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Physiological functions of gene regulatory networks driven by endogenous retroviruses

Research Project

Project/Area Number 20K15767
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 43050:Genome biology-related
Research InstitutionThe University of Tokyo

Principal Investigator

Ito Jumpei  東京大学, 医科学研究所, 助教 (20835540)

Project Period (FY) 2020-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2022: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2021: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2020: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Keywords遺伝子発現調節ネットワーク / トランスポゾン / 内在性レトロウイルス / 進化 / 遺伝子発現制御ネットワーク / 生殖細胞 / ヒト始原生殖細胞 / CRISPR/Cas9新規手法開発
Outline of Research at the Start

内在性レトロウイルス (endogenous retrovirus; ERV) は自身の配列中に転写調節エレメントを含んでおり、近傍の遺伝子の発現に様々な影響を与える。申請者らは、公的データベースに蓄積したマルチオミクスデータの大規模な再解析から、多数のERVが神経・生殖系の細胞においてエンハンサーとして働いていることを明らかにし、さらにはこれらのERVが近傍に存在する遺伝子の発現を制御することで、上述の細胞の機能・分化に重要な役割を果たしている可能性を見出した。本研究課題の目的は、「ERVの駆動する遺伝子発現ネットワーク」の神経・生殖系細胞における生理機能を明らかにすることである。

Outline of Final Research Achievements

Gene regulatory networks controlling germ cell development have diversified significantly during mammalian evolution, suggesting that they have been fine-tuned during evolution. In this study, we show that LTR5_Hs, an ape-specific ERVs, may have modified the gene regulatory network in primordial germ cells. LTR5_Hs was active as an enhancer in human primordial germ cells established from iPS cells. Furthermore, interspecies comparative transcriptome analysis revealed that the insertion of LTR5_Hs likely altered the gene expression regulatory network in primordial germ cells by creating an ape-specific enhancer.

Academic Significance and Societal Importance of the Research Achievements

生物の形質の進化は、遺伝子配列における変異だけでなく、遺伝子発現制御配列における変異により引き起こされることが知られている。本研究では、配列中に様々な転写調節エレメントを有し、遺伝子のプロモーターやエンハンサーとして働く内在性レトロウイルス(ERV)が、類人猿の進化過程においてゲノムの中で大量に増殖したことで、生殖細胞で働く遺伝子制御ネットワークが大きく書き換えられた可能性を示した。

Report

(4 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Research-status Report
  • 2020 Research-status Report
  • Research Products

    (32 results)

All 2022 2021 2020 Other

All Int'l Joint Research (3 results) Journal Article (19 results) (of which Int'l Joint Research: 11 results,  Peer Reviewed: 19 results,  Open Access: 18 results) Presentation (10 results) (of which Int'l Joint Research: 2 results,  Invited: 4 results)

  • [Int'l Joint Research] ペンシルベニア大学(米国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] ペンシルベニア大学(米国)

    • Related Report
      2021 Research-status Report
  • [Int'l Joint Research] ペンシルベニア大学(米国)

    • Related Report
      2020 Research-status Report
  • [Journal Article] A hominoid-specific endogenous retrovirus may have rewired the gene regulatory network shared between primordial germ cells and naive pluripotent cells2022

    • Author(s)
      Ito Jumpei、Seita Yasunari、Kojima Shohei、Parrish Nicholas F.、Sasaki Kotaro、Sato Kei
    • Journal Title

      PLOS Genetics

      Volume: 18 Issue: 5 Pages: e1009846-e1009846

    • DOI

      10.1371/journal.pgen.1009846

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant2022

    • Author(s)
      Suzuki Rigel、Yamasoba Daichi、Kimura Izumi、Wang Lei他
    • Journal Title

      Nature

      Volume: 603 Issue: 7902 Pages: 700-705

    • DOI

      10.1038/s41586-022-04462-1

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation2021

    • Author(s)
      Saito Akatsuki、Irie Takashi、Suzuki Rigel、Maemura Tadashi、Nasser Hesham、Uriu Keiya、Kosugi Yusuke、Other 43 authors、Tanaka Shinya、Nakagawa So、Ikeda Terumasa、Fukuhara Takasuke、Kawaoka Yoshihiro、Sato Kei、The Genotype to Phenotype Japan (G2P-Japan) Consortium
    • Journal Title

      Nature

      Volume: 602 Issue: 7896 Pages: 300-306

    • DOI

      10.1038/s41586-021-04266-9

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Clonality of HIV-1 and HTLV-1 infected cells in naturally coinfected individuals2021

    • Author(s)
      Katsuya H, Cook L, Rowan AG, Melamed A, Turpin J, Ito J, Islam S, Miyazato P, Tan B, Matsuo M, Miyakawa T, Nakata H, Matsushita S, Taylor GP, Bangham CRM, Kimura S, Satou Y.
    • Journal Title

      The Journal of Infectious Diseases

      Volume: 0 Issue: 2 Pages: 0-0

    • DOI

      10.1093/infdis/jiab202

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Elucidation of the Complicated Scenario of Primate APOBEC3 Gene Evolution2021

