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疾患に関わる非AUG型上流ORFの情報工学的網羅同定法の開発

Publicly Offered Research

Project AreaNascent-chain Biology
Project/Area Number 17H05659
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 InstitutionKanazawa University

Principal Investigator

高橋 広夫  金沢大学, 薬学系, 准教授 (30454367)

Project Period (FY) 2017-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥7,540,000 (Direct Cost: ¥5,800,000、Indirect Cost: ¥1,740,000)
Fiscal Year 2018: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2017: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Keywordsバイオインフォマティクス / データ科学 / 新生鎖 / uORF / 翻訳制御 / データベース横断解析 / データサイエンス / 上流ORF / オミックス
Outline of Annual Research Achievements

上流ORF上の翻訳制御配列を網羅的に同定するために、コンピュータ解析による配列ビッグデータ横断解析に基づく情報工学的な方法論を確立し、ESUCA法と名付け、論文として発表した(Takahashi et al., , BMC Genomics, 2020)。ESUCA法の支援手法として、翻訳制御とタンパク質酵素活性配列のmicro syntenyを活用したクラスタリング手法を開発して、ESUCA法の出力結果をクラスタリングして、新生鎖による翻訳制御を類似性の高いホモロジーグループ(HG)に分類することが出来た。ESUCA法を5つの植物ゲノム(シロイヌナズナ、イネ、ポプラ、ブドウ、トマト)に応用することで、新規の翻訳制御配列を抽出し、100近くの新規HGを発見した。植物に関する11個のアレスト配列候補配列をルシフェラーゼによる実験的に検証することで、少なくとも5個アレスト配列を発見しこの成果を論文として発表することが出来た(Takahashi et al., , BMC Genomics, 2020)。さらに、完成させたESUCA法の非AUG(CTG, TTG, GTG, ACG, ATT, ATA, ATC)の対応化を行い、シロイヌナズナゲノムから、多数の新規非AUG型CPuORFを同定できた。これらの一部については、実験的に検証し、翻訳抑制非AUG型uORFも見つかっている。ヒトゲノムにも応用し、多数の新規非AUG型CPuORFを同定し、実験的に検証している。

Research Progress Status

平成30年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

平成30年度が最終年度であるため、記入しない。

Report

(2 results)
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • Research Products

    (42 results)

All 2020 2019 2018 2017 Other

All Journal Article (13 results) (of which Int'l Joint Research: 9 results,  Peer Reviewed: 12 results,  Open Access: 11 results) Presentation (28 results) (of which Int'l Joint Research: 5 results,  Invited: 2 results) Remarks (1 results)

  • [Journal Article] The formation of perinucleolar bodies is important for normal leaf development and requires the zinc‐finger DNA‐binding motif in Arabidopsis ASYMMETRIC LEAVES22020

    • Author(s)
      Luo Lilan、Ando Sayuri、Sakamoto Yuki、Suzuki Takanori、Takahashi Hiro、Ishibashi Nanako、Kojima Shoko、Kurihara Daisuke、Higashiyama Tetsuya、Yamamoto Kotaro T.、Matsunaga Sachihiro、Machida Chiyoko、Sasabe Michiko、Machida Yasunori
    • Journal Title

      The Plant Journal

      Volume: 101 Issue: 5 Pages: 1118-1134

    • DOI

      10.1111/tpj.14579

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA2020

    • Author(s)
      Takahashi Hiro、Hayashi Noriya、Hiragori Yuta、Sasaki Shun、Motomura Taichiro、Yamashita Yui、Naito Satoshi、Takahashi Anna、Fuse Kazuyuki、Satou Kenji、Endo Toshinori、Kojima Shoko、Onouchi Hitoshi
    • Journal Title

      BMC Genomics

      Volume: 21 Issue: 1 Pages: 260-260

    • DOI

      10.1186/s12864-020-6662-5

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Excess sterols disrupt plant cellular activity by inducing stress-responsive gene expression2020

    • Author(s)
      Shimada Takashi L、Yamaguchi Katsuki、Shigenobu Shuji、Takahashi Hiro、Murase Masataka、Fukuyoshi Shuichi、Hara-Nishimura Ikuko
    • Journal Title

      Journal of Plant Research

      Volume: in press Issue: 3 Pages: 383-392

    • DOI

      10.1007/s10265-020-01181-4

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Draft Genome Sequence of Aspergillus terreus High-Itaconic-Acid- Productivity Strain IFO63652020

    • Author(s)
      Takahashi H., Minami T., Okabe M., Park E.Y., Fujimoto T., Takahashi A., Murase M., Fukuyoshi S., Satou K., and Kanamasa S.
    • Journal Title

      Microbiol. Resour. Announc.

