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The accurate determination of gene loci by genome-wide approach

Research Project

Project/Area Number 23651195
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Medical genome science
Research InstitutionKyushu University

Principal Investigator

OHKAWA Yasuyuki  九州大学, 医学研究院, 准教授 (80448430)

Project Period (FY) 2011 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2012: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2011: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Keywordsクロマチン / 転写 / RNA ポリメラーゼII / 発現プロファイリング / リン酸化 / RNAポリメラーゼII
Research Abstract

Cellular function is regulated by the balance of stringently regulated amounts of mRNA. Previous reports revealed that RNA polymerase II (RNAPII), which transcribes mRNA, c an be classified into the pausing state and the active transcription state according to the phosphorylation state of RPB1, the catalytic subunit of RNAPII. We examined the correlation between the phosphorylation of RNAPII and mRNA expression levels using acombined analysis by ChIPseq and RNAseq. We could visualized the recruitment of various phosphorylated RNAPIIs. Our analysis indicated that the complexity of quantitative regulation of mRNA levels could be classified into three categories according to thephosphorylation state of RNAPII.

Report

(3 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Research-status Report
  • Research Products

    (56 results)

All 2013 2012 2011 Other

All Journal Article (16 results) (of which Peer Reviewed: 14 results) Presentation (30 results) (of which Invited: 6 results) Book (7 results) Remarks (3 results)

  • [Journal Article] A co-localization model of paired ChIP-seq data using a large ENCODE data set enables comparison of multiple samples2013

    • Author(s)
      Maehara K, Odawara J, Harada A, Yoshimi T, Nagao K, Obuse C, Akashi K, Tachibana T, Sakata T, and Ohkawa Y
    • Journal Title

      Nucleic Acids Res

      Volume: 41 Issue: 1 Pages: 54-62

    • DOI

      10.1093/nar/gks1010

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Ly6C+ Ly6G- Myeloid-derived suppressor cells play a critical role in the resolution of acute inflammation and the subsequent tissue repair process after spinal cord injury.2013

    • Author(s)
      Saiwai H, Kumamaru H, Ohkawa Y, Kubota K, Kobayakawa K, Yamada H, Yokomizo T, Iwamoto Y, Okada S.
    • Journal Title

      J Neurochem.

      Volume: 125 Issue: 1 Pages: 74-88

    • DOI

      10.1111/jnc.12135

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Chd2 interacts with H3.3 to determine myogenic cell fate2012

    • Author(s)
      Harada A, Okada S, Konno D, Odawara J, Yoshimi T, Yoshimura S, Kumamaru H, Saiwai H, Tsubota T, Kurumizaka H, Akashi K, Tachibana T, Imbalzano AN, Ohkawa Y
    • Journal Title

      EMBO J

      Volume: 31 Issue: 13 Pages: 2994-3007

    • DOI

      10.1038/emboj.2012.136

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Direct isolation and RNA-Seq reveal environment-dependent properties of engrafted neural stem/progenitor cells2012

    • Author(s)
      Kumamaru H, Ohkawa Y, Saiwai H, Yamada H, Kubota K, Kobayakawa K, Akashi K, Okano H, Iwamoto Y, Okada S
    • Journal Title

      Nat Commun

      Volume: 3 Issue: 1 Pages: 1140-1140

    • DOI

      10.1038/ncomms2132

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Surf4 modulates STIM1-dependent calcium entry.2012

    • Author(s)
      Fujii, Y. et al
    • Journal Title

      Biochem. Biophys. Res. Commun.

      Volume: 422 Issue: 4 Pages: 615-620

    • DOI

      10.1016/j.bbrc.2012.05.037

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Age-related differences in the cellular and molecular profiles of inflammatory responses after spinal cord injury2012

    • Author(s)
      Kumamaru H, Saiwai H, Ohkawa Y, Yamada H, Iwamoto Y, Okada S
    • Journal Title

      Journal of Cellular Physiology

      Volume: 227 Issue: 4 Pages: 1335-46

    • DOI

      10.1002/jcp.22845

    • Related Report
      2012 Annual Research Report 2012 Final Research Report 2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Isolation of nuclei from skeletal muscle satellite cells and myofibers for use in chromatin immunoprecipitation assays.2012

    • Author(s)
      Ohkawa Y, Mallappa C, Vallaster CS, Imbalzano AN.
    • Journal Title

      Methods Mol Biol.

