Arimura Lab

Arimura Lab

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Publications

  • MagIC-Cryo-EM: Structural determination on magnetic beads for scarce macromolecules in heterogeneous samples
    Arimura Y, Konishi HA, Funabiki H
    eLife. 2024 Nov 27. doi: 10.7554/eLife.103486.1.
  • MagIC-Cryo-EM: Structural determination on magnetic beads for scarce macromolecules in heterogeneous samples
    Arimura Y, Konishi HA, Funabiki H
    bioRxiv. 2024 Sep 16;. doi: 10.1101/2024.01.21.576499. PMID: 38328033 
  • Electrostatic Ratchet for Successive Peptide Synthesis in Nonribosomal Molecular Machine RimK.
    Ohnuki J, Arimura Y, Kono T, Kino K, Kurumizaka H, Takano M.
    J Am Chem Soc. 2023 Jul 26;145(29):15963-15970. doi: 10.1021/jacs.3c03926. Epub 2023 Jul 15.
    PMID: 37452763
  • Characteristic H3 N-tail dynamics in the nucleosome core particle, nucleosome, and chromatosome.
    Furukawa A, Wakamori M, Arimura Y, Ohtomo H, Tsunaka Y, Kurumizaka H, Umehara T, Nishimura Y.
    iScience. 2022 Feb 17;25(3):103937. doi: 10.1016/j.isci.2022.103937. eCollection 2022 Mar 18.
    PMID: 35265811
  • Structural Mechanics of the Alpha-2-Macroglobulin Transformation.
    Arimura Y, Funabiki H.
    J Mol Biol. 2022 Mar 15;434(5):167413. doi: 10.1016/j.jmb.2021.167413. Epub 2021 Dec 20.
    PMID: 34942166 
  • Structural features of nucleosomes in interphase and metaphase chromosomes.
    Arimura Y, Shih RM, Froom R, Funabiki H.
    Mol Cell. 2021 Nov 4;81(21):4377-4397.e12. doi: 10.1016/j.molcel.2021.08.010. Epub 2021 Sep 2.
    PMID: 34478647
  • The N-terminal Tails of Histones H2A and H2B Adopt Two Distinct Conformations in the Nucleosome with Contact and Reduced Contact to DNA.
    Ohtomo H, Kurita JI, Sakuraba S, Li Z, Arimura Y, Wakamori M, Tsunaka Y, Umehara T, Kurumizaka H, Kono H, Nishimura Y.
    J Mol Biol. 2021 Jul 23;433(15):167110. doi: 10.1016/j.jmb.2021.167110. Epub 2021 Jun 18.
    PMID: 34153285
  • Histone variant H2A.B-H2B dimers are spontaneously exchanged with canonical H2A-H2B in the nucleosome.
    Hirano R, Arimura Y, Kujirai T, Shibata M, Okuda A, Morishima K, Inoue R, Sugiyama M, Kurumizaka H.
    Commun Biol. 2021 Feb 12;4(1):191. doi: 10.1038/s42003-021-01707-z.
    PMID: 33580188 
  • Structural basis of nucleosomal histone H4 lysine 20 methylation by SET8 methyltransferase.
    Ho CH, Takizawa Y, Kobayashi W, Arimura Y, Kimura H, Kurumizaka H.
    Life Sci Alliance. 2021 Feb 11;4(4):e202000919. doi: 10.26508/lsa.202000919. Print 2021 Apr.
    PMID: 33574035
  • Cryo-EM structure of the CENP-A nucleosome in complex with phosphorylated CENP-C.
    Ariyoshi M, Makino F, Watanabe R, Nakagawa R, Kato T, Namba K, Arimura Y, Fujita R, Kurumizaka H, Okumura EI, Hara M, Fukagawa T.
    EMBO J. 2021 Mar 1;40(5):e105671. doi: 10.15252/embj.2020105671. Epub 2021 Jan 19.
    PMID: 33463726
  • Essentiality of CENP-A Depends on Its Binding Mode to HJURP.
