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Functional analyses of novel lncRNAs using reverse genetics

Research Project

Project/Area Number 17H03604
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Genome biology
Research InstitutionHokkaido University

Principal Investigator

Nakagawa Shinichi  北海道大学, 薬学研究院, 教授 (50324679)

Co-Investigator(Kenkyū-buntansha) 横井 佐織  北海道大学, 薬学研究院, 助教 (10772048)
Project Period (FY) 2017-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥16,640,000 (Direct Cost: ¥12,800,000、Indirect Cost: ¥3,840,000)
Fiscal Year 2021: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2020: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2019: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2018: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Fiscal Year 2017: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
KeywordsノンコーディングRNA / 核内構造体 / iGONAD / ゲノム編集 / ノックイン / ノックアウトマウス / 選択的スプライシング / 4.5SH / lncRNA / RNA-Seq / ES細胞 / 未分化状態 / ペプチド / x / 長鎖ノンコーディングRNA / 変異マウス / GONAD / メダカ / CRISPR-Cas9 / ゲノム
Outline of Final Research Achievements

Large numbers of non-protein-coding RNAs are transcribed from the genomes of higher organisms including human and mouse. In this study, we aimed to systematically select functional lncRNA candidate genes and to establish an efficient method for functional analyses. We found that functional lncRNAs that form tight complexes with proteins can be predicted based on the amount of RNAs recovered from the aqueous phase after UV irradiation. We also established a method to efficiently generate mutant mice lacking lncRNA function using the iGONAD method, a recently developed method that enables a low-cost, high-efficient genome editing.

Academic Significance and Societal Importance of the Research Achievements

膨大な数のlncRNAが重要な機能を持っているのか。あるいはそれらは単なる転写のノイズであり機能的な役割を果たしていないのか。この問題に関してはlncRNAの発見以来20年以上に渡って議論が続いており、変異体を作製してその表現型解析を行うことの重要性が指摘されている。本研究の成果によって効率よく機能性のlncRNAを予測することが可能となり、機能未知のlncRNAの役割について、実験的な検証が加速することが期待される。

Report

(6 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • Research Products

    (35 results)

All 2022 2021 2020 2019 2018 2017 Other

All Int'l Joint Research (3 results) Journal Article (19 results) (of which Int'l Joint Research: 13 results,  Peer Reviewed: 19 results,  Open Access: 9 results,  Acknowledgement Compliant: 1 results) Presentation (12 results) (of which Int'l Joint Research: 6 results,  Invited: 7 results) Remarks (1 results)

  • [Int'l Joint Research] University of Western Australia(Australia)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] Stanford University School of Medicine(米国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] University of Berlin(Germany)

    • Related Report
      2017 Annual Research Report
  • [Journal Article] MiR-150 Attenuates Maladaptive Cardiac Remodeling Mediated by Long Noncoding RNA MIAT and Directly Represses Profibrotic <i>Hoxa4</i>2022

    • Author(s)
      Aonuma Tatsuya、Moukette Bruno、Kawaguchi Satoshi、Barupala Nipuni P.、Sep?lveda Marisa N.、Frick Kyle、Tang Yaoliang、Guglin Maya、Raman Subha V.、Cai Chenleng、Liangpunsakul Suthat、Nakagawa Shinichi、Kim Il-man
    • Journal Title

      Circulation: Heart Failure

      Volume: - Issue: 4

    • DOI

      10.1161/circheartfailure.121.008686

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] lncRNA Neat1 regulates neuronal dysfunction post sepsis via stabilization of hemoglobin subunit beta2022

    • Author(s)
      Wu Yan、Li Pengfei、Liu Liu、Goodwin Andrew J.、Halushka Perry V.、Hirose Tetsuro、Nakagawa Shinichi、Zhou Jiliang、Liu Meng、Fan Hongkuan
    • Journal Title

      Molecular Therapy

      Volume: - Issue: 7 Pages: 2618-2632

    • DOI

      10.1016/j.ymthe.2022.03.011

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Paraspeckles are constructed as block copolymer micelles.2021

    • Author(s)
      Tomohiro Yamazaki, Tetsuya Yamamoto, Hyura Yoshino, Sylvie Souquere, Shinichi Nakagawa, Gerard Pierron, Tetsuro Hirose
    • Journal Title

      EMBO Journal

      Volume: - Issue: 12

    • DOI

      10.15252/embj.2020107270

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Ablation of lncRNA Miat attenuates pathological hypertrophy and heart failure2021

    • Author(s)
      Yang Liu、Deng Jianxin、Ma Wenxia、Qiao Aijun、Xu Shiyue、Yu Yang、Boriboun Chan、Kang Xiang、Han Dunzheng、Ernst Patrick、Zhou Lufang、Shi Jiawei、Zhang Eric、Li Tao-Sheng、Qiu Hongyu、Nakagawa Shinichi、Blackshaw Seth、Zhang Jianyi、Qin Gangjian
    • Journal Title

      Theranostics

      Volume: 11 Issue: 16 Pages: 7995-8007

    • DOI

      10.7150/thno.50990

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] A histone modifier, ASXL1, interacts with NONO and is involved in paraspeckle formation in hematopoietic cells2021