      Volume: 798 Pages: 517-30

    • Related Report
      2011 Research-status Report
  • [Journal Article] An improved restriction enzyme accessibility assay for analyzing changes in chromatin structure in samples of limited cell number.2012

    • Author(s)
      Ohkawa Y, Mallappa C, Vallaster CS, Imbalzano AN.
    • Journal Title

      Methods Mol Biol.

      Volume: 798 Pages: 531-42

    • Related Report
      2011 Research-status Report
  • [Journal Article] Myeloperoxidase Exacerbates Secondary Injury by Generating Highly Reactive Oxygen Species and Mediating Neutrophil Recruitment in Experimental Spinal Cord Injury.2012

    • Author(s)
      Kubota K, Saiwai H, Kumamaru H, Maeda T, Ohkawa Y, Aratani Y, Nagano T, Iwamoto Y, Okada S.
    • Journal Title

      Spine.

      Volume: In press

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Chromatin accessibility and transcription factor binding at the PPARγ2promoter during adipogenesis is protein kinase A-dependent2011

    • Author(s)
      Xiao H, Leblanc SE, Wu Q, Konda S, Salma N, Marfella CG, Ohkawa Y,Imbalzano AN
    • Journal Title

      J Cell Physiol

      Volume: Vol.226、NO.1 Issue: 1 Pages: 86-93

    • DOI

      10.1002/jcp.22308

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Flow cytometric sorting of neuronal and glial nuclei from central nervous system tissue2011

    • Author(s)
      Okada S, Saiwai H, Kumamaru H, Kubota K, Harada A, Yamaguchi M, Iwamoto Y, Ohkawa Y
    • Journal Title

      Journal of Cellular Physiology

      Volume: 226 Issue: 2 Pages: 552-558

    • DOI

      10.1002/jcp.22365

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on geneome-wide approach2011

    • Author(s)
      Odawara J, Harada A, Yoshimi T, Maehara K, Tachbana T, Okada S, Akashi K, Ohkawa Y
    • Journal Title

      BMC Genomics

      Volume: 12 Issue: 1 Pages: 516-516

    • DOI

      10.1186/1471-2164-12-516

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Chromatin accessibility and transcription factor binding at the PPARγ2 promoter during adipogenesis is protein kinase A-dependent.2011

    • Author(s)
      Xiao H, Leblanc SE, Wu Q, Konda S, Salma N, Marfella CG, Ohkawa Y, Imbalzano AN.
    • Journal Title

      J Cell Physiol.

      Volume: 226 Pages: 86-93

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Flow cytometric sorting of neuronal and glial nuclei from central nervous system tissue.2011

    • Author(s)
      Okada S, Saiwai H, Kumamaru H, Kubota K, Harada A, Yamaguchi M, Iwamoto Y, Ohkawa Y.
    • Journal Title

      J Cell Physiol.

      Volume: 226 Pages: 552-8

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Generation of a rat monoclonal antibody specific for hsp72.2011

    • Author(s)
      Tanaka M, Shiota M, Okada S, Harada A, Odawara J, Mun S, Iwao H, Ohkawa Y.
    • Journal Title

      Hybridoma

      Volume: 30 Pages: 397-400

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach.2011

    • Author(s)
      Odawara J, Harada A, Yoshimi T, Maehara K, Tachibana T, Okada S, Akashi K, Ohkawa Y.
    • Journal Title

      BMC Genomics.