    • Author(s)
      Uriu Keiya、Kosugi Yusuke、Suzuki Narumi、Ito Jumpei、Sato Kei
    • Journal Title

      Journal of Virology

      Volume: 95 Issue: 12 Pages: 00-00

    • DOI

      10.1128/jvi.00144-21

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: Viruses, plasmids, and more2021

    • Author(s)
      Sugimoto Ryota、Nishimura Luca、Nguyen Phuong Thanh、Ito Jumpei、Parrish Nicholas F.、Mori Hiroshi、Kurokawa Ken、Nakaoka Hirofumi、Inoue Ituro
    • Journal Title

      PLOS Computational Biology

      Volume: 17 Issue: 10 Pages: e1009428-e1009428

    • DOI

      10.1371/journal.pcbi.1009428

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity2021

    • Author(s)
      Motozono Chihiro、Toyoda Mako、Zahradnik Jiri、Saito Akatsuki、Other 19 authors、Ikeda Terumasa、Nakagawa So、Ueno Takamasa、Sato Kei
    • Journal Title

      Cell Host & Microbe

      Volume: 29 Issue: 7 Pages: 1124-1136

    • DOI

      10.1016/j.chom.2021.06.006

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A comprehensive investigation on the interplay between feline APOBEC3Z3 proteins and feline immunodeficiency virus Vif proteins. Journal of Virology.2021

    • Author(s)
      Yusuke Kosugi‡, Keiya Uriu‡, Narumi Suzuki‡, Keisuke Yamamoto‡, Shumpei Nagaoka‡, Izumi Kimura‡, Yoriyuki Konno‡, Hirofumi Aso‡, Brian J Willett, Tomoko Kobayashi, Yoshio Koyanagi, Mahoko Takahashi Ueda, Jumpei Ito and Kei Sato. ‡Equal contribution.
    • Journal Title

      Journal of Virology

      Volume: 00178-21 Issue: 13 Pages: 00-00

    • DOI

      10.1128/jvi.00178-21

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Virus-like insertions with sequence signatures similar to those of endogenous non-retroviral RNA viruses in the human genome.2021

    • Author(s)
      Kojima S, Yoshikawa K, Ito J, Nakagawa S, Parrish NF, Horie M, Kawano S, Tomonaga K.
    • Journal Title

      Proceedings of the National Academy of Sciences of the United States of America

      Volume: 118 Issue: 5

    • DOI

      10.1073/pnas.2010758118

    • Related Report
      2021 Research-status Report 2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] The Battle between Retroviruses and APOBEC3 Genes: Its Past and Present2021

    • Author(s)
      Uriu Keiya、Kosugi Yusuke、Ito Jumpei、Sato Kei
    • Journal Title

      Viruses

      Volume: 13 Issue: 1 Pages: 124-124

    • DOI

      10.3390/v13010124

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] A tissue level atlas of the healthy human virome2020

    • Author(s)
      Kumata Ryuichi、Ito Jumpei、Takahashi Kenta、Suzuki Tadaki、Sato Kei
    • Journal Title

      BMC Biology

      Volume: 18 Issue: 1 Pages: 1-15

    • DOI

      10.1186/s12915-020-00785-5

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Inherited chromosomally integrated HHV-6 possibly modulates human gene expression2020

    • Author(s)
      Kumata Ryuichi、Ito Jumpei、Sato Kei
    • Journal Title

      Virus Genes

      Volume: 56 Issue: 3 Pages: 386-389

    • DOI

      10.1007/s11262-020-01745-5

    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [Journal Article] Multiomics Investigation Revealing the Characteristics of HIV-1-Infected Cells In?Vivo2020

    • Author(s)
      Aso Hirofumi、Nagaoka Shumpei、Kawakami Eiryo、Ito Jumpei、Islam Saiful、Tan Benjy Jek Yang、Nakaoka Shinji、Ashizaki Koichi、Shiroguchi Katsuyuki、Suzuki Yutaka、Satou Yorifumi、Koyanagi Yoshio、Sato Kei
    • Journal Title

      Cell Reports

      Volume: 32 Issue: 2 Pages: 107887-107887

    • DOI

      10.1016/j.celrep.2020.107887

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Phosphoregulation of a Conserved Herpesvirus Tegument Protein by a Virally Encoded Protein Kinase in Viral Pathogenicity and Potential Linkage between Its Evolution and Viral Phylogeny2020

    • Author(s)
      Shibazaki Misato、Kato Akihisa、Takeshima Kosuke、Ito Jumpei、Suganami Mai、Koyanagi Naoto、Maruzuru Yuhei、Sato Kei、Kawaguchi Yasushi
    • Journal Title

      Journal of Virology

      Volume: 94 Issue: 18 Pages: 1-4

    • DOI

      10.1128/jvi.01055-20

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Endogenization and excision of human herpesvirus 6 in human genomes.2020

    • Author(s)
      Xiaoxi Liu, Shunichi Kosugi, Rie Koide, Yoshiki Kawamura, Jumpei Ito, Hiroki Miura, Nana Matoba, Motomichi Matsuzaki , and other 14 authors
    • Journal Title

