Development of a new functional genomics mothod to perform single-cell enhancer identification

• Project/Area Number: 20K21407
• Research Category: Grant-in-Aid for Challenging Research (Exploratory)
• Allocation Type: Multi-year Fund
• Review Section: Medium-sized Section 43:Biology at molecular to cellular levels, and related fields
• Research Institution: Institute of Physical and Chemical Research
• Principal Investigator: Murakawa Yasuhiro 国立研究開発法人理化学研究所, 生命医科学研究センター, チームリーダー (50765469)
• Project Period (FY): 2020-07-30 – 2022-03-31
• Project Status: Completed (Fiscal Year 2021)
• Budget Amount: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000); Fiscal Year 2021: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000); Fiscal Year 2020: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
• Keywords: エンハンサー / シングルセル解析 / 遺伝子発現制御 / ヒトゲノム解析 / 遺伝子発現ネットワーク / バイオインフォマティクス / ゲノムサイエンス / シングルセル / 機能性ゲノム学 / オミックス解析

Outline of Research at the Start

エンハンサーは、非コーディング領域に存在し、極めて時空間特異的に活性化し、遠位から標的遺伝子の発現を強力に増強する。本研究では、１細胞レベルで各々の細胞のエンハンサー活性を解析できる画期的な新技術を確立する。さらに、病気のゲノム情報と統合した解析を行う基盤を構築し、従来の全ゲノム配列解析をより機能的な方向性に転換・発展させ、新たな機能性ゲノム学の潮流を生み出す。

Outline of Final Research Achievements

Enhancers are one of the key cis-regulatory elements that control gene expression in a cell type-specific manner. To enable enhancer analysis at single-cell level, we established a novel ReapTEC approach. By applying this approach to approximately 500,000 CD4 positive T cells, we profiled the activation states of approximately 70,000 enhancers in over 100 cell types identified. We integrated this enhancer activity map with large-scale human genetic data to provide a systematic functional interpretation of DNA variation associated with autoimmune and infectious diseases.

Academic Significance and Societal Importance of the Research Achievements

本研究では、１細胞レベルで各々の細胞のエンハンサー活性を解析できる画期的な新技術を確立した。将来的には、ヒトの全身の様々な細胞でのエンハンサーマップを高精細に作成するための基盤技術になりえる。病気SNPやがんゲノム変異の大部分はエンハンサー領域に存在するため、こうしたエンハンサーマップとヒトゲノム解析結果を統合していくことで、ヒトの病気の発症メカニズムの理解に大きく貢献することが期待される。また、これにより新しい治療標的やバイオマーカーが発見される可能性がある。

