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Functional analyses of physiological function of ncRNA according to the neo-taxonomy

Planned Research

Project AreaNeo-taxonomy of noncoding RNAs
Project/Area Number 26113005
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionHokkaido University (2016-2018)
Institute of Physical and Chemical Research (2014-2015)

Principal Investigator

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

Project Period (FY) 2014-07-10 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥137,280,000 (Direct Cost: ¥105,600,000、Indirect Cost: ¥31,680,000)
Fiscal Year 2018: ¥27,690,000 (Direct Cost: ¥21,300,000、Indirect Cost: ¥6,390,000)
Fiscal Year 2017: ¥27,690,000 (Direct Cost: ¥21,300,000、Indirect Cost: ¥6,390,000)
Fiscal Year 2016: ¥27,300,000 (Direct Cost: ¥21,000,000、Indirect Cost: ¥6,300,000)
Fiscal Year 2015: ¥27,170,000 (Direct Cost: ¥20,900,000、Indirect Cost: ¥6,270,000)
Fiscal Year 2014: ¥27,430,000 (Direct Cost: ¥21,100,000、Indirect Cost: ¥6,330,000)
KeywordslncRNA / 長鎖ノンコーディングRNA / Neat1 / パラスペックル / RNAseq / 液ー液相分離 / 1,6ヘキサンジオール / tSNE / ノンコーディングRNA / 核内構造体 / 高脂肪食 / 超解像顕微鏡
Outline of Final Research Achievements

A number of noncoding RNAs that do not encode proteins are transcribed from the genome. The ncRNAs can be divided into two large groups: "small RNA", which are involved in RNA silencing, and "Long noncoding RNA (lncRNA)", which are more than 200 bases long. It is not clear how many of the lncRNAs actually have physiological functions. We have developed a method to identify novel functional lncRNA candidate genes using the property that known functional lncRNAs are highly efficiently cross-linked to proteins by mild UV irradiation. We also established a technique to analyze the fine structure formed by lncRNA using a super-resolution microscope.

Academic Significance and Societal Importance of the Research Achievements

lncRNAのうち機能解析が行われたものは全体の1%にも満たず、転写のノイズに過ぎないと考えられているものも多い。また、転写されたRNAではなくその領域をRNAポリメラーゼが通過することに生理的意義があるlncRNAも報告されており、実際にRNA分子が生理機能を持つlncRNAを効率よく同定する方法が求められていた。我々が開発した手法は極めて簡便に機能性lncRNAの候補を同定することが可能であり、今後の効率的な個別の遺伝子の機能解析への道筋をつけることができた。また、lncRNAが形成するサブミクロンオーダーの構造体の内部構造の解析が可能となり、構造に基づいた分子作動機構予測が可能となった。

Report

(6 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • Research Products

    (55 results)

All 2019 2018 2017 2016 2015 2014 Other

All Int'l Joint Research (16 results) Journal Article (26 results) (of which Int'l Joint Research: 14 results,  Peer Reviewed: 26 results,  Open Access: 19 results,  Acknowledgement Compliant: 6 results) Presentation (13 results) (of which Int'l Joint Research: 6 results,  Invited: 9 results)

  • [Int'l Joint Research] DZHK(ドイツ)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] The Icahn School of Med. at Mt. Sinai(米国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] The University of Texas(米国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] University of Western Australia(オーストラリア)

    • Related Report
      2018 Annual Research Report
  • [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
  • [Int'l Joint Research] University of Illinois Urbana/Harvad Medical School(米国)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] Chinese University of Hong Kong(China)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] University of Oxford(英国)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] The University of Western Australia(Australia)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] VIB(Belgium)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] Harvard Medical School/University of Illinois(米国)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] University of Western Australia(Australia)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] DZHK(Germany)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] Maastricht University(オランダ)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] The expression of long noncoding RNA NEAT1 is reduced in schizophrenia and modulates oligodendrocytes transcription.2019

    • Author(s)
      Katsel P, Roussos P, Fam P, Khan S, Tan W, Hirose T, Nakagawa S, Pletnikov MV, Haroutunian V.
    • Journal Title

      NPJ Schizophr.

      Volume: 5 Issue: 1 Pages: 3-3

    • DOI

      10.1038/s41537-019-0071-2

    • Related Report
      2018 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] Long noncoding RNA NEAT1 (nuclear paraspeckle assembly transcript 1) is critical for phenotypic switching of vascular smooth muscle cells.2018

    • Author(s)
      Ahmed ASI, Dong K, Liu J, Wen T, Yu L, Xu F, Kang X, Osman I, Hu G, Bunting KM, Crethers D, Gao H, Zhang W, Liu Y, Wen K, Agarwal G, Hirose T, Nakagawa S, Vazdarjanova A, Zhou J.
    • Journal Title

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

      Volume: 115 Issue: 37

    • DOI

      10.1073/pnas.1803725115

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Immune system-mediated atherosclerosis caused by deficiency of long noncoding RNA MALAT1 in ApoE-/- mice.2018

