Hitoshi Kurumizaka

Hitoshi Kurumizaka

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Hitoshi Kurumizaka

Publications by authors named "Hitoshi Kurumizaka"

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Nucleosome destabilization by nuclear non-coding RNAs.

Commun Biol 2020 Feb 11;3(1):60. Epub 2020 Feb 11.

Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.

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http://dx.doi.org/10.1038/s42003-020-0784-9DOI Listing
February 2020

Cryo-EM Structures of Centromeric Tri-nucleosomes Containing a Central CENP-A Nucleosome.

Structure 2020 Jan 8;28(1):44-53.e4. Epub 2019 Nov 8.

Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; Graduate School of Advanced Science & Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.str.2019.10.016DOI Listing
January 2020

Native Mass Spectrometry of Protein and DNA Complexes Prepared in Nonvolatile Buffers.

J Am Soc Mass Spectrom 2020 Jan 31. Epub 2020 Jan 31.

Graduate School of Medical Life Science , Yokohama City University , 1-7-29 Suehiro-cho, Tsurumi-ku , Yokohama , Kanagawa 230-0045 , Japan.

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http://dx.doi.org/10.1021/jasms.9b00145DOI Listing
January 2020

Structural transition of the nucleosome during chromatin remodeling and transcription.

Curr Opin Struct Biol 2019 Dec 29;59:107-114. Epub 2019 Aug 29.

Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S0959440X183021
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http://dx.doi.org/10.1016/j.sbi.2019.07.011DOI Listing
December 2019

A novel mode of DnaA-DnaA interaction promotes ADP dissociation for reactivation of replication initiation activity.

Nucleic Acids Res 2019 Dec;47(21):11209-11224

Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan.

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http://dx.doi.org/10.1093/nar/gkz795DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6868365PMC
December 2019

Incorporation and influence of Leishmania histone H3 in chromatin.

Nucleic Acids Res 2019 Dec;47(22):11637-11648

Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1093/nar/gkz1040DOI Listing
December 2019

Biochemical and structural analyses of the nucleosome containing human histone H2A.J.

J Biochem 2019 Dec 3. Epub 2019 Dec 3.

Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan.

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http://dx.doi.org/10.1093/jb/mvz109DOI Listing
December 2019

Structural Studies of Overlapping Dinucleosomes in Solution.

Biophys J 2019 Dec 18. Epub 2019 Dec 18.

Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2019.12.010DOI Listing
December 2019

Transcription through the nucleosome.

Curr Opin Struct Biol 2019 Nov 29;61:42-49. Epub 2019 Nov 29.

Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2019.10.007DOI Listing
November 2019

Structure determination of the nucleosome core particle by selenium SAD phasing.

Acta Crystallogr D Struct Biol 2019 Oct 24;75(Pt 10):930-936. Epub 2019 Sep 24.

Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino-shi, Tokyo 191-8506, Japan.

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http://dx.doi.org/10.1107/S2059798319012713DOI Listing
October 2019

Structure-based design of an H2A.Z.1 mutant stabilizing a nucleosome in vitro and in vivo.

Biochem Biophys Res Commun 2019 Aug 8;515(4):719-724. Epub 2019 Jun 8.

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan; Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2019.06.012DOI Listing
August 2019

Biochemical analysis of nucleosome targeting by Tn5 transposase.

Open Biol 2019 08 14;9(8):190116. Epub 2019 Aug 14.

Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1098/rsob.190116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6731594PMC
August 2019

Biochemical characterization of the placeholder nucleosome for DNA hypomethylation maintenance.

Biochem Biophys Rep 2019 Jul 10;18:100634. Epub 2019 Apr 10.

Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.

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http://dx.doi.org/10.1016/j.bbrep.2019.100634DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6458450PMC
July 2019

Intrabody-based FRET probe to visualize endogenous histone acetylation.

Sci Rep 2019 Jul 15;9(1):10188. Epub 2019 Jul 15.

Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan.

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http://dx.doi.org/10.1038/s41598-019-46573-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6629662PMC
July 2019

Mitotic phosphorylation of HP1α regulates its cell cycle-dependent chromatin binding.