    Hori T, Cao J, Nishimura K, Ariyoshi M, Arimura Y, Kurumizaka H, Fukagawa T.
    Cell Rep. 2020 Nov 17;33(7):108388. doi: 10.1016/j.celrep.2020.108388.
    PMID: 33207191
  • Acetylated histone H4 tail enhances histone H3 tail acetylation by altering their mutual dynamics in the nucleosome.
    Furukawa A, Wakamori M, Arimura Y, Ohtomo H, Tsunaka Y, Kurumizaka H, Umehara T, Nishimura Y.
    Proc Natl Acad Sci U S A. 2020 Aug 18;117(33):19661-19663. doi: 10.1073/pnas.2010506117. Epub 2020 Aug 3.
    PMID: 32747537
  • Linker DNA and histone contributions in nucleosome binding by p53.
    Nishimura M, Arimura Y, Nozawa K, Kurumizaka H.
    J Biochem. 2020 Dec 26;168(6):669-675. doi: 10.1093/jb/mvaa081.
    PMID: 32702132
  • The N-terminal and C-terminal halves of histone H2A.Z independently function in nucleosome positioning and stability.
    Sato S, Tanaka N, Arimura Y, Kujirai T, Kurumizaka H.
    Genes Cells. 2020 Aug;25(8):538-546. doi: 10.1111/gtc.12791. Epub 2020 Jul 22.
    PMID: 32500630
  • Crystal structure of α-glucosyl transfer enzyme XgtA from Xanthomonas campestris WU-9701.
    Watanabe R, Arimura Y, Ishii Y, Kirimura K.
    Biochem Biophys Res Commun. 2020 Jun 4;526(3):580-585. doi: 10.1016/j.bbrc.2020.03.109. Epub 2020 Apr 1.
    PMID: 32247611
  • Nucleosome destabilization by nuclear non-coding RNAs.
    Fujita R, Yamamoto T, Arimura Y, Fujiwara S, Tachiwana H, Ichikawa Y, Sakata Y, Yang L, Maruyama R, Hamada M, Nakao M, Saitoh N, Kurumizaka H.
    Commun Biol. 2020 Feb 11;3(1):60. doi: 10.1038/s42003-020-0784-9.
    PMID: 32047236
  • Cryo-EM Structures of Centromeric Tri-nucleosomes Containing a Central CENP-A Nucleosome.
    Takizawa Y, Ho CH, Tachiwana H, Matsunami H, Kobayashi W, Suzuki M, Arimura Y, Hori T, Fukagawa T, Ohi MD, Wolf M, Kurumizaka H.
    Structure. 2020 Jan 7;28(1):44-53.e4. doi: 10.1016/j.str.2019.10.016. Epub 2019 Nov 8.
    PMID: 31711756
  • Biochemical analysis of nucleosome targeting by Tn5 transposase.
    Sato S, Arimura Y, Kujirai T, Harada A, Maehara K, Nogami J, Ohkawa Y, Kurumizaka H.
    Open Biol. 2019 Aug 30;9(8):190116. doi: 10.1098/rsob.190116. Epub 2019 Aug 14.
    PMID: 31409230
  • The CENP-A centromere targeting domain facilitates H4K20 monomethylation in the nucleosome by structural polymorphism.
    Arimura Y, Tachiwana H, Takagi H, Hori T, Kimura H, Fukagawa T, Kurumizaka H.
    Nat Commun. 2019 Feb 4;10(1):576. doi: 10.1038/s41467-019-08314-x.
    PMID: 30718488
  • A chromatin integration labelling method enables epigenomic profiling with lower input.
    Harada A, Maehara K, Handa T, Arimura Y, Nogami J, Hayashi-Takanaka Y, Shirahige K, Kurumizaka H, Kimura H, Ohkawa Y.
    Nat Cell Biol. 2019 Feb;21(2):287-296. doi: 10.1038/s41556-018-0248-3. Epub 2018 Dec 10.
