizer
      特定領域研究「生殖系列の世代サイクルとエピゲノムネットワーク」第5回シンポジウム
    • Place of Presentation
      京都大学医学部構内芝蘭会館
    • Related Report
      2012 Annual Research Report
  • [Presentation] マウス始原生殖細胞におけるDNAメチローム解析

    • Author(s)
      小林久人
    • Organizer
      第35回日本分子生物学会
    • Place of Presentation
      福岡国際会議場
    • Related Report
      2012 Annual Research Report
  • [Presentation] マウス卵母細胞の成熟過程におけるミトコンドリアの動態

    • Author(s)
      若井拓哉
    • Organizer
      第35回日本分子生物学会
    • Place of Presentation
      福岡国際会議場
    • Related Report
      2012 Annual Research Report
  • [Presentation] 生殖系列のリプログラミングはどこまで理解できたか ― 体細胞から生殖系列への転換 ―

    • Author(s)
      河野友宏
    • Organizer
      NIAS/NILGS合同シンポジウム
    • Place of Presentation
      エポカルつくば
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Amplification-free whole-genome shotgun bisulfite sequencing of mouse primordial germ cells

    • Author(s)
      小林久人
    • Organizer
      Epigenetics & Chromatin: Interactions and Processes 2013
    • Place of Presentation
      ハーバードメディカルセンター、ボストン・アメリカ
    • Related Report
      2012 Annual Research Report
  • [Book] 卵子学2011

    • Author(s)
      河野友宏
    • Publisher
      京都大学学術出版会
    • Related Report
      2011 Annual Research Report
  • [Book] 生命の誕生に向けて<第二版>生殖補助医療(ART)胚培養の理論と実際2011

    • Author(s)
      河野友宏
    • Publisher
      近代出版
    • Related Report
      2010 Annual Research Report
  • [Remarks] 動物発生工学研究室(河野研究室)

    • URL

      http://nodai-konolab.net/

    • Related Report
      2013 Annual Research Report
  • [Remarks] 動物発生工学研究室

    • URL

      http://nodai-konolab.net

    • Related Report
      2012 Annual Research Report
  • [Remarks]

    • URL

      http://www.nodai-genome.org/

    • Related Report
      2011 Annual Research Report
  • [Remarks]

    • URL

      http://nodai.cc-town.net/laboratory/single.php?id=27

    • Related Report
      2010 Annual Research Report

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

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