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Nuclear and chromatin structure dynamics and gene regulatioin

Planned Research

Project AreaChromatin potential for gene regulation
Project/Area Number 18H05527
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 InstitutionTokyo Institute of Technology

Principal Investigator

Kimura Hiroshi  東京工業大学, 科学技術創成研究院, 教授 (30241392)

Co-Investigator(Kenkyū-buntansha) 伊藤 由馬  東京工業大学, 生命理工学院, 助教 (70803245)
大川 恭行  九州大学, 生体防御医学研究所, 教授 (80448430)
Project Period (FY) 2018-06-29 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥235,690,000 (Direct Cost: ¥181,300,000、Indirect Cost: ¥54,390,000)
Fiscal Year 2022: ¥46,150,000 (Direct Cost: ¥35,500,000、Indirect Cost: ¥10,650,000)
Fiscal Year 2021: ¥46,150,000 (Direct Cost: ¥35,500,000、Indirect Cost: ¥10,650,000)
Fiscal Year 2020: ¥46,150,000 (Direct Cost: ¥35,500,000、Indirect Cost: ¥10,650,000)
Fiscal Year 2019: ¥46,150,000 (Direct Cost: ¥35,500,000、Indirect Cost: ¥10,650,000)
Fiscal Year 2018: ¥51,090,000 (Direct Cost: ¥39,300,000、Indirect Cost: ¥11,790,000)
Keywordsクロマチン / 遺伝子発現 / 転写制御 / エピジェネティクス / ヒストン修飾 / 遺伝子発現制御 / 転写調節 / エピジェネティクス制御 / 転写 / ヒストン / 細胞核
Outline of Final Research Achievements

This research aimed to elucidate the function of chromatin structure through histone modifications from the perspective of transcriptional activation potential. Through live-cell imaging of zebrafish embryos, we revealed that histone acetylation enhances the potential for transcriptional activation. We also developed genetically encoded single-stranded variable region antibody probes that specifically recognize phosphorylation of RNA polymerase II at the transcription initiation and elongation stages. Based on the distinct localization and dynamics of transcription initiation and elongation foci in living cells, a model of transcription organization was proposed. In addition, we have developed low-input epigenome analysis techniques.

Academic Significance and Societal Importance of the Research Achievements

ヒトなどの真核生物の細胞核に存在するDNAはヒストンタンパク質と結合しクロマチン構造をとって存在している。このクロマチン構造が遺伝子発現の制御に働くことが最近明らかになってきたが、生きた細胞中でどのように転写が起こるのについてはよくわかっていない。本研究では、ヒストンや転写を担う酵素であるRNAポリメラーゼIIの翻訳後修飾を生細胞観察することにより、転写の活性化や抑制にヒストン修飾が働くこと、および、転写が開始する場所と伸長する場所が異なることを明らかにした。本研究による転写の基本メカニズムに関する知見は、再生医療や細胞治療などの研究に波及効果がある。

Report

(6 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • Research Products

    (165 results)

All 2023 2022 2021 2020 2019 2018 Other

All Int'l Joint Research (17 results) Journal Article (85 results) (of which Int'l Joint Research: 37 results,  Peer Reviewed: 65 results,  Open Access: 69 results) Presentation (45 results) (of which Int'l Joint Research: 20 results,  Invited: 27 results) Book (1 results) Remarks (17 results)

  • [Int'l Joint Research] Hubrecht Institute(オランダ)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Memorial Sloan Kettering Cencer Center/Colorado State University(米国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Lausanne University(スイス)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Cambridge University(英国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Colorado State University/Florida State University(米国)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] Hubrecht Institute(オランダ)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] European Moleclar Biology Laboratory/Max Planck Institute-CBG/Karlsruhe Institute of Technology(ドイツ)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] University of Copenhagen(デンマーク)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] University of Cambridge/Crick Institute(英国)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] Colorado State University(米国)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] New York University/Colorado State University/Florida State University(米国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Cambridge University/New Castle University(英国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] EMBL/Max Panck Institute, Dresden/Karlsruhe Institute of Technology(ドイツ)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Colorado State University/HHMI Janelia Research Campus(米国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] Cambridge University(英国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] MPI - Molecular Cell Biology & Genetics/Karlsruhe Institute of Technology/EMBL(ドイツ)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] Curie Insitute(フランス)

    • Related Report
      2018 Annual Research Report
  • [Journal Article] Epigenetic plasticity safeguards heterochromatin configuration in mammals2023

    • Author(s)
      Fukuda Kei、Shimi Takeshi、Shimura Chikako、Ono Takao、Suzuki Takehiro、Onoue Kenta、Okayama Satoko、Miura Hisashi、Hiratani Ichiro、Ikeda Kazuho、Okada Yasushi、Dohmae Naoshi、Yonemura Shigenobu、Inoue Azusa、Kimura Hiroshi、Shinkai Yoichi
    • Journal Title

      Nucleic Acids Research

      Volume: - Issue: 12 Pages: 6190-6207

    • DOI

      10.1093/nar/gkad387

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Actin filaments accumulated in the nucleus and remain in the vicinity of condensing chromosomes during prophase in zebrafish early embryo2023

    • Author(s)
      Oda Haruka、Sato Yuko、Kawashima Shigehiro A.、Fujiwara Yusuke、Palfy Mate、Wu Edlyn、Vastenhouw Nadine L.、Kanai Motomu、Kimura Hiroshi
    • Journal Title

      Biology Open

      Volume: 12 Issue: 5

    • DOI

      10.1242/bio.059783

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Live-cell tracking of γ-H2AX kinetics reveals the distinct modes of ATM and DNA-PK in the immediate response to DNA damage2023

    • Author(s)
      Trakarnphornsombat Watanya、Kimura Hiroshi
    • Journal Title

      Journal of Cell Science

      Volume: 136 Issue: 8

    • DOI

      10.1242/jcs.260698

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Dense and Acidic Organelle-Targeted Visualization in Living Cells: Application of Viscosity-Responsive Fluorescence Utilizing Restricted Access to Minimum Energy Conical Intersection2023

    • Author(s)
      Adachi Junya、Oda Haruka、Fukushima Toshiaki、Lestari Beni、Kimura Hiroshi、Sugai Hiroka、Shiraki Kentaro、Hamaguchi Rei、Sato Kohei、Kinbara Kazushi
    • Journal Title

      Analytical Chemistry

      Volume: 95 Issue: 12 Pages: 5196-5204

    • DOI

      10.1021/acs.analchem.2c04133

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Nanog organizes transcription bodies2023

    • Author(s)
      Kuznetsova Ksenia、Chabot No?mie M.、Ugolini Martino、Wu Edlyn、Lalit Manan、Oda Haruka、Sato Yuko、Kimura Hiroshi、Jug Florian、Vastenhouw Nadine L.
    • Journal Title

      Current Biology

      Volume: 33 Issue: 1 Pages: 164-173.e5

    • DOI

      10.1016/j.cub.2022.11.015

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Transient Methionine Deprivation Triggers Histone Modification and Potentiates Differentiation of Induced Pluripotent Stem Cells.2023

    • Author(s)
      Ozawa H, Kambe A, Hibi K, Murakami S, Oikawa A, Handa T, Fujiki K, Nakato R, Shirahige K, Kimura H, Shiraki N, Kume S
    • Journal Title

      Stem Cells.