J Biochem 2019 May;165(5):433-446

Graduate School of Natural Sciences, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Japan.

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http://dx.doi.org/10.1093/jb/mvy117DOI Listing
May 2019

Author Correction: CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language.

Nat Commun 2019 May 2;10(1):2079. Epub 2019 May 2.

CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada.

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http://dx.doi.org/10.1038/s41467-019-10161-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6497626PMC
May 2019

Structural and biochemical analyses of the nuclear pore complex component ELYS identify residues responsible for nucleosome binding.

Commun Biol 2019 3;2:163. Epub 2019 May 3.

1Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032 Japan.

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http://www.nature.com/articles/s42003-019-0385-7
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http://dx.doi.org/10.1038/s42003-019-0385-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499780PMC
May 2019

Methods for Preparing Nucleosomes Containing Histone Variants.

Methods Mol Biol 2018 ;1832:3-20

Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, 113-0032, Tokyo, Japan.

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http://dx.doi.org/10.1007/978-1-4939-8663-7_1DOI Listing
April 2019

Homologous pairing activities of Arabidopsis thaliana RAD51 and DMC1.

J Biochem 2019 Mar;165(3):289-295

Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan.

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https://academic.oup.com/jb/advance-article/doi/10.1093/jb/m
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http://dx.doi.org/10.1093/jb/mvy105DOI Listing
March 2019

A chromatin integration labelling method enables epigenomic profiling with lower input.

Nat Cell Biol 2019 02 10;21(2):287-296. Epub 2018 Dec 10.

Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.

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http://dx.doi.org/10.1038/s41556-018-0248-3DOI Listing
February 2019

The CENP-A centromere targeting domain facilitates H4K20 monomethylation in the nucleosome by structural polymorphism.

Nat Commun 2019 02 4;10(1):576. Epub 2019 Feb 4.

Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.

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http://dx.doi.org/10.1038/s41467-019-08314-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6362020PMC
February 2019

Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.

Science 2019 02 7;363(6428):744-747. Epub 2019 Feb 7.

RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

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http://dx.doi.org/10.1126/science.aav8912DOI Listing
February 2019

Author Correction: CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language.

Nat Commun 2019 02 15;10(1):883. Epub 2019 Feb 15.

CHU Sainte-Justine Research Center, Montreal, QC, H3T 1C5, Canada.

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http://dx.doi.org/10.1038/s41467-019-08800-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377600PMC
February 2019

Crystallographic analysis of the overlapping dinucleosome as a novel chromatin unit.

Biophys Physicobiol 2018 19;15:251-254. Epub 2018 Dec 19.

Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.2142/biophysico.15.0_251DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6353640PMC
December 2018

Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome.

Nucleic Acids Res 2018 11;46(19):10007-10018

Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1093/nar/gky661DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6212774PMC
November 2018

Structural basis of the nucleosome transition during RNA polymerase II passage.

Science 2018 11 4;362(6414):595-598. Epub 2018 Oct 4.

Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://www.sciencemag.org/lookup/doi/10.1126/science.aau9904
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http://dx.doi.org/10.1126/science.aau9904DOI Listing
November 2018

CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language.

Nat Commun 2018 11 5;9(1):4619. Epub 2018 Nov 5.

CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada.

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http://www.nature.com/articles/s41467-018-06014-6
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http://dx.doi.org/10.1038/s41467-018-06014-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218476PMC
November 2018

Histone H2A variants confer specific properties to nucleosomes and impact on chromatin accessibility.

Nucleic Acids Res 2018 09;46(15):7675-7685

Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.

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https://academic.oup.com/nar/article/46/15/7675/5045337
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http://dx.doi.org/10.1093/nar/gky540DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125630PMC
September 2018

MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast.

Nucleic Acids Res 2018 08;46(14):7124-7137

Molecular Modeling and Simulation Group, Department of Quantum Beam Life Science, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto 619-0215, Japan.

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http://dx.doi.org/10.1093/nar/gky502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6101533PMC
August 2018

Structural Diversity of Nucleosomes Characterized by Native Mass Spectrometry.