Research Products

• [Int'l Joint Research] IFOM/Human Technopole(イタリア)
• [Int'l Joint Research] カロリンスカ研究所(スウェーデン)
• [Int'l Joint Research] ヘルシンキ大学(フィンランド)
• [Journal Article] Expression of matrix metalloproteinase‐3 and ‐10 is up‐regulated in the periodontal tissues of aged mice (2022)
  • Author(s): Kageyama Yoko、Nakamura Megumi、Igari Yohei、Yamaguchi Satoshi、Oguchi Akiko、Murakawa Yasuhiro、Hattori Yoshinori、Sasano Yasuyuki
  • Journal Title: Journal of Periodontal Research Volume: - Issue: 4 Pages: 733-741
  • DOI: 10.1111/jre.12996
  • Peer Reviewed / Open Access
• [Journal Article] DUX4 is a multifunctional factor priming human embryonic genome activation (2022)
  • Author(s): Vuoristo Sanna、Bhagat Shruti、et al.
  • Journal Title: iScience Volume: 25 Issue: 4 Pages: 104137-104137
  • DOI: 10.1016/j.isci.2022.104137
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Two ovarian candidate enhancers, identified by time series enhancer RNA analyses, harbor rare genetic variations identified in ovarian insufficiency (2022)
  • Author(s): Nakagawa Ryuichi et al.
  • Journal Title: Human Molecular Genetics Volume: - Issue: 13 Pages: 2223-2235
  • DOI: 10.1093/hmg/ddac023
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] PAX6-positive microglia evolve locally in hiPSC-derived ocular organoids (2022)
  • Author(s): Shiraki Nobuhiko、Maruyama Kazuichi、Hayashi Ryuhei、Oguchi Akiko、Murakawa Yasuhiro、Katayama Tomohiko、Takigawa Toru、Sakimoto Susumu、Quantock Andrew J.、Tsujikawa Motokazu、Nishida Kohji
  • Journal Title: Stem Cell Reports Volume: 17 Issue: 2 Pages: 221-230
  • DOI: 10.1016/j.stemcr.2021.12.009
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] CD153/CD30 signaling promotes age-dependent tertiary lymphoid tissue expansion and kidney injury (2022)
  • Author(s): Sato Yuki et al.
  • Journal Title: Journal of Clinical Investigation Volume: 132 Issue: 2
  • DOI: 10.1172/jci146071
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Cap analysis of gene expression (CAGE) and noncoding regulatory elements (2021)
  • Author(s): Guerrini Matteo Maurizio、Oguchi Akiko、Suzuki Akari、Murakawa Yasuhiro
  • Journal Title: Seminars in Immunopathology Volume: 44 Issue: 1 Pages: 127-136
  • DOI: 10.1007/s00281-021-00886-5
  • Peer Reviewed
• [Journal Article] Chromosomal-scale de novo genome assemblies of Cynomolgus Macaque and Common Marmoset (2021)
  • Author(s): Jayakumar Vasanthan、Nishimura Osamu、Kadota Mitsutaka、Hirose Naoki、Sano Hiromi、Murakawa Yasuhiro、Yamamoto Yumiko、Nakaya Masataka、Tsukiyama Tomoyuki、Seita Yasunari、Nakamura Shinichiro、Kawai Jun、Sasaki Erika、Ema Masatsugu、Kuraku Shigehiro、Kawaji Hideya、Sakakibara Yasubumi
  • Journal Title: Scientific Data Volume: 8 Issue: 1 Pages: 59-59
  • DOI: 10.1038/s41597-021-00935-6
  • Peer Reviewed / Open Access
• [Journal Article] Intravital Imaging Identifies the VEGF?TXA2 Axis as a Critical Promoter of PGE2 Secretion from Tumor Cells and Immune Evasion (2021)
  • Author(s): Konishi Yoshinobu、Ichise Hiroshi、Watabe Tetsuya、Oki Choji、Tsukiji Shinya、Hamazaki Yoko、Murakawa Yasuhiro、Takaori-Kondo Akifumi、Terai Kenta、Matsuda Michiyuki
  • Journal Title: Cancer Research Volume: 81 Issue: 15 Pages: 4124-4132
  • DOI: 10.1158/0008-5472.can-20-4245
  • Peer Reviewed
• [Journal Article] The embryonic ontogeny of the gonadal somatic cells in mice and monkeys (2021)
  • Author(s): Sasaki Kotaro、Oguchi Akiko、Cheng Keren、Murakawa Yasuhiro、Okamoto Ikuhiro、Ohta Hiroshi、Yabuta Yukihiro、Iwatani Chizuru、Tsuchiya Hideaki、Yamamoto Takuya、Seita Yasunari、Saitou Mitinori
  • Journal Title: Cell Reports Volume: 35 Issue: 5 Pages: 109075-109075
  • DOI: 10.1016/j.celrep.2021.109075
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Identification of candidate PAX2-regulated genes implicated in human kidney development (2021)