      Volume: 12

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Presentation] ヒストンバリアントによる骨格筋分化制御機構2013

    • Author(s)
      大川 恭行
    • Organizer
      第1回ヒストンバリアント研究会
    • Place of Presentation
      九州大学総合研究棟、福岡
    • Year and Date
      2013-03-08
    • Related Report
      2012 Final Research Report
  • [Presentation] Cd2 incorporates H3.3 to mark myogenic genes2013

    • Author(s)
      大川 恭行
    • Organizer
      新学術領域「ゲノム支援」国際シンポジウム"Expanding Frontiers of Genome Science"
    • Place of Presentation
      東京大学 伊藤国際学術研究センター、東京
    • Year and Date
      2013-01-10
    • Related Report
      2012 Final Research Report
  • [Presentation] 共局在回帰モデルと ENCODE データセットを介した ChIP-seq データの多サンプル比較解析2012

    • Author(s)
      前原 一満, 小田原 淳, 原田 哲仁, 吉見 智彦, 長尾 恒治, 小布施 力史, 立花 太郎, 坂田 年男, 大川 恭行
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場・マリンメッセ福岡、福岡
    • Year and Date
      2012-12-14
    • Related Report
      2012 Final Research Report
  • [Presentation] CHD5(Chromodomain helicase DNA binding protein 5)はマウスの胚性幹細胞において H3.1 と結合して遺伝子発現を抑制しうる2012

    • Author(s)
      林 正康, 小田原 淳, 原田 哲仁, 前原一満, 立花 太郎, 赤司 浩一, 大川 恭行
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場・マリンメッセ福岡、福岡
    • Year and Date
      2012-12-13
    • Related Report
      2012 Final Research Report
  • [Presentation] 高次クロマチン構造制御による骨格筋分化制御2012

    • Author(s)
      大川 恭行
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場・マリンメッセ福岡、福岡
    • Year and Date
      2012-12-12
    • Related Report
      2012 Final Research Report
  • [Presentation] Chd-2 dependent deposition of H3.3 is required for myogenic cell fate2012

    • Author(s)
      Akihito Harada, Anthony N. Imbalzano, Yasuyuki Ohkawa
    • Organizer
      KEYSTONE SYMPOSIA
    • Place of Presentation
      コロラド,USA
    • Year and Date
      2012-01-19
    • Related Report
      2012 Final Research Report
  • [Presentation] Control of gene expression through the phosphorylation of Ser2 and Ser5 of RNAP II : A combined analysis for ChIPseq and RNAseq2012

    • Author(s)
      Jun Odawara, Akihito Harada, Yasuyuki Ohkawa
    • Organizer
      KEYSTONE SYMPOSIA
    • Place of Presentation
      コロラド,USA
    • Year and Date
      2012-01-19
    • Related Report
      2012 Final Research Report
  • [Presentation] Chd-2 dependent deposition of H3.3 is required for myogenic cell fate.2012

    • Author(s)
      大川恭行
    • Organizer
      KEYSTONE SYMPOSIA
    • Place of Presentation
      KEYSTONE RESORT,USA
    • Related Report
      2011 Research-status Report
  • [Presentation] Control of gene expression through the phosphorylation of Ser2 and Ser5 of RNAPII: A combined analysis for ChIPseq and RNAseq.2012

    • Author(s)
      原田哲仁, 大川恭行
    • Organizer
      KEYSTONE SYMPOSIA
    • Place of Presentation
      KEYSTONE RESORT,USA
    • Related Report
      2011 Research-status Report
  • [Presentation] The deposition of histone varients is the basis of chromatin structual changes in cell fate decision2011

    • Author(s)
      Yasuyuki Ohkawa, Jun Odawara, Akihito Harada
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜、神奈川
    • Year and Date
      2011-12-16
    • Related Report
      2012 Final Research Report
  • [Presentation] Chd-2 dependent deposition of H3.3 is crucial for Brg1 recruitment in myogenesis2011

    • Author(s)
      Akihito Harada, Jun Odawara, Kazumitu Maehara, Tomohiko Yoshimi, Saori Yoshimura, Taro Tachibana, Hitoshi Kurumizaka, Hiroshi Kimura, Yasuyuki Ohkawa
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜、神奈川
    • Year and Date
      2011-12-15
    • Related Report
      2012 Final Research Report
  • [Presentation] ヒストンバリアントH3.3取り込みによる骨格筋分化運命決定

