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Identification of the role of transcription termination and polyadenylation in the pathogenesis of ALS using multiple high-throughput sequencing analyses

Research Project

Project/Area Number 15K06755
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Nerve anatomy/Neuropathology
Research InstitutionNagoya University

Principal Investigator

Masuda Akio  名古屋大学, 医学系研究科, 准教授 (10343203)

Project Period (FY) 2015-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2017: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2015: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
KeywordstRIP / CLIP法 / RNA代謝 / ポリアデニル化 / RNA-タンパク相互作用 / ALS / FUS / RNA-蛋白相互作用 / CLIP / RNAP II / mRNA / 次世代シークエンサー
Outline of Final Research Achievements

RNA metabolism occurs in specific machineries of RNA, including RNA polymerase II (RNAP II), spliceosome, and 3’ end processing machinery. However, the transcriptome-wide detection of protein-RNA interactions in a subcellular component is challenging. Here, we developed the tRIP method (targeted RNA immunoprecipitation) to increase efficiency of RNA immunoprecipitation, which enables detection of UV-crosslinked protein-RNA interactions from thousands of cells. Application of tRIP to identification of protein-protein-RNA interactions revealed that FUS, a multifunctional RNA-binding protein associated with ALS, binds specifically upstream to alternative polyadenylation (APA) sites of nascent RNA engaged to RNAP II. Further tRIP analysis demonstrated that the FUS-U1 snRNP-RNA complex is the entity that suppresses APA.

Academic Significance and Societal Importance of the Research Achievements

本研究は、生命の基本現象である、遺伝・転写・翻訳のうち、転写に関するものである。本研究により、従来の100倍以上の感度を持った転写制御解析法を確立した。この方法により、従来、解析することの出来なかった、細胞内の小器官内での転写の様子を見ることが可能になった。実際、本研究で、疾患原因因子FUSによる、従来知られていなかった新たな転写制御様式を発見している。本研究成果は、転写研究や転写異常が原因となる神経疾患の研究の進展に大いに貢献することが期待される。

Report

(5 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (38 results)

All 2019 2018 2017 2016 2015 Other

All Int'l Joint Research (3 results) Journal Article (22 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 21 results,  Open Access: 18 results,  Acknowledgement Compliant: 9 results) Presentation (6 results) Book (2 results) Remarks (4 results) Patent(Industrial Property Rights) (1 results)

  • [Int'l Joint Research] University of Southern Denmark(Denmark)

    • Related Report
      2017 Research-status Report
  • [Int'l Joint Research] Mahidol University(Thailand)

    • Related Report
      2017 Research-status Report
  • [Int'l Joint Research] University of Southern Denmark(Denmark)

    • Related Report
      2016 Research-status Report
  • [Journal Article] Mianserin suppresses R-spondin 2-induced activation of Wnt/β-catenin signaling in chondrocytes and prevents cartilage degradation in a rat model of osteoarthritis2019

    • Author(s)
      Okura Toshiaki、Ohkawara Bisei、Takegami Yasuhiko、Ito Mikako、Masuda Akio、Seki Taisuke、Ishiguro Naoki、Ohno Kinji
    • Journal Title

      Scientific Reports

      Volume: 9 Issue: 1 Pages: 2808-2808

    • DOI

      10.1038/s41598-019-39393-x

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Differential effects of spinal motor neuron-derived and skeletal muscle-derived Rspo2 on acetylcholine receptor clustering at the neuromuscular junction2018

    • Author(s)
      Li Jin、Ito Mikako、Ohkawara Bisei、Masuda Akio、Ohno Kinji
    • Journal Title

      Scientific Reports

      Volume: 8 Issue: 1 Pages: 13577-13577

    • DOI

      10.1038/s41598-018-31949-7

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Lack of Fgf18 causes abnormal clustering of motor nerve terminals at the neuromuscular junction with reduced acetylcholine receptor clusters2018

    • Author(s)
      Ito Kenyu、Ohkawara Bisei、Yagi Hideki、Nakashima Hiroaki、Tsushima Mikito、Ota Kyotaro、Konishi Hiroyuki、Masuda Akio、Imagama Shiro、Kiyama Hiroshi、Ishiguro Naoki、Ohno Kinji
    • Journal Title