    • Author(s)
      Gast M, Rauch BH, Nakagawa S, Haghikia A, Jasina A, Haas J, Nath N, Jensen L, Stroux A, Bohm A, Friebel J, Rauch U, Skurk C, Blankenberg S, Zeller T, Prasanth KV, Meder B, Kuss A, Landmesser U, Poller W
    • Journal Title

      Cardiovascular research

      Volume: 115 Issue: 2 Pages: 302-314

    • DOI

      10.1093/cvr/cvy202

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation2018

    • Author(s)
      Yamazaki Tomohiro、Souquere Sylvie、Chujo Takeshi、Kobelke Simon、Chong Yee Seng、Fox Archa H.、Bond Charles S.、Nakagawa Shinichi、Pierron Gerard、Hirose Tetsuro
    • Journal Title

      Molecular Cell

      Volume: 70 Issue: 6 Pages: 1038-1053

    • DOI

      10.1016/j.molcel.2018.05.019

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] CO2-sensitive tRNA modification associated with human mitochondrial disease2018

    • Author(s)
      Lin, H., Kenjyo, M., Harada, T., Okita, R., Takeshita, E., Komaki, H., Yagasaki, H., Fujioka, K., Goto, Y., Yanaka, K., Nakagawa, S., Sakaguchi, Y. and *Suzuki, T.
    • Journal Title

      Nature Commun.

      Volume: in press Issue: 1 Pages: 1875-1875

    • DOI

      10.1038/s41467-018-04250-4

    • 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] Long noncoding RNA MALAT1 suppresses breast cancer metastasis2018

    • Author(s)
      Kim, J., Piao, H.L., Kim, B.J., Yao, F., Han, Z., Wang, Y., Xiao, Z., Siverly, A.N., Lawhon, S.E., Ton, B.N., Lee, H., Zhou, Z., Gan, B., Nakagawa, S., Ellis, M.J., Liang, H., Hung, M.C., You, M.J., Sun, Y. & Ma, L.
    • Journal Title

      Nature Genetics

      Volume: 50 Issue: 12 Pages: 1705-1715

    • DOI

      10.1038/s41588-018-0252-3

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [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 2016 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
  • [Journal Article] Malat1 regulates myogenic differentiation and muscle regeneration through modulating MyoD transcriptional activity.2017

    • Author(s)
      Chen X, He L, Zhao Y, Li Y, Zhang S, Sun K, So K, Chen F, Zhou L, Lu L, Wang L, Zhu X, Bao X, Esteban MA, Nakagawa S, Prasanth KV, Wu Z, Sun H, Wang H.
    • Journal Title

      Cell Discov

      Volume: in press Issue: 1

    • DOI

      10.1038/celldisc.2017.2

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Control of Chromosomal Localization of Xist by hnRNP U Family Molecules.2016

    • Author(s)
      Sakaguchi, T., Hasegwa, Y., Brockdorff, N., Tsutusi, K., Tsutsui, K., *Sado, T., and *Nakagawa, S
    • Journal Title

      Developmental Cell

      Volume: 39 Issue: 1 Pages: 11-12

    • DOI

      10.1016/j.devcel.2016.09.022

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Regulation of membrane KCNQ1/KCNE1 channel density by sphingomyelin synthase 1.2016

    • Author(s)
      Wu M, Takemoto M, Taniguchi M, Takumi T, Okazaki T, Song WJ
    • Journal Title

      Am J Physiol Cell Physiol

      Volume: 311 Issue: 7 Pages: 817-830

    • DOI

      10.1083/jcb.201601071

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Natural antisense RNA promotes 3' end processing and maturation of MALAT1 lncRNA.2016

    • Author(s)
      Zong X, Nakagawa S, Freier SM, Fei J, Ha T, Prasanth SG, Prasanth KV.
    • Journal Title

      Nucleic Acids Res

      Volume: 44 Issue: 6 Pages: 2898-2908

    • DOI

      10.1093/nar/gkw047

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] MALAT1 long non-coding RNA in cancer.2016

    • Author(s)
      Yoshimoto R, Mayeda A, Yoshida M, Nakagawa S.
    • Journal Title

      Biochim Biophys Acta

      Volume: 1859 Issue: 1 Pages: 192-199

    • DOI

      10.1016/j.bbagrm.2015.09.012

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Regulation of gene expression via retrotransposon insertions and the noncoding RNA 4.5S RNAH.2015

    • Author(s)
      Ishida K, Miyauchi K, Kimura Y, Mito M, Okada S, Suzuki T, Nakagawa S.
    • Journal Title

      Genes Cells

      Volume: 20 Issue: 11 Pages: 887-901

    • DOI

      10.1111/gtc.12280

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Xist Exon 7 Contributes to the Stable Localization of Xist RNA on the Inactive X-Chromosome.2015

    • Author(s)
      Yamada N, Hasegawa Y, Yue M, Hamada T, Nakagawa S, Ogawa Y.
    • Journal Title

      PLoS Genet.

