The physicochemical field for genetic activities

2012 Fiscal Year Final Research Report

• Project Area: The physicochemical field for genetic activities
• Project/Area Number: 20114001
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Osaka University
• Principal Investigator: HIRAOKA Yasushi 大阪大学, 生命機能研究科, 教授 (10359078)
• Co-Investigator(Renkei-kenkyūsha): OHYAMA Takashi 早稲田大学, 教育・総合科学学術院, 教授 (60268513) ; TOKUNAGA Makio 東京工業大学, 生命理工学研究科, 教授 (00192659) ; KURUMIZAKA Hitoshi 早稲田大学, 理工学術院, 教授 (80300870) ; OBUSE Chikashi 北海道大学, 先端生命科学研究院, 教授 (00273855) ; SUEMORI Hirofumi 京都大学, 再生医科学研究所, 准教授 (90261198) ; KIMURA Akatsuki 国立遺伝学研究所, 構造遺伝学研究センター, 准教授 (10365447)
• Project Period (FY): 2008-11-13 – 2014-03-31
• Keywords: 分子細胞生物学

Research Abstract

This study aims to understand the physicochemical filed in the cell nucleus ensuring genetic activities for chromosomes. This study has organized group meetings and workshops to promote interdisciplinary collaborations within the group. We organized an international symposium in related fields, and circulated our understandings and opinions through the web page and newsletters. We organized workshops and practical courses for students and young researchers.

Research Products

• [Journal Article] Human inactive X chromosome is compacted through a PRC2-independent SMCHD1-HBiX1 pathway (2013)
  • Author(s): Nozawa RS, Nagao K, Igami K, Shibata S, Shirai N, Nozaki N, Sado T, Kimura H, and Obuse C
  • Journal Title: Nat. Struct. Mol. Biol Volume: 20 Pages: 566-573
  • DOI: doi: 10.1038/nsmb.2532.
  • Peer Reviewed
• [Journal Article] A co-localization model of paired ChIP-seq data using a large ENCODE data set enables comparison of multiple samples (2013)
  • 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 Pages: 54-62
  • DOI: doi:10.1093/nar/gks1010
  • Peer Reviewed
• [Journal Article] Vertebrate Spt2 is a novel nucleolar histone chaperone that assists in ribosomal DNA transcription (2013)
  • Author(s): Osakabe A, Tachiwana H, Takaku M, Hori T, Obuse C, Kimura H, Fukagawa T, Kurumizaka H
  • Journal Title: J. Cell Sci Volume: 126 Pages: 1323-1332
  • DOI: doi:10.1242/jcs.112623
  • Peer Reviewed
• [Journal Article] Nap1 regulates proper CENP-B binding to nucleosomes (2013)
  • Author(s): Tachiwana H, Miya Y, Shono N, Ohzeki J, Osakabe A, Otake K, Larionov V, Earnshaw WC, Kimura H, Masumoto H, Kurumizaka H
  • Journal Title: Nucleic Acids Res Volume: 5 Pages: 2869-2880
  • DOI: doi:10.1093/nar/gks1464
  • Peer Reviewed
• [Journal Article] Human PSF concentrates DNA and stimulates duplex capture in DMC1-mediated homologous pairing (2012)
  • Author(s): Morozumi Y, Ino R, Takaku M, Hosokawa M, Chuma S, Kurumizaka H
  • Journal Title: Nucleic Acids Res Volume: 40 Pages: 3031-3041
  • DOI: doi:10.1093/nar/gkr1229
  • Peer Reviewed
• [Journal Article] Meiosis-specific non-coding RNA mediates robust pairing of homologous chromosomes in meiosis (2012)
  • Author(s): Ding D-Q, Okamasa K, Yamane M, Tsutsumi C, Haraguchi T, Yamamoto M, and Hiraoka Y
  • Journal Title: Science Volume: 336 Pages: 732-736
  • DOI: doi:10.1126/science.1219518
  • Peer Reviewed
• [Journal Article] Lamin B receptor recognizes specific modifications of histone H4 in heterochromatin formation (2012)
  • Author(s): Hirano Y, Hizume K, Kimura H, Takeyasu K, Haraguchi T, Hiraoka Y