      Volume: 41(3) Issue: 3 Pages: 271-286

    • DOI

      10.1093/stmcls/sxac082

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The role of H3K9me3 in oral squamous cell carcinoma2023

    • Author(s)
      Tanaka Misako、Harada Hiroyuki、Kimura Hiroshi
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 640 Pages: 56-63

    • DOI

      10.1016/j.bbrc.2022.11.102

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Euchromatin factors HULC and Set1C affect heterochromatin organization and mating-type switching in fission yeast <i>Schizosaccharomyces pombe</i>2022

    • Author(s)
      Esquivel-Chavez Alfredo、Maki Takahisa、Tsubouchi Hideo、Handa Testuya、Kimura Hiroshi、Haber James E.、Thon Genevieve、Iwasaki Hiroshi
    • Journal Title

      Genes & Genetic Systems

      Volume: 97 Issue: 3 Pages: 123-138

    • DOI

      10.1266/ggs.22-00012

    • ISSN
      1341-7568, 1880-5779
    • Year and Date
      2022-06-01
    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity2022

    • Author(s)
      Ohishi Hiroaki、Shimada Seiru、Uchino Satoshi、Li Jieru、Sato Yuko、Shintani Manabu、Owada Hitoshi、Ohkawa Yasuyuki、Pertsinidis Alexandros、Yamamoto Takashi、Kimura Hiroshi、Ochiai Hiroshi
    • Journal Title

      Nature Communications

      Volume: 13 Issue: 1 Pages: 7672-7672

    • DOI

      10.1038/s41467-022-35286-2

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Single-cell profiling of transcriptome and histone modifications with EpiDamID2022

    • Author(s)
      Rang Franka J.、de Luca Kim L.、de Vries Sandra S.、Valdes-Quezada Christian、Boele Ellen、Nguyen Phong D.、Guerreiro Isabel、Sato Yuko、Kimura Hiroshi、Bakkers Jeroen、Kind Jop
    • Journal Title

      Molecular Cell

      Volume: 82 Issue: 10 Pages: 1956-1970.e14

    • DOI

      10.1016/j.molcel.2022.03.009

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Nucleoplasmic lamin C rapidly accumulates at sites of nuclear envelope rupture with BAF and cGAS2022

    • Author(s)
      Kono Yohei、Adam Stephen A.、Sato Yuko、Reddy Karen L.、Zheng Yixian、Medalia Ohad、Goldman Robert D.、Kimura Hiroshi、Shimi Takeshi
    • Journal Title

      Journal of Cell Biology

      Volume: 221 Issue: 12

    • DOI

      10.1083/jcb.202201024

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Superfluid helium nanoscope insert with millimeter working range2022

    • Author(s)
      Kamiya Naoki、Kuramoto Kazuki、Takishima Kento、Yumoto Tatsuya、Oda Haruka、Shimi Takeshi、Kimura Hiroshi、Matsushita Michio、Fujiyoshi Satoru
    • Journal Title

      Review of Scientific Instruments

      Volume: 93 Issue: 10 Pages: 103703-103703

    • DOI

      10.1063/5.0107395

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Intra Q-body: an antibody-based fluorogenic probe for intracellular proteins that allows live cell imaging and sorting2022

    • Author(s)
      Dai Yancen、Sato Yuko、Zhu Bo、Kitaguchi Tetsuya、Kimura Hiroshi、Ghadessy Farid J.、Ueda Hiroshi
    • Journal Title

      Chemical Science

      Volume: 13 Issue: 33 Pages: 9739-9748

    • DOI

      10.1039/d2sc02355e

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Imaging transcription elongation dynamics by new technologies unveils the organization of initiation and elongation in transcription factories2022

    • Author(s)
      Kimura Hiroshi、Sato Yuko
    • Journal Title

      Current Opinion in Cell Biology

      Volume: 74 Pages: 71-79

    • DOI

      10.1016/j.ceb.2022.01.002

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Live imaging of transcription sites using an elongating RNA polymerase II-specific probe.2022

    • Author(s)
      Uchino S, Ito Y, Sato Y, Handa T, Ohkawa Y, Tokunaga M, Kimura H.
    • Journal Title

      J Cell Biol.

      Volume: 221 Issue: 2 Pages: 1-23

    • DOI

      10.1083/jcb.202104134

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq).2021

    • Author(s)
      Bartlett DA, Dileep V, Handa T, Ohkawa Y, Kimura H, Henikoff S, Gilbert DM.
    • Journal Title

      J Cell Biol.

      Volume: 220 Issue: 12

    • DOI

      10.1083/jcb.202103078

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Chromatin loading of MCM hexamers is associated with di-/tri-methylation of histone H4K20 toward S phase entry.2021

    • Author(s)
      Hayashi-Takanaka Y, Hayashi Y, Hirano Y, Miyawaki-Kuwakado A, Ohkawa Y, Obuse C, Kimura H, Haraguchi T, Hiraoka Y.
    • Journal Title

      Nucleic Acids Res.

      Volume: 49 Issue: 21 Pages: 12152-12166

    • DOI

      10.1093/nar/gkab1068

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Recent advances in single-cell epigenomics2021

    • Author(s)
      Harada Akihito、Kimura Hiroshi、Ohkawa Yasuyuki
    • Journal Title

      Current Opinion in Structural Biology

      Volume: 71 Pages: 116-122

    • DOI

      10.1016/j.sbi.2021.06.010

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Visualizing looping of two endogenous genomic loci using synthetic zinc‐finger proteins with anti‐FLAG and anti‐HA frankenbodies in living cells2021

    • Author(s)
      Liu Yang、Zhao Ning、Kanemaki Masato T.、Yamamoto Yotaro、Sadamura Yoshifusa、Ito Yuma、Tokunaga Makio、Stasevich Timothy J.、Kimura Hiroshi
    • Journal Title

      Genes to Cells

      Volume: 26 Issue: 11 Pages: 905-926

    • DOI

      10.1111/gtc.12893

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Modeling population size independent tissue epigenomes by ChIL‐seq with single thin sections2021

    • Author(s)
      Maehara Kazumitsu、Tomimatsu Kosuke、Harada Akihito、Tanaka Kaori、Sato Shoko、Fukuoka Megumi、Okada Seiji、Handa Tetsuya、Kurumizaka Hitoshi、Saitoh Noriko、Kimura Hiroshi、Ohkawa Yasuyuki
    • Journal Title

      Molecular Systems Biology

      Volume: 17 Issue: 11 Pages: 8934-8946

    • DOI

      10.15252/msb.202110323

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Multiplexed Imaging of Posttranslational Modifications of Endogenous Proteins in Live Cells2021

    • Author(s)
      Sato Yuko、Kimura Hiroshi
    • Journal Title

      Methods in Molecular Biology

      Volume: 2350 Pages: 31-41

    • DOI

      10.1007/978-1-0716-1593-5_3

    • ISBN
      9781071615928, 9781071615935
    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Live-cell imaging probes to track chromatin modification dynamics2021

