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Molecular dynamics of siRNA-AGO complexes in complex cellular environments

Research Project

Project/Area Number 21K20630
Research Category

Grant-in-Aid for Research Activity Start-up

Allocation TypeMulti-year Fund
Review Section 0701:Biology at molecular to cellular levels, and related fields
Research InstitutionThe University of Tokyo

Principal Investigator

Kobayashi Yoshiaki  東京大学, 大学院理学系研究科(理学部), 特任研究員 (20907381)

Project Period (FY) 2021-08-30 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Fiscal Year 2022: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2021: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
KeywordssiRNA / RNAi / Argonaute2 / Argonaute / AGO2 / RNA結合タンパク質 / ライブセルイメージング
Outline of Research at the Start

siRNA-AGO2複合体の作用機序は、これまでin vitroな生化学的解析および構造解析により明らかにされてきた。しかしながら、実際の細胞内環境を反映した解析がほとんど行われていない。細胞内には多種のRNA結合タンパク質が存在しており、siRNA-AGO2複合体と競合的に働く可能性がある。そこで本研究では、細胞内のsiRNA-AGO2複合体をイメージングする手法を新たに開発し、多種のRNA結合タンパク質が存在する複雑な細胞環境における分子動態の解明を目指す。

Outline of Final Research Achievements

Previous biochemical analyses have revealed that small interfering RNA (siRNA) recognized target mRNAs via the seed region (nucleotides 2~8 counting from the 5´ end of siRNA), but the role of the seed region by its position was not well understood. By measuring siRNA activity in human cells, we found that the seed region of siRNA is divided into two functional domains, nucleotides 2-5 and 6-8. Nucleotides 2-5 are domains that do not contribute significantly to RNAi activity, while nucleotides 6-8 are the domains that determine the degree of RNAi activity.

Academic Significance and Societal Importance of the Research Achievements

この研究成果は、従来の生化学的解析のみでは明らかにできなかったsiRNAの作用機序を実際の細胞内環境を反映した解析により明らかにした。siRNA のシード領域のうち、6-8番ヌクレオチドはRNAi活性の程度を規定するドメインであることから、今後活性の強弱を制御する手法の開発が期待される。また、siRNAは薬としての応用が期待されているものの、その作用機序に立脚した医薬品の設計が不十分であることから、本成果はsiRNAの治療応用に向けた知見を広げるものであると示唆される。

Report

(3 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Research-status Report
  • Research Products

    (31 results)

All 2023 2022 2021

All Journal Article (7 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 6 results,  Open Access: 4 results) Presentation (20 results) (of which Int'l Joint Research: 3 results,  Invited: 1 results) Book (4 results)

  • [Journal Article] SNPD-CRISPR: Single Nucleotide Polymorphism-Distinguishable Repression or Enhancement of a Target Gene Expression by CRISPR System2023

    • Author(s)
      Maruyama Shohei、Kusakabe Takashi、Zou Xinyi、Kobayashi Yoshiaki、Asano Yoshimasa、Wang Qingbo S.、Ui-Tei Kumiko
    • Journal Title

      Methods in Molecular Biology

      Volume: 2637 Pages: 49-62

    • DOI

      10.1007/978-1-0716-3016-7_4

    • ISBN
      9781071630150, 9781071630167
    • Related Report
      2022 Annual Research Report
  • [Journal Article] siRNAが働く仕組みと医薬品としての研究開発の現状2023

    • Author(s)
      小林 芳明 , 浅野 吉政 , 程 久美子
    • Journal Title

      循環器内科 = Cardioangiology / 循環器内科編集委員会 編

      Volume: 93 Pages: 346-354

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A 2′-modified uridine analog, 2′-O-(methylthiomethoxy)methyl uridine, for siRNA applications2022

    • Author(s)
      Fangjie Lyu, Seongjin An, Yoshiaki Kobayashi, Kohei Nomura, Rintaro Baba, Naoko Abe, Haruka Hiraoka, Fumitaka Hashiya, Zhaoma Shu, Kumiko Ui-Tei, Yasuaki Kimura, Hiroshi Abe
    • Journal Title

      Bioorganic & Medicinal Chemistry Letters

      Volume: 74 Pages: 128939-128939

    • DOI

      10.1016/j.bmcl.2022.128939

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Knockdown of 15-bp Deletion-Type v-raf Murine Sarcoma Viral Oncogene Homolog B1 mRNA in Pancreatic Ductal Adenocarcinoma Cells Repressed Cell Growth In Vitro and Tumor Volume In Vivo2022

    • Author(s)
      Song Jiaxuan、Kobayashi Yoshiaki、Asano Yoshimasa、Sato Atsushi、Taniguchi Hiroaki、Ui-Tei Kumiko
    • Journal Title