      Sceintific Reports

      Volume: 8 Issue: 1 Pages: 434-434

    • DOI

      10.1038/s41598-017-18753-5

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] MYRF is associated with encephalopathy with reversible myelin vacuolization2018

    • Author(s)
      Kurahashi Hirokazu、Azuma Yoshiteru、Masuda Akio、Okuno Tatsuya、Nakahara Eri、Imamura Takuji、Saitoh Makiko、Mizuguchi Masashi、Shimizu Toshiaki、Ohno Kinji、Okumura Akihisa
    • Journal Title

      Annals of Neurology

      Volume: 83 Issue: 1 Pages: 98-106

    • DOI

      10.1002/ana.25125

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Rules and tools to predict the splicing effects of exonic and intronic mutations2018

    • Author(s)
      Ohno K, Takeda J, Masuda A.
    • Journal Title

      Wiley Interdiscip Rev RNA

      Volume: 印刷中 Issue: 1

    • DOI

      10.1002/wrna.1451

    • NAID

      120006473502

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Competitive regulation of alternative splicing and alternative polyadenylation by hnRNP H and CstF64 determines acetylcholinesterase isoforms2017

    • Author(s)
      Nazim M, Masuda A, Rahman MA, Nasrin F, Takeda JI, Ohe K, Ohkawara B, Ito M, Ohno K.
    • Journal Title

      Nucleic Acids Res

      Volume: - Pages: 1455-1468

    • DOI

      10.1093/nar/gkw823

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] SRSF1 suppresses selection of intron-distal 5′ splice site of DOK7 intron 4 to generate functional full-length Dok-7 protein2017

    • Author(s)
      Ahsan Khalid Bin、Masuda Akio、Rahman Mohammad Alinoor、Takeda Jun-ichi、Nazim Mohammad、Ohkawara Bisei、Ito Mikako、Ohno Kinji
    • Journal Title

      Sceintific Reports

      Volume: 7 Issue: 1 Pages: 10446-10446

    • DOI

      10.1038/s41598-017-11036-z

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Splicing regulation and dysregulation of cholinergic genes expressed at the neuromuscular junction2017

    • Author(s)
      Ohno, K. Rahman, M. A. Nazim, M. Nasrin, F. Lin, Y. Takeda, J. I. Masuda, A.
    • Journal Title

      J Neurochem

      Volume: 印刷中 Issue: S2 Pages: 64-72

    • DOI

      10.1111/jnc.13954

    • Related Report
      2017 Research-status Report 2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Six GU-rich (6GUR) FUS-binding motifs detected by normalization of CLIP-seq by Nascent-seq2017

    • Author(s)
      Takeda J, Masuda A, Ohno K.
    • Journal Title

      Gene

      Volume: 618 Pages: 57-64

    • DOI

      10.1016/j.gene.2017.04.008

    • NAID

      120006331826

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Competitive regulation of alternative splicing and alternative polyadenylation by hnRNP H and CstF64 determines acetylcholinesterase isoforms2017

    • Author(s)
      Nazim, M. Masuda, A. Rahman, M. A. Nasrin, F. Takeda, J. I. Ohe, K. Ohkawara, B. Ito, M. Ohno, K.
    • Journal Title

      Nucleic Acids Res

      Volume: 3 Pages: 1455-1468

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] FUS-mediated regulation of alternative RNA processing in neurons: insights from global transcriptome analysis2016

    • Author(s)
      Akio Masuda. Takeda, J. I. Ohno, K.
    • Journal Title

      Wiley Interdiscip Rev RNA

      Volume: in press Issue: 3 Pages: 330-340

    • DOI

      10.1002/wrna.1338

    • NAID

      120005893268

    • Related Report
      2016 Research-status Report 2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] FUSによるmRNA長の制御2016

    • Author(s)
      増田章男、大野欽司
    • Journal Title

      生化学

      Volume: 88 Pages: 244-247

    • NAID

      40020843436

    • Related Report
      2016 Research-status Report 2015 Research-status Report
    • Acknowledgement Compliant
  • [Journal Article] R-spondin 2 facilitates differentiation of proliferating chondrocytes into hypertrophic chondrocytes by enhancing Wnt/β-catenin signaling in endochondral ossification.2016

    • Author(s)
      Takegami Y, Ohkawara B, Ito M, Masuda A, Nakashima H, Ishiguro N, Ohno K.
    • Journal Title

      Biochem Biophys Res Commun.