    • Author(s)
      Yamamoto Keita、Goyama Susumu、Asada Shuhei、Fujino Takeshi、Yonezawa Taishi、Sato Naru、Takeda Reina、Tsuchiya Akiho、Fukuyama Tomofusa、Tanaka Yosuke、Yokoyama Akihiko、Toya Hikaru、Kon Ayana、Nannya Yasuhito、Onoguchi-Mizutani Rena、Nakagawa Shinichi、Hirose Tetsuro、Ogawa Seishi、Akimitsu Nobuyoshi、Kitamura Toshio
    • Journal Title

      Cell Reports

      Volume: 36 Issue: 8 Pages: 109576-109576

    • DOI

      10.1016/j.celrep.2021.109576

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Spliceostatin A interaction with SF3B1 limits U1 snRNP availability and causes premature cleavage and polyadenylation.2021

    • Author(s)
      Yoshimoto, R., Chhipi-Shrestha, J.K., Schneider-Poetsch, T., Furuno, M., Burroughs, A.M., Noma, S., Suzuki, H., Hayashizaki, Y., Mayeda, A., Nakagawa, S., Kaida, D., Iwasaki, S., Yoshida, M.
    • Journal Title

      Cell Chem. Biol.

      Volume: - Issue: 9 Pages: 1356-1365

    • DOI

      10.1016/j.chembiol.2021.03.002

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] NEAT1 lncRNA and amyotrophic lateral sclerosis2021

    • Author(s)
      Nishimoto Yoshinori、Nakagawa Shinichi、Okano Hideyuki
    • Journal Title

      Neurochemistry International

      Volume: 150 Pages: 105175-105175

    • DOI

      10.1016/j.neuint.2021.105175

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] NEAT1 is essential for metabolic changes that promote breast cancer growth and metastasis.2021

    • Author(s)
      Mi Kyung Park, Li Zhang, Kyung-Won Min, 中略, Tetsuro Hirose, Je-Hyun Yoon, Min Sup Song
    • Journal Title

      Cell metabolism

      Volume: 33 Issue: 12 Pages: 2380-2397

    • DOI

      10.1016/j.cmet.2021.11.011

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The cell type‐specific ER membrane protein UGS148 is not essential in mice2021

    • Author(s)
      Takahashi Osamu、Tanahashi Mayuko、Yokoi Saori、Kaneko Mari、Yanaka Kaori、Nakagawa Shinichi、Maita Hiroshi
    • Journal Title

      Genes to Cells

      Volume: 27 Issue: 1 Pages: 43-60

    • DOI

      10.1111/gtc.12910

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Long non-coding RNA Neat1 regulates adaptive behavioural response to stress in mice2020

    • Author(s)
      Kukharsky Michail S.、Ninkina Natalia N.、An Haiyan、Telezhkin Vsevolod、Wei Wenbin、Meritens Camille Rabesahala de、Cooper-Knock Johnathan、Nakagawa Shinichi、Hirose Tetsuro、Buchman Vladimir L.、Shelkovnikova Tatyana A.
    • Journal Title

      Translational Psychiatry

      Volume: 10 Issue: 1 Pages: 171-171

    • DOI

      10.1038/s41398-020-0854-2

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Sexually dimorphic role of oxytocin in medaka mate choice2020

    • Author(s)
      Yokoi Saori、Naruse Kiyoshi、Kamei Yasuhiro、Ansai Satoshi、Kinoshita Masato、Mito Mari、Iwasaki Shintaro、Inoue Shuntaro、Okuyama Teruhiro、Nakagawa Shinichi、Young Larry J.、Takeuchi Hideaki
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 117 Issue: 9 Pages: 4802-4808

    • DOI

      10.1073/pnas.1921446117

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Forced isoform switching of Neat1_1 to Neat1_2 leads to the loss of Neat1_1 and the hyperformation of paraspeckles but does not affect the development and growth of mice2019

    • Author(s)
      Isobe Momo、Toya Hikaru、Mito Mari、Chiba Tomoki、Asahara Hiroshi、Hirose Tetsuro、Nakagawa Shinichi
    • Journal Title

      RNA

      Volume: 26 Issue: 3 Pages: 251-264

    • DOI

      10.1261/rna.072587.119

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The long noncoding RNA NEAT1_1 is seemingly dispensable for normal tissue homeostasis and cancer cell growth2019

    • Author(s)
      Adriaens Carmen、Rambow Florian、Bervoets Greet、Silla Toomas、Mito Mari、Chiba Tomoki、Asahara Hiroshi、Hirose Tetsuro、Nakagawa Shinichi、Jensen Torben Heick、Marine Jean-Christophe
    • Journal Title

      RNA

      Volume: 25 Issue: 12 Pages: 1681-1695

    • DOI

      10.1261/rna.071456.119

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] UPA-seq: prediction of functional lncRNAs using differential sensitivity to UV crosslinking2018

    • Author(s)
      Komatsu T, Yokoi S, Fujii K, Mito M, Kimura Y, Iwasaki S, Nakagawa S.
    • Journal Title

