The structure and dynamics of chromatin harboring specific histone modifications

• Project/Area Number: 19370076
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Molecular biology
• Research Institution: Osaka University
• Principal Investigator: KIMURA Hiroshi Osaka University, 生命機能研究科, 准教授 (30241392)
• Project Period (FY): 2007 – 2009
• Project Status: Completed (Fiscal Year 2009)
• Budget Amount: ¥18,200,000 (Direct Cost: ¥14,000,000、Indirect Cost: ¥4,200,000); Fiscal Year 2009: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000); Fiscal Year 2008: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000); Fiscal Year 2007: ¥6,760,000 (Direct Cost: ¥5,200,000、Indirect Cost: ¥1,560,000)
• Keywords: 染色体構造・機能・分配 / クロマチン / 核構造 / 細胞周期 / 細胞構造 / 機能 / ヒストン / エピジェネティクス / 細胞核 / 蛋白質翻訳後修 / 生細胞観察 / 転写制御回 / 翻訳後修飾 / アセチル化 / モノクローナル抗体 / メチル化 / 遺伝子発現

Research Abstract

To understand the structure and dynamics of specialized chromatin harboring distinct histone modifications, we employed chromatin immunoprecipitation followed by mass spectrometry analysis and live cell imaging by using modification-specific monoclonal antibodies. Using affinity beads coated with different antibodies, distinct sets of proteins were identified as components of chromatin enriched in specific modifications. A method for visualizing specific histone modifications in living cells was also developed.

Research Products

• [Journal Article] Human POGZ modulates HP1 dissociation from mitotic chromosome arms through Aurora B activation. (2010)
  • Author(s): Nozawa, R.-S., Nagao, K., Masuda, H.-T., Iwasaki, O., Hirota, T., Nozaki, N., Kimura, H., Obuse, C
  • Journal Title: Nature Cell Biol (in press)
  • Peer Reviewed
• [Journal Article] Structural basis of instability of the nucleosome containing a testis-specific histone variant (2010)
  • Author(s): Tachiwana, H., Kagawa, W., Osakabe, A., Kawaguchi, K., Shiga, T., Hayashi-Takanaka, Y., Kimura, H., Kurumizaka, H
  • Journal Title: human H3T. Proc. Natl Acad. Sci (in press)
  • Peer Reviewed
• [Journal Article] 特異的モノクローナル抗体を用いたメチル化ヒストンダイナミクスの可視化 (2010)
  • Author(s): 木村宏, 林陽子
  • Journal Title: 実験医学 増刊号(印刷中)
• [Journal Article] Visualization of DNA methylation and histone modifications in living cells. (2010)
  • Author(s): Kimura, H., Hayashi-Takanaka, Y., Yamagata, K
  • Journal Title: Curr. Opin. Cell Biol doi:10.1016/j.ceb.2010.02.0041
  • Peer Reviewed
• [Journal Article] Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. (2010)
  • Author(s): Matsui, T., Leung, D., Miyashita, H., Maksakova, I.A., Miyachi, H., Kimura, H., Tachibana, M., Lorincz, M.C., Shinkai, Y
  • Journal Title: Nature 464 Pages: 927-931
  • NAID: 120002140757
  • Peer Reviewed
• [Journal Article] Histone H1 null vertebrate cells exhibit altered nucleosome architecture. (2010)
  • Author(s): Hashimoto, H., Takami, Y., Sonoda, E., Iwasaki, T., Iwano, H., Tachibana, M., Takeda, S., Nakayama, T., Kimura, H., Shinkai, Y
  • Journal Title: Nucleic Acids Res doi:10.1093/nar/gkq076
  • Peer Reviewed
• [Journal Article] Transduction of RNA-directed DNA methylation signals to repressive histone marks in Arabidopsis thaliana. (2010)
  • Author(s): Numa, H., Kim, J.M., Matsui, A., Kurihara, Y., Morosawa, T., Ishida, J., Mochizuki, Y., Kimura, H., Shinozaki, K., Toyoda, T., Seki, M., Yoshikawa, M., Habu Y
  • Journal Title: EMBO J. 29 Pages: 352-362
  • Peer Reviewed
• [Journal Article] Visualization of DNA methylation and histone modifications in living cells. (2010)
  • Author(s): Kimura, H.