      Cancers

      Volume: 14 Issue: 13 Pages: 3162-3162

    • DOI

      10.3390/cancers14133162

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] siRNA Seed Region Is Divided into Two Functionally Different Domains in RNA Interference in Response to 2′-OMe Modifications2022

    • Author(s)
      Kobayashi Yoshiaki、Fukuhara Daiki、Akase Dai、Aida Misako、Ui-Tei Kumiko
    • Journal Title

      ACS Omega

      Volume: 7 Issue: 2 Pages: 2398-2410

    • DOI

      10.1021/acsomega.1c06455

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] The siRNA Off-Target Effect Is Determined by Base-Pairing Stabilities of Two Different Regions with Opposite Effects2022

    • Author(s)
      Kobayashi Yoshiaki、Tian Shen、Ui-Tei Kumiko
    • Journal Title

      Genes

      Volume: 13 Issue: 2 Pages: 319-319

    • DOI

      10.3390/genes13020319

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Thermodynamic stabilities in the siRNA seed and non-seed regions regulate siRNA off-target effect in opposite direction2022

    • Author(s)
      Kobayashi Yoshiaki、Tian Shen、Ui-Tei Kumiko
    • Journal Title

      Research Aspects in Biological Science

      Volume: 2 Pages: 117-130

    • DOI

      10.9734/bpi/rabs/v2/6153f

    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Presentation] The siRNA Seed Region Is Composed of Two Functionally Different Domains Which Have Different Effects On RNA Interference and Off-target Activities in Response to 2´-OMe Modifications.2022

    • Author(s)
      Yoshiaki Kobayashi, Daiki Fukuhara, Dai Akase, Misako Aida, Kumiko Ui-Tei
    • Organizer
      The Fourth RAS Initiative Symposium
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] SNPD-siRNA: an siRNA Specifically Suppresses the Expression of a Target Gene with Single Nucleotide Mutation.2022

    • Author(s)
      Kumiko Ui-Tei, Yoshiaki Kobayashi, Yoshimasa Asano, Hiroaki Taniguchi
    • Organizer
      The Fourth RAS Initiative Symposium
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Development of siRNA for KRAS and BRAF mutations using a cancer cell-derived Xenograft.2022

    • Author(s)
      Yoshimasa Asano, Yoshiaki Kobayashi, Sato Atsushi, Hiroaki Taniguchi, Kumiko Ui-Tei
    • Organizer
      The Fourth RAS Initiative Symposium
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Molecular design of single nucleotide polymorphism-distinguishable SNPD-siRNA 1塩基変異を区別して遺伝子発現を抑制するSNPD-siRNAの分子設計2022

    • Author(s)
      Kumiko Ui-Tei, Yoshiaki Kobayashi, Yoshimasa Asano
    • Organizer
      第45回日本分子生物学会
    • Related Report
      2022 Annual Research Report
  • [Presentation] The 2’-formamide modification in the siRNA seed region reduces off-target effects by two different mechanisms 2’-formamide修飾をseed領域にもつsiRNAは2つの異なるメカニズムによってoff-target効果を減弱させる2022

    • Author(s)
      Seongjin An, Yoshiaki Kobayashi, Kohei Nomura, Yasuaki Kimura, Hiroshi Abe, Dai Akase, Misako Aida, Kumiko Ui-Tei
    • Organizer
      第45回日本分子生物学会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Verification of SNPD-siPIK3CA targeting single nucleotide mutation in PIK3CA oncogene in breast cancer-derived cells PIK3CAがん原遺伝子の一塩基多型を識別する小分子干渉RNA (SNPD-siPIK3CA)のがん細胞に対する効果の検証2022

    • Author(s)
      Toshinori Ohyama, Yoshiaki Kobayashi, Kumiko Ui-Tei
    • Organizer
      第45回日本分子生物学会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Development of siRNA which specifically represses the expression of oncogenic fusion gene がんの原因となる融合遺伝子を特異的に抑制する小分子干渉RNAの開発2022

    • Author(s)
      Soto Okubo, Yoshiaki Kobayashi, Kumiko Ui-Tei
    • Organizer
      第45回日本分子生物学会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Development of the CRISPR system to regulate TERT expression utilizing single nucleotide mutations in the promoter region プロモーター領域における一塩基変異を識別してTERT遺伝子の発現を制御するCRISPRシステムの構築2022

    • Author(s)
      Hiromu Matsui, Yoshiaki Kobayashi, Kumiko Ui-Tei
    • Organizer
      第45回日本分子生物学会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Verification of CRISPR-Cas9 system for sequence-specific regulation of the gut microbiota CRISPR-Cas9システムによる塩基配列特異的な腸内細菌叢制御の検証2022

    • Author(s)
      Ryuichi Ono, Yoshiaki Kobayashi, Kumiko Ui-Tei
    • Organizer
      第45回日本分子生物学会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Specific knockdown of KRAS mutant gene using SNPD-siRNA repressed cell proliferation of pancreatic cancer cells in vitro and in vivo2022