      Volume: S0006-291X(16) Issue: 1 Pages: 30400-4

    • DOI

      10.1016/j.bbrc.2016.03.089

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] IntSplice: prediction of the splicing consequences of intronic single-nucleotide variations in the human genome2016

    • Author(s)
      Shibata, A. Okuno, T. Rahman, M. A. Azuma, Y. Takeda, J. Masuda, A. Selcen, D. Engel, A. G. Ohno, K.
    • Journal Title

      J Hum Genet

      Volume: 61 Issue: 7 Pages: 633-640

    • DOI

      10.1038/jhg.2016.23

    • NAID

      120005851030

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] R-spondin 2 promotes acetylcholine receptor clustering at the neuromuscular junction via Lgr5.2016

    • Author(s)
      Nakashima H., Ohkawara B., Ishigaki S., Fukudome T., Ito K., Tsushima M., Konishi H., Okuno T., Yoshimura T., Ito M., Masuda A., Sobue G., Kiyama H., Ishiguro N., Ohno K.
    • Journal Title

      Sci Rep

      Volume: 22 Issue: 1 Pages: 28512-28512

    • DOI

      10.1038/srep28512

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Arginine methylation of ubiquitin-associated protein 2-like is required for the accurate distribution of chromosomes.2016

    • Author(s)
      Maeda M, Hasegawa H, Sugiyama M, Hyodo T, Ito S, Chen D, Asano E, Masuda A, Hasegawa Y, Hamaguchi M, Senga T
    • Journal Title

      FASEB Journal

      Volume: 30 Issue: 1 Pages: 312-323

    • DOI

      10.1096/fj.14-268987

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Molecular hydrogen suppresses activated Wnt-catenin signaling.2016

    • Author(s)
      Y. Lin, B. Ohkawara, M. Ito, N. Misawa, K. Miyamoto, Y. Takegami, A. Masuda, S. Toyokuni, K Ohno
    • Journal Title

      Scientific Report

      Volume: 25 Issue: 1 Pages: 31986-31986

    • DOI

      10.1038/srep31986

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Tranilast stimulates endochondral ossification by upregulating SOX9 and RUNX2 promoters.2016

    • Author(s)
      Hasegawa S, Kitoh H, Ohkawara B, Mishima K, Matsushita M, Masuda A, Ishiguro N, Ohno K
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 470(2) Issue: 2 Pages: 356-61

    • DOI

      10.1016/j.bbrc.2016.01.044

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Phenylbutazone induces expression of MBNL1 and suppresses formation of MBNL1-CUG RNA foci in a mouse model of myotonic dystrophy2016

    • Author(s)
      1.Chen G, Masuda A, Konishi H, Ohkawara B, Ito M, Kinoshita M, Kiyama H, Matsuura T, Ohno K.
    • Journal Title

      Sci Rep

      Volume: 6 Issue: 1 Pages: 25317-25317

    • DOI

      10.1038/srep25317

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Global identification of hnRNP A1 binding sites for SSO-based splicing modulation2016

    • Author(s)
      Bruun GH, Doktor TK, Borch J-J, Masuda A, Krainer AR, Ohno K, Andresen BS.
    • Journal Title

      BMC Biol

      Volume: 14 Issue: 1 Pages: 54-54

    • DOI

      10.1186/s12915-016-0279-9

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Position-specific binding of FUS to nascent RNA regulates mRNA length.2015

    • Author(s)
      Masuda A, Takeda J, Okuno T, Okamoto T, Ohkawara B, Ito M, Ishigaki S, Sobue G, Ohno K.
    • Journal Title

      Genes Dev.

      Volume: 29(10) Issue: 10 Pages: 1045-57

    • DOI

      10.1101/gad.255737.114

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] SRSF1 and hnRNP H antagonistically regulate splicing of COLQ exon 16 in a congenital myasthenic syndrome.2015

    • Author(s)
      Rahman MA, Azuma Y, Nasrin F, Takeda J, Nazim M, Bin Ahsan K, Akio Masuda, Engel AG, Ohno K.
    • Journal Title

      Sci Rep.

