Single cell mapping of epigenetic modifications through super-nucleosome construction

• Project/Area Number: 18H03931
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Review Section: Medium-sized Section 37:Biomolecular chemistry and related fields
• Research Institution: The University of Tokyo
• Principal Investigator: Okamoto Akimitsu 東京大学, 先端科学技術研究センター, 教授 (60314233)
• Project Period (FY): 2018-04-01 – 2021-03-31
• Project Status: Completed (Fiscal Year 2020)
• Budget Amount: ¥44,200,000 (Direct Cost: ¥34,000,000、Indirect Cost: ¥10,200,000); Fiscal Year 2020: ¥14,170,000 (Direct Cost: ¥10,900,000、Indirect Cost: ¥3,270,000); Fiscal Year 2019: ¥14,170,000 (Direct Cost: ¥10,900,000、Indirect Cost: ¥3,270,000); Fiscal Year 2018: ¥15,860,000 (Direct Cost: ¥12,200,000、Indirect Cost: ¥3,660,000)
• Keywords: ヌクレオソーム / DNA / クロマチン / ヒストン / パラジウム / ルテニウム / ペプチド / タンパク質化学合成 / エピジェネティクス / タンパク質合成 / 遺伝子制御 / 化学合成 / 合成化学 / 1細胞イメージング

Outline of Final Research Achievements

(1) Establishment of a chemical synthesis method for artificial nucleosomes: We established a new peptide ligation method using organometallic complexes, and synthesized four types of core histones (H2A, H2B, H3, and H4) and linker histone H1.
(2) Creation of supernucleosomes: In order to discover the essence of the regulation of cell functions by atoms, we investigated protein modification methods and established a method for the chemical synthesis of "supernucleosomes" with functions not found in nature.

Academic Significance and Societal Importance of the Research Achievements

独自の化学合成の確立を通して、天然にはない標識や反応性官能基、複数の複雑な機能性ユニットをヒストン構造に入れることが可能になるので、機能解明を支援する創造的スーパーヌクレオソームを作成して未知のヌクレオソーム機能を明らかにすることができる。これによって、ヌクレオソーム内DNAへ働きかけることができる新たな抗がん剤設計などに利用することができる。

Research Products

• [Journal Article] Floxuridine Oligomers Activated under Hypoxic Environment (2021)
  • Author(s): Morihiro, K.; Ishinabe, T.; Takatsu, M.; Osumi, H.; Osawa, T.; Okamoto, A.
  • Journal Title: J. Am. Chem. Soc. Volume: 143 Issue: 9 Pages: 3340-3347
  • DOI: 10.1021/jacs.0c10732
  • Peer Reviewed / Open Access
• [Journal Article] Organoruthenium-Catalyzed Chemical Protein Synthesis to Elucidate the Functions of Epigenetic Modifications on Heterochromatin Factors (2021)
  • Author(s): Kamo, N.; Kujirai, T.; Kurumizaka, H.; Murakami, H.; Hayashi, G.; Okamoto, A.
  • Journal Title: Chem. Sci. Volume: 12 Issue: 16 Pages: 5926-5937
  • DOI: 10.1039/d1sc00731a
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Light-inducible control of cellular proliferation and differentiation by a Hedgehog signaling inhibitor (2021)
  • Author(s): Misawa Ryuji、Minami Tsuyoshi、Okamoto Akimitsu、Ikeuchi Yoshiho
  • Journal Title: Bioorganic & Medicinal Chemistry Volume: 38 Pages: 116144-116144
  • DOI: 10.1016/j.bmc.2021.116144
  • Peer Reviewed
• [Journal Article] Toolbox for chemically synthesized histone proteins (2020)
  • Author(s): Nakatsu, K.; Hayashi, G.; Okamoto, A.
  • Journal Title: Curr. Opin. Chem. Biol. Volume: 58 Pages: 10-19
  • DOI: 10.1016/j.cbpa.2020.04.016
  • Peer Reviewed
• [Journal Article] A light-inducible Hedgehog signaling activator modulates proliferation and differentiation of neural cells. (2020)
  • Author(s): Ryuji Misawa, Tsuyoshi Minami, Akimitsu Okamoto, Yoshiho Ikeuchi.