  • Author(s): Yuta Yamamura, Kengo Furuichi, Yasuhiro Murakawa, Shigeki Hirabayashi, Masahito Yoshihara, Keisuke Sako, Shinji Kitajima, Tadashi Toyama, Yasunori Iwata, Norihiko Sakai, Kazuyoshi Hosomichi, Philip M Murphy, Atsushi Tajima, Keisuke Okita, Kenji Osafune, Shuichi Kaneko, Takashi Wada
  • Journal Title: Scientific reports Volume: 11 Issue: 1 Pages: 9123-9123
  • DOI: 10.1038/s41598-021-88743-1
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] APOBEC3B is preferentially expressed at the G2/M phase of cell cycle (2021)
  • Author(s): Hirabayashi Shigeki、Shirakawa Kotaro、Horisawa Yoshihito、Matsumoto Tadahiko、Matsui Hiroyuki、Yamazaki Hiroyuki、Sarca Anamaria Daniela、Kazuma Yasuhiro、Nomura Ryosuke、Konishi Yoshinobu、Takeuchi Suguru、Stanford Emani、Kawaji Hideya、Murakawa Yasuhiro、Takaori-Kondo Akifumi
  • Journal Title: Biochemical and Biophysical Research Communications Volume: 546 Pages: 178-184
  • DOI: 10.1016/j.bbrc.2021.02.008
  • Peer Reviewed / Open Access
• [Journal Article] CAGE-Seq Reveals that HIV-1 Latent Infection Does Not Trigger Unique Cellular Responses in a Jurkat T Cell Model (2021)
  • Author(s): Matsui Hiroyuki、Shirakawa Kotaro、Konishi Yoshinobu、Hirabayashi Shigeki、Sarca Anamaria Daniela、Fukuda Hirofumi、Nomura Ryosuke、Stanford Emani、Horisawa Yoshihito、Kazuma Yasuhiro、Matsumoto Tadahiko、Yamazaki Hiroyuki、Murakawa Yasuhiro、Battivelli Emilie、Verdin Eric、Koyanagi Yoshio、Takaori-Kondo Akifumi
  • Journal Title: Journal of Virology Volume: 95 Issue: 8 Pages: 1-18
  • DOI: 10.1128/jvi.02394-20
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Significance of HMGA2 expression as independent poor prognostic marker in perihilar and distal cholangiocarcinoma resected with curative intent (2021)
  • Author(s): Takahashi Tomoaki、Kawaji Hideya、Murakawa Yasuhiro、Hayashizaki Yoshihide、Murakami Takashi、Yabushita Yasuhiro、Homma Yuki、Kumamoto Takafumi、Matsuyama Ryusei、Endo Itaru
  • Journal Title: European Journal of Surgical Oncology Volume: 47 Issue: 2 Pages: 394-400
  • DOI: 10.1016/j.ejso.2020.08.005
  • Peer Reviewed
• [Journal Article] CAGE-seq analysis of osteoblast derived from cleidocranial dysplasia human induced pluripotent stem cells (2020)
  • Author(s): Ooki Akio、Onodera Shoko、Saito Akiko、Oguchi Akiko、Murakawa Yasuhiro、Sakamoto Teruo、Sueishi Kenji、Nishii Yasushi、Azuma Toshifumi
  • Journal Title: Bone Volume: 141 Pages: 115582-115582
  • DOI: 10.1016/j.bone.2020.115582
  • Peer Reviewed
• [Presentation] Functional characterization of human disease pathways using high-resolution chromatin contact maps (2021)
  • Author(s): Yasuhiro Murakawa
  • Organizer: Dovetail Epigenetics Summit
  • Int'l Joint Research / Invited
• [Presentation] Functional characterization of human disease pathways using high-resolution chromatin contact maps (2021)
  • Author(s): Yasuhiro Murakawa
  • Organizer: Immuno UK: In-Person
  • Int'l Joint Research / Invited
• [Presentation] A compendium of active enhancers in human helper T cells to decode genetic architecture of immune-mediated diseases (2021)
  • Author(s): Yasuhiro Murakawa
  • Organizer: 5th RIKEN IMS-Stanford ISCBRM Joint Symposium
  • Int'l Joint Research / Invited
• [Presentation] A new genomic and computational approach to study human genomic enhancers and its association with diseases (2021)
  • Author(s): 村川泰裕
  • Organizer: 1st International Symposium of CCII
  • Int'l Joint Research / Invited
• [Presentation] Identification of Transcriptional Regulators Using Novel Next-generation Sequencing Technology (2021)
  • Author(s): 村川泰裕
  • Organizer: 85th Annual Scientific Meeting of the Japanese Circulation Society
  • Invited
• [Presentation] Decoding functional DNA elements in the human genome (2021)
  • Author(s): 村川泰裕
  • Organizer: 1st ASHBi SignAC Workshop
  • Invited
• [Presentation] RNAの生死から俯瞰する遺伝⼦発現制御 (2021)
  • Author(s): 村川泰裕
  • Organizer: IPR – Seminar
  • Invited