      Volume: 5 Issue: 1 Pages: 13208-13208

    • DOI

      10.1038/srep13208

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 新規RNA免疫沈降法(tRIP法)による、FUS-U1 snRNP依存性 転写終結制御の解明2018

    • Author(s)
      Akio Masuda, Toshihiko Kawachi, Junichi Takeda, Kinji Ohno
    • Organizer
      第41回日本分子生物学会 年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 新規RNA免疫沈降法による生体内protein-protein-RNA interactionの検出2017

    • Author(s)
      増田章男、河地利彦、武田淳一、大野欽司
    • Organizer
      第19回日本RNA学会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] FUSはプロモーター領域のアンチセンス鎖RNA (PROMPTs) に結合し、転写制御を行う2016

    • Author(s)
      Takaaki Okamoto, Akio Masuda, Jun-ichi Takeda, Kinji Ohno
    • Organizer
      日本分子生物学会
    • Place of Presentation
      パシフィコ横浜(神奈川県横浜市)
    • Year and Date
      2016-11-30
    • Related Report
      2016 Research-status Report
  • [Presentation] Binding of FUS to promoter upstream transcripts, PROMPTs, globally regulates gene transcription2016

    • Author(s)
      Akio Masuda, Jun-ichi Takeda, Takaaki Okamoto, Kinji Ohno
    • Organizer
      RNA society
    • Place of Presentation
      国立京都国際会館(京都府京都市)
    • Year and Date
      2016-06-28
    • Related Report
      2016 Research-status Report
  • [Presentation] Interaction between NIFK and ncRNA arising from Ccnd1 promoter region regulates myogenic differentiation2016

    • Author(s)
      Yoshihiro Yamashita, Akio Masuda, Kinji Ohno
    • Organizer
      RNA society
    • Place of Presentation
      国立京都国際会館(京都府京都市)
    • Year and Date
      2016-06-28
    • Related Report
      2016 Research-status Report
  • [Presentation] 神経疾患関連RNA結合蛋白FUSによる転写開始・終結制御2015

    • Author(s)
      増田章男、武田淳一、大野欽司
    • Organizer
      第17回RNAミーティング
    • Place of Presentation
      ホテルライフォート札幌(北海道札幌市)
    • Year and Date
      2015-07-13
    • Related Report
      2015 Research-status Report
  • [Book] Neurodegeneration-associated RNA-binding protein, FUS, regulates mRNA length2016

    • Author(s)
      Masuda, A. Ohno, K.
    • Total Pages
      1
    • Publisher
      ATLAS of Science
    • Related Report
      2016 Research-status Report
  • [Book] "Neurodegeneration-associated RNA-binding protein, FUS, regulates mRNA length" in Atlas of Science. Ed. by Lynn C Yeoman. http://atlasofscience.org/neurodegeneration-associated-rna-binding-protein-fus-regulates-mrna-length/2016

    • Author(s)
      Akio Masuda. Ohno, K.
    • Publisher
      AoS Nordic AB, Stockholm
    • Related Report
      2015 Research-status Report
  • [Remarks] 名古屋大学大学院医学系研究科神経遺伝情報公式ホームページ

    • URL

      https://www.med.nagoya-u.ac.jp/neurogenetics/

    • Related Report
      2018 Annual Research Report
  • [Remarks] 名古屋大学大学院医学系研究科先端応用医学部門神経遺伝情報分野

    • URL

      https://www.med.nagoya-u.ac.jp/neurogenetics/

    • Related Report
      2017 Research-status Report
  • [Remarks]

    • URL

      https://www.med.nagoya-u.ac.jp/neurogenetics/

    • Related Report
      2016 Research-status Report
  • [Remarks] 神経変性疾患の発症に関わる“RNA結合タンパクFUS”の機能解明

    • URL

      http://www.med.nagoya-u.ac.jp/medical/dbps_data/_material_/nu_medical/_res/topix/2015/fus_20150515jp.pdf

    • Related Report
      2015 Research-status Report
  • [Patent(Industrial Property Rights)] タンパク質-RNA相互作用の検出2017

    • Inventor(s)
      増田章男、大野欽司
    • Industrial Property Rights Holder
      名古屋大学
    • Industrial Property Rights Type
      特許
    • Filing Date
      2017
    • Related Report
      2017 Research-status Report

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Published: 2015-04-16   Modified: 2020-03-30  

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