Elucidating the roles of higher-order chromatin structure in the formation of chromosomal domains

2009 Fiscal Year Final Research Report

• Project/Area Number: 17080012
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: The Institute of Physical and Chemical Research
• Principal Investigator: NAKAYAMA Jun-ichi The Institute of Physical and Chemical Research, クロマチン動態研究チーム, チームリーダー (60373338)
• Co-Investigator(Kenkyū-buntansha): MURAKAMI Yota 北海道大学, 先端生命科学研究院, 教授 (20260622) ; OKI Masaya 福井大学, 工学研究科, 准教授 (60420626)
• Project Period (FY): 2005 – 2009
• Keywords: 遺伝子 / 発現制御 / ヘテロクロマチン / RNA干渉 / 分裂酵母 / 出芽酵母

Research Abstract

In this research program, we tried to gain a better understanding of the molecular mechanisms underlying the establishment and maintenance of higher-order chromatin structure, heterochromatin. We successfully identified ARC and Eri1 as novel regulatory factors of heterochromatin assembly in fission yeast. We also demonstrated that the HP1 function is regulated by dosage balance and posttranslational modifications. Furthermore, using budding yeast, we defined the molecular mechanisms to form heterochromatin boundaries.

Research Products

• [Journal Article] MRG15 directly binds to PALB2 and stimulates homology-directed repair of chromosomal breaks. (2010)
  • Author(s): Hayakawa, T., Zhang, F., Hayakawa, N., Ohtani, Y., Shinmyozu, K., Nakayama, J., Andressen, P.R.
  • Journal Title: J. Cell Sci. 123(in press) Pages: 1124-1130
  • Peer Reviewed
• [Journal Article] Dynamic regulation of heterochromatin via phosphorylation of HP1-family proteins. (2010)
  • Author(s): Shimada, A., Murakami, Y.
  • Journal Title: Epigenetics 5 Pages: 30-33
• [Journal Article] Reconstitution of Arabidopsis thaliana SUMO pathways in E. coli: functional evaluation of SUMO machinery proteins and mapping of SUMOylation sites by mass spectrometry. (2009)
  • Author(s): Okada, S., Nagabuchi, M., Takamura, Y., Nakagawa, T., Shinmyozu, K., Nakayama, J., Tanaka, K.
  • Journal Title: Plant Cell Physiol. 50 Pages: 1049-1061
  • Peer Reviewed
• [Journal Article] Phosphorylation of Swi6/HP1 regulates transcriptional gene silencing at heterochromatin. (2009)
  • Author(s): Shimada, A., Dohke, K., Sadaie, M., Shinmyozu, K., Nakayama, J., Urano, T., Murakami, Y.
  • Journal Title: Genes Dev. 23 Pages: 18-23
  • Peer Reviewed
• [Journal Article] The heterochromatin protein Swi6/HP1 activates replication origins at pericentromeres and silent mating-type locus. (2009)
  • Author(s): Hayashi, M.T., Takahashi, T.S., Nakagawa, T., Nakayama, J., Masukata, H.
  • Journal Title: Nat. Cell Biol. 11 Pages: 357-362
  • Peer Reviewed
• [Journal Article] Balance between distinct HP1 family proteins controls heterochromatin assembly in fission yeast (2008)
  • Author(s): Sadaie, M., Kawaguchi, R., Ohtani, Y., Arisaka, F., Tanaka, K., Shirahige, K., Nakayama, J.
  • Journal Title: Mol. Cell. Biol. 28 Pages: 6973-6988
  • Peer Reviewed
• [Journal Article] siRNA-mediated heterochromatin establishment requires HP1 and is associated with antisense transcription. (2008)
  • Author(s): Iida, T., Nakayama, J., Moazed, D.
  • Journal Title: Mol. Cell 31 Pages: 178-189
  • Peer Reviewed
• [Journal Article] A conserved SET-domain methyltransferase, Set11, modifies ribosomal protein Rpl12 in fission yeast. (2008)
  • Author(s): Sadaie, M., Shinmyozu, K., Nakayama, J.