  • Journal Title: ACS Chemical Biology Volume: - Issue: 6 Pages: 1595-1603
  • DOI: 10.1021/acschembio.0c00195
  • Peer Reviewed / Open Access
• [Journal Article] Fmoc-Compatible and C-terminal-Sequence-Independent Peptide Alkyl Thioester Formation Using Cysteinylprolyl Imide (2020)
  • Author(s): Nakatsu, K.; Yanase, M.; Hayashi, G.; Okamoto, A.
  • Journal Title: Org. Lett. Volume: 22 Issue: 12 Pages: 4670-4674
  • DOI: 10.1021/acs.orglett.0c01450
  • Peer Reviewed
• [Journal Article] Single cell array enclosed with a photodegradable hydrogel in microwells for image-based cell classification and selective photorelease of cells (2020)
  • Author(s): Yamaguchi, S.; Takagi, R.; Hosogane, T.; Ohashi, Y.; Sakai, Y.; Sakakihara, S.; Iino, R.; Tabata, K.; Noji, H.; Okamoto, A.
  • Journal Title: ACS Appl. Bio Mater. Volume: 3 Issue: 9 Pages: 5887-5895
  • DOI: 10.1021/acsabm.0c00583
  • Peer Reviewed
• [Journal Article] Monitoring intracellular metal ion complexation with acetylene-tagged ligand by Raman spectroscopy (2020)
  • Author(s): Takemura, S.; Watanabe, H.; Nishihara, T.; Okamoto, A.; Tanabe, K.
  • Journal Title: RSC Adv. Volume: 10 Issue: 59 Pages: 36119-36123
  • DOI: 10.1039/d0ra06329k
  • Peer Reviewed / Open Access
• [Journal Article] L-DNA-tagged fluorescence in situ hybridization for highly sensitive imaging of RNAs in single cells (2020)
  • Author(s): Ogata, M.; Hayashi, G.; Ichiu, A.; Okamoto, A.
  • Journal Title: Org. Biomol. Chem. Volume: 18 Issue: 40 Pages: 8084-8088
  • DOI: 10.1039/d0ob01635g
  • Peer Reviewed
• [Journal Article] Acetylation-modulated communication between the H3 N-terminal tail domain and the intrinsically disordered H1 C-terminal domain (2020)
  • Author(s): Hao, F; Murphy, K. J.; Kujirai, T.; Kamo, N.; Kato, J.; Koyama, M.; Okamato, A.; Hayashi, G.; Kurumizaka, H.; Hayes, J. J.
  • Journal Title: Nucleic Acids Res. Volume: 48 Issue: 20 Pages: 11510-11520
  • DOI: 10.1093/nar/gkaa949
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A highly constrained nucleic acid analog based on α-L-threosamine (2020)
  • Author(s): Morihiro, K.; Okamoto, A.
  • Journal Title: Nucleosides Nucleotides Nucleic Acids Volume: 39 Issue: 1-3 Pages: 270-279
  • DOI: 10.1080/15257770.2019.1666278
  • Peer Reviewed
• [Journal Article] Live Cell Sensing of Telomerase Activity Using Hybridization-Sensitive Fluorescent Oligonucleotide Probes (2020)
  • Author(s): Chen, J.; Morihiro, K.; Fukui, D.; Guo, L.; Okamoto, A.
  • Journal Title: ChemBioChem Volume: 21 Issue: 7 Pages: 1022-1027
  • DOI: 10.1002/cbic.201900555
  • Peer Reviewed
• [Journal Article] Efficient Ketose Production by Hydroxyapatite Catalyst in a Continuous Flow Module (2019)
  • Author(s): Usami, K.; Xiao, K.; Okamoto, A.
  • Journal Title: ACS Sustainable Chem. Eng. Volume: 7 Issue: 3 Pages: 3372-3377
  • DOI: 10.1021/acssuschemeng.8b05574
  • Peer Reviewed
• [Journal Article] Reversible and Photoresponsive Immobilization of Nonadherent Cells by Spiropyran-Conjugated PEG-Lipids (2019)
  • Author(s): Izuta, S.; Yamaguchi, S.; Kosaka, T.; Okamoto, A.
