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Genetic approaches to physiological functions of long noncoding RNA machinery

Planned Research

Project AreaFunctional machinery for non-coding RNAs
Project/Area Number 21115007
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 InstitutionKobe University (2011-2013)
National Institutes of Natural Sciences Okazaki Research Facilities (2009-2010)

Principal Investigator

KAGEYAMA Yuji  神戸大学, 遺伝子実験センター, 准教授 (90335480)

Co-Investigator(Kenkyū-buntansha) NAKAGAWA Shinichi  独立行政法人理化学研究所, 中川RNA生物学研究室, 准主任研究員 (50324679)
Project Period (FY) 2009-07-23 – 2014-03-31
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥131,560,000 (Direct Cost: ¥101,200,000、Indirect Cost: ¥30,360,000)
Fiscal Year 2013: ¥28,340,000 (Direct Cost: ¥21,800,000、Indirect Cost: ¥6,540,000)
Fiscal Year 2012: ¥28,340,000 (Direct Cost: ¥21,800,000、Indirect Cost: ¥6,540,000)
Fiscal Year 2011: ¥24,830,000 (Direct Cost: ¥19,100,000、Indirect Cost: ¥5,730,000)
Fiscal Year 2010: ¥24,830,000 (Direct Cost: ¥19,100,000、Indirect Cost: ¥5,730,000)
Fiscal Year 2009: ¥25,220,000 (Direct Cost: ¥19,400,000、Indirect Cost: ¥5,820,000)
Keywordsショウジョウバエ / マウス / 非コードRNA / 神経発生 / 不活性化X / Xist / ペプチド / 遺伝学 / 発生生物学 / noncoding RNA / 中枢神経系 / キイロショウジョウバエ / ノンコーディングRNA / 神経細胞 / 発生遺伝学
Research Abstract

Current research project demonstrates biological importance of long noncoding RNA by genetic approaches using fruit flies and mice. Mutational studies showed that 1) high-molecular weight long noncoding RNA plays an impotent role in formation of neural circuits in the adult fly brain and 2) RNA binding protein hnRNP U, which carries both an RNA binding domain and a chromatin binding domain, is essential for localization of Xist RNA, an essential component in dosage compensation in mammals. In the course of study, we found that some of the putative long noncoding RNA include short ORFs that encodes extremely small peptides and those peptides, at least in some cases, regulate gene expression in transcriptional network.

Report

(6 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • 2009 Annual Research Report
  • Research Products

    (53 results)

All 2014 2013 2012 2011 2010 2009 Other

All Journal Article (17 results) (of which Peer Reviewed: 7 results) Presentation (35 results) (of which Invited: 1 results) Book (1 results)

  • [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 JA, Vanichkina DP, Poth EM, Beveridge NJ, Ratnu VS, Nayler SP, Nones K, Hu J, Bredy TW, Nakagawa S, Rigo F, Taft RJ, Cairns MJ, Blackshaw S, Wolvetang EJ, Mattick JS
    • Journal Title

      Mol Psychiatry

      Volume: 19(4) Pages: 486-494

    • Related Report
      2013 Final Research Report
  • [Journal Article]2014

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

      Mol Biol Cell

      Volume: 25(1) Pages: 169-183

    • Related Report
      2013 Final Research Report
  • [Journal Article] Nuclear lncRNAs as epigenetic regulators-beyond skepticism.2014

    • Author(s)
      Nakagawa, S., Kageyama, Y.
    • Journal Title

      Biochim. Biophys. Acta.

      Volume: 1839 Issue: 3 Pages: 215-222

    • DOI

      10.1016/j.bbagrm.2013.10.009

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The binding of multiple nuclear receptors to a single regulatory region is important for the proper expression of EDG84A in Drosophila melanogaster2013

    • Author(s)
      Akagi K, Kageyama Y, Kayashima Y, Takakura Y, Hirose S, Ueda H.
    • Journal Title

      J. Mol. Biol

      Volume: 425(1) Pages: 71-81

    • Related Report
      2013 Final Research Report
  • [Journal Article] The long non-coding RNA nuclear-enriched abundant transcript 1_2 induces paraspeckle formation in the motor neuron during the early phase of amyotrophic lateral sclerosis2013

    • Author(s)
      Nishimoto Y, Nakagawa S, Hirose T, Okano HJ, Takao M, Shibata S, Suyama S, Kuwako K, Imai T, Murayama S, Suzuki N, Okano H
    • Journal Title

