Study on nucleosomes and chromatin-demodifying enzymes

• Project/Area Number: 24613007
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: epigenetics
• Research Institution: The Institute of Physical and Chemical Research
• Principal Investigator: UMEHARA Takashi 独立行政法人理化学研究所, ライフサイエンス技術基盤研究センター, ユニットリーダー (20415095)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000); Fiscal Year 2014: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2013: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2012: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
• Keywords: 遺伝子発現 / エピジェネティクス / エピゲノム / クロマチン / 染色体 / ヒストン / ヌクレオソーム / 構造解析 / 転写 / メチル化 / 阻害剤

Outline of Final Research Achievements

Purpose of this study is to establish biochemical assay systems for understanding of regulatory mechanisms of lysine-methylated nucleosome core particles through the histone demethylase family of LSD1/LSD2 (Lysine-specific demethylase-1/2) which is assumed in the onsets of intractable cancers and/or lifestyle-related diseases. We achieved cell-free protein production methodology to synthesize full-length histone H3 protein containing a site-specific mono-methyl-lysine, which is the demethylation substrates for LSD1/LSD2 in the context of chromatin, through the combination of site-specific incorporation of Boc-protected mono-methyl-lysine into a protein during translation and chemical removal of the Boc group.

Research Products

• [Journal Article] New Frontiers of Epigenetics Researches in Pharmaceutical Sciences (2015)
  • Author(s): Umehara. T., Hori, Y.
  • Journal Title: YAKUGAKU ZASSHI Volume: 135 Issue: 1 Pages: 1-2
  • DOI: 10.1248/yakushi.14-00202-F
  • NAID: 130004756463
  • ISSN: 0031-6903, 1347-5231
  • Year and Date: 2015-01-01
  • Open Access
• [Journal Article] Lysine-specific demethylase LSD2 suppresses lipid influx and metabolism in hepatic cells (2015)
  • Author(s): Nagaoka, K., Hino, S., Sakamoto, A., Anan, K., Takase, R., Umehara, T., Yokoyama, S., Sasaki, Y., Nakao, M.
  • Journal Title: Mol. Cell. Biol. Volume: 35 (7) Issue: 7 Pages: 1068-1080
  • DOI: 10.1128/mcb.01404-14
  • Peer Reviewed / Open Access
• [Journal Article] Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT (2015)
  • Author(s): *Tochio, N., *Umehara, T., Nakabayashi, K., Yoneyama, M., Tsuda, K., Shirouzu, M., Koshiba, S., Watanabe, S., Kigawa, T., Sasazuki, T., Shirasawa, S., Yokoyama, S.
  • Journal Title: J. Struct. Funct. Genomics Volume: 16 (2)
  • Peer Reviewed / Open Access
• [Journal Article] Multiple site-specific installations of N(ε)-monomethyl-L-lysine into histone proteins by cell-based and cell-free protein synthesis (2014)
  • Author(s): Yanagisawa, T., Takahashi, M., Mukai, T., Sato, S., Wakamori, M., Shirouzu, M., Sakamoto, K., and Umehara, T. and Yokoyama, S.
  • Journal Title: ChemBioChem Volume: 15 Issue: 12 Pages: 1830-1838
  • DOI: 10.1002/cbic.201402291
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Expanded genetic code technologies for modified lysine installation at multiple sites (2014)
  • Author(s): Yanagisawa, T., Umehara, T., Sakamoto, K., and Yokoyama, S.
  • Journal Title: ChemBioChem Volume: 15 Issue: 15 Pages: 2181-2187
  • DOI: 10.1002/cbic.201402266
  • Peer Reviewed
• [Journal Article] Development of a hexahistidine-3× FLAG-tandem affinity purification method for endogenous protein complexes in Pichia pastoris (2014)
