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Development of molecules that control gene networks and their application to cells

Research Project

Project/Area Number 21H04705
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Review Section Medium-sized Section 37:Biomolecular chemistry and related fields
Research InstitutionKyoto University

Principal Investigator

SUGIYAMA Hiroshi  京都大学, 高等研究院, 研究員 (50183843)

Co-Investigator(Kenkyū-buntansha) 板東 俊和  京都大学, 理学研究科, 准教授 (20345284)
ナマシヴァヤム パンディアン  京都大学, 高等研究院, 講師 (20625446)
Project Period (FY) 2021-04-05 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥42,120,000 (Direct Cost: ¥32,400,000、Indirect Cost: ¥9,720,000)
Fiscal Year 2023: ¥13,000,000 (Direct Cost: ¥10,000,000、Indirect Cost: ¥3,000,000)
Fiscal Year 2022: ¥13,780,000 (Direct Cost: ¥10,600,000、Indirect Cost: ¥3,180,000)
Fiscal Year 2021: ¥15,340,000 (Direct Cost: ¥11,800,000、Indirect Cost: ¥3,540,000)
Keywordsケミカルバイオロジー / 生物有機化学 / 遺伝子発現制御 / ヌクレオソーム / DNAナノ構造体 / AFM解析 / ミトコンドリア / 遺伝子発現
Outline of Research at the Start

細胞内でおこる生命現象は、生物学的な構成単位であるヌクレオソーム中のヒストンや核酸塩基の化学修飾よって誘導され、エピジェネティックに制御されている。遺伝子発現機構を分子レベルで解明することができれば、細胞の運命を自在にコントロールし、再生医療や基礎研究への応用が期待できる。本研究申請では、ヌクレオソームを中心とした遺伝子発現の機構を1分子レベルの可視化技術を確立し、我々の構築した「遺伝子スイッチ」の作用を評価する。これらの知見に基づき遺伝子ネットワークを制御するための新たな分子の開発と細胞への応用を目指す。

Outline of Final Research Achievements

If we can elucidate the gene expression mechanism mediated by the nucleosome network at the molecular level, we can expect its application to biofunctional molecular research. The research and development representative succeeded in visualizing the dynamics of gene expression centered on nucleosomes using DNA origami-AFM measurement technology. Furthermore, we developed cyclic polyamide molecules and chlorambucil polyamide molecules as functional molecules to control gene expression networks, and analyzed and evaluated them in cultured human cancer cells and mice with Huntington's disease. We believe that the results obtained through this research have enabled us to successfully elucidate biological phenomena using nanoscale molecular arrangement and single molecule analysis, and have established a technological foundation for the creation of functional molecules.

Academic Significance and Societal Importance of the Research Achievements

遺伝子発現はヌクレオソーム中のヒストンや核酸塩基の化学修飾よって制御され、ヌクレオソーム間の距離や配向によってクロマチンの高次構造が形成される。分子レベルの解像度のクロマチン構造の動態や反応機構の詳細は解明されておらず、研究代表者らが分子科学の立場からナノスケールでの遺伝子発現機構の解明と機能分子による制御技術の開拓を行ったことに、学術的な意義があると考える。本研究で得られた遺伝子発現制御技術に関する知見は、大学研究機関や企業へ広がっており、核酸領域研究に関連する新概念の創出や将来的な医薬品分野への発展の可能性が見込まれている。

Report

(5 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Annual Research Report
  • 2021 Comments on the Screening Results   Annual Research Report
  • Research Products

    (29 results)

All 2023 2022 2021

All Journal Article (29 results) (of which Int'l Joint Research: 9 results,  Peer Reviewed: 29 results,  Open Access: 19 results)

  • [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] A cyclic pyrrole-imidazole polyamide reduces pathogenic RNA in CAG/CTG triplet repeat neurological disease models2023

    • Author(s)
      Ikenoshita Susumu、Matsuo Kazuya、Yabuki Yasushi、Kawakubo Kosuke、Asamitsu Sefan、Hori Karin、Usuki Shingo、Hirose Yuki、Bando Toshikazu、Araki Kimi、Ueda Mitsuharu、Sugiyama Hiroshi、Shioda Norifumi
    • Journal Title

      Journal of Clinical Investigation

      Volume: 133 Issue: 22

    • DOI

      10.1172/jci164792

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural Expansion of Catalytic RNA Nanostructures through Oligomerization of a Cyclic Trimer of Engineered Ribozymes2023

    • Author(s)
      Siddika Mst. Ayesha、Oi Hiroki、Hidaka Kumi、Sugiyama Hiroshi、Endo Masayuki、Matsumura Shigeyoshi、Ikawa Yoshiya
    • Journal Title

