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Macro level cellular adaptation by lncRNA mediated gene regulation

Research Project

Project/Area Number 16K18477
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field System genome science
Research InstitutionThe University of Tokyo

Principal Investigator

Oda Arisa  東京大学, 教養学部, 特任助教 (00760084)

Research Collaborator Hatakeyama Tetsuhiro S.  
Project Period (FY) 2016-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2018: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2017: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2016: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Keywords酵母 / ストレス応答 / グルコース飢餓ストレス応答 / 発現制御
Outline of Final Research Achievements

Long noncoding RNAs serve critical regulatory functions in many biological phenomena. Some sense and antisense long noncoding RNAs are known to have antagonistic regulation. In S. pombe, glucose starvation induces sense long noncoding RNA transcription which leads to chromatin changes around fbp1 promoter. fbp1 codes for a gluconeogenesis enzyme, fructose-1,6-bisphosphatase and is repressed in glucose rich condition. Importantly, overlapping with the regions for sense long noncoding RNA transcription, small amounts of antisense RNAs are antagonistically transcribed in glucose rich condition. To estimate the effect of sense and antisense long noncoding RNA transcription, we conducted mathematical modeling of transcriptional dynamics at the fbp1 locus during changes in glucose concentration. From this study, it is suggested that the long noncoding RNA mediated gene regulation system is beneficial for survival of yeast cells under stressed condition.

Academic Significance and Societal Importance of the Research Achievements

lncRNA依存的な遺伝子発現の制御メカニズムを分子レベルで解明するだけでなく、マクロな細胞集団レベルでの適応における役割を検証し、従来の分子生物学の枠にとらわれない新たな切り口で現象を説明した。厳しい栄養飢餓環境下で、能動的な移動手段を持たない単細胞生物が、環境にうまく適応して自らのリネージが生き延びるリスクヘッジの様子を、実験・数理モデルの両面から説明した。

Report

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

    (23 results)

All 2018 2017 2016

All Journal Article (7 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 6 results,  Open Access: 7 results,  Acknowledgement Compliant: 2 results) Presentation (16 results) (of which Int'l Joint Research: 5 results,  Invited: 2 results)

  • [Journal Article] Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double-strand breaks2018

    • Author(s)
      Muramoto Nobuhiko、Oda Arisa、Tanaka Hidenori、Nakamura Takahiro、Kugou Kazuto、Suda Kazuki、Kobayashi Aki、Yoneda Shiori、Ikeuchi Akinori、Sugimoto Hiroki、Kondo Satoshi、Ohto Chikara、Shibata Takehiko、Mitsukawa Norihiro、Ohta Kunihiro
    • Journal Title

      Nature Communications

      Volume: 9 Issue: 1 Pages: 1995-1995

    • DOI

      10.1038/s41467-018-04256-y

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Linear Regression Links Transcriptomic Data and Cellular Raman Spectra2018

    • Author(s)
      Kobayashi-Kirschvink, K. J., Nakaoka, H., Oda, A., Kamei, K. F., Nosho, K., Fukushima, H., Kanesaki, Y., Yajima, S., Masaki, H., Ohta, K., Wakamoto, Y.
    • Journal Title

      Cell Systems

      Volume: 7 Issue: 1 Pages: 104-117

    • DOI

      10.1016/j.cels.2018.05.015

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Replication stress induces accumulation of FANCD2 at central region of large fragile genes.2018

    • Author(s)
      Okamoto Y, Iwasaki WM, Kugou K, Takahashi KK, Oda A, Sato K, Kobayashi W, Kawai H, Sakasai R, Takaori-Kondo A, Yamamoto T, Kanemaki MT, Taoka M, Isobe T, Kurumizaka H, Innan H, Ohta K, Ishiai M, Takata M.
    • Journal Title

      Nucleic Acids Res.

      Volume: 46(6) Issue: 6 Pages: 2932-2944

    • DOI

      10.1093/nar/gky058

    • NAID

      120006488604

    • Related Report
      2018 Annual Research Report 2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Correlation of Meiotic DSB Formation and Transcription Initiation Around Fission Yeast Recombination Hotspots.2017

    • Author(s)
      . Yamada, M. Okamura, H. Murakami, K.Ohta, T. Yamada
    • Journal Title

      Genetics

      Volume: in press Issue: 2 Pages: 801-809

    • DOI

      10.1534/genetics.116.197954

    • Related Report
      2017 Research-status Report 2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Transcriptomes and Raman spectra are linked linearly through a shared low-dimensional subspace2017

    • Author(s)
      Kobayashi-Kirschvink, K. J., Nakaoka, H., Oda, A., Kamei, K. F., Nosho, K., Fukushima, H., Kanesaki, Y., Yajima, S., Masaki, H., Ohta, K., Wakamoto, Y.
    • Journal Title

      bioRxiv

      Volume: NA Pages: 235580-235580

    • DOI

      10.1101/235580

    • Related Report
      2017 Research-status Report
    • Open Access
  • [Journal Article] Three-dimensional reconstruction of single-cell chromosome structure using recurrence plots2016

    • Author(s)
      Hirata Y, Oda A, Ohta K, Aihara K
    • Journal Title

      Scientific Reports

      Volume: 6 Issue: 1 Pages: 34982-34982

    • DOI

      10.1038/srep34982

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Local potentiation of stress-responsive genes by upstream noncoding transcription.2016

    • Author(s)
      Takemata N, Oda A, Yamada T, Galipon J, Miyoshi T, Suzuki Y, Sugano S, Hoffman CS, Hirota K, Ohta K.
    • Journal Title

      Nucleic Acids Res.