  • Journal Title: J. Biol. Chem. 283 Pages: 7185-7195
  • Peer Reviewed
• [Journal Article] Gene expression and distribution of Swi6 in partial aneuploids of the fission yeast Schizosaccharomyces pombe. (2008)
  • Author(s): Chikashige, Y., Nakayama, J. (8人中5番目), Hiraoka, Y.
  • Journal Title: Cell Struct. Funct. 32 Pages: 149-161
  • Peer Reviewed
• [Journal Article] Schizosaccharomyces pombe Orc5 plays multiple roles in the maintenance of genome stability throughout the cell cycle. (2008)
  • Author(s): Kato, H., Matsunaga, F., Miyazaki, S., Yin, L., D'Urso, G., Tanaka, K., Murakami, Y.
  • Journal Title: Cell Cycle 7 Pages: 1085-1096
  • Peer Reviewed
• [Journal Article] Fission yeast chromatin assembly factor 1 assists in the replication-coupled maintenance of heterochromatin. (2008)
  • Author(s): Dohke, K., Miyazaki, S., Tanaka, K., Urano, T., Grewal, S.I., Murakami, Y.
  • Journal Title: Genes Cells. 13 Pages: 1027-43
  • Peer Reviewed
• [Journal Article] RBP2 is an MRG15 complex component and downregulates intragenic histone H3 lysine 4 methylation. (2007)
  • Author(s): Hayakawa, T., Ohtani, Y., Hayakawa, N., Shinmyozu, K., Saito, M., Ishikawa, F., Nakayama, J.
  • Journal Title: Genes Cells 12 Pages: 811-826
  • Peer Reviewed
• [Journal Article] Two different Argonaute complexes are required for siRNA generation and heterochromatin assembly in fission yeast. (2007)
  • Author(s): Buker, S.M., Iida, T., Buhler, M., Villen, J., Gygi, S.P., Nakayama, J., Moazed, D.
  • Journal Title: Nat. Struct. Mol. Biol. 14 Pages: 200-207
  • Peer Reviewed
• [Journal Article] Faster and easier chromatin immunoprecipitation assay with high sensitivity. (2007)
  • Author(s): Kohzaki, H., Murakami, Y.
  • Journal Title: Proteomics 7 Pages: 10-14
  • Peer Reviewed
• [Journal Article] Transcription factor Runx1 recruits the polyomavirus replication origin to replication factories. (2007)
  • Author(s): Murakami, Y., Chen, LF., Sanechika, N., Kohzaki, H., Ito, Y.
  • Journal Title: J. Cell Biochem. 100 Pages: 1313-1323
  • Peer Reviewed
• [Journal Article] The novel gene mus7(+) is involved in the repair of replication-associated DNA damage in fission yeast. (2007)
  • Author(s): Yokoyama, M., Inoue, H., Ishii, C., Murakami, Y.
  • Journal Title: DNA Repair (Amst) 6 Pages: 770-780
  • Peer Reviewed
• [Journal Article] Identification of novel suppressors for Mog1 implies its involvement in RNA metabolism, lipid metabolism and signal transduction. (2007)
  • Author(s): Oki, M. (9名中1番目), Nishimoto T.
  • Journal Title: Gene 400 Pages: 114-121
  • Peer Reviewed
• [Journal Article] Role of histone phosphorylation in chromatin dynamics and its implications in diseases. (2007)
  • Author(s): Oki, M., Aihara, H., Ito, T.
  • Journal Title: Subcell. Biochem. 41 Pages: 319-336
  • Peer Reviewed
• [Journal Article] Temperature-sensitive defects of the GSP1gene, yeast Ran homologue, activate the Tel1-dependent pathway. Biochem. Biophys. (2007)
  • Author(s): Hayashi, N., Oki, M. (10名中5番目), Nishimoto T.