    • Author(s)
      大川 恭行
    • Organizer
      第6回日本エピジェネティクス研究会年会
    • Place of Presentation
      学術総合センター(東京)
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 高次クロマチン構造における細胞分化運命決定

    • Author(s)
      大川 恭行
    • Organizer
      第33回日本炎症・再生医学会
    • Place of Presentation
      ホテル日航福岡(福岡)
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 遺伝子をすべて見る研究への挑戦

    • Author(s)
      大川 恭行
    • Organizer
      「京」シンポジウム:新生命科学分野開拓とスーパーコンピュータ「京」
    • Place of Presentation
      九州大学医学部百年講堂(福岡)
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 遺伝子をすべて見る研究への試み-多様化するエピゲノム解析-

    • Author(s)
      大川 恭行
    • Organizer
      HPCIワークショップ2012(日本バイオインフォマティクス学会 創薬インフォマティクス研究会)
    • Place of Presentation
      産総研臨海副都心センター(東京)
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] ヒストンバリアントH3.3取り込みによる骨格筋分化運命決定

    • Author(s)
      大川 恭行
    • Organizer
      平成24年度遺伝研研究会「染色体ドメインの形成と機能発現機構」
    • Place of Presentation
      国立遺伝学研究所(静岡)
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Chd2 incorporates H3.3 to mark myogenic genes.

    • Author(s)
      大川 恭行
    • Organizer
      新学術領域「ゲノム支援」国際シンポジウム”Expanding Frontiers of Genome Science”
    • Place of Presentation
      東京大学 伊藤国際学術研究センター(東京)
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] The deposition of histone variant H3.3 mediated by transcription factors determines hematopoietic cell fate.

    • Author(s)
      Jun Odawara, Kohta Miyawaki, Kentaro Kohno, Takahiro Shima, Masao Nagasaki, Yasuyuki Ohkawa, Koichi Akashi.
    • Organizer
      第10回幹細胞シンポジウム
    • Place of Presentation
      淡路夢舞台国際会議場(兵庫)
    • Related Report
      2012 Annual Research Report
  • [Presentation] 骨格筋分化における高次クロマチン構造制御機構の解明

    • Author(s)
      大川 恭行
    • Organizer
      新学術領域「遺伝情報収納・発現・継承の時空間場」・第5回班会議
    • Place of Presentation
      ルスツリゾート(北海道)
    • Related Report
      2012 Annual Research Report
  • [Presentation] 高次クロマチン構造制御による骨格筋分化制御

    • Author(s)
      大川 恭行
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場・マリンメッセ福岡(福岡)
    • Related Report
      2012 Annual Research Report
  • [Presentation] Chd2依存的なH3.3マーキングが筋発生における骨格筋遺伝子のbivalent geneの形成に必要である

    • Author(s)
      原田 哲仁, 小田原 淳, 前原 一満, 立花 太郎, 木村 宏, 大川 恭行
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場・マリンメッセ福岡(福岡)
    • Related Report
      2012 Annual Research Report
  • [Presentation] CHD5(Chromodomain helicase DNA binding protein 5)はマウスの胚性幹細胞においてH3.1と結合して遺伝子発現を抑制しうる

    • Author(s)
      林 正康, 小田原 淳, 原田 哲仁, 前原 一満, 立花 太郎, 赤司 浩一, 大川 恭行
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場・マリンメッセ福岡(福岡)
    • Related Report
      2012 Annual Research Report
  • [Presentation] 共局在回帰モデルとENCODEデータセットを介したChIP-seqデータの多サンプル比較解析

    • Author(s)
      前原 一満, 小田原 淳, 原田 哲仁, 吉見 智彦, 長尾 恒治, 小布施 力史, 立花 太郎, 坂田 年男, 大川 恭行
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場・マリンメッセ福岡(福岡)
    • Related Report
      2012 Annual Research Report
  • [Presentation] モノクローナル抗体を用いたリン酸化ヒストンH3の解析

    • Author(s)
      吉見 智彦, 大川 恭行, 東 雅之, 立花 太郎
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場・マリンメッセ福岡(福岡)
    • Related Report
      2012 Annual Research Report
  • [Presentation] 選択的なヒストンバリアントH3.3の取り込みによる造血細胞分化運命決定機構の解明