      Volume: - Issue: 16 Pages: 1-2

    • DOI

      10.1128/mra.00080-20

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] SIMON: Simple methods for analyzing DNA methylation by targeted bisulfite next-generation sequencing2019

    • Author(s)
      Vial-Pradel Simon、Hasegawa Yoshinori、Nakagawa Ayami、Miyaki Shido、Machida Yasunori、Kojima Shoko、Machida Chiyoko、Takahashi Hiro
    • Journal Title

      Plant Biotechnology

      Volume: 36 Issue: 4 Pages: 213-222

    • DOI

      10.5511/plantbiotechnology.19.0822a

    • NAID

      130007776104

    • ISSN
      1342-4580, 1347-6114
    • Year and Date
      2019-12-25
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Patient‐derived xenograft models of non‐small cell lung cancer for evaluating targeted drug sensitivity and resistance2019

    • Author(s)
      Kenji Kita, Koji Fukuda, Hiro Takahashi, Azusa Tanimoto, Akihiro Nishiyama, Sachiko Arai, Shinji Takeuchi, Kaname Yamashita, Koshiro Ohtsubo, Sakiko Otani, Naohiro Yanagimura, Chiaki Suzuki, Hiroko Ikeda, Masaya Tamura, Isao Matsumoto, Seiji Yano
    • Journal Title

      Cancer Science

      Volume: 110(10) Issue: 10 Pages: 3215-3224

    • DOI

      10.1111/cas.14171

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Draft Genome Sequence of Saccharomyces cerevisiae Strain Pf-1, Isolated from Prunus mume2019

    • Author(s)
      Kanamasa Shin、Yamaguchi Daiki、Machida Chiyoko、Fujimoto Tsukasa、Takahashi Anna、Murase Masataka、Fukuyoshi Shuichi、Oda Akifumi、Satou Kenji、Takahashi Hiro
    • Journal Title

      Microbiology Resource Announcements

      Volume: 8 Issue: 46

    • DOI

      10.1128/mra.01169-19

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Draft Genome Sequence of Aspergillus terreus High-Itaconic-Acid-Productivity Mutant TN-4842019

    • Author(s)
      Kanamasa Shin、Minami Tomoyuki、Okabe Mitsuyasu、Park Enoch Y.、Fujimoto Tsukasa、Takahashi Anna、Murase Masataka、Fukuyoshi Shuichi、Oda Akifumi、Satou Kenji、Takahashi Hiro
    • Journal Title

      Microbiology Resource Announcements

      Volume: 8 Issue: 49

    • DOI

      10.1128/mra.01170-19

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] バイオインフォマティクスによる配列データベース横断解析に基づく機能上流ORFの推定2019

    • Author(s)
      高橋広夫・伊藤素行・尾之内均
    • Journal Title

      生物工学会誌

      Volume: 97 Pages: 496-499

    • Related Report
      2018 Annual Research Report
  • [Journal Article] Arabidopsis Zinc-Finger-Like Protein ASYMMETRIC LEAVES2 (AS2) and Two Nucleolar Proteins Maintain Gene Body DNA Methylation in the Leaf Polarity Gene ETTIN (ARF3)2018

    • Author(s)
      Vial-Pradel Simon、Keta Sumie、Nomoto Mika、Luo Lilan、Takahashi Hiro、Suzuki Masataka、Yokoyama Yuri、Sasabe Michiko、Kojima Shoko、Tada Yasuomi、Machida Yasunori、Machida Chiyoko
    • Journal Title

      Plant and Cell Physiology

      Volume: Epub ahead of print Pages: 1385-1397

    • DOI

      10.1093/pcp/pcy031

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Draft Genome Sequence of Saccharomyces cerevisiae Strain Hm-1, Isolated from Cotton Rosemallow2018

    • Author(s)
      Takahashi H., Sakagawa E., Sakakibara I., Machida C., Miyaki S., Takahashi A., Onai S., Fukuyoshi S., Ohta A., Satou K., Kanamasa S.
    • Journal Title

      Microbiology Resource Announcements

      Volume: 7 Issue: 13 Pages: 1-2

    • DOI

      10.1128/mra.01184-18

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Draft Genome Sequence of Trebouxiophyceae sp. Strain KSI-1, Isolated from an Island Hot Spring2018

    • Author(s)
      Takahashi H., Tanaka S., Hayashi S., Miyaki S., Takahashi A., Onai S., Fukuyoshi S., and Miyasaka H.
    • Journal Title

      Microbiology Resource Announcements

      Volume: 7 Issue: 16

    • DOI

      10.1128/mra.01185-18

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Identification of Arabidopsis thaliana upstream open reading frames encoding peptide sequences that cause ribosomal arrest2017

    • Author(s)
      1.Hayashi N., Sasaki S., Takahashi H., Naito S., and Onouchi H.
    • Journal Title