  • Journal Title: Curr.Opin.Cell Biol. (印刷中)
  • Peer Reviewed
• [Journal Article] Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. (2010)
  • Author(s): Matsui, T.
  • Journal Title: Nature (印刷中)
  • Peer Reviewed
• [Journal Article] Histone H1 null vertebrate cells exhibit altered nucleosome architecture. (2010)
  • Author(s): Hashimoto, H.
  • Journal Title: Nucl.Acids Res. (印刷中)
  • Peer Reviewed
• [Journal Article] Transduction of RNA-directed DNA methylation signals to repressive histone marks in Arabidopsis thaliana. (2010)
  • Author(s): Numa, H.
  • Journal Title: EMBO J. 29 Pages: 352-362
  • Peer Reviewed
• [Journal Article] Visualizing histone modifications in living cells: spatiotemporal dynamics of H3 phosphorylation during interphase. (2009)
  • Author(s): Hayashi-Takanaka, Y., Yamagata, K., Nozaki, N., Kimura, H
  • Journal Title: J. Cell Biol 187 Pages: 781-790
  • Peer Reviewed
• [Journal Article] Inactive X chromosome-specific histone H3 modifications and CpG hypomethylation flank a chromatin boundary between an X-inactivated and an escape gene. (2009)
  • Author(s): Goto, Y., Kimura, H
  • Journal Title: Nucleic Acids Res 37 Pages: 7416-7428
  • Peer Reviewed
• [Journal Article] A wave of nascent transcription on activated human genes. (2009)
  • Author(s): Wada, Y., Ohta, Y., Xu, M., Tsutsumi, S., Minami, T., Inoue, K., Komura, D., Kitakami, J., Oshida, N, Papantonis, A., Izumi, A., Kobayashi, M., Meguro, H, Kanki, Y., Mimura, I., Yamamoto, K., Mataki, C., Hamakubo, T., Shirahige, K., Aburatani, H., Kimura, Wada, Y., Ohta, Y., Xu, M., Tsutsumi
  • Journal Title: Proc. Natl Acad. Sci. USA 106 Pages: 18357-18361
  • Peer Reviewed
• [Journal Article] Hierarchical inactivation of a synthetic human kinetochore by a chromatin modifier. (2009)
  • Author(s): Cardinale, S., Bergmann, J.H., Kelly, D., Nakano, M., Valdivia, M.M., Kimura, H., Masumoto, H., Larionov, V., Earnshaw, W. C
  • Journal Title: Mol. Biol. Cell 20 Pages: 4194-4204
  • Peer Reviewed
• [Journal Article] Histone demethylase Jmjd2c increases the expression of Mdm2 oncogene. (2009)
  • Author(s): Ishimura, A., Terashima, M., Kimura, H., Akagi, K., Suzuki, Y., Sugano, S., Suzuki, T
  • Journal Title: Biochem. Biophys. Res. Commun 389 Pages: 366-371
  • Peer Reviewed
• [Journal Article] ヒストンダイナミクスの可視化と膜透過化細胞による再構成 (2009)
  • Author(s): 木村宏, 林陽子
  • Journal Title: 実験医学 増刊号,27 Pages: 2833-2838
• [Journal Article] Visualizing histone modifications in living cells : spatiotemporal dynamics of H3 phosphorylation during interphase. (2009)
  • Author(s): Hayashi-Takanaka, Y.
  • Journal Title: J.Cell Biol. 187 Pages: 781-790
  • Peer Reviewed
• [Journal Article] Inactive X chromosome-specific histone H3 modifications and CpG hypomethylation flank a chromatin boundary between an X-inactivated and an escape gene. (2009)
  • Author(s): Goto, Y.
  • Journal Title: Nucl.Acids Res. 37 Pages: 7416-7428
  • Peer Reviewed
• [Journal Article] A wave of nascent transcription on activated human genes. (2009)
  • Author(s): Wada, Y.
  • Journal Title: Proc.Natl Acad.Sci.USA 106 Pages: 18357-18361
  • Peer Reviewed
• [Journal Article] Hierarchical inactivation of a synthetic human kinetochore by a chromatin modifier. (2009)
  • Author(s): Cardinale, S.