  • Journal Title: Res. Commun. 353 Pages: 330-336
  • Peer Reviewed
• [Journal Article] Cytoplasmic siRNA-degrading ribonuclease, Eri1, negatively regulates heterochromatin assembly in fission yeast. (2006)
  • Author(s): Iida, T., Kawaguchi, R., Nakayama, J.
  • Journal Title: Curr. Biol. 16 Pages: 1459-1464
  • Peer Reviewed
• [Journal Article] Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b (2006)
  • Author(s): Tsumura, A., Nakayama, J. (11名中10番目), Okano, M.
  • Journal Title: Genes Cells 11 Pages: 805-814
  • Peer Reviewed
• [Journal Article] Nuclear RanGAP is required for the heterochromatin assembly and reciprocally regulated by histones and Clr4 histone methyltransferase in S. (2006)
  • Author(s): Nishijima, H., Nakayama, J., Yoshioka, T., Kusano, A., Nishitani, H., Shibahara, K., Nishimoto, T.
  • Journal Title: pombe. Mol. Biol. Cell 17 Pages: 2524-2536
  • Peer Reviewed
• [Journal Article] The CENP-B homolog, Abp1, interacts with the initiation protein Cdc23 (MCM10) and is required for efficient DNA replication in fission yeast. (2006)
  • Author(s): Locovei, AM., Spiga, MG., Tanaka, K., Murakami, Y., D'Urso, G.
  • Journal Title: Cell Div. 1 Pages: 27
  • Peer Reviewed
• [Journal Article] Different mating-type-regulated genes affect the DNA repair defects of Saccharomyces RAD51, RAD52 and RAD55 mutants. (2006)
  • Author(s): Valencia-Burton, M., Oki, M., Johnson, J., Seier, TA., Kamakaka, R., Haber, JE.
  • Journal Title: Genetics 174 Pages: 41-55
  • Peer Reviewed
• [Presentation] エピジェネティックな遺伝子発現切り替わりメカニズムの解析 (2010)
  • Author(s): 沖昌也
  • Organizer: 第27回染色体ワークショップ
  • Place of Presentation: 御殿場市
  • Year and Date: 2010-01-20
• [Presentation] Dynamic Regulation of heterochromatin sturucture/function in the cell cycle. (2009)
  • Author(s): 村上洋太
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: 横浜市
  • Year and Date: 20091209-20091212
• [Presentation] トランスポゼース由来の分裂酵母CENP-Bホモログはキネトコアとヘテロクロマチンの境界で機能する (2009)
  • Author(s): 村上洋太
  • Organizer: 第82回日本生化学会大会
  • Place of Presentation: 神戸市
  • Year and Date: 20091021-20091024
• [Presentation] Dynamic Regulation of Heterochrimatin (2009)
  • Author(s): 村上洋太
  • Organizer: 第24回内藤カンファレンス"Nuclear Dynamics and RNA [II]
  • Place of Presentation: 札幌市
  • Year and Date: 20090623-20090626
• [Presentation] Chromodomain Protein and RNAi-mediated Heterochromatin Assembly. (2009)
  • Author(s): 中山潤一
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: 横浜市
  • Year and Date: 2009-12-09
• [Presentation] Analysis of the heredity change of the boundary (2009)
  • Author(s): 沖昌也
  • Organizer: UNIA Current Trends in Biomedical Workshop 2009 on: Chromatin domains and Insulators
  • Place of Presentation: Baeza, Spain
  • Year and Date: 2009-11-09
• [Presentation] Distinct Roles of Chromodomain Proteins in the Formation of Higher-Order Chromatin Structure. (2009)