      Nucleic Acids Research

      Volume: 45 Issue: 15 Pages: 8844-8858

    • DOI

      10.1093/nar/gkx528

    • NAID

      120006360096

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] ゲノムのジャンク領域における機能領域予測とその実験的検証2020

    • Author(s)
      本村汰一朗・宮木至道・林憲哉・尾之内均・伊藤素行・高橋広夫
    • Organizer
      第48回東海ファジィ研究会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 植物間で保存された翻訳調節に関与する非AUG型uORFのゲノムワイド探索2020

    • Author(s)
      平郡雄太・高橋広夫・林憲哉・佐々木駿・山下由衣・内藤哲・尾之内均
    • Organizer
      第61回日本植物生理学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 過剰なステロール蓄積が植物の生理機能に与える影響2020

    • Author(s)
      島田貴士・重信秀治・山口勝司・高橋広夫・福吉修一・上田貴志・西村いくこ
    • Organizer
      第61回日本植物生理学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] シロイヌナズナのAS2が関わる葉の向背軸分化とAS2の標的遺伝子のDNAメチル化における核小体タンパク質の役割の解明2020

    • Author(s)
      町田千代子・日比野哲紀・三谷恭平・水谷優斗・ヴィアルプラデルシモン・高橋広夫・小島晶子・町田泰則
    • Organizer
      第61回日本植物生理学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 上流ORFの新生ペプチドを含む翻訳複合体が細胞内のマグネシウム濃度を感知して翻訳を制御する2020

    • Author(s)
      林憲哉・佐々木駿・平郡雄太・Feng Zhihang・藤原徹・渡部敏裕・町田幸大・今高寛晃・高橋広夫・山下由衣・内藤哲・尾之内均
    • Organizer
      第61回日本植物生理学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 上流ORFの新生ペプチドを含む翻訳複合体が細胞内のマグネシウム濃度を感知して翻訳を制御する2019

    • Author(s)
      林憲哉・佐々木駿・平郡雄太・Feng Zhihang・藤原徹・高橋広夫・山下由衣・内藤哲・尾之内均
    • Organizer
      第60回日本植物生理学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] シロイヌナズナのAS2を介した葉の発生に関わるサイトカイニン合成酵素遺伝子の解析2019

    • Author(s)
      小島晶子・西本珠美・香田加那・石橋菜々子・小嶋美紀子・高橋広夫・榊原均・町田泰則・町田千代子
    • Organizer
      第60回日本植物生理学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 選択的スプライシングと上流ORFによる翻訳制御を介した植物の核小体ストレス応答機構2019

    • Author(s)
      佐々木駿・工藤凛・笹原大暉・高橋広夫・渡部俊・大林祝・杉山宗隆・内藤哲・尾之内均
    • Organizer
      第60回日本植物生理学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] シロイヌナズナのzinc-finger-like protein AS2が関わる葉の向背軸分化とDNA メチル化における核小体タンパク質の役割の解明2019

    • Author(s)
      鈴木雅貴・ヴィアルプラデルシモン・高橋広夫・杉山宗隆・氣多澄江・小島晶子・町田泰則・町田千代子
    • Organizer
      第60回日本植物生理学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 翻訳制御上流ORFのバイオインフォマティクスによる推定と実験的検証2019

    • Author(s)
      宮木至道・林憲哉・尾之内均・伊藤素行・高橋広夫
    • Organizer
      日本遺伝学会第91回大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 葉にオイルボディを過剰蓄積するシロイヌナズナ変異体lipid rich 1の解析2019

    • Author(s)
      山口萌・重信秀治・山口勝司・高橋広夫・福吉修一・島田貴士
    • Organizer
      第32回植物脂質シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] 植物ステロール過剰蓄積が及ぼす植物体への影響2019

    • Author(s)
      島田貴士・重信秀治・山口勝司・高橋広夫・福吉修一・上田貴志・西村いくこ
    • Organizer
      第32回植物脂質シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] 植物間で保存された翻訳調節に関与する非AUG型uORFのゲノムワイド探索2019

    • Author(s)
      平郡雄太・高橋広夫・林憲哉・佐々木駿・山下由衣・内藤哲・尾之内均
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Development of bioinformatics methods and their applications: from plant to medical sciences2019

    • Author(s)
      Takahashi H., Machida C., Muto M., Kojima S., Itoh M., Onouchi H., and Sasaki H.
    • Organizer
      International Conference for Leading and Young Medical Scientists - IC-LYMS 2019 -
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Roles of Nucleolar Proteins and Zinc-Finger Protein ASYMMETRIC LEAVES2 in establishment of leaf adaxial-abaxial polarity in Arabidopsis thaliana2019