  • Author(s): Toshiaki Higo, Noriyuki Suka, Haruhiko Ehara, Masatoshi Wakamori, Shin Sato, Hideaki Maeda, Shun-ichi Sekine, Takashi Umehara, and Shigeyuki Yokoyama
  • Journal Title: J Struct Funct Genomics Volume: 15 Issue: 4 Pages: 191-199
  • DOI: 10.1007/s10969-014-9190-1
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Structures of histone methyltransferase SET7/9 in complexes with adenosylmethionine derivatives (2013)
  • Author(s): Hideaki Niwa, Noriko Handa, Yuri Tomabechi, Keiko Honda, Mitsutoshi Toyama, Noboru Ohsawa, Mikako Shirouzu, Hiroyuki Kagechika, Tomoya Hirano, Takashi Umehara, Shigeyuki Yokoyama
  • Journal Title: Acta Crystallographica Section D Volume: 69 Issue: 4 Pages: 595-602
  • DOI: 10.1107/s0907444912052092
  • Peer Reviewed
• [Journal Article] A tandem insertion vector for large-scale preparation of nucleosomal DNA (2012)
  • Author(s): Wakamori, M., Umehara, T., Yokoyama, S.
  • Journal Title: Anal.Biochem. Volume: (印刷中) Issue: 1 Pages: 184-186
  • DOI: 10.1016/j.ab.2012.01.010
  • Peer Reviewed
• [Journal Article] Structural biology toward rational drug development in collaboration with molecular imaging (2012)
  • Author(s): Umehara, T., Shirouzu, M., Yokoyama, S.
  • Journal Title: Curr. Med. Imaging Rev. Volume: 8 Issue: 4 Pages: 308-313
  • DOI: 10.2174/157340512803759794
• [Presentation] 「エピヌクレオソーム」の再構成に基づいた創薬技術開発」 (2015)
  • Author(s): 梅原崇史
  • Organizer: 第135回日本薬学会年会
  • Place of Presentation: 神戸市
  • Year and Date: 2015-03-26
• [Presentation] Structure-based development of inhibitors targeting histone demethylase LSD1/KDM1 (2014)
  • Author(s): Umehara, T., Yokoyama, S.
  • Organizer: 第37回日本分子生物学会年会
  • Place of Presentation: 横浜市
  • Year and Date: 2014-11-26
• [Presentation] Functional and structural analyses of H4-acetylated nucleosome core particles (2014)
  • Author(s): Umehara, T., Wakamori, M., Fujii, Y., Suka, N., Shirouzu, M., Sakamoto, K., Yokoyama, S.
  • Organizer: 11th EMBL Conference of Transcription and Chromatin
  • Place of Presentation: Heidelberg, Germany
  • Year and Date: 2014-08-24
• [Presentation] Synthesis of histone proteins containing multiple and site-specific monomethyl-lysines (2014)
  • Author(s): Umehara, T., Yanagisawa, T., Takahashi, M., Mukai, T., Sato, S., Wakamori, M., Shirouzu, M., Sakamoto, K., Yokoyama, S.
  • Organizer: FASEB Science Research Conference on Biological Methylation: Regulation of Chromatin, Epigenetics, and Disease
  • Place of Presentation: Nassau, Bahamas
  • Year and Date: 2014-07-07
• [Presentation] Reconstitution of ‘epi-nucleosomes’ with pinpoint epigenetic information (2014)
  • Author(s): Umehara, T., Yokoyama, S.
  • Organizer: 広島大学 クロマチン動態数理研究拠点セミナー
  • Place of Presentation: 広島市
  • Year and Date: 2014-06-13
  • Invited
• [Presentation] Structure-based development of epigenetics-regulating inhibitors and ‘Epi-nucleosomes’
  • Author(s): Takashi Umehara, Shin Sato, Hideaki Niwa, Masatoshi Wakamori, Kensaku Sakamoto, Mikako Shirouzu, Shigeyuki Yokoyama
  • Organizer: 7th International Conference on Structural Genomics
  • Place of Presentation: Sapporo, Japan
• [Presentation] Reconstitution of epigenetic nucleosomes through genetic code expansion
  • Author(s): Takashi Umehara, Masatoshi Wakamori, Mihoko Takahashi, Takahito Mukai, Mikako Shirouzu, Kensaku Sakamoto, Shigeyuki Yokoyama