  • Journal Title: J. Biol. Chem Volume: 287 Pages: 42654-42663
  • DOI: doi:10.1074/jbc.M112.397950
  • Peer Reviewed
• [Journal Article] Histone chaperone activity of Fanconi anemia proteins, FANCD2 and FANCI, is required for DNA crosslink repair (2012)
  • Author(s): Sato K, Ishiai M, Toda K, Furukoshi S, Osakabe A, Tachiwana H, Takizawa Y, Kagawa W, Kitao H, Dohmae N, Obuse C, Kimura H, Takata M, Kurumizaka H
  • Journal Title: EMBO J Volume: 31 Pages: 3524-3536
  • DOI: doi:10.1038/emboj.2012.197
  • Peer Reviewed
• [Journal Article] Chd2 interacts with H3.3 to determine myogenic cell fate (2012)
  • 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 Pages: 2994-3007
  • DOI: doi:10.1038/emboj.2012.136
  • Peer Reviewed
• [Journal Article] Halenaquinone, a chemical compound that specifically inhibits the secondary DNA binding of RAD51 (2011)
  • Author(s): Takaku M, Kainuma T, Ishida-Takaku T, Ishigami S, Suzuki H, Tashiro S, van Soest RWM, Nakao Y, Kurumizaka H
  • Journal Title: Genes Cells Volume: 6 Pages: 427-436
  • DOI: doi:10.1111/j.1365-2443.2011.01494.x
  • Peer Reviewed
• [Journal Article] Structures of human nucleosomes containing major histone H3 variants (2011)
  • Author(s): Tachiwana H, Osakabe A, Shiga T, Miya Y, Kimura H, Kagawa W, Kurumizaka H
  • Journal Title: Acta Cryst Volume: D67 Pages: 578-583
  • DOI: doi:10.1107/S0907444911014818
  • Peer Reviewed
• [Journal Article] Inner nuclear membrane protein Ima1 is dispensable for intranuclear positioning of centromeres (2011)
  • Author(s): Hiraoka Y, Maekawa H, Asakawa H, Chikashige Y, Kojidani T, Osakada H, Matsuda A, Haraguchi T
  • Journal Title: Genes Cells Volume: 16 Pages: 1000-1011
  • DOI: doi:10.1111/j.1365-2443.2011.01544.x
  • Peer Reviewed
• [Journal Article] The involvement of SLX4 in interstrand cross-link repair is regulated by the Fanconi anemia pathway (2011)
  • Author(s): Yamamoto KN, Kobayashi S, Tsuda M, Kurumizaka H, Takata M, Kono K, Jiricny J, Takeda S, Hirota K
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 108 Pages: 6492-6496
  • DOI: doi:10.1073/pnas.1018487108
  • Peer Reviewed
• [Journal Article] Physical breakdown of the nuclear envelope is not necessary for breaking its barrier function (2011)
  • Author(s): Asakawa H, Hiraoka Y, Haraguchi T
  • Journal Title: Nucleus Volume: 2 Pages: 523-526
  • DOI: doi:10.4161/nucl.2.6.16117
  • Peer Reviewed
• [Journal Article] Crystal structure of the human centromeric nucleosome containing CENP-A (2011)
  • Author(s): Tachiwana H, Kagawa W, Shiga T, Osakabe A, Miya Y, Saito K, Hayashi-Takanaka Y, Oda T, Sato M, Park S-Y, Kimura H, Kurumizaka H
  • Journal Title: Nature Volume: 476 Pages: 232-235
  • DOI: doi:10.1038/nature10258
  • Peer Reviewed
• [Journal Article] Tracking epigenetic histone modifications in single cells using Fab-based live endogenous modification labeling (2011)
  • Author(s): Hayashi-Takanaka Y, Yamagata K, Wakayama T, Stasevich TJ, Kainuma T, Tsurimoto T, Tachibana M, Shinkai Y, Kurumizaka H, Nozaki N, and Kimura H
  • Journal Title: Nucleic Acids Res Volume: 39 Pages: 6475-6488
  • DOI: doi:10.1093/nar/gkr343
  • Peer Reviewed
• [Journal Article] Human POGZ modulates dissociation of HP1alpha from mitotic chromosome arms through Aurora B activation (2010)