      Mol Brain

      Volume: 6 Pages: 31-31

    • Related Report
      2013 Final Research Report
  • [Journal Article] Alternative 3'-end processing of long noncoding RNA initiates construction of nuclear paraspeckles2012

    • Author(s)
      Naganuma T, Nakagawa S, Tanigawa A, Sasaki YF, Goshima N, Hirose T
    • Journal Title

      EMBO J

      Volume: 31(20) Pages: 4020-4034

    • Related Report
      2013 Final Research Report
  • [Journal Article] Malat1 is not an essential component of nuclear speckles in mice2012

    • Author(s)
      Nakagawa S, Ip JY, Shioi G, Tripathi V, Zong X, Hirose T, Prasanth KV
    • Journal Title

      RNA

      Volume: 18(8) Pages: 1487-1499

    • Related Report
      2013 Final Research Report
  • [Journal Article] Malat1 is not an essential component of nuclear speckles in mice2012

    • Author(s)
      Nakagawa, S., Ip, J. Y., Shioi, G., Tripathi, V., Zong, X., Hirose, T., and Prasanth, K. V
    • Journal Title

      RNA

      Volume: 18 Issue: 8 Pages: 1487-1499

    • DOI

      10.1261/rna.033217.112

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice2011

    • Author(s)
      Nakagawa S, Naganuma T, Shioi G, Hirose T
    • Journal Title

      J Cell Biol

      Volume: 193(1) Pages: 31-39

    • Related Report
      2013 Final Research Report
  • [Journal Article] Competition between a noncoding exon and introns : Gomafu contains tandem UACUAAC repeats and associates with splicing factor-12011

    • Author(s)
      Tsuiji H, Yoshimoto R, Hasegawa Y, Furuno M, Yoshida M, Nakagawa S
    • Journal Title

      Genes Cells

      Volume: 16(5) Pages: 479-490

    • Related Report
      2013 Final Research Report
  • [Journal Article] Long non-coding RNAs in nuclear bodies2011

    • Author(s)
      Ip JY, Nakagawa S
    • Journal Title

      Dev Growth Differ

      Volume: 54 Issue: 1 Pages: 44-54

    • DOI

      10.1111/j.1440-169x.2011.01303.x

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Coding vs non-coding : Translatability of short ORFs found in putative non-coding transcripts2011

    • Author(s)
      Kageyama Y, Kondo T, Hashimoto Y
    • Journal Title

      Biochimie

      Volume: 93 Pages: 1981-1986

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice2011

    • Author(s)
      Nakagawa, S., Naganuma, T., Shioi, G., Hirose, T.
    • Journal Title

      J Cell Biol

      Volume: 193 Pages: 31-39

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Long non-coding RNAs in nuclear bodies2011

    • Author(s)
      Ip, J., Nakagawa, S.
    • Journal Title

      Dev Growth Differ

      Volume: 54 Pages: 321-327

    • NAID

      10030404653

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Small peptides switch the transcriptional activity of Shavenbaby during Drosophila embryogenesis2010

    • Author(s)
      Kondo T, Plaza S, Zanet J, Benrabah E, Valenti P, Hashimoto Y, Kobayashi S, Payre F, Kageyama Y
    • Journal Title

      Science

      Volume: 329(5989) Pages: 336-339

    • Related Report
      2013 Final Research Report
  • [Journal Article] The matrix protein hnRNP U is required for chromosomal localization of Xist RNA2010

    • Author(s)
      Hasegawa Y, Brockdorff N, Kawano S, Tsutui K, Tsutui K, Nakagawa S
    • Journal Title

      Dev Cell

      Volume: 19(3) Pages: 469-476

    • Related Report
      2013 Final Research Report
  • [Journal Article] Small peptides switch the transcriptional activity of Shavenbaby during Drosophila Embryogenesis.2010

    • Author(s)
      Kondo, T., Plaza, S., Zanet, J., Benrabah, E., Valenti, P., Hashimoto, Y., Kobayashi, S., Payre, F. Kageyama, Y.
    • Journal Title

      Science

      Volume: 329 Pages: 469-476

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] Lobe-less RNA is essential for mushroom body morphogenesis in Drosophila2014