  • Journal Title: Mol.Biol. Cell 20 Pages: 4194-4204
  • Peer Reviewed
• [Journal Article] Histone demethylase Jmjd2c increases the expression of Mdm2 oncogene (2009)
  • Author(s): Ishimura, A.
  • Journal Title: Biochem.Biophys.Res.Commun. 389 Pages: 366-371
  • Peer Reviewed
• [Journal Article] ヒストンダイナミクスの可視化と膜透過化細胞による再構成 (2009)
  • Author(s): 木村宏
  • Journal Title: 実験医学(増刊号) 27 Pages: 2833-2838
• [Journal Article] G9a/GLP complexes independently mediate H3K9 and DNA methylation to silence transcription. (2008)
  • Author(s): Tachibana, M., Matsumura, Y., Fukuda, M., Kimura, H., Shinkai, Y
  • Journal Title: EMBO J. 27 Pages: 2681-2690
  • Peer Reviewed
• [Journal Article] Alterations of lysine modifications on histone H3 N-tail under drought stress conditions in Arabidopsis thaliana (2008)
  • Author(s): Kim, J.-M., Kim To, T., Ishida, J., Morosawa, T., Kawashima, M., Matsui, A., Toyoda, T., Kimura, H., Shinozaki, K., Seki, M
  • Journal Title: Plant Cell Physiol 49 Pages: 1580-1588
  • NAID: 10027334715
  • Peer Reviewed
• [Journal Article] Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro. (2008)
  • Author(s): Tachiwana, H., Osakabe, A., Kimura, H., Kurumizaka, H
  • Journal Title: Nucl. Acids Res 36 Pages: 2208-2218
  • Peer Reviewed
• [Journal Article] Organization of histone H3 modifications revealed by a panel of specific monoclonal antibodies. (2008)
  • Author(s): Kimura, H., Hayashi-Takanaka, Y., Goto, Y., Takizawa, N., Nozaki, N
  • Journal Title: Cell Struct. Funct 33 Pages: 61-73
  • NAID: 40016794072
  • Peer Reviewed
• [Journal Article] ビフォー&アフターフォトブリーチ (2008)
  • Author(s): 木村宏
  • Journal Title: 蛋白質核酸酵素 53 Pages: 1992-1999
• [Journal Article] Alterations of lysine modifications on histone H3 N-tai under drought stress conditions in Arabidopsis thaliana (2008)
  • Author(s): Kim, J. -M.
  • Journal Title: Plant Cell Physiology 49 Pages: 1580-1588
  • Peer Reviewed
• [Journal Article] G9a/GLP complexes independently mediate H3K9 and DNA methylation to silence transcription (2008)
  • Author(s): Tachibana, M.
  • Journal Title: EMBO Journal 27 Pages: 2681-2690
  • Peer Reviewed
• [Journal Article] ビフォー&アフター フォトブリーチ (2008)
  • Author(s): 木村 宏
  • Journal Title: 蛋白質核酸酵素 53 Pages: 1992-1999
• [Journal Article] The organization of histone H3 modifications as revealed by a panel of specific monoclonal antibodies (2008)
  • Author(s): Kimura, H.
  • Journal Title: Cell Structure and Function 33(in press)
  • NAID: 40016794072
  • Peer Reviewed
• [Journal Article] Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro (2008)
  • Author(s): Tachiwana, H.
