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An integrated approach for mapping RNA protein interactions in the ribosome

Research Project

Project/Area Number 22K19291
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 43:Biology at molecular to cellular levels, and related fields
Research InstitutionKyoto University

Principal Investigator

NAMASIVAYAM Ganesh Pandian  京都大学, 高等研究院, 講師 (20625446)

Co-Investigator(Kenkyū-buntansha) Packwood Daniel  京都大学, 高等研究院, 准教授 (40640884)
Project Period (FY) 2022-06-30 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000)
Fiscal Year 2023: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Fiscal Year 2022: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
KeywordsTranscriptomics / RNA Structures / Nanopore technology / Chemical probes / Informatics / RNA protein interactions / RNA modifications / ナノポアシークエンシング / リボソーム / RNA-たんぱく質相互作用 / ケミカルプローブ / バイオインフォマティクス / Nanopore / Direct RNA sequencing / RNA-protein interactions / Chemical probe / Machine learning
Outline of Research at the Start

本研究は、学際的なアプローチを使用して、RNP-BI-NANO-Seqと呼ばれる迅速に適応できるシーケンス技術を開発することを目的としている。これにより、癌のリボソームにおけるRNA-タンパク質相互作用を調べる既存の方法における欠点を克服することが可能である。癌だけでなく他の多くの病気でもリボソームの機能不全は見られる。これら疾患に対する既存の薬剤の多く はリボソームを標的にしており、結果として得られたデータセットは、新しい創薬可能な RNA構造を明らかにし、新しい創薬に役立つ。

Outline of Final Research Achievements

Using this grant, we have successfully demonstrated the proof-of-concept (POC) studies to verify an integrated approach of harnessing the selective reactivity of chemical probes in the nanopore direct RNA sequencing platform and improving the prediction accuracy using an informatics workflow called Indo-C that can be programmed on demand. Using this methodology, we published initial results on deciphering the inosine and pseudouridine RNA modifications, the nano-bio interaction of the functionalized quantum dot probes as original articles and have summarized the potential of computational-aided discovery of natural product-derived small molecule probes as review articles. Currently, we are extending our strategy to map RNA structural and base modifications and their interaction using programmable nucleic acid-based nanopores in varied sizes, shapes, and constrictions and developing a universally adaptable biomolecular sequencing technology under a JST program.

Academic Significance and Societal Importance of the Research Achievements

近年のCovid-19の世界的流行により健康についての信頼性の高い指標として、RNAから細胞内環境に関する正確な情報が得られることが明らかになった。本研究により開発された、ケミカルプローブを用いたディレクトRNAシークエンシング法は、他の研究室でも取り入れることのできる簡便なものである。したがって、感染症であれがんのような非感染性疾患であれ、未知のRNA修飾やその相互作用の場所を特定するマッピング研究への波及効果が期待できる。そうして得られたデータセットの解析は、診断用疾患マーカーあるいは新薬の標的となるようなRNAの新規構造の発見や、不治の希少疾患に対する核酸医薬の創出に役立つ可能性がある。

Report

(3 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Research-status Report
  • Research Products

    (27 results)

All 2024 2023 2022 Other

All Int'l Joint Research (8 results) Journal Article (10 results) (of which Int'l Joint Research: 10 results,  Peer Reviewed: 10 results,  Open Access: 10 results) Presentation (7 results) (of which Int'l Joint Research: 2 results,  Invited: 7 results) Remarks (2 results)

  • [Int'l Joint Research] University of Zurich/AO Research Institute(スイス)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] MacDiarmid Institute(ニュージーランド)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] Vellore Institute of Technology/Anna University/University of Madras(インド)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] National Cheg Kung University(その他の国・地域(台湾))

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] Rutgers University(米国)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] University of Zurich/AO Research Institute(スイス)

    • Related Report
      2022 Research-status Report
  • [Int'l Joint Research] National Chemical Laboratory - Pune(インド)

    • Related Report
      2022 Research-status Report
  • [Int'l Joint Research] Rutgers University(米国)

    • Related Report
      2022 Research-status Report
  • [Journal Article] Chalcone derivatives' interaction with human serum albumin and cyclooxygenase-22024

    • Author(s)
      Karthikeyan Subramani、Thirunarayanan Ayyavu、Shano Leon Bernet、Hemamalini Arasappan、Sundaramoorthy Anandh、Mangaiyarkarasi Rajendiran、Abu Norhidayah、Ganesan Singaravelu、Chinnathambi Shanmugavel、Pandian Ganesh N.
    • Journal Title

      RSC Advances

      Volume: 14 Issue: 4 Pages: 2835-2849

    • DOI

      10.1039/d3ra07438b

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] An ultra-sensitive detection of Melamine in milk using Rare-earth doped Graphene Quantum Dots- Synthesis and Optical Spectroscopic approach2024

    • Author(s)
      Anjila P.K Fathima、Tharani G.R.、Sundaramoorthy Anand、Kumar Shanmugam Venkat、Subramani Karthikeyan、Chinnathambi Shanmugavel、Pandian Ganesh N.、Raghavan Vimala、Grace Andrews Nirmala、Ganesan Singaravelu、Rajendiran Mangaiyarkarasi
    • Journal Title

      Microchemical Journal

      Volume: 196 Pages: 109670-109670

    • DOI

      10.1016/j.microc.2023.109670

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Surface charge-dependent cytokine production using near-infrared emitting silicon quantum dots2024

    • Author(s)
      Chinnathambi Shanmugavel、Shirahata Naoto、Lesani Pooria、Thangavel Vaijayanthi、Pandian Ganesh N.
    • Journal Title