      Molecules

      Volume: 28 Issue: 18 Pages: 6465-6465

    • DOI

      10.3390/molecules28186465

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Isothermal self-assembly of multicomponent and evolutive DNA nanostructures2023

    • Author(s)
      Rossi-Gendron Caroline、El Fakih Farah、Bourdon Laura、Nakazawa Koyomi、Finkel Julie、Triomphe Nicolas、Chocron Lea、Endo Masayuki、Sugiyama Hiroshi、Bellot Ga?tan、Morel Mathieu、Rudiuk Sergii、Baigl Damien
    • Journal Title

      Nature Nanotechnology

      Volume: 18 Issue: 11 Pages: 1311-1318

    • DOI

      10.1038/s41565-023-01468-2

    • 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
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Corrigendum to “Chlorambucil-conjugated PI-polyamide (Chb-M’), a transcription inhibitor of the RUNX family, has anti-tumor activity against SHH-type medulloblastoma with p53 mutation” [Biochem. Biophys. Res. Commun. 620 (10 September 2022) 150?157]2023

    • Author(s)
      Matsui Yasuzumi、Mineharu Yohei、Noguchi Yuki、Hattori Etsuko Yamamoto、Kubota Hirohito、Hirata Masahiro、Miyamoto Susumu、Sugiyama Hiroshi、Arakawa Yoshiki、Kamikubo Yasuhiko
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 656 Pages: 146-147

    • DOI

      10.1016/j.bbrc.2023.03.022

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Two-Dimensional DNA Origami Lattices Assembled on Lipid Bilayer Membranes2023

    • Author(s)
      Suzuki Yuki、Sugiyama Hiroshi、Endo Masayuki
    • Journal Title

      Methods in Molecular Biology

      Volume: 2639 Pages: 83-90

    • DOI

      10.1007/978-1-0716-3028-0_5

    • ISBN
      9781071630273, 9781071630280
    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Single-Molecule Visualization of B-Z Transition in DNA Origami Using High-Speed AFM2023

    • Author(s)
      Endo Masayuki、Sugiyama Hiroshi
    • Journal Title

      Methods in Molecular Biology

      Volume: 2651 Pages: 241-250

    • DOI

      10.1007/978-1-0716-3084-6_17

    • ISBN
      9781071630839, 9781071630846
    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Substitution to hydrophobic linker and formation of host-guest complex enhanced the effect of synthetic transcription factor made of pyrrole-imidazole polyamide.2023

    • Author(s)
      Junnosuke Hatanaka and Kaori Hashiya and Toshikazu Bando and Hiroshi Sugiyama
    • Journal Title

      Bioorganic & medicinal chemistry

      Volume: 81 Pages: 117208-117208

    • DOI

      10.1016/j.bmc.2023.117208

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] RNA G-quadruplex organizes stress granule assembly through DNAPTP6 in neurons2023

    • Author(s)
      Asamitsu Sefan、Yabuki Yasushi、Matsuo Kazuya、Kawasaki Moe、Hirose Yuki、Kashiwazaki Gengo、Chandran Anandhakumar、Bando Toshikazu、Wang Dan Ohtan、Sugiyama Hiroshi、Shioda Norifumi
    • Journal Title

      Science Advances

      Volume: 9 Issue: 8

    • DOI

      10.1126/sciadv.ade2035

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Photocontrolled DNA nanotubes as stiffness tunable matrices for controlling cellular behavior2023

    • Author(s)
      Sethi Soumya、Emura Tomoko、Hidaka Kumi、Sugiyama Hiroshi、Endo Masayuki
    • Journal Title

      Nanoscale

      Volume: 15 Issue: 6 Pages: 2904-2910

    • DOI

      10.1039/d2nr05202d

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] RUNX1-Survivin Axis Is a Novel Therapeutic Target for Malignant Rhabdoid Tumors2022

    • Author(s)
      Mikami Masamitsu、Masuda Tatsuya、Kanatani Takuya、Noura Mina、Umeda Katsutsugu、Hiramatsu Hidefumi、Kubota Hirohito、Daifu Tomoo、Iwai Atsushi、Hattori Etsuko Yamamoto、Furuichi Kana、Takasaki Saho、Tanaka Sunao、Matsui Yasuzumi、Matsuo Hidemasa、Hirata Masahiro、Kataoka Tatsuki R. et al.
    • Journal Title

      Molecules and Cells

      Volume: 45 Issue: 12 Pages: 886-895

    • DOI

      10.14348/molcells.2022.2031

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Twelve Colors of Streptavidin-Fluorescent Proteins (SA-FPs): A Versatile Tool to Visualize Genetic Information in Single-Molecule DNA2022