  • Journal Title: Nucleic Acids Research (in press)
  • Peer Reviewed
• [Presentation] Live cell imaging of histone H3 phosphorylation in G2/M phase (2009)
  • Author(s): Hiroshi Kimura
  • Organizer: Mitosis and Cancer Symposium
  • Place of Presentation: オランダ国アムステルダム
  • Year and Date: 2009-02-26
• [Presentation] Visualizing histone modifications in living cells. (2009)
  • Author(s): H. Kimura
  • Organizer: 第32回日本分子生物学会
  • Place of Presentation: 横浜
• [Presentation] 染色体の損傷と分配異常に伴うヒストン修飾のダイナミクス (2009)
  • Author(s): 木村宏
  • Organizer: 日本放射線影響学会第52回大会
  • Place of Presentation: 広島
• [Presentation] 正常細胞とがん細胞におけるヒストンH3リン酸化ダイナミクスの差異 (2009)
  • Author(s): 木村宏, 林(高中)陽子, 山縣一夫, 野崎直仁
  • Organizer: 第82回日本生化学会大会
  • Place of Presentation: 神戸
• [Presentation] Visualization of histone modifications in living cells. (2009)
  • Author(s): H. Kimura, Y. Hayashi-Takanaka, K. Yamagata, N. Nozaki
  • Organizer: EMBO Conference on Nuclear Structure and Dynamics
  • Place of Presentation: L'Isle-sur-la-Sorgue, France
• [Presentation] Visualization of histone modifications in living cells. (2009)
  • Author(s): Y. Hayashi-Takanaka, K. Yamagata, N. Nozaki, H. Kimura
  • Organizer: 第61回日本細胞生物学会大会
  • Place of Presentation: 名古屋
• [Presentation] 生細胞内ヒストン修飾の可視化 (2009)
  • Author(s): 林(高中)陽子, 山縣一夫, 野崎直仁, 木村宏
  • Organizer: 第3回日本エピジェネティクス研究会年会
  • Place of Presentation: 東京
• [Presentation] Live-cell imaging of histone H3 phosphorylation in G2/M phase. (2009)
  • Author(s): Y. Hayashi-Takanaka, N. Nozaki, H. Kimura
  • Organizer: Mitosis and Cancer Symposium
  • Place of Presentation: Amsterdam, The Netherlands
• [Presentation] Visualizing histone modifications in living cells (2009)
  • Author(s): Hiroshi Kimura
  • Organizer: 第32回日本分子生物学会
  • Place of Presentation: 横浜
• [Presentation] 染色体の損傷と分配異常に伴うピストン修飾のダイナミクス (2009)
  • Author(s): 木村宏
  • Organizer: 日本放射線影響学会第52回大会
  • Place of Presentation: 広島
• [Presentation] 正常細胞とがん細胞におけるピストンH3リン酸化ダイナミクスの差異 (2009)
  • Author(s): 木村宏
  • Organizer: 第82回日本生化学会大会
  • Place of Presentation: 神戸
• [Presentation] Visualization of histone modifications in living cells (2009)
  • Author(s): Hiroshi Kimura
  • Organizer: 第61回日本細胞生物学会大会
  • Place of Presentation: 名古屋
• [Presentation] 生細胞内ピストン修飾の可視化 (2009)
  • Author(s): 木村宏
  • Organizer: 第3回日本エピジェネティクス研究会年会
  • Place of Presentation: 東京
• [Presentation] Visualization of histone modifications in living cells (2009)
  • Author(s): Hiroshi Kimura
  • Organizer: EMBO Conference on Nuclear Structure and Dynamics
  • Place of Presentation: フランスL'Isle-Sur-la-Sorgue
• [Presentation] Dynamics of histone modifications in living cells (2008)
  • Author(s): Hiroshi Kimura
  • Organizer: International Symposium Decoding Epigenetic Code
  • Place of Presentation: 東京
  • Year and Date: 2008-12-15
• [Presentation] ヒストン修飾ダイナミクスの可視化 (2008)
  • Author(s): 木村 宏
  • Organizer: クロマチン研究会 -細胞核・染色体・クロマチンの機能構造構築と動態-
  • Place of Presentation: 三島
  • Year and Date: 2008-10-22
• [Presentation] The modification and dynamics of histones in human cells as revealed by a panel of specific monoclonal antibodies (2008)
  • Author(s): Hiroshi Kimura
  • Organizer: ICHC2008 (XIII International Congress of Histochemistry and Cytochemistry)
  • Place of Presentation: ポーランド国グダンスク
  • Year and Date: 2008-08-26