    • Author(s)
      小田原 淳, 植野 和子, 成相 直樹, 林 正康, 前原 一満, 原田 哲仁, 宮脇 恒太, 河野 健太郎, 島 隆宏, 吉見 智彦, 立花 太郎, 赤司 浩一, 長崎 正朗, 大川 恭行
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場・マリンメッセ福岡(福岡)
    • Related Report
      2012 Annual Research Report
  • [Presentation] ヒストンバリアントによる骨格筋分化制御機構

    • Author(s)
      大川 恭行
    • Organizer
      第1回ヒストンバリアント研究会
    • Place of Presentation
      九州大学総合研究棟(福岡)
    • Related Report
      2012 Annual Research Report
  • [Presentation] The deposition of histone varients is the basis of chromatin structual changes in cell fate decision.

    • Author(s)
      大川恭行
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(神奈川)
    • Related Report
      2011 Research-status Report
  • [Presentation] Chd-2 dependent deposition of H3.3 is crucial for Brg1 recruitment in myogenesis.

    • Author(s)
      原田哲仁, 大川恭行
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(神奈川)
    • Related Report
      2011 Research-status Report
  • [Presentation] Control of gene expression through the phosphorylation of Ser2 and Ser5 of RNAPII: A combined analysis for ChIPseq and RNAseq.

    • Author(s)
      前原一満, 大川恭行
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(神奈川)
    • Related Report
      2011 Research-status Report
  • [Presentation] Visualization for nuclear distribution of PPARδ in myoblast.

    • Author(s)
      澤野祥子, 大川恭行
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(神奈川)
    • Related Report
      2011 Research-status Report
  • [Book] 実験医学2013

    • Author(s)
      大川 恭行, 小田原 淳, 原田 哲仁
    • Publisher
      羊土社
    • Related Report
      2012 Final Research Report
  • [Book] 実験医学 Vol.31 No.42013

    • Author(s)
      大川恭行, 小田原淳, 原田哲仁
    • Publisher
      羊土社
    • Related Report
      2012 Annual Research Report
  • [Book] 細胞工学2012

    • Author(s)
      原田 哲仁, 大川 恭行
    • Publisher
      秀潤社
    • Related Report
      2012 Final Research Report
  • [Book] Methods Mol Biol"Isolation of nuclei from skeletal muscle satellite cells and myofibers for use in chromatin immunoprecipitation assays."2012

    • Author(s)
      Ohkawa Y, Mallappa C, Vallaster CS, Imbalzano AN
    • Publisher
      Springer 社
    • Related Report
      2012 Final Research Report
  • [Book] Methods Mol Biol"An improved restriction enzyme accessibility assay for analyzing changes in chromatin structure insamples of limited cell number."2012

    • Author(s)
      Ohkawa Y, Mallappa C, Vallaster CS, Imbalzano AN
    • Publisher
      Springer 社
    • Related Report
      2012 Final Research Report
  • [Book] Methods Mol Biol.2012

    • Author(s)
      Ohkawa Y, Mallappa C, Vallaster CS, Imbalzano AN.
    • Publisher
      Springer社
    • Related Report
      2012 Annual Research Report
  • [Book] 細胞工学 Vol.31 No.82012

    • Author(s)
      原田哲仁, 大川恭行
    • Publisher
      秀潤社
    • Related Report
      2012 Annual Research Report
  • [Remarks] 九州大学 医学研究院 先端医療医学部門エピジェネティクス分野 / 大川研究室

    • URL

      http://chromatin.med.kyushu-u.ac.jp/

    • Related Report
      2012 Final Research Report
  • [Remarks] 九州大学 医学研究院 先端医療医学部門 エピジェネティクス分野 / 大川研究室

    • URL

      http://chromatin.med.kyushu-u.ac.jp/

    • Related Report
      2012 Annual Research Report
  • [Remarks]

    • URL

      http://chromatin.med.kyushu-u.ac.jp/

    • Related Report
      2011 Research-status Report

URL: 

Published: 2011-08-05   Modified: 2020-04-17  

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