  • Journal Title: ACS Appl. Bio Mater. Volume: 2 Issue: 1 Pages: 33-38
  • DOI: 10.1021/acsabm.8b00656
  • Peer Reviewed
• [Journal Article] Supramolecular Polymeric Hydrogels for Ultrasound-guided Protein Release (2019)
  • Author(s): Yamaguchi, S; Higashi, K.; Azuma, T.; Okamoto, A.
  • Journal Title: Biotechnol. J. Volume: 14 Issue: 5 Pages: 1800530-1800530
  • DOI: 10.1002/biot.201800530
  • Peer Reviewed
• [Journal Article] Cysteinylprolyl imide (CPI) peptide: a highly reactive and easily accessible crypto-thioester for chemical protein synthesis (2019)
  • Author(s): Yanase Masafumi、Nakatsu Koki、Cardos Charlane Joy、Konda Yoshiki、Hayashi Gosuke、Okamoto Akimitsu
  • Journal Title: Chemical Science Volume: 10 Issue: 23 Pages: 5967-5975
  • DOI: 10.1039/c9sc00646j
  • Peer Reviewed / Open Access
• [Journal Article] Simultaneous and Traceless Ligation of Peptide Fragments on DNA Scaffold. (2019)
  • Author(s): Hayashi G, Yanase M, Nakatsuka Y, Okamoto A.
  • Journal Title: Biomaclomolecules Volume: 20 Issue: 3 Pages: 1246-1253
  • DOI: 10.1021/acs.biomac.8b01655
  • Peer Reviewed
• [Journal Article] Chemical Synthesis of Cys-Containing Protein via Chemoselective Deprotection with Different Palladium Complexes (2019)
  • Author(s): Kamo, N.; Hayashi, G.; Okamoto, A.
  • Journal Title: Org. Lett. Volume: 21 Issue: 20 Pages: 8378-8382
  • DOI: 10.1021/acs.orglett.9b03152
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Photo-responsive materials with strong cell trapping ability for light-guided manipulation of nonadherent cells (2019)
  • Author(s): Jarzebska, N. A.; Yamaguchi, S.; Izuta, S.; Kosaka, T.; Yamahira, S.; Nagamune, T.; Okamoto, A.
  • Journal Title: Biomater. Sci. Volume: 7 Issue: 11 Pages: 4514-4518
  • DOI: 10.1039/c9bm01200a
  • Peer Reviewed
• [Journal Article] Photophysical properties of fluorescent imaging biological probes of nucleic acids: SAC-CI and TD-DFT Study (2018)
  • Author(s): Shiraogawa Takafumi、Candel Gaelle、Fukuda Ryoichi、Ciofini Ilaria、Adamo Carlo、Okamoto Akimitsu、Ehara Masahiro
  • Journal Title: Journal of Computational Chemistry Volume: 40 Issue: 1 Pages: 127-134
  • DOI: 10.1002/jcc.25553
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Triple Function of 4-Mercaptophenylacetic Acid Promotes One-Pot Multiple Peptide Ligation (2018)
  • Author(s): Kamo Naoki、Hayashi Gosuke、Okamoto Akimitsu
  • Journal Title: Angewandte Chemie International Edition Volume: 57 Issue: 50 Pages: 16533-16537
  • DOI: 10.1002/anie.201809765
  • Peer Reviewed
• [Journal Article] Chemistry‐Driven Epigenetic Investigation of Histone and DNA Modifications (2018)