      Scientific Reports

      Volume: 14 Issue: 1 Pages: 9618-9618

    • DOI

      10.1038/s41598-024-60536-2

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Pyrrole Imidazole Polyamides A Frontrunner in Nucleic Acid‐Based Small Molecule Drugs2023

    • Author(s)
      Vaijayanthi Thangavel、Pandian Ganesh N.、Sugiyama Hiroshi
    • Journal Title

      Advanced Therapeutics

      Volume: - Issue: 7 Pages: 2300022-2300022

    • DOI

      10.1002/adtp.202300022

    • Related Report
      2023 Annual Research Report 2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Identification of genes responsible for the social skill in the earthworm, Eudrilus eugeniae2023

    • Author(s)
      Lathakumari Saranya、Seenipandian Sumitha、Balakrishnan Subburathinam、Raj Audre Preena Maria Sundar、Sugiyama Hiroshi、Pandian Ganesh N、Sivasubramaniam Sudhakar
    • Journal Title

      Gene Reports

      Volume: 31 Pages: 101774-101774

    • DOI

      10.1016/j.genrep.2023.101774

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Bat-associated microbes: Opportunities and perils, an overview2023

    • Author(s)
      Dhivahar J.、Parthasarathy Anutthaman、Krishnan Kathiravan、Kovi Basavaraj S.、Pandian Ganesh N.
    • Journal Title

      Heliyon

      Volume: 9 Issue: 12 Pages: e22351-e22351

    • DOI

      10.1016/j.heliyon.2023.e22351

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Nucleic acid‐based small molecules as targeted transcription therapeutics for immunoregulation2023

    • Author(s)
      Bai Dan、Ziadlou Reihane、Vaijayanthi Thangavel、Karthikeyan Subramani、Chinnathambi Shanmugavel、Parthasarathy Anutthaman、Cai Li、Br?ggen Marie‐Charlotte、Sugiyama Hiroshi、Pandian Ganesh N.
    • Journal Title

      Allergy

      Volume: 79 Issue: 4 Pages: 843-860

    • DOI

      10.1111/all.15959

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Nano bio interaction between human immunoglobulin G and nontoxic, near-infrared emitting water-borne silicon quantum dot micelles2023

    • Author(s)
      Chinnathambi Shanmugavel、Shirahata Naoto、Kumar Mahima、Karthikeyan Subramani、Abe Katsuhiko、Thangavel Vaijayanthi、Pandian Ganesh N.
    • Journal Title

      RSC Advances

      Volume: 13 Issue: 9 Pages: 6051-6064

    • DOI

      10.1039/d3ra00552f

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Artificial intelligence in microbial natural product drug discovery: current and emerging role2022

    • Author(s)
      Sahayasheela Vinodh J.、Lankadasari Manendra B.、Dan Vipin Mohan、Dastager Syed G.、Pandian Ganesh N.、Sugiyama Hiroshi
    • Journal Title

      Natural Product Reports

      Volume: 39 Issue: 12 Pages: 2215-2230

    • DOI

      10.1039/d2np00035k

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Chemical Probe-Based Nanopore Sequencing to Selectively Assess the RNA Modifications2022

    • Author(s)
      Ramasamy Soundhar、Sahayasheela Vinodh J.、Sharma Surbhi、Yu Zutao、Hidaka Takuya、Cai Li、Thangavel Vaijayanthi、Sugiyama Hiroshi、Pandian Ganesh N.
    • Journal Title

      ACS Chemical Biology

      Volume: 17 Issue: 10 Pages: 2704-2709

    • DOI

      10.1021/acschembio.2c00221

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Scripting an Eco-system for Precision Medicine: Navigating the Journey to Bridge Boundaries for Synergistic Integration?"2024

    • Author(s)
      Ganesh Pandian NAMASIVAYAM
    • Organizer
      Kyoto winter school-2024, `Quantifying Dynamics of Life`
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Harnessing Informatics for Personalized Medicine2023

    • Author(s)
      Ganesh Pandian NAMASIVAYAM
    • Organizer
      MacDiarmid Institute-Kyoto University Workshop
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Programmable small molecules to regulate genetic information inside live cells on demand2023

    • Author(s)
      Ganesh Pandian NAMASIVAYAM
    • Organizer
      MacDiarmid Institute-iCeMS symposium
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Chemical Biology approach for precision medicine2023

    • Author(s)
      Ganesh Pandian Namasivayam
    • Organizer
      Next Generation Healthcare - Interdisciplinary Approaches
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Targeted transcription therapeutics for skin cell reprogramming2023

    • Author(s)
      NAMASIVAYAM Ganesh Pandian
    • Organizer
      Skintegrity - Mini symposium
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Nucleic acid-based small molecule therapeutics2023

    • Author(s)
      NAMASIVAYAM Ganesh Pandian
    • Organizer
      Swiss Institute of Allergy and Asthma Research - University of Zurich Lecture Series
    • Related Report
      2022 Research-status Report
    • Invited
  • [Presentation] DNA-based targeted transcription therapeutics for precision medicine2022

    • Author(s)
      NAMASIVAYAM Ganesh Pandian
    • Organizer
      Functional nucleic acids: Recent landscapes and therapeutic applications - EMBO Lecture Series
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research / Invited
  • [Remarks] Reading RNA modifications more precisely

    • URL

      https://www.asiaresearchnews.com/content/reading-rna-modifications-more-precisely

    • Related Report
      2022 Research-status Report
  • [Remarks] Oxford nanopore social media site

    • URL

      https://twitter.com/nanopore/status/1562411398881505284?lang=bg

    • Related Report
      2022 Research-status Report

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Published: 2022-07-05   Modified: 2025-01-30  

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