    • Author(s)
      Sachi Inagaki, Masanao Sato, Tomoyuki Miyashita, Natsuki Nakamura, Satoru Kobayashi and Yuji Kageyama
    • Organizer
      55th Annual Drosophila Research Conference
    • Place of Presentation
      San Diego (USA)
    • Related Report
      2013 Final Research Report
  • [Presentation] Lobe-less RNA is essential for mushroom body morphogenesis in Drosophila.2014

    • Author(s)
      Sachi Inagaki, Masanao Sato, Tomoyuki Miyashita, Natsuki Nakamura, Satoru Kobayashi and Yuji Kageyama
    • Organizer
      55th Annual Drosophila Research Conference
    • Place of Presentation
      San Diego, USA
    • Related Report
      2013 Annual Research Report
  • [Presentation] 長鎖非コードRNA の局在と機能に対するRNA 結合タンパク質hnRNP U の役割2013

    • Author(s)
      長谷川優子、中川真一
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2013-12-03
    • Related Report
      2013 Final Research Report
  • [Presentation] MRE32 RNA is essential for mushroom body morphogenesis in Drosophila adult brain2013

    • Author(s)
      Sachi Inagaki, Masanao Sato, Yuji Kageyama
    • Organizer
      The 23rd CDB Meeting: Building multicellular systems from cellular cross-talk
    • Place of Presentation
      Kobe
    • Related Report
      2013 Final Research Report
  • [Presentation] Lobe-less RNA is essential for mushroom body morphogenesis in Drosophila2013

    • Author(s)
      Sachi Inagaki, Natsuki Nakamura, Masanao Sato, Satoru Kobayashi and Yuji Kageyama
    • Organizer
      第46回日本発生生物学会年会
    • Place of Presentation
      松江
    • Related Report
      2013 Final Research Report
  • [Presentation] MRE32/Lobe-less RNA is essential for mushroom body morphogenesis in Drosophila2013

    • Author(s)
      稲垣幸、佐藤昌直、中村奈月、小林悟、影山裕二
    • Organizer
      第15回日本RNA 学会年会
    • Place of Presentation
      松山
    • Related Report
      2013 Final Research Report
  • [Presentation] Drosophila Lobe-less RNA is essential for axon guidance in development of mushroom body neurons2013

    • Author(s)
      Sachi Inagaki, Natsuki Nakamura, Masanao Sato, Satoru Kobayashi and Yuji Kageyama
    • Organizer
      2013 Riboclub Annual Meeting
    • Place of Presentation
      Orford (Canada)
    • Related Report
      2013 Final Research Report
  • [Presentation] Lobe-less RNAはショウジョウバエキノコ体の形態形成を介して学習・記憶を制御している2013

    • Author(s)
      稲垣幸、佐藤昌直、宮下知之、中村奈月、小林悟、斉藤実、影山裕二
    • Organizer
      第36回日本分子生物学会
    • Place of Presentation
      神戸
    • Related Report
      2013 Final Research Report
  • [Presentation] ショウジョウバエ成虫脳の形態形成と記憶・学習を制御する長鎖ノンコーディングRNA2013

    • Author(s)
      影山裕二、稲垣幸
    • Organizer
      第36回日本分子生物学会ワークショップ「non-coding RNA の分子機能と動作原理」
    • Place of Presentation
      神戸
    • Related Report
      2013 Final Research Report
  • [Presentation] レトロトランスポゾンSINE B1と相同配列を持つ核内ノンコーディングRNAによるグローバルな遺伝子発現制御2013

    • Author(s)
      中川真一
    • Organizer
      日本遺伝学会ワークショップ「転移因子と宿主の相互作用」
    • Place of Presentation
      慶応大学日吉キャンパス
    • Related Report
      2013 Final Research Report
  • [Presentation] Lobe-less RNA is essential for mushroom body morphogenesis in Drosophila.2013

    • Author(s)
      Sachi Inagaki, Natsuki Nakamura, Masanao Sato, Satoru Kobayashi and Yuji Kageyama
    • Organizer
      第46回日本発生生物学会年会
    • Place of Presentation
      松江
    • Related Report
      2013 Annual Research Report
  • [Presentation] MRE32/Lobe-less RNA is essential for mushroom body morphogenesis in Drosophila.2013