      Volume: 印刷中 Issue: 11 Pages: 5174-89

    • DOI

      10.1093/nar/gkw142

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Presentation] Artificial Genome Rearrangement System using a Restriction Enzyme2018

    • Author(s)
      Arisa Oda, Takahiro Nakamura, Nobuhiko Muramoto, Hidenori Tanaka,Kazuto Kugou, Kunihiro Ohta
    • Organizer
      CSHL meetings 2018, The Biology of Genomes
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] TAQing: 制限酵素を用いたゲノムシャッフリング技術2018

    • Author(s)
      小田有沙,中村隆宏,村本伸彦,田中秀典,久郷和人,光川典宏,太田邦史
    • Organizer
      生命科学系フロンティアミーティング2018(国立遺伝学研究所研究会)
    • Related Report
      2018 Annual Research Report
  • [Presentation] Hi-C データで得られる染色体の距離情報を扱う2018

    • Author(s)
      小田 有沙、平田 祥人、太田 邦史、合原 一幸
    • Organizer
      日本遺伝学会第90回大会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 耐熱性制限酵素による大規模ゲノム再編成2018

    • Author(s)
      中村隆宏、小田有沙、村本伸彦、田中秀典,久郷和人、須田一毅、太田邦史
    • Organizer
      酵母遺伝学フォーラム第51回研究報告会
    • Related Report
      2018 Annual Research Report
  • [Presentation] ヒストンバリアント H2A.Z のクロマチン導入部位決定機構解析2018

    • Author(s)
      高橋大輔、北川紗帆、小田有沙、仮屋園遼、尾間由佳子、太田邦史、原田昌彦
    • Organizer
      第36回染色体ワークショップ・第17回核ダイナミクス研究会
    • Related Report
      2018 Annual Research Report
  • [Presentation] CRISPR/dCas9 を用いた転写制御における off-target 解析2018

    • Author(s)
      安心院祥、小田有沙、仮屋園遼、太田邦史
    • Organizer
      第36回染色体ワークショップ・第17回核ダイナミクス研究会
    • Related Report
      2018 Annual Research Report
  • [Presentation] metabolic stress-induced lncRNA(mlonRNA)転写を介したクロマチン再編成が、転写と減数分裂期組換えを制御する2018

    • Author(s)
      千松賢史、浅田隆大、小田有沙、Charles S Hoffman, 太田邦史、廣田耕志
    • Organizer
      第36回染色体ワークショップ・第17回核ダイナミクス研究会
    • Related Report
      2018 Annual Research Report
  • [Presentation] TAQing : Artificial Genome Rearrangement by a Restriction Enzyme, Taq??.2018

    • Author(s)
      A. Oda, T.Nakamura, N.Muramoto, H.Tanaka, K. Kugou, K.Ohta
    • Organizer
      The 11th 3R&3C Symposium
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] The novel cis-acting element for metabolic stress-induced lncRNA(mlonRNA) and meiotic recombination in fisson yeast.2018

    • Author(s)
      S. Senmatsu, R. Asada, A. Oda, C.S. Hoffman, K. Ohta, K. Hirota
    • Organizer
      The 11th 3R&3C Symposium
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 3D chromosome structure reconstruction from single-cell Hi-C data using recurrence plots2018

    • Author(s)
      Arisa Oda, Yoshito Hirata, Kunihiro Ohta & Kazuyuki Aihara
    • Organizer
      6th Annual Winter q-bio Meeting
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Reconstruction of single-cell chromosome 3D structure using recurrence plots2017

    • Author(s)
      Arisa Oda, Yoshito Hirata, Kunihiro Ohta, Kazuyuki Aihara
    • Organizer
      winter Qbio 2017
    • Place of Presentation
      アメリカ合衆国、Hawaii
    • Year and Date
      2017-02-20
    • Related Report
      2016 Research-status Report
  • [Presentation] 1細胞Hi-Cデータを用いた染色体三次元構造解析手法2017

    • Author(s)
      小田有沙、平田祥人、太田邦史、合原一幸
    • Organizer
      染色体ワークショップ
    • Place of Presentation
      千葉県木更津市、かずさDNA研究所
    • Year and Date
      2017-01-11
    • Related Report
      2016 Research-status Report
  • [Presentation] 制限酵素を用いた人為的ゲノム再編誘導2017

    • Author(s)
      小田有沙、中村隆宏、村本伸彦、田中秀典、 久郷和人、光川典宏、太田邦史
    • Organizer
      第35回染色体ワークショップ 第16回各ダイナミクス研究会
    • Related Report
      2017 Research-status Report
  • [Presentation] Hi-Cのデータから染色体の立体構造を解く2017

    • Author(s)
      小田 有沙、平田 祥人、太田 邦史、合原 一幸
    • Organizer
      2017年度生命科学系学会合同年次大会
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] Transcriptional dynamics of sense and antisense long noncoding RNAs during glucose starvation2017

    • Author(s)
      Arisa Oda, Tetsuhiro Hatakeyama, Kunihiko Kaneko & Kunihiro Ohta
    • Organizer
      The 9th International Fission Yeast Meeting
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] 1細胞Hi-Cによる染色体3次元構造解析手法2016

    • Author(s)
      小田有沙、平田祥人、太田邦史、合原一幸
    • Organizer
      第39回日本分子生物学会年会
    • Place of Presentation
      神奈川県横浜市、パシフィコ横浜
    • Year and Date
      2016-11-30
    • Related Report
      2016 Research-status Report

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Published: 2016-04-21   Modified: 2023-12-25  

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