      RNA

      Volume: 24 Issue: 12 Pages: 1785-1802

    • DOI

      10.1261/rna.067611.118

    • NAID

      120006545959

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Molecular dissection of nuclear paraspeckles: towards understanding the emerging world of the RNP milieu.2018

    • Author(s)
      Nakagawa S, Yamazaki T, Hirose T.
    • Journal Title

      Open Biology

      Volume: 8 Issue: 10 Pages: 180150-180150

    • DOI

      10.1098/rsob.180150

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing2018

    • Author(s)
      Mito Mari、Kadota Mitsutaka、Tanaka Kaori、Furuta Yasuhide、Abe Kuniya、Iwasaki Shintaro、Nakagawa Shinichi
    • Journal Title

      Scientific Reports

      Volume: 8 Issue: 1 Pages: 1143-1143

    • DOI

      10.1038/s41598-018-19494-9

    • NAID

      120006398777

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Unusual semi‐extractability as a hallmark of nuclear body‐associated architectural noncoding RNAs2017

    • Author(s)
      Chujo T, Yamazaki T, Kawaguchi T, Kurosaka S, Takumi T, Nakagawa S, Hirose T
    • Journal Title

      The EMBO Journal

      Volume: - Issue: 10 Pages: 861-868

    • DOI

      10.15252/embj.201695848

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Neat1 is a p53-inducible lincRNA essential for transformation suppression.2017

    • Author(s)
      Mello SS, Sinow C, Raj N, Mazur PK, Bieging-Rolett K, Broz DK, Imam JFC, Vogel H, Wood LD, Sage J, Hirose T, Nakagawa S, Rinn J, Attardi LD.
    • Journal Title

      Genes Dev.

      Volume: 31(11) Issue: 11 Pages: 1095-1108

    • DOI

      10.1101/gad.284661.116

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Paraspeckles: Where Long Noncoding RNA Meets Phase Separation.2017

    • Author(s)
      Fox AH, Nakagawa S, Hirose T, Bond CS.
    • Journal Title

      Trends Biochem Sci.

      Volume: 43(2) Issue: 2 Pages: 124-135

    • DOI

      10.1016/j.tibs.2017.12.001

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Presentation] Regulation of Mouse Development by Retrotransposon-Related short RNA4.5SH2021

    • Author(s)
      Shinichi Nakagawa
    • Organizer
      Noncoding RNA World: From Mechanism to Therapy
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] マウス目特異的なリピート関連ノンコーディングRNA 4.5SHによる生体制御2021

    • Author(s)
      中川 真一
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Rodent specific 4.5SH RNA is essential for the early development in mouse2020

    • Author(s)
      Ikuko Yamamoto, Michiko Sugimoto, Kimi Araki, Yu Suzuki, Takehiko Kobayashi, Shinichi Nakagawa
    • Organizer
      The 25th Annual Meeting of the RNA Society
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Myodonta属特異的4.5SHクラスタはマウスの発生に必須である2019

    • Author(s)
      山本育子、杉本道彦、荒木喜美、鈴木雄、小林武彦、中川真一
    • Organizer
      日本進化学会第21回大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 小型齧歯類特異的4.5SHクラスタの欠損マウスは胎生致死となる2019

    • Author(s)
      山本育子、杉本道彦、荒木喜美、鈴木雄、小林武彦、中川真一
    • Organizer
      第21回日本RNA学会
    • Related Report
      2019 Annual Research Report
  • [Presentation] UPA‐Seq:UVへの感受性を利用した機能性lncRNAの同定2018

    • Author(s)
      中川真一, 小松太和, 水戸麻理, 竹本愛菜, 藤居光一, 岩崎信太郎
    • Organizer
      第20回日本RNA学会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Towards Identification of Novel Functional Long noncoding RNAs2017

    • Author(s)
      Shinichi Nakagawa
    • Organizer
      Kumamoto Key Forum
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Identification of novel functional lncRNA candidates using differential sensitivities to UV-irradiation2017

    • Author(s)
      Shinichi Nakagawa
    • Organizer
      ConBio 2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 長鎖ノンコーディングRNAの個体レベルでの機能解析2017

    • Author(s)
      中川 真一
    • Organizer
      第6回生命医薬情報学連合大会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 長鎖ノンコーディングRNAにできること2017

    • Author(s)
      中川 真一
    • Organizer
      千里ライフサイエンスセミナー
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Observation of sub-micron size nuclear bodies using super-resolution microscopy2017

    • Author(s)
      Shinichi Nakagawa
    • Organizer
      The 43th Naito Conference「Noncoding RNA: Biology, Chemistry, & Diseases」
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Fine structural analyses of nuclear body paraspeckle using SIM2017

    • Author(s)
      Shinichi Nakagawa
    • Organizer
      50th JSDB meeting
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Remarks] RNA Biology Laboratory

    • URL

      https://sites.google.com/rnabiol.com/home

    • Related Report
      2017 Annual Research Report

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Published: 2017-04-28   Modified: 2023-01-30  

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