    • Author(s)
      Sato Yuko、Nakao Masaru、Kimura Hiroshi
    • Journal Title

      Microscopy

      Volume: 70 Issue: 5 Pages: 415-422

    • DOI

      10.1093/jmicro/dfab030

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Dynamic Behavior of Inactive X During the Cell Cycle as Revealed by H3K27me3-Specific Intracellular Antibody2021

    • Author(s)
      Sato Yuko、Kimura Hiroshi
    • Journal Title

      Methods in Molecular Biology

      Volume: 2329 Pages: 237-247

    • DOI

      10.1007/978-1-0716-1538-6_17

    • ISBN
      9781071615379, 9781071615386
    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene2021

    • Author(s)
      Forero-Quintero Linda S.、Raymond William、Handa Tetsuya、Saxton Matthew N.、Morisaki Tatsuya、Kimura Hiroshi、Bertrand Edouard、Munsky Brian、Stasevich Timothy J.
    • Journal Title

      Nature Communications

      Volume: 12 Issue: 1 Pages: 3158-3158

    • DOI

      10.1038/s41467-021-23417-0

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A live imaging system to analyze spatiotemporal dynamics of RNA polymerase II modification in Arabidopsis thaliana2021

    • Author(s)
      M. Shibuta, T. Sakamoto, T. Yamaoka, M. Yoshikawa, S. Kasamatsu, N. Yagi, S. Fujimoto, T. Suzuki, S. Uchino, Y. Sato. H. Kimura, and S. Matsunaga
    • Journal Title

      Communications Biology

      Volume: 4 Issue: 1 Pages: 580-580

    • DOI

      10.1038/s42003-021-02106-0

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay2021

    • Author(s)
      Hiroaki Tachiwana, Mariko Dacher, Kazumitsu Maehara, Akihito Harada, Yosuke Seto, Ryohei Katayama, Yasuyuki Ohkawa, Hiroshi Kimura, Hitoshi Kurumizaka, Noriko Saitoh
    • Journal Title

      eLife

      Volume: 10

    • DOI

      10.7554/elife.66290

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] RNA polymerase II condensate formation and association with Cajal and histone locus bodies in living human cells2021

    • Author(s)
      Imada Takashi、Shimi Takeshi、Kaiho Ai、Saeki Yasushi、Kimura Hiroshi
    • Journal Title

      Genes to Cells

      Volume: - Issue: 5 Pages: 298-312

    • DOI

      10.1111/gtc.12840

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Simple Fluorogenic Cellular Assay for Histone Deacetylase Inhibitors Based on Split-Yellow Fluorescent Protein and Intrabodies2021

    • Author(s)
      Ohmuro-Matsuyama Yuki、Kitaguchi Tetsuya、Kimura Hiroshi、Ueda Hiroshi
    • Journal Title

      ACS Omega

      Volume: 6 Issue: 15 Pages: 10039-10046

    • DOI

      10.1021/acsomega.0c06281

    • NAID

      120007034011

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural basis of nucleosomal histone H4 lysine 20 methylation by SET8 methyltransferase2021

    • Author(s)
      Ho Cheng-Han、Takizawa Yoshimasa、Kobayashi Wataru、Arimura Yasuhiro、Kimura Hiroshi、Kurumizaka Hitoshi
    • Journal Title

      Life Science Alliance

      Volume: 4 Issue: 4 Pages: e202000919-e202000919

    • DOI

      10.26508/lsa.202000919

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] H4K20me1 and H3K27me3 are concurrently loaded onto the inactive X chromosome but dispensable for inducing gene silencing2021

    • Author(s)
      Tjalsma Sjoerd J D、Hori Mayako、Sato Yuko、Bousard Aurelie、Ohi Akito、Raposo Ana Claudia、Roensch Julia、Le Saux Agnes、Nogami Jumpei、Maehara Kazumitsu、Kujirai Tomoya、Handa Tetsuya、Bages‐Arnal Sandra、Ohkawa Yasuyuki、Kurumizaka Hitoshi、da Rocha Simao Teixeira、Zylicz Jan J、Kimura Hiroshi、Heard Edith
    • Journal Title

      EMBO reports

      Volume: 22 Issue: 3

    • DOI

      10.15252/embr.202051989

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Dynamics of transcription-mediated conversion from euchromatin to facultative heterochromatin at the Xist promoter by Tsix2021

    • Author(s)
      Ohhata Tatsuya、Yamazawa Kazuki、Miura-Kamio Asuka、Takahashi Saori、Sakai Satoshi、Tamura Yuka、Uchida Chiharu、Kitagawa Kyoko、Niida Hiroyuki、Hiratani Ichiro、Kobayashi Hisato、Kimura Hiroshi、Wutz Anton、Kitagawa Masatoshi
    • Journal Title

      Cell Reports

      Volume: 34 Issue: 13 Pages: 108912-108912

    • DOI

      10.1016/j.celrep.2021.108912

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Live-cell epigenome manipulation by synthetic histone acetylation catalyst system2021

    • Author(s)
      Fujiwara Yusuke、Yamanashi Yuki、Fujimura Akiko、Sato Yuko、Kujirai Tomoya、Kurumizaka Hitoshi、Kimura Hiroshi、Yamatsugu Kenzo、Kawashima Shigehiro A.、Kanai Motomu
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 118 Issue: 4

    • DOI

      10.1073/pnas.2019554118

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Genome-wide analysis of chromatin structure changes upon MyoD binding in proliferative myoblasts during the cell cycle2021

    • Author(s)
      Wu Qianmei、Fujii Takeru、Harada Akihito、Tomimatsu Kosuke、Miyawaki-Kuwakado Atsuko、Fujita Masatoshi、Maehara Kazumitsu、Ohkawa Yasuyuki
    • Journal Title

      The Journal of Biochemistry

      Volume: - Issue: 6 Pages: 653-661

    • DOI

      10.1093/jb/mvab001

    • NAID

      40022687719

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Transcription organizes euchromatin via microphase separation2021

    • Author(s)
      Hilbert Lennart、Sato Yuko、Kuznetsova Ksenia、Bianucci Tommaso、Kimura Hiroshi、Julicher Frank、Honigmann Alf、Zaburdaev Vasily、Vastenhouw Nadine L.
    • Journal Title

      Nature Communications

      Volume: 12 Issue: 1 Pages: 1360-1360

    • DOI

      10.1038/s41467-021-21589-3

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Variable immersion microscopy with a high numerical aperture2021

    • Author(s)
      Keita Ishida, Kanta Naruse, Yuta Mizouchi, Yoshihiro Ogawa, Michio Matsushita, Takeshi Shimi, Hiroshi Kimura, Satoru Fujiyoshi
    • Journal Title

      Optics Letters

      Volume: 46 Issue: 4 Pages: 856-859

    • DOI

      10.1364/ol.416006

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Visualizing transcription sites in living cells using a genetically encoded probe specific for the elongating form of RNA polymerase II2021