    • Author(s)
      Jin Yu、Bae Jaeyoung、Kim Tehee Yurie、Hwang Hyeseung、Kim Taesoo、Yu Myungheon、Oh Hyesoo、Hashiya Kaori、Bando Toshikazu、Sugiyama Hiroshi、Jo Kyubong
    • Journal Title

      Analytical Chemistry

      Volume: 94 Issue: 48 Pages: 16927-16935

    • DOI

      10.1021/acs.analchem.2c04344

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Catalytic RNA Oligomers Formed by Co-Oligomerization of a Pair of Bimolecular RNase P Ribozymes2022

    • Author(s)
      Siddika Mst. Ayesha、Yamada Takahiro、Aoyama Risako、Hidaka Kumi、Sugiyama Hiroshi、Endo Masayuki、Matsumura Shigeyoshi、Ikawa Yoshiya
    • Journal Title

      Molecules

      Volume: 27 Issue: 23 Pages: 8298-8298

    • DOI

      10.3390/molecules27238298

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Author Correction: A RUNX-targeted gene switch-off approach modulates the BIRC5/PIF1-p21 pathway and reduces glioblastoma growth in mice2022

    • Author(s)
      Hattori Etsuko Yamamoto、Masuda Tatsuya、Mineharu Yohei、Mikami Masamitsu、Terada Yukinori、Matsui Yasuzumi、Kubota Hirohito、Matsuo Hidemasa、Hirata Masahiro、Kataoka Tatsuki R.、Nakahata Tatsutoshi、Ikeda Shuji、Miyamoto Susumu、Sugiyama Hiroshi、Arakawa Yoshiki、Kamikubo Yasuhiko
    • Journal Title

      Communications Biology

      Volume: 5 Issue: 1 Pages: 1021-1021

    • DOI

      10.1038/s42003-022-04006-3

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Zeptoliter DNA Origami Reactor to Reveal Cosolute Effects on Nanoconfined G-Quadruplexes2022

    • Author(s)
      Pandey Shankar、Jonchhe Sagun、Mishra Shubham、Emura Tomoko、Sugiyama Hiroshi、Endo Masayuki、Mao Hanbin
    • Journal Title

      The Journal of Physical Chemistry Letters

      Volume: 13 Issue: 37 Pages: 8692-8698

    • DOI

      10.1021/acs.jpclett.2c02253

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Chlorambucil-conjugated PI-polyamides (Chb-M’), a transcription inhibitor of RUNX family, has an anti-tumor activity against SHH-type medulloblastoma with p53 mutation2022

    • Author(s)
      Matsui Yasuzumi、Mineharu Yohei、Noguchi Yuki、Hattori Etsuko Yamamoto、Kubota Hirohito、Hirata Masahiro、Miyamoto Susumu、Sugiyama Hiroshi、Arakawa Yoshiki、Kamikubo Yasuhiko
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 620 Pages: 150-157

    • DOI

      10.1016/j.bbrc.2022.06.090

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A RUNX-targeted gene switch-off approach modulates the BIRC5/PIF1-p21 pathway and reduces glioblastoma growth in mice2022

    • Author(s)
      Hattori Etsuko Yamamoto、Masuda Tatsuya、Mineharu Yohei、Mikami Masamitsu、Terada Yukinori、Matsui Yasuzumi、Kubota Hirohito、Matsuo Hidemasa、Hirata Masahiro、Kataoka Tatsuki R.、Nakahata Tatsutoshi、Ikeda Shuji、Miyamoto Susumu、Sugiyama Hiroshi、Arakawa Yoshiki、Kamikubo Yasuhiko
    • Journal Title

      Communications Biology

      Volume: 5 Issue: 1 Pages: 939-939

    • DOI

      10.1038/s42003-022-03917-5

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] N-terminal Cationic Modification of Linear Pyrrole-Imidazole Polyamide Improves Its Binding to DNA.2022

    • Author(s)
      Junnosuke Hatanaka and Yuki Hirose and Kaori Hashiya and Toshikazu Bando and Hiroshi Sugiyama
    • Journal Title

      Chembiochem : a European journal of chemical biology

      Volume: 23 Issue: 14

    • DOI

      10.1002/cbic.202200124

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] DNA-Based Daisy Chain Rotaxane Nanocomposite Hydrogels as Dual-Programmable Dynamic Scaffolds for Stem Cell Adhesion2022