• [Presentation] Histone modifications associated with transcription activation and silencing as revealed by a panel of specific monoclonal antibodies (2008)
  • Author(s): Hiroshi Kimura
  • Organizer: Benzon Symposium No. 55-Transcription, Chromatin and Disease
  • Place of Presentation: デンマーク国コペンハーゲン
  • Year and Date: 2008-08-19
• [Presentation] Dynamics of histone modifications during the cell cycle and gene activation (2008)
  • Author(s): Hiroshi Kimura
  • Organizer: International Symposium on Chromosome Dynamics in Ise
  • Place of Presentation: 志摩
  • Year and Date: 2008-05-28
• [Presentation] 転写の活性化に伴うヒストン修飾のダイナミクス (2008)
  • Author(s): 木村 宏
  • Organizer: 第2回 日本エピジェネティクス研究会
  • Place of Presentation: 三島
  • Year and Date: 2008-05-10
• [Presentation] Histone dynamics and modification in human cells. (2008)
  • Author(s): H. Kimura
  • Organizer: Millipore Bio Forum 2008
  • Place of Presentation: Tokyo, Japan
  • Year and Date: 2008-03-07
• [Presentation] 修飾ヒストン特異的モノクローナル抗体を用いたエピゲノム解析 (2008)
  • Author(s): 木村 宏
  • Organizer: 文部科学省科学研究費補助金特定領域研究「生殖系列の世代サイクルとエピゲノムネットワーク」発足記念キックオフシンポジウム
  • Place of Presentation: 東京
  • Year and Date: 2008-03-05
• [Presentation] クロマチン制御とがん (2008)
  • Author(s): 木村 宏
  • Organizer: 第10回癌治療増感研究シンポジウム
  • Place of Presentation: 奈良
  • Year and Date: 2008-02-10
• [Presentation] 細胞周期と転写の活性化に伴うヒストン修飾のダイナミクス (2008)
  • Author(s): 木村宏, 林(高中)陽子, 野崎直仁
  • Organizer: BMB2008
  • Place of Presentation: 神戸
• [Presentation] The modification and dynamics of histones in human cells as revealed by a panel of specific monoclonal antibodies. (2008)
  • Author(s): H. Kimura, Y. Hayashi-Takanaka, N. Nozaki
  • Organizer: ICHC2008: 13th Congress of the International Federation of Societies for Histochemistry and Cytochemistry
  • Place of Presentation: Gdansk, Poland
• [Presentation] Histone modifications associated with transcription activation and silencing as revealed by a panel of specific monoclonal antibodies. (2008)
  • Author(s): H. Kimura, Y. Hayashi-Takanaka, Y. Goto, N. Nozaki
  • Organizer: Benzon Symposium No. 55. Transcription, Chromatin and Disease
  • Place of Presentation: Copenhagen, Denmark
• [Presentation] Dynamics of histone modifications during the cell cycle and gene activation. (2008)
  • Author(s): Y. Hayashi-Takanaka, N. Nozaki, H. Kimura
  • Organizer: International Symposium on Chromosome Dynamics in Ise '08
  • Place of Presentation: Shima, Japan
• [Presentation] ヒストン交換と修飾のダイナミクス (2007)
  • Author(s): 木村 宏
  • Organizer: BMB2008
  • Place of Presentation: 横浜
  • Year and Date: 2007-12-15
• [Presentation] ヒストン交換と修飾のダイナミクス (2007)
  • Author(s): 木村宏, 林(高中)陽子, 立和名博昭, 越坂部晃永, 胡桃坂仁志, 野崎直仁
  • Organizer: BMB2007
  • Place of Presentation: 横浜
• [Book] 細胞核-遺伝情報制御と疾患:染色体・核輸送のダイナミクスと細胞分化から個体発生,破綻による疾患まで (2009)
  • Author(s): 平岡泰, 原田昌彦, 木村宏, 田代聡:編
  • Total Pages: 239
  • Publisher: 羊土社
• [Book] エピジェネティクス実験プロトコール(牛島俊和・眞貝洋一/編) (2008)
  • Author(s): 林陽子, 後藤友二, 木村宏
  • Publisher: 羊土社
• [Book] エピジェネティクス実験プロトコール(牛島俊和・ 眞貝洋一 編) (2008)
  • Author(s): 林 陽子
  • Total Pages: 267
  • Publisher: 羊土社
• [Book] 講義と実習:生細胞蛍光イメージング-阪大・北大顕微鏡コースブック- (2007)
  • Author(s): 原口徳子, 木村宏, 平岡泰:編
  • Total Pages: 302
  • Publisher: 共立出版
• [Book] 講義と実習:生細胞蛍光イメージング 阪大・北大顕微鏡コースブック (2007)
  • Author(s): 原口徳子
  • Total Pages: 302
  • Publisher: 共立出版
• [Remarks]
  • URL: http://www.dma.jim.osaka-u.ac.jp/kg-portal/aspi/RX0011D.asp?UNO=17710&page=