  • Author(s): Sueoka Takuma、Koyama Kenta、Hayashi Gosuke、Okamoto Akimitsu
  • Journal Title: The Chemical Record Volume: 18 Issue: 12 Pages: 1727-1744
  • DOI: 10.1002/tcr.201800040
  • Peer Reviewed
• [Journal Article] Efficient peptide ligation between allyl-protected Asp and Cys followed by palladium-mediated deprotection (2018)
  • Author(s): Kamo Naoki、Hayashi Gosuke、Okamoto Akimitsu
  • Journal Title: Chemical Communications Volume: 54 Issue: 34 Pages: 4337-4340
  • DOI: 10.1039/c8cc01965g
  • Peer Reviewed
• [Presentation] ニトロ基およびアゾ基の生体還元を利用したFloxuridineオリゴマーの低酸素活性化 (2021)
  • Author(s): 森廣 邦彦、石鍋 拓郎、高津 正子、大澤 毅、岡本 晃充
  • Organizer: 日本化学会第101春季年会
• [Presentation] 細胞内タンパク質送達を指向した刺激溶解性タンパク質凝集体の開発 (2021)
  • Author(s): 山本 一穂、山口 哲志、岡本 晃充
  • Organizer: 日本化学会第101春季年会
• [Presentation] 光化学インターナリゼーションに有効な近赤外光吸収色素の合成と評価 (2021)
  • Author(s): 濵邉 美佳子、出羽 和花子、大橋 瑠子、浜窪 隆雄、岡本 晃充
  • Organizer: 日本化学会第101春季年会
• [Presentation] 細胞膜透過性を指向する含フッ素オリゴヌクレオチドの合成と評価 (2021)
  • Author(s): 渡邉 ほの香、相川 光介、森廣 邦彦、岡本 晃充、岡添 隆
  • Organizer: 日本化学会第101春季年会
• [Presentation] 光誘起型伸長反応を用いたポリユビキチンの鎖長制御手法の確立 (2021)
  • Author(s): 村山 伊織、古畑 隆史、岡本 晃充
  • Organizer: 日本化学会第101春季年会
• [Presentation] 固相合成に適したチオエステル前駆体システイニルプロリルイミドによるタンパク質化学合成 (2021)
  • Author(s): 中津 幸輝、梁瀬 将史、林 剛介、岡本 晃充
  • Organizer: 日本化学会第101春季年会
• [Presentation] 生体分子の選択的可視化を実現する光活性化アルキンタグ (2021)
  • Author(s): 中村 聖、山口 哲志、小阪 高広、中村 元直、岡本 晃充
  • Organizer: 日本化学会第101春季年会
• [Presentation] 細胞膜裏側の定量的1細胞解析のための細胞膜シートアレイの開発 (2021)
  • Author(s): 梅田 侑生、山口 哲志、山平 真也、中村 元直、岡本 晃充
  • Organizer: 日本化学会第101春季年会
• [Presentation] Ru触媒を用いたリンカーヒストンH1.2とHP1αの化学合成とその翻訳後修飾の機能解析 (2021)
  • Author(s): 加茂 直己、鯨井 智也、胡桃坂 仁志、村上 裕、林 剛介、岡本 晃充
  • Organizer: 日本化学会第101春季年会
• [Presentation] The use of cysteinylprolyl imide peptide as an Fmoc-compatible crypto-thioester (2020)
  • Author(s): Koki Nakatsu、Masafumi Yanase、Gosuke Hayashi、Akimitsu Okamoto
  • Organizer: 第57回ペプチド討論会
• [Presentation] Total chemical synthesis of linker histone H1.2 and heterochromatin protein 1 alpha through one-pot multiple peptide ligation using Ru catalyst (2020)
  • Author(s): Naoki Kamo、Gosuke Hayashi、Tomoya Kujirai、Hitoshi Kurumizaka、Hiroshi Murakami、Akimitsu Okamoto
  • Organizer: 第57回ペプチド討論会
• [Presentation] 低酸素環境下で活性化するFluoxuridineオリゴマーの開発 (2020)
  • Author(s): 森廣 邦彦、石鍋 拓郎、高津 正子、岡本 晃充
  • Organizer: 第14回バイオ関連化学シンポジウム
• [Presentation] 金属イオン曝露によるDNAメチル化レベル変化の蛍光解析 (2020)
  • Author(s): 森廣 邦彦、劉 杉、竹内 芙美香、岡本 晃充
  • Organizer: 第42回日本光医学・光生物学会
• [Presentation] 感光性クリック試薬を用いた異種細胞位置制御技術の開発 (2019)
  • Author(s): 小阪 高広、山口 哲志、泉田 森、岡本 晃充
  • Organizer: 生体機能関連化学部会若手の会 第31回サマースクール
• [Presentation] タンパク質化学合成を指向したチオエステル前駆体CPI(Cysteinylprolyl imide) の設計と機能評価 (2019)