      PLOS Genetics

      Volume: 16 Issue: 8 Pages: 1008915-1008915

    • DOI

      10.1371/journal.pgen.1008915

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A role for gorilla APOBEC3G in shaping lentivirus evolution including transmission to humans2020

    • Author(s)
      Nakano Yusuke、Yamamoto Keisuke、Ueda Mahoko Takahashi、Soper Andrew、Konno Yoriyuki、Kimura Izumi、Uriu Keiya、Kumata Ryuichi、Aso Hirofumi、Misawa Naoko、Nagaoka Shumpei、Shimizu Soma、Mitsumune Keito、Kosugi Yusuke、Juarez-Fernandez Guillermo、Ito Jumpei、...、Koyanagi Yoshio、Harris Reuben S.、Sato Kei
    • Journal Title

      PLOS Pathogens

      Volume: 16 Issue: 9 Pages: 1008812-1008812

    • DOI

      10.1371/journal.ppat.1008812

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Endogenous retroviruses drive KRAB zinc-finger protein family expression for tumor suppression2020

    • Author(s)
      Ito Jumpei、Kimura Izumi、Soper Andrew、Coudray Alexandre、Koyanagi Yoshio、Nakaoka Hirofumi、Inoue Ituro、Turelli Priscilla、Trono Didier、Sato Kei
    • Journal Title

      Science Advances

      Volume: 6 Issue: 43 Pages: 3020-3020

    • DOI

      10.1126/sciadv.abc3020

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The significance of disseminated intravascular coagulation on multiple organ dysfunction during the early stage of acute respiratory distress syndrome2020

    • Author(s)
      Gando S、Fujishima S、Saitoh D、Shiraishi A、Yamakawa K、Kushimoto S、Ogura H、Abe T、et al
    • Journal Title

      Thrombosis Research

      Volume: 191 Issue: 1 Pages: 15-21

    • DOI

      10.1093/qjmed/hcaa296

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Reconstitution of prospermatogonial specification in vitro from human induced pluripotent stem cells2020

    • Author(s)
      Hwang Young Sun、Suzuki Shinnosuke、Seita Yasunari、Ito Jumpei、Sakata Yuka、Aso Hirofumi、Sato Kei、Hermann Brian P.、Sasaki Kotaro
    • Journal Title

      Nature Communications

      Volume: 11 Issue: 1 Pages: 5656-5656

    • DOI

      10.1038/s41467-020-19350-3

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 内在性レトロウイルスが駆動した始原生殖細胞における遺伝子発現制御ネットワークの進化2022

    • Author(s)
      伊東潤平
    • Organizer
      日本レトロウイルス研究会
    • Related Report
      2022 Annual Research Report
  • [Presentation] トランスポゾンと多重遺伝子ファミリーの進化生態学2021

    • Author(s)
      伊東潤平、佐藤佳
    • Organizer
      日本遺伝学会第93回大会
    • Related Report
      2021 Research-status Report
    • Invited
  • [Presentation] Coevolutionary dynamics of multigene families and transposable elements in vertebrates.2021

    • Author(s)
      Jumpei Ito, Kei Sato
    • Organizer
      5th Uppsala Transposon Symposium
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] 多重遺伝子ファミリーとトランスポゾンの進化生態学2021

    • Author(s)
      伊東潤平, 佐藤佳
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Research-status Report
  • [Presentation] 内在性レトロウイルスと抗レトロウイルス遺伝子ファミリー間に起こった進化的軍拡競争の描出2020

    • Author(s)
      伊東潤平
    • Organizer
      第92回日本遺伝学会, 紙面開催
    • Related Report
      2020 Research-status Report
    • Invited
  • [Presentation] 内在性レトロウイルスの駆動する生命現象と生物進化2020

    • Author(s)
      伊東潤平
    • Organizer
      山口大学 微生物研究推進体 研究会
    • Related Report
      2020 Research-status Report
    • Invited
  • [Presentation] データ駆動科学で乗り出すウイルス研究の新天地2020

    • Author(s)
      伊東潤平
    • Organizer
      2020年日本バイオインフォマティクス学会年会・第9回生命医薬情報学連合大会
    • Related Report
      2020 Research-status Report
    • Invited
  • [Presentation] 公的シーケンスデータ解析のウイルス研究への応用可能性2020

    • Author(s)
      伊東潤平
    • Organizer
      第43回日本分子生物学会年会
    • Related Report
      2020 Research-status Report
  • [Presentation] 腫瘍の遺伝子発現制御ネットワークを司る「ウイルス由来ジャンクDNA」の同定2020

    • Author(s)
      伊東潤平
    • Organizer
      ウイルス学若手研究集会2020
    • Related Report
      2020 Research-status Report
  • [Presentation] Endogenous retroviruses drive KRAB zinc-finger protein family expression for tumor suppression.2020

    • Author(s)
      Jumpei Ito, Izumi Kimura, Kei Sato
    • Organizer
      Cold Spring Harbor Laboratory Meeting on Transposable Elements
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research

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Published: 2020-04-28   Modified: 2024-01-30  

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