    • Author(s)
      Machida C., Vial-Pradel S., Nomoto M., Takahashi H., Kojima S., Tada Y and Machida Y.
    • Organizer
      Plant Organ Growth Symposium
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Epigenetic role of zinc-finger protein AS2 and nucleolar proteins in the specification of the adaxial cell fate of leaves in Arabidopsis thaliana2019

    • Author(s)
      Machida C., Ando S., Sakamoto Y., Matsunaga S., Kurihara D., Higashiyama T., Takahashi H., Kojima S., Machida Y.
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Zebrafish behavior pattern recognition using three-dimensional tracking and machine learning2018

    • Author(s)
      Yang P., Kajiwara R., Takahashi H., Itoh M.
    • Organizer
      The 24th Japanese medaka and zebrafish meeting (第24回小型魚類研究会)
    • Related Report
      2018 Annual Research Report
  • [Presentation] Arabidopsis zinc-finger-like protein ASYMMETRIC LEAVES2 (AS2) bound exon 1 of ETTIN (ARF3) and maintain gene body DNA methylation in ETTIN together with nucleolar proteins2018

    • Author(s)
      Vial-Pradel S., Nomoto M., Takahashi H., Ando S., Suzuki M., Kojima S., Tada Y., Machida Y., Machida C.
    • Organizer
      日本植物学会第82回大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] がんオミックスデータに基づく治療前診断・治療標的探索2018

    • Author(s)
      高橋広夫・武藤学・佐々木博己
    • Organizer
      化学工学会 第50回秋季大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] シロイヌナズナの葉の極性確立においてAS1-AS2とTOP1αはETTIN (ARF3)を介してCDKインヒビターを抑制する2018

    • Author(s)
      町田千代子・中川彩美・高橋広夫・ビアループラデル シモン・山川 美里・小島晶子・町田泰則
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Arabidopsis zinc-finger-like protein ASYMMETRIC LEAVES2 (AS2) bound exon 1 of ETTIN (ARF3) and maintain gene body DNA methylation in ETTIN together with nucleolar proteins2018

    • Author(s)
      Vial Pradel S., Nomoto M., Takahashi H., Ando S., Suzuki M., Kojima S., Tada Y., Machida Y., Machida C.
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Bioinformatic identification method of evolutional ranges for functional small peptides on genomes2018

    • Author(s)
      Takahashi H., Hayashi N., Takahashi A., Onouchi H.
    • Organizer
      The 2nd edition of Biotech France 2018 International Conference and Exhibition -Biotech France 2018-
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Arabidopsis zinc-finger-like protein ASYMMETRIC LEAVES2 (AS2) binds exon 1 of ETTIN(ARF3) and maintains gene body DNA methylation in ETTIN together with nucleolar proteins2018

    • Author(s)
      Vial-Pradel S., Nomoto M., Takahashi H., Ando S., Suzuki M., Kojima S., Tada Y., Machida Y., Machida C.
    • Organizer
      EMBO Workshop "New shores in land plant"
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] シロイヌナズナTTM3遺伝子の上流ORF は後期促進複合体の構成因子をコードする2018

    • Author(s)
      122.垣内俊哉・伊藤正樹・髙橋広夫・刑部祐里子・刑部敬史・内藤哲・尾之内均
    • Organizer
      第59回日本植物生理学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] シロイヌナズナのzinc-finger様タンパク質AS2と核小体タンパク質は葉の裏側化因子ETT/ARF3のgene body DNAメチル化維持に関わる2018

    • Author(s)
      120.町田千代子・Simon Vial-Pradel・髙橋広夫・鈴木雅貴・安藤沙友里・小島晶子・町田泰則
    • Organizer
      第59回日本植物生理学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Development of bioinformatic method for identification of functional upstream open reading frames on the basis of evolutionary conservation on eukaryotic genomes2017

    • Author(s)
      Takahashi H., Idesako N., Hayashi N, Onouchi H., Itoh M.,
    • Organizer
      International Symposium on Protein Quality Control
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 配列データベース横断解析に基づくタンパク質の翻訳制御配列の網羅同定法開発2017

    • Author(s)
      高橋広夫・井手迫伸夫・林憲哉・尾之内均・伊藤素行
    • Organizer
      化学工学会 第49回秋季大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Epigenetic repressor AS1-AS2 and DNA replication factors control ARF3 in leaf development2017

    • Author(s)
      116.Machida C., Nakagawa A., Luong Quy T., Takahashi H., Kojima S., Machida Y.
    • Organizer
      日本植物学会第81回大会
    • Related Report
      2017 Annual Research Report
  • [Remarks] 高橋広夫研究室

    • URL

      https://www.takahashi-lab.com/

    • Related Report
      2018 Annual Research Report

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Published: 2017-04-28   Modified: 2021-01-27  

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