  • Author(s): Nozawa R, Nagao K, Masuda H, Iwasaki O, Hirota T, Nozaki N, Kimura H. and Obuse C
  • Journal Title: Nat. Cell Biol Volume: 12 Pages: 719-727
  • DOI: doi:10.1038/ncb2075
  • Peer Reviewed
• [Journal Article] Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T (2010)
  • Author(s): Tachiwana H, Kagawa W, Osakabe A, Kawaguchi K, Shiga T, Hayashi -Takanaka Y, Kimura H, and Kurumizaka H
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 107 Pages: 10454-10459
  • DOI: doi:10.1073/pnas.1003064107
  • Peer Reviewed
• [Journal Article] Nucleosome formation activity of human sNASP (2010)
  • Author(s): Osakabe A, Tachiwana H, Matsunaga T, Shiga T, Nozawa R, Obuse C, and Kurumizaka H
  • Journal Title: J. Biol. Chem Volume: 285 Pages: 11913-11921
  • DOI: doi:10.1074/jbc.M109.083238
  • Peer Reviewed
• [Journal Article] The putative nuclear localization signal of the human RAD52 protein is a potential sumoylation site (2010)
  • Author(s): Saito K, Kagawa W, Suzuki T, Suzuki H, Yokoyama S, Saitoh H, Tashiro S, Dohmae N, and Kurumizaka H
  • Journal Title: J. Biochem Volume: 147 Pages: 833-842
  • DOI: doi:10.1093/jb/mvq020
  • Peer Reviewed
• [Journal Article] GEMIN2 promotes accumulation of RAD51 at double-strand breaks in homologous recombination (2010)
  • Author(s): Takizawa Y, Qing Y, Takaku M, Ishida T, Morozumi Y, Tsujita T, Kogame T, Hirota K, Takahashi M, Shibata T, Kurumizaka H, and Takeda S
  • Journal Title: Nucleic Acids Res Volume: 38 Pages: 5059-5074
  • DOI: doi:10.1093/nar/gkq271
  • Peer Reviewed
• [Journal Article] Highly efficient chromatin transcription induced by superhelically curved DNA segments: the underlying mechanism revealed by a yeast system (2010)
  • Author(s): Tanase J, Morohashi N, Fujita M, Nishikawa J, Shimizu M, and Ohyama T
  • Journal Title: Biochemistry Volume: 49 Pages: 2351-2358
  • DOI: doi:10.1021/bi901950w
  • Peer Reviewed
• [Journal Article] Membrane proteins Bqt3 and Bqt4 anchor telomeres to the nuclear envelope to ensure chromosomal bouquet formation (2009)
  • Author(s): Chikashige Y, Yamane M, Okamasa K, Tsutsumi C, Kojidani T, Sato M, Haraguchi T, Hiraoka Y
  • Journal Title: J. Cell Biol Volume: 187 Pages: 413-427
  • DOI: doi:10.1083/jcb.200902122
  • Peer Reviewed
• [Journal Article] The SUN rises on meiotic chromosome dynamics (2009)
  • Author(s): Hiraoka Y, and Dernburg A
  • Journal Title: Dev. Cell Volume: 17 Pages: 598-605
  • DOI: doi:10.1016/j.devcel.2009.10.014
  • Peer Reviewed
• [Journal Article] Cell-size-dependent spindle elongation in the Caenorhabditis elegans early embryo (2009)
  • Author(s): Hara Y, and Kimura A
  • Journal Title: Curr. Biol Volume: 19 Pages: 1549-1554
  • DOI: doi:10.1016/j.cub.2009.07.050
  • Peer Reviewed
• [Journal Article] Positions of pluripotency genes and hepatocyte-specific genes in the nucleus before and after mouse ES cell differentiation
  • Author(s): Udagawa K, and Ohyama T
  • Journal Title: Genet. Mol. Res Volume: (in press)
  • Peer Reviewed
• [Presentation] Dynamics of proteins in the nucleus by single molecule analysis (2011)
  • Author(s): Tokunaga M, Sakata-Sogawa K
  • Organizer: International Symposium on the Physicochemical Field for Genetic Activities
  • Place of Presentation: Awaji, Hyogo, Japan, Awaji Yumebutai International Conference Cemter, Japan