      Volume: 11 Issue: 8 Pages: e1005430-e1005430

    • DOI

      10.1371/journal.pgen.1005430

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Lessons from reverse-genetic studies of lncRNAs.2015

    • Author(s)
      Nakagawa S.
    • Journal Title

      Biochim Biophys Acta

      Volume: 1859 Issue: 1 Pages: 177-183

    • DOI

      10.1016/j.bbagrm.2015.06.011

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] The lncRNA Neat1 is required for corpus luteum formation and the establishment of pregnancy in a subpopulation of mice.2014

    • Author(s)
      Nakagawa S, Shimada M, Yanaka K, Mito M, Arai T, Takahashi E, Fujita Y, Fujimori T, Standaert L, Marine JC, Hirose T.
    • Journal Title

      Development

      Volume: 141 Issue: 23 Pages: 4618-27

    • DOI

      10.1242/dev.110544

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The long noncoding RNA Neat1 is required for mammary gland development and lactation.2014

    • Author(s)
      Standaert, L., Adriaens, C., Radaelli, E., Van Keymeulen, A., Blanpain, C., Hirose, T., Nakagawa, S. & Marine, J.C.
    • Journal Title

      RNA

      Volume: 20 Issue: 12 Pages: 1844-1849

    • DOI

      10.1261/rna.047332.114

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Yb Integrates piRNA Intermediates and Processing Factors into Perinuclear Bodies to Enhance piRISC Assembly.2014

    • Author(s)
      Murota Y, Ishizu H, Nakagawa S, Iwasaki YW, Shibata S, Kamatani MK, Saito K, Okano H, Siomi H, Siomi MC.
    • Journal Title

      Cell Rep.

      Volume: 8 Issue: 1 Pages: 103-113

    • DOI

      10.1016/j.celrep.2014.05.043

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Formation of nuclear bodies by the lncRNA Gomafu-associating proteins Celf3 and SF12014

    • Author(s)
      Ishizuka, A., Hasegawa, Y., Ishida, K., Yanaka, K. & Nakagawa, S
    • Journal Title

      Genes Cells

      Volume: 19 Issue: 9 Pages: 704-721

    • DOI

      10.1111/gtc.12169

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] NEAT1 long noncoding RNA regulates transcription via protein sequestration within2014

    • Author(s)
      Hirose T, Virnicchi G, Tanigawa A, Naganuma T, Li R, Kimura H, Yokoi T, Nakagawa S, Bénard M, Fox AH, Pierron G.
    • Journal Title

      Mol Biol Cell.

      Volume: 25 Issue: 1 Pages: 169-183

    • DOI

      10.1091/mbc.e13-09-0558

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing2014

    • Author(s)
      Barry, G., Briggs, J. A., Vanichkina, D. P., Poth, E. M., Beveridge, N. J., Ratnu, V. S., Nayler, S. P., Nones, K., Hu, J., Bredy, T. W., Nakagawa, S., Rigo, F., Taft, R. J., Cairns, M. J., Blackshaw, S., Wolvetang, E. J., and Mattick, J. S.
    • Journal Title

      Mol. Psychiatry

      Volume: 19 Issue: 4 Pages: 486-494

    • DOI

      10.1038/mp.2013.45

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Presentation] 長鎖ノンコーディングRNAによる生体制御2018

    • Author(s)
      中川 真一
    • Organizer
      第59回日本神経学会学術大会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Prediction of functional lncRNAs using UPA-seq2018

    • Author(s)
      Shinichi Nakagawa
    • Organizer
      EMBO Workshop
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Attempts towards identification of novel functional lncRNAs2018

    • Author(s)
      Shinichi Nakagawa
    • Organizer
      Cold Spring Harbor-Asia Conference
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Towards Identification of Novel Functional Long noncoding RNAs2017

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

    • Author(s)
      Shinichi Nakagawa
    • Organizer
      ConBio 2017(招待講演)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [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
  • [Presentation] Regulation of female fertility by lncRNA Neat12015

    • Author(s)
      Nakagawa, S.
    • Organizer
      日本分子生物学会
    • Place of Presentation
      神戸国際会議場(兵庫県神戸市)
    • Year and Date
      2015-12-02
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Paraspeckles: lncRNA-dependent nuclear bodies regulating multiple physiological processes2015

    • Author(s)
      Nakagawa, S.
    • Organizer
      DZHK symposium
    • Place of Presentation
      Berlin (Germany)
    • Year and Date
      2015-10-16
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 超解像顕微鏡による核内構造体パラスペックルの微細構観察2015

    • Author(s)
      中川 真一、水戸 麻理、廣瀬 哲郎
    • Organizer
      日本RNA学会
    • Place of Presentation
      ホテルライフォート札幌(北海道札幌市)
    • Year and Date
      2015-07-16
    • Related Report
      2015 Annual Research Report
  • [Presentation] RNA-dependent Nuclear Bodies : Evolutionary New Regulation Machinery Build on Long Noncoding RNAs2015

    • Author(s)
      Nakagawa, S.
    • Organizer
      International Symposium of Research Center for Epigenome Regulation
    • Place of Presentation
      Suwang (Korea)
    • Year and Date
      2015-05-13
    • Related Report
      2015 Annual Research Report
    • Invited

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Published: 2014-11-20   Modified: 2022-02-28  

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