    • Author(s)
      Uchino Satoshi、Ito Yuma、Sato Yuko、Handa Tetsuya、Ohkawa Yasuyuki、Tokunaga Makio、Kimura Hitoshi
    • Journal Title

      bioRxiv

      Volume: - Pages: 441582-441582

    • DOI

      10.1101/2021.04.27.441582

    • Related Report
      2020 Annual Research Report
    • Open Access
  • [Journal Article] Discriminative feature of cells characterizes cell populations of interest by a small subset of genes2021

    • Author(s)
      Fujii Takeru、Maehara Kazumitsu、Fujita Masatoshi、Ohkawa Yasuyuki
    • Journal Title

      bioRxiv

      Volume: - Pages: 435089-435089

    • DOI

      10.1101/2021.03.12.435089

    • Related Report
      2020 Annual Research Report
    • Open Access
  • [Journal Article] Cohesin and condensin extrude DNA loops in a cell cycle-dependent manner2020

    • Author(s)
      Golfier Stefan、Quail Thomas、Kimura Hiroshi、Brugues Jan
    • Journal Title

      eLife

      Volume: 9

    • DOI

      10.7554/elife.53885

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence2020

    • Author(s)
      Olan Ioana、Parry Aled J.、Schoenfelder Stefan、Narita Masako、Ito Yoko、Chan Adelyne S. L.、Slater Guy St.C.、Bihary Dora、Bando Masashige、Shirahige Katsuhiko、Kimura Hiroshi、Samarajiwa Shamith A.、Fraser Peter、Narita Masashi
    • Journal Title

      Nature Communications

      Volume: 11 Issue: 1 Pages: 6049-6049

    • DOI

      10.1038/s41467-020-19878-4

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Single-molecule imaging reveals control of parental histone recycling by free histones during DNA replication2020

    • Author(s)
      Gruszka D. T.、Xie S.、Kimura H.、Yardimci H.
    • Journal Title

      Science Advances

      Volume: 6 Issue: 38

    • DOI

      10.1126/sciadv.abc0330

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Histone modification dynamics as revealed by multicolor immunofluorescence-based single-cell analysis2020

    • Author(s)
      Hayashi-Takanaka Yoko、Kina Yuto、Nakamura Fumiaki、Becking Leontine E.、Nakao Yoichi、Nagase Takahiro、Nozaki Naohito、Kimura Hiroshi
    • Journal Title

      Journal of Cell Science

      Volume: 133 Issue: 14

    • DOI

      10.1242/jcs.243444

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells2020

    • Author(s)
      Ochiai Hiroshi、Hayashi Tetsutaro、Umeda Mana、Yoshimura Mika、Harada Akihito、Shimizu Yukiko、Nakano Kenta、Saitoh Noriko、Liu Zhe、Yamamoto Takashi、Okamura Tadashi、Ohkawa Yasuyuki、Kimura Hiroshi、Nikaido Itoshi
    • Journal Title

      Science Advances

      Volume: 6 Issue: 25

    • DOI

      10.1126/sciadv.aaz6699

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genomic Profiling by ALaP-Seq Reveals Transcriptional Regulation by PML Bodies through DNMT3A Exclusion2020

    • Author(s)
      Kurihara Misuzu、Kato Kagayaki、Sanbo Chiaki、Shigenobu Shuji、Ohkawa Yasuyuki、Fuchigami Takeshi、Miyanari Yusuke
    • Journal Title

      Molecular Cell

      Volume: 78 Issue: 3 Pages: 493-505

    • DOI

      10.1016/j.molcel.2020.04.004

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Physics of chromatin dynamics at the 57th Biophysical Society of Japan meeting.2020

    • Author(s)
      Yuma Ito、Akatsuki Kimura
    • Journal Title

      Biophys Rev

      Volume: - Issue: 2 Pages: 265-266

    • DOI

      10.1007/s12551-020-00642-3

    • Related Report
      2020 Annual Research Report 2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Modeling population size independent tissue epigenomes by ChIL-seq with single-thin sections2020

    • Author(s)
      Maehara Kazumitsu、Tomimatsu Kosuke、Harada Akihito、Tanaka Kaori、Sato Shoko、Okada Seiji、Handa Tetsuya、Kurumizaka Hitoshi、Kimura Hiroshi、Ohkawa Yasuyuki
    • Journal Title

      bioRxiv

      Volume: - Pages: 423434-423434

    • DOI

      10.1101/2020.12.18.423434

    • Related Report
      2020 Annual Research Report
    • Open Access
  • [Journal Article] Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene2020

    • Author(s)
      Forero-Quintero Linda S.、Raymond William、Handa Tetsuya、Saxton Matthew、Morisaki Tatsuya、Kimura Hiroshi、Bertrand Edouard、Munsky Brian、Stasevich Timothy J.
    • Journal Title

      bioRxiv

      Volume: - Pages: 024414-024414

    • DOI

      10.1101/2020.04.03.024414

    • Related Report
      2020 Annual Research Report 2019 Annual Research Report
    • Open Access / Int'l Joint Research
  • [Journal Article] Subnuclear gene positioning through lamina association affects copper tolerance2020

    • Author(s)
      Sakamoto Yuki、Sato Mayuko、Sato Yoshikatsu、Harada Akihito、Suzuki Takamasa、Goto Chieko、Tamura Kentaro、Toyooka Kiminori、Kimura Hiroshi、Ohkawa Yasuyuki、Hara-Nishimura Ikuko、Takagi Shingo、Matsunaga Sachihiro
    • Journal Title

      Nature Communications

      Volume: 11 Issue: 1 Pages: 5914-5914

    • DOI

      10.1038/s41467-020-19621-z

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Kinase inhibition profiles as a tool to identify kinases for specific phosphorylation sites2020

    • Author(s)
      Watson Nikolaus A.、Cartwright Tyrell N.、Lawless Conor、Camara-Donoso Marcos、Sen Onur、Sako Kosuke、Hirota Toru、Kimura Hiroshi、Higgins Jonathan M. G.
    • Journal Title

      Nature Communications

      Volume: 11 Issue: 1 Pages: 1684-1684

    • DOI

      10.1038/s41467-020-15428-0

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells2020

    • Author(s)
      Higashijima Y, Matsui Y, Shimamura T, Nakaki R, Nagai N, Tsutsumi S, Abe Y, Link VM, Osaka M, Yoshida M, Watanabe R, Tanaka T, Taguchi A, Miura M, Ruan X, Li G, Inoue T, Nangaku M, Kimura H, Furukawa T, Aburatani H, Wada Y, Ruan Y, Glass CK, Kanki Y
    • Journal Title

      The EMBO Journal

      Volume: 39 Issue: 7 Pages: 1-1

    • DOI

      10.15252/embj.2019103949

    • NAID

      120006902140

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Histone modification dynamics as revealed by a multicolor immunofluorescence-based single-cell analysis2020

    • Author(s)
      Hayashi-Takanaka Yoko、Kina Yuto、Nakamura Fumiaki、Becking Leontine E.、Nakao Yoichi、Nagase Takahiro、Nozaki Naohito、Kimura Hiroshi
    • Journal Title

      bioRxiv

      Volume: - Pages: 892299-892299

    • DOI

      10.1101/2020.01.01.892299

    • Related Report
      2019 Annual Research Report
    • Open Access / Int'l Joint Research
  • [Journal Article] ヒストン修飾解析の最前線2020