    • Author(s)
      稲垣幸、佐藤昌直、中村奈月、小林悟、影山裕二
    • Organizer
      第15回日本RNA学会年会
    • Place of Presentation
      松山
    • Related Report
      2013 Annual Research Report
  • [Presentation] Drosophila Lobe-less RNA is essential for axon guidance in development of mushroom body neurons.2013

    • Author(s)
      Sachi Inagaki, Natsuki Nakamura, Masanao Sato, Satoru Kobayashi and Yuji Kageyama
    • Organizer
      2013 Riboclub Annual Meeting
    • Place of Presentation
      Orford, Canada
    • Related Report
      2013 Annual Research Report
  • [Presentation] Lobe-less RNA はショウジョウバエキノコ体の形態形成を介して学習・記憶を制御している2013

    • Author(s)
      稲垣幸、佐藤昌直、宮下知之、中村 奈月、小林悟、斉藤実、影山裕二
    • Organizer
      第36回日本分子生物学会
    • Place of Presentation
      神戸
    • Related Report
      2013 Annual Research Report
  • [Presentation] Physiological roles of MRE32 RNA in Drosophila optic lobe and wing development.2012

    • Author(s)
      Sachi Inagaki, Masanao Sato, Yasuo Fukami, Yuji Kageyama
    • Organizer
      第14回日本RNA学会年会
    • Place of Presentation
      仙台
    • Year and Date
      2012-07-18
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Physiological roles of MRE32 RNA in Drosophila optic lobe and wing development2012

    • Author(s)
      Sachi Inagaki, Masanao Sato, Yuji Kageyama.
    • Organizer
      The 22nd CDB Meeting : RNA Sciences in Cell and Developmental Biology II
    • Place of Presentation
      Kobe
    • Related Report
      2013 Final Research Report
  • [Presentation] Physiological roles of MRE32 RNA in Drosophila optic lobe and wing development2012

    • Author(s)
      Sachi Inagaki, Masanao Sato, Yasuo Fukami, Yuji Kageyama
    • Organizer
      第14回日本RNA 学会年会
    • Place of Presentation
      仙台
    • Related Report
      2013 Final Research Report
  • [Presentation] Physiological roles of long non-coding RNA MRE32 in the central nervous system and wing development2012

    • Author(s)
      Sachi Inagaki, Masanao Sato, Yuji Kageyama
    • Organizer
      第10回日本ショウジョウバエ研究会
    • Place of Presentation
      東京
    • Related Report
      2013 Final Research Report
  • [Presentation] An Architectural Long Noncoding RNA NEAT1 Controls Corpus Luteum Formation in an Age-Dependent Manner2012

    • Author(s)
      Nakagawa, S
    • Organizer
      Keystone Symposia "Non-Coding RNAs"
    • Place of Presentation
      Snowbird, Utah USA
    • Related Report
      2013 Final Research Report
  • [Presentation] Nuclear Noncoding RNA Neat1 Regulates Corpus Luteum Development in Aged Animals2012

    • Author(s)
      Nakagawa, S
    • Organizer
      22nd CDB meeting "RNA Sciences in Cell and Developmental Biology II"
    • Place of Presentation
      Kobe, Japan
    • Related Report
      2013 Final Research Report
  • [Presentation] 核内ノンコーディングRNAが制御する生理現象2012

    • Author(s)
      中川真一
    • Organizer
      第4回日本RNAi研究会
    • Place of Presentation
      広島
    • Related Report
      2013 Final Research Report
  • [Presentation] 核内構造体パラスペックルの骨格ncRNA であるNeat1 を欠損するマウスは早期に不妊になる2012

    • Author(s)
      中川真一
    • Organizer
      第14回日本RNA学会年会
    • Place of Presentation
      仙台
    • Related Report
      2013 Final Research Report
  • [Presentation] A small peptide gene polished rice is essential for trichome formation and metamorphosis in Drosophila2011

    • Author(s)
      Yoshiko Hashimoto, Kaori Niimi, Takefumi Kondo, Yuji Kageyama
    • Organizer
      第44回日本発生生物学会年会シンポジウム
    • Place of Presentation
      沖縄コンベンションセンター(沖縄県)
    • Year and Date
      2011-05-21
    • Related Report
      2011 Annual Research Report
  • [Presentation] A small peptide gene polished rice is essential for trichome formation and metamorphosis in Drosophila2011