    • Author(s)
      Yao Shengtao、Chang Yongyun、Zhai Zanjing、Sugiyama Hiroshi、Endo Masayuki、Zhu Weiping、Xu Yufang、Yang Yangyang、Qian Xuhong
    • Journal Title

      ACS Applied Materials & Interfaces

      Volume: 14 Issue: 18 Pages: 20739-20748

    • DOI

      10.1021/acsami.2c03265

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] An informatics approach to distinguish RNA modifications in nanopore direct RNA sequencing2022

    • Author(s)
      Ramasamy Soundhar、Mishra Shubham、Sharma Surbhi、Parimalam Sangamithirai Subramanian、Vaijayanthi Thangavel、Fujita Yoto、Kovi Basavaraj、Sugiyama Hiroshi、Pandian Ganesh N.
    • Journal Title

      Genomics

      Volume: - Issue: 3 Pages: 110372-110372

    • DOI

      10.1016/j.ygeno.2022.110372

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Targeted elimination of mutated mitochondrial DNA by a multi-functional conjugate capable of sequence-specific adenine alkylation2022

    • Author(s)
      Hidaka Takuya、Hashiya Kaori、Bando Toshikazu、Pandian Ganesh N.、Sugiyama Hiroshi
    • Journal Title

      Cell Chemical Biology

      Volume: 29 Issue: 4 Pages: 1-6

    • DOI

      10.1016/j.chembiol.2021.08.003

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Targeted epigenetic induction of mitochondrial biogenesis enhances antitumor immunity in mouse model2022

    • Author(s)
      Malinee Madhu、Pandian Ganesh Namasivayam、Sugiyama Hiroshi
    • Journal Title

      Cell Chemical Biology

      Volume: 29 Issue: 3 Pages: 463-475.e6

    • DOI

      10.1016/j.chembiol.2021.08.001

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Dissection of nanoconfinement and proximity effects on the binding events in DNA origami nanocavity2022

    • Author(s)
      Jonchhe Sagun、Pandey Shankar、Beneze Christian、Emura Tomoko、Sugiyama Hiroshi、Endo Masayuki、Mao Hanbin
    • Journal Title

      Nucleic Acids Research

      Volume: 50 Issue: 2 Pages: 697-703

    • DOI

      10.1093/nar/gkab1298

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Strong and Specific Recognition of CAG/CTG Repeat DNA (5’‐dWGCWGCW‐3’) by a Cyclic Pyrrole‐Imidazole Polyamide2021

    • Author(s)
      Hirose Yuki、Ohno Tomo、Asamitsu Sefan、Hashiya Kaori、Bando Toshikazu、Sugiyama Hiroshi
    • Journal Title

      ChemBioChem

      Volume: 23 Issue: 2

    • DOI

      10.1002/cbic.202100533

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Photo-Controllable Phase Transition of Arylazopyrazole-Conjugated Oligonucleotides2021

    • Author(s)
      Hidaka Takuya、Wee Wen Ann、Yum Ji Hye、Sugiyama Hiroshi、Park Soyoung
    • Journal Title

      Bioconjugate Chemistry

      Volume: 32 Issue: 10 Pages: 2129-2133

    • DOI

      10.1021/acs.bioconjchem.1c00302

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Non‐invasive Regulation of Cellular Morphology Using a Photoswitchable Mechanical DNA Polymer2021

    • Author(s)
      Sethi Soumya、Hidaka Kumi、Sugiyama Hiroshi、Endo Masayuki
    • Journal Title

      Angewandte Chemie International Edition

      Volume: 60 Issue: 37 Pages: 20342-20349

    • DOI

      10.1002/anie.202105425

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] HBD1 protein with a tandem repeat of two HMG-box domains is a DNA clip to organize chloroplast nucleoids in <i>Chlamydomonas reinhardtii</i>2021

    • Author(s)
      Takusagawa Mari、Kobayashi Yusuke、Fukao Yoichiro、Hidaka Kumi、Endo Masayuki、Sugiyama Hiroshi、Hamaji Takashi、Kato Yoshinobu、Miyakawa Isamu、Misumi Osami、Shikanai Toshiharu、Nishimura Yoshiki
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 118 Issue: 20 Pages: 463-475

    • DOI

      10.1073/pnas.2021053118

    • NAID

      120007035840

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Application of DNA‐Alkylating Pyrrole‐Imidazole Polyamides for Cancer Treatment2021

    • Author(s)
      Maeda Rina、Bando Toshikazu、Sugiyama Hiroshi
    • Journal Title

      ChemBioChem

      Volume: 22 Issue: 9 Pages: 1538-1545

    • DOI

      10.1002/cbic.202000752

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access

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Published: 2021-04-28   Modified: 2025-01-30  

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