    • Author(s)
      半田哲也、木村 宏
    • Journal Title

      遺伝子医学

      Volume: 10 Pages: 124-129

    • NAID

      40022142663

    • Related Report
      2019 Annual Research Report
  • [Journal Article] タンパク質1分子を翻訳過程からイメージング可能なプローブ「HA Frankenbody」2020

    • Author(s)
      趙 寧、森崎達也、小田春佳、佐藤優子、木村 宏、Stasevich Timothy J
    • Journal Title

      実験医学

      Volume: 38 Pages: 617-613

    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Journal Article] Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells2019

    • Author(s)
      Nakato R, Wada Y, Nakaki R, Nagae G, Katou Y, Tsutsumi S, Nakajima N, Fukuhara H, Iguchi A, Kohro T, Kanki Y, Saito Y, Kobayashi M, Izumi-Taguchi A, Osato N, Tatsuno K, Kamio A, Hayashi-Takanaka Y, Wada H, Ohta S, Aikawa M, Nakajima H, Nakamura M, McGee RC, Heppner KW, Kawakatsu T, Genno M, Yanase H, Kume H, et al.
    • Journal Title

      Epigenetics & Chromatin

      Volume: 12 Issue: 1 Pages: 77-77

    • DOI

      10.1186/s13072-019-0319-0

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A genetically encoded probe for imaging nascent and mature HA-tagged proteins in vivo2019

    • Author(s)
      Zhao Ning、Kamijo Kouta、Fox Philip D.、Oda Haruka、Morisaki Tatsuya、Sato Yuko、Kimura Hiroshi、Stasevich Timothy J.
    • Journal Title

      Nature Communications

      Volume: 10 Issue: 1 Pages: 2947-2947

    • DOI

      10.1038/s41467-019-10846-1

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Intrabody-based FRET probe to visualize endogenous histone acetylation2019

    • Author(s)
      Chung Chan-I、Sato Yuko、Ohmuro-Matsuyama Yuki、Machida Shinichi、Kurumizaka Hitoshi、Kimura Hiroshi、Ueda Hiroshi
    • Journal Title

      Scientific Reports

      Volume: 9 Issue: 1 Pages: 10188-10188

    • DOI

      10.1038/s41598-019-46573-2

    • NAID

      120006936925

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Incorporation and influence of Leishmania histone H3 in chromatin2019

    • Author(s)
      Dacher Mariko、Tachiwana Hiroaki、Horikoshi Naoki、Kujirai Tomoya、Taguchi Hiroyuki、Kimura Hiroshi、Kurumizaka Hitoshi
    • Journal Title

      Nucleic Acids Research

      Volume: 47 Issue: 22 Pages: 11637-11648

    • DOI

      10.1093/nar/gkz1040

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The CENP-A centromere targeting domain facilitates H4K20 monomethylation in the nucleosome by structural polymorphism.2019

    • Author(s)
      Arimura Y, Tachiwana H, Takagi H, Hori T, Kimura H, Fukagawa T, Kurumizaka H
    • Journal Title

      Nature Commun.

      Volume: 10 Issue: 1 Pages: 576-576

    • DOI

      10.1038/s41467-019-08314-x

    • Related Report
      2019 Annual Research Report 2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live cell analysis.2019

    • Author(s)
      Sato Y, Hilbert L, Oda H, Wan Y, Heddleston JM, Chew T-L, Zaburdaev V, Keller P, Lionnet T, Vastenhouw N, and Kimura H
    • Journal Title

      Development

      Volume: 146 Issue: 19

    • DOI

      10.1242/dev.179127

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Structure-based design of an H2A.Z.1 mutant stabilizing a nucleosome in vitro and in vivo2019

    • Author(s)
      Horikoshi Naoki、Kujirai Tomoya、Sato Koichi、Kimura Hiroshi、Kurumizaka Hitoshi
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 515 Issue: 4 Pages: 719-724

    • DOI

      10.1016/j.bbrc.2019.06.012

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Effect of mycalolides isolated from a marine sponge Mycale aff. nullarosette on actin in living cells2019

    • Author(s)
      Hayashi-Takanaka Yoko、Kina Yuto、Nakamura Fumiaki、Yamazaki Shota、Harata Masahiko、Soest Rob W. M. van、Kimura Hiroshi、Nakao Yoichi
    • Journal Title

      Scientific Reports

      Volume: 9 Issue: 1 Pages: 7540-7540

    • DOI

      10.1038/s41598-019-44036-2

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Chromatin-bound CRM1 recruits SET-Nup214 and NPM1c onto HOX clusters causing aberrant HOX expression in leukemia cells.2019

    • Author(s)
      Oka M, Mura S, Otani M, Miyamoto Y, Nogami J, Maehara K, Harada A, Tachibana T, Yoneda Y, Ohkawa Y
    • Journal Title

      Elife

      Volume: 8

    • DOI

      10.7554/elife.46667

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Cell competition corrects noisy Wnt morphogen gradients to achieve robust patterning in the zebrafish embryo2019

    • Author(s)
      Akieda Yuki、Ogamino Shohei、Furuie Hironobu、Ishitani Shizuka、Akiyoshi Ryutaro、Nogami Jumpei、Masuda Takamasa、Shimizu Nobuyuki、Ohkawa Yasuyuki、Ishitani Tohru
    • Journal Title

      Nature Communications

      Volume: 10 Issue: 1 Pages: 4710-4710

    • DOI

      10.1038/s41467-019-12609-4

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The Eleanor ncRNAs activate the topological domain of the ESR1 locus to balance against apoptosis.2019

    • Author(s)
      †Abdalla MOA, †Yamamoto T, Maehara K, Ohkawa Y, Miura H, Hiratani I, Nakayama H, Nakao M, *Saitoh N
    • Journal Title

      Nat Commun

      Volume: 10 Issue: 1 Pages: 3778-3778

    • DOI

      10.1038/s41467-019-11378-4

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Dmrt factors determine the positional information of cerebral cortical progenitors via differential suppression of homeobox genes.2019

    • Author(s)
      Konno D, Kishida C, Maehara K, Ohkawa Y, Kiyonari H, Okada S, Matsuzaki F
    • Journal Title

      Development

      Volume: 146 Issue: 15 Pages: 174243-174243

    • DOI

      10.1242/dev.174243

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Calcineurin Broadly Regulates the Initiation of Skeletal Muscle-Specific Gene Expression by Binding Target Promoters and Facilitating the Interaction of the SWI/SNF Chromatin Remodeling Enzyme.2019

    • Author(s)
      Witwicka H, Nogami J, Syed SA, Maehara K, Padilla-Benavides T, Ohkawa Y, Imbalzano AN
    • Journal Title

      Mol Cell Biol.