  • Year and Date: 20110124-26
• [Presentation] The Cell Nucleus: A Physicochemical Field for Genetic Activities of the Chromosome (2011)
  • Author(s): Hiraoka Y, Chikashige Y, Haraguchi T
  • Organizer: International Symposium on the Physicochemical Field for Genetic Activities
  • Place of Presentation: Awaji Yumebutai International Conference Cemter, Japan
  • Year and Date: 2011-01-26
• [Presentation] Atomic Resolution Structures of the Human Nucleosomes Containing Histone Variants (2011)
  • Author(s): Kurumizaka H
  • Organizer: International Symposium of the Physicochemical Field for Genetic Activities
  • Place of Presentation: Awaji Yumebutai International Conference Cemter, Japan
  • Year and Date: 2011-01-25
• [Presentation] Proteomic Approach Identification and Characterization Hetereochromatic HP1-binding Proteins (2011)
  • Author(s): Obuse C
  • Organizer: International Symposium Physicochemical Field for Genetic Activities
  • Place of Presentation: Awaji Yumebutai International Conference Cemter, Japan
  • Year and Date: 2011-01-25
• [Presentation] Changes Expression Of Chromatin Modification Factors During The Early Embryonic Germ Layer Determination (2011)
  • Author(s): Suemori H
  • Organizer: International Symposium Physicochemical Field for Genetic Activities
  • Place of Presentation: Awaji Yumebutai International Conference Cemter, Japan
  • Year and Date: 2011-01-25
• [Presentation] Structure of yeast interphase chromosomes and the genome folding principle (2011)
  • Author(s): Ohyama T, Kimura H, Nishikawa J, Shimooka Y, Arakawa J, Seki M, Miura O, Sugiyama S, Yamada S
  • Organizer: International Symposium on the Physicochemical Field for Genetic Activities
  • Place of Presentation: Awaji Yumebutai International Conference Cemter, Japan
  • Year and Date: 2011-01-24
• [Presentation] Size-dependency/independency in the spatial organization of the cell: nuclear positioning and chromosome dynamics in C. elegans embryos (2011)
  • Author(s): Kimura A
  • Organizer: International Symposium Physicochemical Field for Genetic Activities
  • Place of Presentation: Awaji Yumebutai International Conference Center, Japan
  • Year and Date: 2011-01-24
• [Book] 遺伝情報の時空間場の理解に向けて. 実験医学 増刊 細胞核-遺伝情報制御と疾患 (2009)
  • Author(s): 平岡 泰
  • Total Pages: 27,.2708-2714
  • Publisher: 羊土社
• [Remarks]
  • URL: http://www.genofield.osaka-u.ac.jp/pfga_index.html
• [Remarks] (1)平岡泰(1)産経新聞朝刊1面電子透かし(東日本管内)、2012年5月16日「遺伝情報組み換えメカニズムの解明に大きな前進」 MSNトピックス(電子版):以下に同様の報道神戸新聞2012年5月11日、日刊工業新聞2012年5月11日、日経産業新聞2012年5月11日、科学新聞2012年5月18日
• [Remarks] (2)胡桃坂仁志(1)日本経済新聞、2010年5月25日「不妊・がん関与?変異体 早大 たんぱく質構造解明」:以下に同様の報道日刊工業新聞2010年5月25日、化学工業日報2010年5月26日、日経産業新聞2010年5月27日、日刊工業新聞2010年5月28日、科学新聞2010年6月4日
• [Remarks] (2)胡桃坂仁志(2)日本経済新聞、2011年7月13日「ヒト染色体の中心構造を詳細に解明 早大教授ら」:以下に同様の報道日経産業新聞2011年7月12日、化学工業日報2010年7月11日
• [Remarks] (2)胡桃坂仁志(3)日刊工業新聞、2012年7月25日「がん化抑制因子特定 遺伝子の修復機能解明 早大」:以下に同様の報道化学工業日報、2012年7月25日
• [Remarks] (3)小布施力史(1)北海道医療新聞、 2010年7月2日「POGZがオーロラBを制御」
• [Remarks] (3)小布施力史(2)北海道新聞、2013年4月1日「(性染色体の仕組み解明 iPS細胞作製に期待):以下に同様の報道北海道医療新聞2013年4月5日
• [Patent(Industrial Property Rights)] 顕微鏡システム (2010)
  • Inventor(s): 宮脇成礼、徳永万喜洋、十川久美子、江部康平、堀博文
  • Industrial Property Rights Holder: オリンパスソフトウェアテクノロジー(株)、東京大学、(独)理化学研究所
  • Industrial Property Number: 特許権、特願2010-145571
  • Filing Date: 2010-06-25