  • Organizer: The 65th Fujihara Seminar, International Symposium on Synthetic Biology of Unnatural Base Pairs and Amino Acids
  • Place of Presentation: Tomakomai, Japan
• [Presentation] 残基特異的な修飾を導入した「エピヌクレオソーム」の調製技術開発と機能解析
  • Author(s): 梅原崇史, 若森昌聡, 須賀則之, 高橋美穂子, 佐藤 心, 柳沢達男, 向井崇人, 白水美香子, 坂本健作, 横山茂之
  • Organizer: 第7回日本エピジェネティクス研究会年会
  • Place of Presentation: 奈良市
• [Presentation] 合理的創薬を指向したヒストン脱メチル化酵素LSD1/KDM1の構造基盤阻害剤開発
  • Author(s): 梅原崇史, 日野信次朗, 佐藤 心, 丹羽英明, 白水美香子, 中尾光善, 横山茂之
  • Organizer: 日本ケミカルバイオロジー学会 第8回年会
  • Place of Presentation: 東京都文京区
• [Presentation] BETファミリーのヒストン認識ポケットに対する構造基盤阻害剤開発
  • Author(s): 梅原崇史, 横山茂之
  • Organizer: 第86回日本生化学会大会
  • Place of Presentation: 横浜市
• [Presentation] 薬学が拓くエピジェネティクス研究の最前線
  • Author(s): 梅原崇史, 堀雄一郎
  • Organizer: 第134回日本薬学会年会
  • Place of Presentation: 熊本市
• [Presentation] Structural study and drug development of a histone demethylase involved in repressive KLF pathway
  • Author(s): Takashi Umehara
  • Organizer: FASEB Summer Research Conference on Biology and Pathobiology of Krueppel-like Factors
  • Place of Presentation: Base Village, Snowmass Village, CO, USA
  • Invited
• [Presentation] Structure analysis and drug development of transcription factor complexes
  • Author(s): Takashi Umehara and Shigeyuki Yokoyama
  • Organizer: International Symposium on Development of Medical Technologies for Treating Intractable Cancers and Cardiovascular Diseases
  • Place of Presentation: Univ. Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
  • Invited
• [Presentation] 複数の残基特異的アセチル化を含む「エピヌクレオソーム」の再構成と機能解析
  • Author(s): 梅原崇史, 若森昌聡, 須賀則之, 向井崇人, 寺田貴帆, 白水美香子, 坂本健作, 横山茂之
  • 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（東京都千代田区）
• [Presentation] ヒストン脱メチル化酵素LSD1/KDM1の結晶構造解析と阻害剤開発
  • Author(s): 梅原崇史, 三桝信哉, 佐藤 心, 須賀則之, 丹羽英明, 半田徳子, 横山茂之
  • Organizer: 第12回日本蛋白質科学会年会
  • Place of Presentation: 名古屋国際会議場（愛知県名古屋市）
• [Presentation] エピジェネティックなヌクレオソームの調製技術
  • Author(s): 梅原崇史
  • Organizer: 大阪大学蛋白質研究所セミナー
  • Place of Presentation: 大阪大学吹田キャンパス（大阪府吹田市）
  • Invited
• [Presentation] クロマチンを創る：エピジェネティック情報を持つヌクレオソームの試験管内再構成
  • Author(s): 梅原崇史, 若森昌聡, 須賀則之, 向井崇人, 寺田貴帆, 白水美香子, 坂本健作, 横山茂之
  • Organizer: 細胞を創る研究会5.0
  • Place of Presentation: 東京工業大学すずかけ台キャンパス（神奈川県横浜市）
• [Presentation] 創薬を指向した疾患関連タンパク質とその阻害剤複合体のX線結晶構造解析
  • Author(s): 梅原崇史, 丹羽英明, 半田徳子, 影近弘之, 平野智也, 白水美香子, 横山茂之
  • Organizer: 第30回Photon Factoryシンポジウム
  • Place of Presentation: つくば国際会議場（茨城県つくば市）
• [Presentation] 創薬を指向したエピジェネティクス研究の最前線
  • Author(s): 梅原崇史
  • Organizer: 第133回日本薬学会年会
  • Place of Presentation: パシフィコ横浜（神奈川県横浜市）
• [Book] 生体の科学 「生命動態システム科学」 エピヌクレオソームの再構成による遺伝子発現制御解析 65 (5) 462-463 (2014)
  • Author(s): 梅原崇史
  • Total Pages: 2
  • Publisher: 医学書院
• [Book] 「エピジェネティクスを標的とした医薬品開発」 構造活性相関部会ニュースレター No. 25, pp. 9-16 (2013)
  • Author(s): 梅原崇史
  • Total Pages: 8
  • Publisher: 日本薬学会
• [Remarks]
  • URL: http://www.riken.jp/research/labs/clst/struct_synth_biol/bio_funct_mol_dev/epigen_drug_discov/
• [Remarks]
  • URL: http://researchmap.jp/ume/
• [Remarks] 理化学研究所 ライフサイエンス技術基盤研究センター エピジェネティクス制御研究ユニット
  • URL: http://www.clst.riken.jp/activity/structuralbiology_group2_team4.html
• [Remarks] 理化学研究所 ライフサイエンス技術基盤研究センター エピジェネティクス制御研究ユニット
  • URL: http://www.riken.jp/research/labs/clst/struct_synth_biol/bio_funct_mol_dev/epigen_drug_discov/