      Volume: 39 Issue: 19

    • DOI

      10.1128/mcb.00063-19

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Cohesin and condensin extrude loops in a cell-cycle dependent manner2019

    • Author(s)
      Golfier Stefan、Quail Thomas、Kimura Hiroshi、Brugues Jan
    • Journal Title

      bioRxiv

      Volume: - Pages: 821306-821306

    • DOI

      10.1101/821306

    • Related Report
      2019 Annual Research Report
    • Open Access / Int'l Joint Research
  • [Journal Article] Single-molecule imaging reveals control of parental histone recycling by free histones during DNA replication2019

    • Author(s)
      Gruszka Dominika T.、Xie Sherry、Kimura Hiroshi、Yardimci Hasan
    • Journal Title

      bioRxiv

      Volume: - Pages: 789578-789578

    • DOI

      10.1101/789578

    • Related Report
      2019 Annual Research Report
    • Open Access / Int'l Joint Research
  • [Journal Article] Transcription-driven cohesin repositioning rewires chromatin loops in cellular senescence2019

    • Author(s)
      Olan Ioana、Parry Aled J.、Schoenfelder Stefan、Narita Masako、Ito Yoko、Chan Adelyne S.L.、Slater Guy St.C.、Bihary Dora、Bando Masashige、Shirahige Katsuhiko、Kimura Hiroshi、Samarajiwa Shamith A.、Fraser Peter、Narita Masashi
    • Journal Title

      bioRxiv

      Volume: - Pages: 823831-823831

    • DOI

      10.1101/823831

    • Related Report
      2019 Annual Research Report
    • Open Access / Int'l Joint Research
  • [Journal Article] 遺伝子発現の理解と制御のための「ヌクレオーム」研究とエピゲノム編集2019

    • Author(s)
      木村 宏、佐藤優子
    • Journal Title

      JATAFFジャーナル

      Volume: 7 Pages: 3-6

    • Related Report
      2019 Annual Research Report
  • [Journal Article] クロマチン挿入標識法(ChIL)による単一細胞エピゲノム解析2019

    • Author(s)
      原田 哲仁、大川 恭行
    • Journal Title

      実験医学(増刊)

      Volume: 37 Pages: 178-183

    • Related Report
      2019 Annual Research Report
  • [Journal Article] Signs of biological activities of 28,000-year-old mammoth nuclei in mouse oocytes visualized by live-cell imaging2019

    • Author(s)
      Kazuo Yamagata, Kouhei Nagai, Hiroshi Miyamoto, ...., Tetsuya Handa (17番目), Hiroshi Kimura, Yoshihiko Hosoi, Tasuku Mitani, Kazuya Matsumoto, Akira Iritani
    • Journal Title

      Scientific Reports

      Volume: 9 巻 Issue: 1 Pages: 4050-4050

    • DOI

      10.1038/s41598-019-40546-1

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A mosaic of old and young nucleoporins2019

    • Author(s)
      Shimi Takeshi、Kimura Hiroshi
    • Journal Title

      The Journal of Cell Biology

      Volume: 218 Issue: 2 Pages: 385-386

    • DOI

      10.1083/jcb.201811170

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Heterochromatin suppresses gross chromosomal rearrangements at centromeres by repressing Tfs1/TFIIS-dependent transcription2019

    • Author(s)
      Okita Akiko K.、Zafar Faria、Su Jie、Weerasekara Dayalini、Kajitani Takuya、Takahashi Tatsuro S.、Kimura Hiroshi、Murakami Yota、Masukata Hisao、Nakagawa Takuro
    • Journal Title

      Communications Biology

      Volume: 2 Issue: 1 Pages: 17-17

    • DOI

      10.1038/s42003-018-0251-z

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Quantitative measurements of chromatin modification dynamics during zygotic genome activation2019

    • Author(s)
      Yuko Sato, Lennart Hilbert, Haruka Oda, Yinan Wan, John M. Heddleston, Teng-Leong Chew, Vasily Zaburdaev, Philipp Keller, Timothee Lionnet, Nadine Vastenhouw, Hiroshi Kimura
    • Journal Title

      bioRxiv

      Volume: 601393 Pages: 601393-601393

    • DOI

      10.1101/601393

    • Related Report
      2018 Annual Research Report
    • Open Access / Int'l Joint Research
  • [Journal Article] 生細胞内の1分子動態と相互作用の定量解析2019

    • Author(s)
      伊藤由馬、徳永万喜洋
    • Journal Title

      パリティ

      Volume: 36 Pages: 72-74

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Modeling latent flows on single-cell data using the Hodge decomposition2019

    • Author(s)
      Maehara Kazumitsu、Ohkawa Yasuyuki
    • Journal Title

      bioRxiv

      Volume: - Pages: 592089-592089

    • DOI

      10.1101/592089

    • Related Report
      2018 Annual Research Report
    • Open Access
  • [Journal Article] A chromatin integration labelling method enables epigenomic profiling with lower input2018

    • Author(s)
      Harada Akihito、Maehara Kazumitsu、Handa Tetsuya、Arimura Yasuhiro、Nogami Jumpei、Hayashi-Takanaka Yoko、Shirahige Katsuhiko、Kurumizaka Hitoshi、Kimura Hiroshi、Ohkawa Yasuyuki
    • Journal Title

      Nature Cell Biology

      Volume: 21 Issue: 2 Pages: 287-296

    • DOI

      10.1038/s41556-018-0248-3

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Visualizing the Dynamics of Inactive X Chromosomes in Living Cells Using Antibody-Based Fluorescent Probes2018

    • Author(s)
      Sato Yuko、Stasevich Timothy J.、Kimura Hiroshi
    • Journal Title

      Methods in Molecular Biology

      Volume: 1861 Pages: 91-102

    • DOI

      10.1007/978-1-4939-8766-5_8

    • ISBN
      9781493987658, 9781493987665
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] 遺伝子不活性化マークを生細胞で観察できる蛍光プローブ2018

    • Author(s)
      佐藤優子、木村宏
    • Journal Title

      化學工業

      Volume: 69 Pages: 589-594

    • Related Report
      2018 Annual Research Report
  • [Journal Article] Nucleome Consortium2018

    • Author(s)
      TASHIRO Satoshi、KIMURA Hiroshi
    • Journal Title

      Seibutsu Butsuri

      Volume: 58 Issue: 4 Pages: 221-222

    • DOI

      10.2142/biophys.58.221

    • NAID

      130007420879

    • ISSN
      0582-4052, 1347-4219
    • Related Report
      2018 Annual Research Report
    • Open Access
  • [Journal Article] A genetically encoded probe for imaging HA-tagged protein translation, localization, and dynamics in living cells and animals2018

    • Author(s)
      Zhao Ning、Kamijo Kouta、Fox Philip、Oda Haruka、Morisaki Tatsuya、Sato Yuko、Kimura Hiroshi、Stasevich Timothy J.
    • Journal Title

      bioRxiv

      Volume: - Pages: 474668-474668

    • DOI

      10.1101/474668

    • Related Report
      2018 Annual Research Report
    • Open Access / Int'l Joint Research
  • [Journal Article] Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells2018

    • Author(s)
      Higashijima Y, Matsui Y, Shimamura T, Tsutsumi S, Nakaki R, Abe Y, Link VM, Osaka M, Yoshida M, Watanabe R, Tanaka T, Taguchi A, Miura M, Inoue T, Nangaku M, Kimura H, Furukawa T, Aburatani H, Wada Y, Glass CK, Kanki Y
    • Journal Title

      bioRxiv

      Volume: - Pages: 456491-456491

    • DOI

      10.1101/456491

    • NAID

      120006902140

    • Related Report
      2018 Annual Research Report
    • Open Access / Int'l Joint Research
  • [Journal Article] CLIP-170 is essential for MTOC repositioning during T cell activation by regulating dynein localisation on the cell surface2018