    PMID: 30532068
  • Methods for Preparing Nucleosomes Containing Histone Variants.
    Kujirai T, Arimura Y, Fujita R, Horikoshi N, Machida S, Kurumizaka H.
    Methods Mol Biol. 2018;1832:3-20. doi: 10.1007/978-1-4939-8663-7_1.
    PMID: 30073519
  • Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome.
    Arimura Y, Ikura M, Fujita R, Noda M, Kobayashi W, Horikoshi N, Sun J, Shi L, Kusakabe M, Harata M, Ohkawa Y, Tashiro S, Kimura H, Ikura T, Kurumizaka H.
    Nucleic Acids Res. 2018 Nov 2;46(19):10007-10018. doi: 10.1093/nar/gky661.
    PMID: 30053102
  • Structural polymorphism of the Escherichia coli poly-α-L-glutamate synthetase RimK.
    Arimura Y, Kono T, Kino K, Kurumizaka H.
    Acta Crystallogr F Struct Biol Commun. 2018 Jul 1;74(Pt 7):385-390. doi: 10.1107/S2053230X18007689. Epub 2018 Jun 26.
    PMID: 29969101
  • Association of M18BP1/KNL2 with CENP-A Nucleosome Is Essential for Centromere Formation in Non-mammalian Vertebrates.
    Hori T, Shang WH, Hara M, Ariyoshi M, Arimura Y, Fujita R, Kurumizaka H, Fukagawa T.
    Dev Cell. 2017 Jul 24;42(2):181-189.e3. doi: 10.1016/j.devcel.2017.06.019.
    PMID: 28743004
  • Synthetic Posttranslational Modifications: Chemical Catalyst-Driven Regioselective Histone Acylation of Native Chromatin.
    Amamoto Y, Aoi Y, Nagashima N, Suto H, Yoshidome D, Arimura Y, Osakabe A, Kato D, Kurumizaka H, Kawashima SA, Yamatsugu K, Kanai M.
    J Am Chem Soc. 2017 Jun 7;139(22):7568-7576. doi: 10.1021/jacs.7b02138. Epub 2017 May 23.
    PMID: 28534629
  • Crystal structure of the overlapping dinucleosome composed of hexasome and octasome.
    Kato D, Osakabe A, Arimura Y, Mizukami Y, Horikoshi N, Saikusa K, Akashi S, Nishimura Y, Park SY, Nogami J, Maehara K, Ohkawa Y, Matsumoto A, Kono H, Inoue R, Sugiyama M, Kurumizaka H.
    Science. 2017 Apr 14;356(6334):205-208. doi: 10.1126/science.aak9867.
    PMID: 28408607
  • Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8.
    Taguchi H, Xie Y, Horikoshi N, Maehara K, Harada A, Nogami J, Sato K, Arimura Y, Osakabe A, Kujirai T, Iwasaki T, Semba Y, Tachibana T, Kimura H, Ohkawa Y, Kurumizaka H.
    Biochemistry. 2017 Apr 25;56(16):2184-2196. doi: 10.1021/acs.biochem.6b01098. Epub 2017 Apr 10.
    PMID: 28374988
  • Polymorphism of apyrimidinic DNA structures in the nucleosome.
    Osakabe A, Arimura Y, Matsumoto S, Horikoshi N, Sugasawa K, Kurumizaka H.
    Sci Rep. 2017 Jan 31;7:41783. doi: 10.1038/srep41783.
    PMID: 28139742
  • Crystal structures of heterotypic nucleosomes containing histones H2A.Z and H2A.
    Horikoshi N, Arimura Y, Taguchi H, Kurumizaka H.
    Open Biol. 2016 Jun;6(6):160127. doi: 10.1098/rsob.160127.
    PMID: 27358293
  • Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA.
    Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y, Kurumizaka H.
    Open Biol. 2015 Oct;5(10):150128. doi: 10.1098/rsob.150128.
    PMID: 26446621
  • Stable complex formation of CENP-B with the CENP-A nucleosome.