  • Author(s): 中山潤一
  • Organizer: The Fifth International Fission Yeast Meeting
  • Place of Presentation: 東京都
  • Year and Date: 2009-10-29
• [Presentation] Dynamic Regulation of Heterochromatin (2009)
  • Author(s): 村上洋太
  • Organizer: The Fifth International Fission Yeast Meeting
  • Place of Presentation: 東京都
  • Year and Date: 2009-10-29
• [Presentation] 分裂酵母のSETドメインタンパク質はリボソームタンパク質のメチル化修飾してリボソーム機能を制御する (2009)
  • Author(s): 中山潤一
  • Organizer: 第11回RNAミーティング
  • Place of Presentation: 新潟市
  • Year and Date: 2009-07-29
• [Presentation] Analysis of the heredity change of the gene expression in the single cell (2009)
  • Author(s): 沖昌也
  • Organizer: FASEB Summer Research Conference
  • Place of Presentation: Colorado, USA
  • Year and Date: 2009-07-13
• [Presentation] 単一細胞におけるエピジェネティックな遺伝子発現切り替わりメカニズムの解析 (2009)
  • Author(s): 沖昌也
  • Organizer: 第8回核ダイナミクス研究会
  • Place of Presentation: 伊豆市
  • Year and Date: 2009-06-19
• [Presentation] 哺乳類HP1のリン酸化修飾の同定とその機能の解析 (2009)
  • Author(s): 中山潤一
  • Organizer: 第26回染色体ワークショップ
  • Place of Presentation: 姫路市
  • Year and Date: 2009-01-27
• [Presentation] 生体内におけるサイレンシング領域伸長停止メカニズムの解析 (2009)
  • Author(s): 沖昌也
  • Organizer: 第26回染色体ワークショップ
  • Place of Presentation: 姫路市
  • Year and Date: 2009-01-27
• [Presentation] ヘテロクロマチン領域伸長停止とTy因子の関与 (2008)
  • Author(s): 沖昌也
  • Organizer: 第31回日本分子生物学会
  • Place of Presentation: 神戸市
  • Year and Date: 2008-12-11
• [Presentation] HMR left boundaryの機能解明 (2008)
  • Author(s): 沖昌也
  • Organizer: 酵母遺伝学フォーラム第41回研究報告会
  • Place of Presentation: 札幌市
  • Year and Date: 2008-09-11
• [Presentation] 分裂酵母SETドメインタンパク質の機能解析 (2008)
  • Author(s): 中山潤一
  • Organizer: 酵母遺伝学フォーラム第41回研究報告会
  • Place of Presentation: 札幌市
  • Year and Date: 2008-09-10
• [Presentation] 生体内におけるヘテロクロマチン領域伸長停止メカニズムの解析 (2008)
  • Author(s): 沖昌也
  • Organizer: 第80回日本遺伝学会
  • Place of Presentation: 名古屋市
  • Year and Date: 2008-09-05
• [Presentation] Distinct roles of chromodomain proteins in the formation of higher-order chromatin structure (2008)
  • Author(s): 中山潤一
  • Organizer: The 21th NAITO Conference
  • Place of Presentation: 北杜市
  • Year and Date: 2008-06-26
• [Presentation] Balance between distinct HP1 proteins controls heterochromatin assembly in fission yeast (2008)
  • Author(s): 中山潤一
  • Organizer: International Symposium on Chromosome Dynamics in Ise, 2008
  • Place of Presentation: 志摩市
  • Year and Date: 2008-05-28
• [Presentation] 高次クロマチン構造形成とRNA代謝ネットワーク (2008)
  • Author(s): 中山潤一
  • Organizer: 第2回日本エピジェネティクス研究会年会
  • Place of Presentation: 三島市
  • Year and Date: 2008-05-10
• [Book] 染色体サイクルのクロマチン制御:概論, 蛋白質核酸酵素増刊「染色体サイクル」(正井久雄、升方久夫、釣本敏樹、仁木宏典、篠原彰編) (2009)
  • Author(s): 中山潤一
  • Total Pages: 485-487
  • Publisher: 共立出版
• [Book] RNAiによるヘテロクロマチン制御機構, 実験医学増刊「染色体サイクル」(正井久雄・渡辺良典編) (2007)
  • Author(s): 飯田哲史・中山潤一
  • Total Pages: 186-190
  • Publisher: 羊土社