    • Author(s)
      Lim Wei Ming、Ito Yuma、Sakata-Sogawa Kumiko、Tokunaga Makio
    • Journal Title

      Scientific Reports

      Volume: 8 Issue: 1 Pages: 17747-17747

    • DOI

      10.1038/s41598-018-35593-z

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 全反射照明蛍光顕微鏡 ― 対物レンズ型2018

    • Author(s)
      徳永万喜洋、伊藤由馬
    • Journal Title

      実験医学増刊

      Volume: 36 Pages: 36-37

    • Related Report
      2018 Annual Research Report
  • [Journal Article] 共焦点レーザー走査顕微鏡 iii. FRAP/FLIP2018

    • Author(s)
      木村 宏
    • Journal Title

      実験医学増刊

      Volume: 36 Pages: 50-51

    • Related Report
      2018 Annual Research Report
  • [Presentation] クロマチン修飾と転写の生細胞ダイナミクス2023

    • Author(s)
      木村 宏
    • Organizer
      第4回ゲノム生物物理学セミナー
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Dynamics of chromatin organization and transcription in early zebrafish embryos2023

    • Author(s)
      Hiroshi Kimura
    • Organizer
      RIKEN BDR Symposium 2023
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Dynamics of histone RNA polymerase II modifications in living cells2022

    • Author(s)
      Hiroshi Kimura
    • Organizer
      EMBO Workshop “Nuclear structure and dynamics”
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Dynamics of histone and RNA polymerase II modifications in living cells2022

    • Author(s)
      Hiroshi Kimura
    • Organizer
      Japan-UK Regulation through Chromatin Conference 2022
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Histone modification dynamics during transcription activation in living cells and embryos2022

    • Author(s)
      Hiroshi Kimura
    • Organizer
      Gordon Research Conference “Chromatin Structure and Function: Chromatin Modifications, RNA and Metabolism”
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Chromatin domain organization and dynamics in zebrafish embryos as revealed by live-cell imaging2022

    • Author(s)
      Hiroshi Kimura
    • Organizer
      EMBO Workshop “Awakening of the genome: The maternal-to-zygotic transition”
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 生細胞プローブを用いた不活性X染色体動態と転写制御の解析2021

    • Author(s)
      佐藤 優子, 内野 哲志, 伊藤 由馬, 前原 一満, 大川 恭行, 徳永 万喜洋, 木村 宏
    • Organizer
      第94回日本生化学会大会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] アセチル化H3K9特異的生細胞プローブの改良とin vitro可溶性評価法の確立2021

    • Author(s)
      岡 翔平, 佐藤 優子, 木村 宏
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 酵母ディスプレイ法による細胞内修飾特異的抗体の特異性改変2021

    • Author(s)
      小松原 新大, 木村 宏, 小田 春佳
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] PHIP/ICEN4 centromere function depends on CENP-B2021

    • Author(s)
      Marinela Perpelescu, 小布施 力史, 舛本 寛, 鐘巻 将人, 木村 宏
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] ショウジョウバエ幼虫の脂肪体におけるリソソーム機能の抑制は変態に重要である2021

    • Author(s)
      村川 直柔, 中村 毅, 川口 紘平, 村山 歩駿, 木村 宏, 藤田 尚信
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] ゼブラフィッシュ初期胚における核アクチンの動態と役割2021

    • Author(s)
      小田 春佳, 佐藤 優子, 藤原 侑亮, 川島 茂裕, 金井 求, 木村 宏
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 単一遺伝子イメージングを用いた転写活性と制御因子クラスタリングの時空間的な関連解明2021

    • Author(s)
      大石 裕晃, 島田 聖瑠, 内野 哲志, Li Jieru, 佐藤 優子, Alexandros Pertsinidis, 山本 卓, 木村 宏, 落合 博
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] ライブセルイメージングを用いたウシ受精卵における染色体動態の可視化2021

    • Author(s)
      肖 テイ, 小田 春佳, 八尾 竜馬, 植田 朱音, 朝香 未来, 中橋 美貴子, 木村 宏, 山縣 一夫
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] ChIL法による単一細胞マルチオミクスプロファイリング2021

    • Author(s)
      原田 哲仁, 藤井 健, 前原 一満, 田中 かおり, 木村 宏, 大川 恭行
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 転写伸長型RNAポリメラーゼII可視化プローブによる生細胞内における 転写伸長部位の観察2021

    • Author(s)
      内野 哲志, 伊藤 由馬, Jessica Dai, 佐藤 優子, 半田 哲也, 大川 恭行, 徳永 万喜洋, 木村 宏
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Tracking histone and RNA polymerase II modifications in living cells using genetically encoded probes2021

    • Author(s)
      Hiroshi Kimura
    • Organizer
      RIKEN BDR Symposium
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Gene regulation and chromatin dynamics in living cells2020

    • Author(s)
      Hiroshi Kimura
    • Organizer
      The 79th of Annual Meeting of the Japanese Cancer Association
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] 転写活性化に伴うヒストンアセチル化とクロマチンのダイナミクス2020

    • Author(s)
      木村 宏
    • Organizer
      第93回 日本生化学会大会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Roles of histone acetylation and nuclear F-actin in zebrafish embryo development2020

    • Author(s)
      Hiroshi Kimura
    • Organizer
      Chromosome Dynamics - An international symposium on chromatin and chromosome stability
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ゼブラフィッシュ胚性ゲノム活性化におけるヒストンアセチル化の役割と核内環境変化2019

    • Author(s)
      木村 宏
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Single-cell histone modification analysis: from live-cell imaging to epigenome profiling2019

    • Author(s)
      Hiroshi Kimura
    • Organizer
      Single Cell Omics Germany Workshop "Advances in single cell epigenomics 2019"
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Tracking RNA polymerase II and histone modification dynamics during the zygotic genome activation2019

    • Author(s)
      Hiroshi Kimura
    • Organizer
      第92回日本生化学会大会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Chromatin modification dynamics during the activation and inactivation of transcription2019

    • Author(s)
      Hiroshi Kimura
    • Organizer
      Gordon Research Conference "Genome Architecture in Cell Fate and Disease"
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] クロマチン挿入法による単一細胞エピゲノム解析2019

    • Author(s)
      大川 恭行
    • Organizer
      日本人類遺伝学会第64回大会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Modification-specific intracellular antibodies for monitoring histone modification in vivo2019

    • Author(s)
      Hiroshi Kimura
    • Organizer
      3rd Epigenetics and Bioengineering Conference (EpiBio 2019)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A single-molecule localization approach to quantify the interaction between transcriptional machinery and chromatin structure2019

    • Author(s)
      Yuma Ito, Makio Tokunaga
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Chromatin integration labelling Technology for expanding multi-omics2019

    • Author(s)
      Yasuyuki Ohkawa
    • Organizer
      EMBO Symposia: Multi-Omics
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 遺伝子の発現されやすさはどのように決まるのか?~クロマチンが規定する遺伝子発現制御能力~2019