  • Author(s): 中津 幸輝、梁瀬 将史、林 剛介、岡本 晃充
  • Organizer: 生体機能関連化学部会若手の会 第31回サマースクール
• [Presentation] 細胞内分子動態解析のための光活性化アルキンタグ (2019)
  • Author(s): 中村 聖、山口 哲志、小阪 高広、岡本 晃充
  • Organizer: 2019年度生物工学若手研究者の集い（若手会）夏のセミナー
• [Presentation] ターンオン型蛍光プローブを用いたテロメラーゼ活性の生細胞内センシング (2019)
  • Author(s): 森廣 邦彦、Jiazhuo Chen, 福井 大介、Guo Lihao、岡本 晃充
  • Organizer: 第41回日本光医学・光生物学会
• [Presentation] Inorganic reactions for analysis of epigenetically modified DNA (2019)
  • Author(s): Akimitsu Okamoto
  • Organizer: 19th International Conference on Biological Inorganic Chemistry (ICBIC-19)
  • Int'l Joint Research
• [Presentation] 細胞運理を志向した光溶解性ゲル充填マイクロウェルアレイ (2019)
  • Author(s): 山口 哲志、細金 剛、大橋 友紀、榊原 昇一、田端 和仁、野地 博行、岡本 晃充
  • Organizer: 第13回バイオ関連化学シンポジウム
• [Presentation] ターンオン型蛍光オリゴヌクレオチドプローブを用いたテロメラーゼ活性の生細胞内センシング (2019)
  • Author(s): 森廣 邦彦、Chen Jiazhuo、福井 大介、Guo Lihao、岡本 晃充
  • Organizer: 第13回バイオ関連化学シンポジウム
• [Presentation] 1細胞間相互作用解析のための光誘導型クリック反応表面 (2019)
  • Author(s): 小阪 高広、山口 哲志、泉田 森、岡本 晃充
  • Organizer: 第13回バイオ関連化学シンポジウム
• [Presentation] Chemical Reactions for Analysis of Epigenetically Modified DNA (2019)
  • Author(s): Akimitsu Okamoto
  • Organizer: Epigenetics & Bioengineering Coference (EpiBio 2019)
  • Int'l Joint Research
• [Presentation] 光反応性クリック試薬を用いた細胞間相互作用解析手法の開発 (2019)
  • Author(s): 小阪 高広、山口 哲志、泉田 森、岡本 晃充
  • Organizer: 第68回高分子討論会
• [Presentation] Photo-responsive cell immobilization reagents for cell manipulation on solid phase (2019)
  • Author(s): Satoshi Yamaguchi, Shin Izuta, Shinya Yamahara, Teruyuki Nagamune, Akimitsu Okamoto
  • Organizer: The 18th Asian Pacific Confederation of Chemical Engineering Congress (APCChE2019)
  • Int'l Joint Research
• [Presentation] Live-Cell Sensing of Telomerase Activity (2019)
  • Author(s): Akimitsu Okamoto, Kunihiko Morihiro, Jiazhuo Chen, Daisuke Fukui and Lihao Guo
  • Organizer: Asia 3 Roundtable of Nucleic Acid 2019 (A3RONA)
  • Int'l Joint Research / Invited
• [Presentation] Reaction design for highly efficient chemical protein synthesis (2019)
  • Author(s): Gosuke Hayashi, Takuma Sueoka, Masafumi Yanase, Naoki Kamo, and Akimitsu Okamoto
  • Organizer: ACS Meeting 2019 Spring
  • Int'l Joint Research
• [Presentation] EXCITON-CONTROLLED FLUORESCENT NUCLEIC ACIDS FOR BIOIMAGING (2018)
  • Author(s): Lihao Guo, Akimitsu Okamoto
  • Organizer: PhotoIUPAC2018
  • Int'l Joint Research
• [Patent(Industrial Property Rights)] 光増感色素 (2020)
  • Inventor(s): 岡本晃充、出羽和歌子、浜窪隆雄、戸田奈緒子、須藤幸夫
  • Industrial Property Rights Holder: 岡本晃充、出羽和歌子、浜窪隆雄、戸田奈緒子、須藤幸夫
  • Industrial Property Rights Type: 特許
  • Industrial Property Number: 2020-108318
  • Filing Date: 2020