    • Author(s)
      Yoshiko Hashimoto, Kaori Niimi, Takefumi Kondo, Yuji Kageyama
    • Organizer
      第44回日本発生生物学会年会シンポジウム「Genetic Control of Morophogenesis」
    • Place of Presentation
      沖縄
    • Related Report
      2013 Final Research Report
  • [Presentation] Functional analyses of nuclear enriched abundant long noncoding RNAs2011

    • Author(s)
      Nakagawa, S
    • Organizer
      第34回日本分子生物学会年会シンポジウム
    • Place of Presentation
      横浜
    • Related Report
      2013 Final Research Report
  • [Presentation] Nonessentials for nothing?-Nuclear bodies paraspeckles are not essential for animal's life2011

    • Author(s)
      Nakagawa, S
    • Organizer
      第63回日本細胞生物学会大会シンポジウム
    • Place of Presentation
      札幌
    • Related Report
      2013 Final Research Report
  • [Presentation] Small peptide regulators encoded in extremely short ORFs2010

    • Author(s)
      Yuji Kageyama
    • Organizer
      4th International Symposium on Nanomedicine
    • Place of Presentation
      岡崎カンファレンスセンター(愛知)
    • Year and Date
      2010-11-30
    • Related Report
      2010 Annual Research Report
  • [Presentation] 短鎖ペプチドによる転写因子の活性制御2010

    • Author(s)
      近藤武史、Serge Plaza、Jennifer Zanet、Emilie Benrabah、Philippe Valenti、橋本祥子、小林悟、Francois Payre、影山裕二
    • Organizer
      第12回日本RNA学会年会
    • Place of Presentation
      学術総合センター(東京)
    • Year and Date
      2010-07-28
    • Related Report
      2010 Annual Research Report
  • [Presentation] A small peptide gene, polished rice, participates in Drosophila ecdysone signal pathway.2010

    • Author(s)
      Yoshiko Hashimoto, Kaori Niimi, Takefumi Kondo, Yuji Kageyama.
    • Organizer
      The 18th International Ecdysone Workshop
    • Place of Presentation
      Academy of Science Conference Center (Czech)
    • Year and Date
      2010-07-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] A small peptide gene, polished rice, participates in Drosophila ecdysone signal pathway2010

    • Author(s)
      Yoshiko Hashimoto, Kaori Niimi, Takefumi Kondo, Yuji Kageyama
    • Organizer
      The 18th International Ecdysone Workshop
    • Place of Presentation
      Ceske Budejovice (Czech Republic)
    • Related Report
      2013 Final Research Report
  • [Presentation] 短鎖ペプチドによる転写因子の活性制御2010

    • Author(s)
      近藤武史、Serge Plaza、Jennifer Zanet、Emilie Benrabah、Philippe Valenti、橋本祥子、小林悟、Francois Payre、影山裕二
    • Organizer
      第12回日本RNA 学会年会
    • Place of Presentation
      東京
    • Related Report
      2013 Final Research Report
  • [Presentation] Small peptide regulators encoded in extremely short ORFs2010

    • Author(s)
      Yuji Kageyama
    • Organizer
      4th International Symposium on Nanomedicine
    • Place of Presentation
      岡崎
    • Related Report
      2013 Final Research Report
  • [Presentation] 大量に蓄積する核内ノンコーディングRNA の機能解析-Gomafu を例にとって2010

    • Author(s)
      中川真一
    • Organizer
      第33回日本分子生物学会年会・第83回日本生化学会大会合同大会(BMB2010)シンポジウム
    • Place of Presentation
      神戸
    • Related Report
      2013 Final Research Report
  • [Presentation] 核内長鎖ノンコーディングRNA Gomafu は動物の行動を制御する2010

    • Author(s)
      中川真一
    • Organizer
      第12回日本RNA 学会年会
    • Place of Presentation
      東京
    • Related Report
      2013 Final Research Report
  • [Presentation] Functional analysis of nuclear long noncoding RNAs

    • Author(s)
      Shinichi Nakagawa
    • Organizer
      Riboclub 2013
    • Place of Presentation
      Cheribourg, Canada
    • Related Report
      2013 Final Research Report
  • [Book] 分子昆虫学-ポストゲノムの昆虫研究-2009

    • Author(s)
      影山裕二, 他
    • Total Pages
      426
    • Publisher
      共立出版
    • Related Report
      2009 Annual Research Report

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Published: 2009-04-01   Modified: 2018-03-28  

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