    Fujita R, Otake K, Arimura Y, Horikoshi N, Miya Y, Shiga T, Osakabe A, Tachiwana H, Ohzeki J, Larionov V, Masumoto H, Kurumizaka H.
    Nucleic Acids Res. 2015 May 26;43(10):4909-22. doi: 10.1093/nar/gkv405. Epub 2015 Apr 27.
    PMID: 25916850
  • Two arginine residues suppress the flexibility of nucleosomal DNA in the canonical nucleosome core.
    Kono H, Shirayama K, Arimura Y, Tachiwana H, Kurumizaka H.
    PLoS One. 2015 Mar 18;10(3):e0120635. doi: 10.1371/journal.pone.0120635. eCollection 2015.
    PMID: 25786215
  • Crystal structure and stable property of the cancer-associated heterotypic nucleosome containing CENP-A and H3.3.
    Arimura Y, Shirayama K, Horikoshi N, Fujita R, Taguchi H, Kagawa W, Fukagawa T, Almouzni G, Kurumizaka H.
    Sci Rep. 2014 Nov 19;4:7115. doi: 10.1038/srep07115.
    PMID: 25408271
  • A method for evaluating nucleosome stability with a protein-binding fluorescent dye.
    Taguchi H, Horikoshi N, Arimura Y, Kurumizaka H.
    Methods. 2014 Dec;70(2-3):119-26. doi: 10.1016/j.ymeth.2014.08.019. Epub 2014 Sep 8.
    PMID: 25220913
  • Distinct features of the histone core structure in nucleosomes containing the histone H2A.B variant.
    Sugiyama M, Arimura Y, Shirayama K, Fujita R, Oba Y, Sato N, Inoue R, Oda T, Sato M, Heenan RK, Kurumizaka H.
    Biophys J. 2014 May 20;106(10):2206-13. doi: 10.1016/j.bpj.2014.04.007.
    PMID: 24853749
  • Structural basis of a nucleosome containing histone H2A.B/H2A.Bbd that transiently associates with reorganized chromatin.
    Arimura Y, Kimura H, Oda T, Sato K, Osakabe A, Tachiwana H, Sato Y, Kinugasa Y, Ikura T, Sugiyama M, Sato M, Kurumizaka H.
    Sci Rep. 2013 Dec 16;3:3510. doi: 10.1038/srep03510.
    PMID: 24336483
  • Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2.
    Horikoshi N, Sato K, Shimada K, Arimura Y, Osakabe A, Tachiwana H, Hayashi-Takanaka Y, Iwasaki W, Kagawa W, Harata M, Kimura H, Kurumizaka H.
    Acta Crystallogr D Biol Crystallogr. 2013 Dec;69(Pt 12):2431-9. doi: 10.1107/S090744491302252X. Epub 2013 Nov 19.
    PMID: 24311584
  • L-amino acid ligase from Pseudomonas syringae producing tabtoxin can be used for enzymatic synthesis of various functional peptides.
    Arai T, Arimura Y, Ishikura S, Kino K.
    Appl Environ Microbiol. 2013 Aug;79(16):5023-9. doi: 10.1128/AEM.01003-13. Epub 2013 Jun 14.
    PMID: 23770908
  • Structural analysis of the hexasome, lacking one histone H2A/H2B dimer from the conventional nucleosome.
    Arimura Y, Tachiwana H, Oda T, Sato M, Kurumizaka H.
    Biochemistry. 2012 Apr 17;51(15):3302-9. doi: 10.1021/bi300129b. Epub 2012 Apr 2.
    PMID: 22448809
  • Poly-alpha-glutamic acid synthesis using a novel catalytic activity of RimK from Escherichia coli K-12.
    Kino K, Arai T, Arimura Y.
    Appl Environ Microbiol. 2011 Mar;77(6):2019-25. doi: 10.1128/AEM.02043-10. Epub 2011 Jan 28.
    PMID: 21278279
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