    • Author(s)
      大川 恭行
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Histone H3.3 sub-variants are required for regulating skeletal muscle differentiation2019

    • Author(s)
      Yasuyuki Ohkawa
    • Organizer
      2018 Federation of American Societies for Experimental Biology (FASEB)
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Chromatin Integration Labeling- an Epigenomic Profiling for Single Cell Analysis2019

    • Author(s)
      Yasuyuki Ohkawa
    • Organizer
      Cell Symposium: Single Cells: Technology to Biology
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Chromatin modification dynamics during gene activation and inactivation in living cells2018

    • Author(s)
      Hiroshi Kimura
    • Organizer
      CSHL Meeting "Nuclear Organization & Function"
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Chromatin Modification Dynamics in Living Cells2018

    • Author(s)
      Hiroshi Kimura
    • Organizer
      Gordon Research Conference "Chromatin Structure and Function"
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Sensing Histone Modification and Transcription Dynamics in Living Cells2018

    • Author(s)
      Hiroshi Kimura
    • Organizer
      2nd Epigenetics and Bioengineering Conference
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Chromatin modification dynamics during gene activation in living cells and embryos2018

    • Author(s)
      Hiroshi Kimura
    • Organizer
      Joint Annual Meeting of JSDB 51st and JSCB 70th
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] A chromatin integration labeling method enables epigenomic profiling with lower input2018

    • Author(s)
      Tetsuya Handa, Akihito Harada, Kazumitsu Maehara, Yasuhiro Arimura, Jumpei Nogami, Yoko Hayashi-Takanaka, Katsuhiko Shirahige, Hitoshi Kurumizaka, Yasuyuki Ohkawa and Hiroshi Kimura
    • Organizer
      3R&3C Symposium
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] クロマチン修飾ダイナミクス 生細胞イメージングとエピゲノム解析の融合に向けて2018

    • Author(s)
      木村 宏
    • Organizer
      第91回日本生化学会大会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] ヒストン修飾と転写の生細胞動態から捉えるクロマチンポテンシャル2018

    • Author(s)
      木村 宏
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Chromatin integration labeling (ChIL) technology: an immunoprecipitation-free method for low-input epigenomic profiling2018

    • Author(s)
      Hiroshi Kimura
    • Organizer
      IHEC Meeting 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 蛍光1分子イメージングにおける動態解析法の開発と核内タンパク質挙動の定量解析2018

    • Author(s)
      伊藤由馬
    • Organizer
      第91回大会日本生化学会大会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 骨格筋分化・再生司るクロマチン構造制御機構の解明2018

    • Author(s)
      大川恭行
    • Organizer
      日本筋学会第4回学術集会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 免疫沈降をしない1細胞エピゲノム解析技術の開発2018

    • Author(s)
      大川恭行
    • Organizer
      第91回日本生化学会学大会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 空間トランスクリプトミクスで解明する骨格筋再生2018

    • Author(s)
      大川恭行
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 骨格筋再生におけるヒストン転換2018

    • Author(s)
      大川恭行
    • Organizer
      第7回骨格筋生物学研究会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] ChILT-an Epigenomic Profiling for Single Cell Analysis2018

    • Author(s)
      Yasuyuki Ohkawa
    • Organizer
      Gordon Research Conference"Chromatin Structure and Function"
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Book] クロマチン解析実践プロトコール2020

    • Author(s)
      大川 恭行、宮成 悠介
    • Total Pages
      270
    • Publisher
      羊土社
    • ISBN
      9784758122481
    • Related Report
      2020 Annual Research Report
  • [Remarks] 東工大 木村研究室

    • URL

      http://kimura-lab.bio.titech.ac.jp/

    • Related Report
      2022 Annual Research Report
  • [Remarks] 東工大 細胞制御工学研究センター

    • URL

      http://www.rcb.iir.titech.ac.jp/index.html

    • Related Report
      2022 Annual Research Report
  • [Remarks] 新学術領域「遺伝子制御の基盤となるクロマチンポテンシャル」

    • URL

      http://www.nibb.ac.jp/potentia/index.html

    • Related Report
      2022 Annual Research Report
  • [Remarks] リサーチマップ 木村宏

    • URL

      https://researchmap.jp/hiroshikimura

    • Related Report
      2022 Annual Research Report
  • [Remarks] ORCID Hiroshi Kimura

    • URL

      https://orcid.org/0000-0003-0854-083X

    • Related Report
      2022 Annual Research Report
  • [Remarks] 遺伝子制御の基盤となる クロマチンポテンシャル

    • URL

      http://www.nibb.ac.jp/potentia/

    • Related Report
      2021 Annual Research Report
  • [Remarks] 東京工業大学 木村研究室

    • URL

      http://kimura-lab.bio.titech.ac.jp/

    • Related Report
      2021 Annual Research Report
  • [Remarks] 東京工業大学 科学技術創成研究院 細胞制御工学研究センター

    • URL

      http://www.rcb.iir.titech.ac.jp/

    • Related Report
      2021 Annual Research Report 2018 Annual Research Report
  • [Remarks] 東京工業大学・科学技術創成研究院・細胞制御工学研究センター

    • URL

      http://www.rcb.iir.titech.ac.jp/index.html

    • Related Report
      2020 Annual Research Report
  • [Remarks] 東京工業大学・科学技術創成研究院・細胞制御工学研究センター・木村研究室

    • URL

      http://kimura-lab.bio.titech.ac.jp/

    • Related Report
      2020 Annual Research Report
  • [Remarks] 東京工業大学リサーチディボジトリ/木村宏

    • URL

      http://t2r2.star.titech.ac.jp/cgi-bin/researcherinfo.cgi?q_researcher_content_number=CTT100673940

    • Related Report
      2020 Annual Research Report
  • [Remarks] 新学術領域「クロマチン潜在能」

    • URL

      http://www.nibb.ac.jp/potentia/

    • Related Report
      2020 Annual Research Report 2018 Annual Research Report
  • [Remarks] 東工大 木村研

    • URL

      http://kimura-lab.bio.titech.ac.jp/

    • Related Report
      2019 Annual Research Report
  • [Remarks] 東工大 科学技術創成研究院 細胞制御工学研究センター

    • URL

      http://www.rcb.iir.titech.ac.jp/

    • Related Report
      2019 Annual Research Report
  • [Remarks] 東工大 T2R2 リサーチディポジトリ

    • URL

      http://t2r2.star.titech.ac.jp/cgi-bin/researcherinfo.cgi?q_researcher_content_number=CTT100673940

    • Related Report
      2019 Annual Research Report
  • [Remarks] 東京工業大学 木村宏研究室

    • URL

      http://kimura-lab.bio.titech.ac.jp/

    • Related Report
      2018 Annual Research Report
  • [Remarks] 東京工業大学 研究者情報

    • URL

      https://t2r2.star.titech.ac.jp/cgi-bin/researcherinfo.cgi?q_researcher_content_number=CTT100673940

    • Related Report
      2018 Annual Research Report

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Published: 2018-07-20   Modified: 2024-01-30  

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