    • Author(s)
      Yoshiaki Kobayashi, Yoshimasa Asano, Atsushi Sato, Hiroaki Taniguchi, Kumiko Ui-Tei
    • Organizer
      CBI学会2022年大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Prediction of Structural Change of siRNA by 2'-formamide, a Newly-synthesized Chemical Modification, via Density Functional Theory.2022

    • Author(s)
      Seongjin An, Yoshiaki Kobayashi, Kohei Nomura, Yasuaki Kimura, Hiroshi Abe, Dai Akase, Misako Aida, Kumiko Ui-Tei
    • Organizer
      CBI学会2022年大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 1塩基の違いを区別して特異的に抑制するsingle-nucleotide polymorphism-distinguishable siRNA (SNPD-siRNA)の開発とその機能解析2022

    • Author(s)
      小林芳明,佐藤淳,浅野吉政,谷口博昭,程久美子
    • Organizer
      日本核酸医薬学会第7回年会・若手シンポジウム
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 2’-formamide修飾をseed領域にもつsiRNAは塩基の向きを変えることで off-target効果を減弱させる2022

    • Author(s)
      安成鎮、小林芳明、野村浩平、木村康明、阿部洋、赤瀬大、相田美砂子、 程 久美子
    • Organizer
      日本核酸医薬学会第7回年会・若手シンポジウム
    • Related Report
      2022 Annual Research Report
  • [Presentation] Cell-derived Xenograftモデルを用いたKRASやBRAFの変異部位を対象としたsiRNAの有効性の検証2022

    • Author(s)
      浅野吉政、小林芳明、佐藤淳、谷口博昭、程久美子
    • Organizer
      日本核酸医薬学会第7回年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] PIK3CAがん原遺伝子の一塩基多型を識別する小分子干渉RNA (SNPD-siRNA)の開発2022

    • Author(s)
      大山隼礼、小林芳明、程久美子
    • Organizer
      日本核酸医薬学会第7回年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] The siRNA seed region is divided into two functionally different domains in RNA interference in response to 2´-OMe modifications.2022

    • Author(s)
      Yoshiaki Kobayashi, Daiki Fukuhara, Dai Akase, Misako Aida, Kumiko Ui-Tei
    • Organizer
      第23回日本RNA学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 2´-OMe修飾したsiRNAのseed領域は2つの機能ドメインをもつ2021

    • Author(s)
      小林芳明, 田申, 福原大輝, 赤瀬大, 相田美砂子, 程久美子
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Research-status Report
  • [Presentation] トリプレットリピート病の原因遺伝子における一塩基多型を識別する小分子干渉RNA(SNPD-siRNA)の構築とマカド・ジョセフ病由来細胞における検証2021

    • Author(s)
      鈴木ゆりあ, 小林芳明, 程久美子
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Research-status Report
  • [Presentation] PIK3CAがん原遺伝子の一塩基変異を識別して抑制する小分子干渉RNA(SNPD-siRNA)の有効性の検証2021

    • Author(s)
      大山隼礼, 小林芳明, 程久美子
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Research-status Report
  • [Presentation] BaseとSugar修飾を利用したsiRNAのoff-target効果の回避2021

    • Author(s)
      Seongjin An, Yoshiaki Kobayashi, Kohei Nomura, Akase Dai, Yasuaki Kimura, Hiroshi Abe, Misako Aida, Kumiko Ui-Tei
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Research-status Report
  • [Book] Clinical Neuroscience_核酸医薬と神経疾患2023

    • Author(s)
      小林芳明 , 程久美子
    • Total Pages
      736
    • Publisher
      中外医学社
    • Related Report
      2022 Annual Research Report
  • [Book] 核酸医薬・mRNA医薬の製造分析の基礎と基盤技術開発2023

    • Author(s)
      小林芳明 , 程久美子 (小比賀聡, 井上貴雄監修)
    • Total Pages
      290
    • Publisher
      シーエムシー・リサーチ
    • Related Report
      2022 Annual Research Report
  • [Book] 核酸医薬 本領を発揮する創薬モダリティ2021

    • Author(s)
      浅野吉政、小林芳明、程久美子 (編集:横田 隆徳)
    • Total Pages
      204
    • Publisher
      羊土社
    • ISBN
      9784758103985
    • Related Report
      2021 Research-status Report
  • [Book] 日本薬学会医薬化学部会機関誌「MEDCHEM NEWS」31-4号「ESSAY特集」2021

    • Author(s)
      小林芳明、程久美子 (編集:MEDCHEM NEWS編集委員会)
    • Total Pages
      60
    • Publisher
      じほうMEDCHEM NEWS
    • Related Report
      2021 Research-status Report

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Published: 2021-10-22   Modified: 2024-01-30  

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