Anal Chem 2018 07 12;90(13):8217-8226. Epub 2018 Jun 12.

Graduate School of Medical Life Science , Yokohama City University , 1-7-29 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan.

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http://pubs.acs.org/doi/10.1021/acs.analchem.8b01649
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http://dx.doi.org/10.1021/acs.analchem.8b01649DOI Listing
July 2018

Histone Methylation by SETD1A Protects Nascent DNA through the Nucleosome Chaperone Activity of FANCD2.

Mol Cell 2018 07 21;71(1):25-41.e6. Epub 2018 Jun 21.

Genome Stability and Human Disease Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.05.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6039718PMC
July 2018

Structural polymorphism of the Escherichia coli poly-α-L-glutamate synthetase RimK.

Acta Crystallogr F Struct Biol Commun 2018 Jul 26;74(Pt 7):385-390. Epub 2018 Jun 26.

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

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http://dx.doi.org/10.1107/S2053230X18007689DOI Listing
July 2018

Structural Basis of Homology-Directed DNA Repair Mediated by RAD52.

iScience 2018 May 12;3:50-62. Epub 2018 Apr 12.

Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino-shi, Tokyo 191-8506, Japan. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S25890042183003
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http://dx.doi.org/10.1016/j.isci.2018.04.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6137706PMC
May 2018

Cryo-EM structure of the nucleosome containing the enhancer DNA sequence.

Open Biol 2018 03;8(3)

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan

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http://dx.doi.org/10.1098/rsob.170255DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5881032PMC
March 2018

Structural diversity of the nucleosome.

J Biochem 2018 Feb;163(2):85-95

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

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http://dx.doi.org/10.1093/jb/mvx081DOI Listing
February 2018

Structural Basis of Heterochromatin Formation by Human HP1.

Mol Cell 2018 02 11;69(3):385-397.e8. Epub 2018 Jan 11.

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Institute for Medical-Oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.12.011DOI Listing
February 2018

LC-MS/MS-based quantitative study of the acyl group- and site-selectivity of human sirtuins to acylated nucleosomes.

Sci Rep 2018 02 8;8(1):2656. Epub 2018 Feb 8.

Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.

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http://dx.doi.org/10.1038/s41598-018-21060-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5805777PMC
February 2018

Phosphorylation of CBX2 controls its nucleosome-binding specificity.

J Biochem 2017 Nov;162(5):343-355

Division of Chromatin Regulation, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan.

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http://dx.doi.org/10.1093/jb/mvx040DOI Listing
November 2017

Parallel mapping with site-directed hydroxyl radicals and micrococcal nuclease reveals structural features of positioned nucleosomes in vivo.

PLoS One 2017 26;12(10):e0186974. Epub 2017 Oct 26.

Department of Chemistry, Graduate School of Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, Hino, Tokyo, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0186974PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5658119PMC
November 2017

Activation of the FA pathway mediated by phosphorylation and ubiquitination.

Mutat Res 2017 10 5;803-805:89-95. Epub 2017 May 5.

Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.mrfmmm.2017.05.003DOI Listing
October 2017

SYCP3 regulates strand invasion activities of RAD51 and DMC1.

Genes Cells 2017 Sep 26;22(9):799-809. Epub 2017 Jul 26.

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.

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http://dx.doi.org/10.1111/gtc.12513DOI Listing
September 2017

Histone H3 Methylated at Arginine 17 Is Essential for Reprogramming the Paternal Genome in Zygotes.

Cell Rep 2017 Sep;20(12):2756-2765

RIKEN BioResource Center, Ibaraki 305-0074, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan; Center for Disease Biology and Integrative Medicine, Faculty of Medicine, University of Tokyo, Tokyo 113-0033, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.08.088DOI Listing
September 2017

Association of M18BP1/KNL2 with CENP-A Nucleosome Is Essential for Centromere Formation in Non-mammalian Vertebrates.

Dev Cell 2017 07;42(2):181-189.e3

Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2017.06.019DOI Listing
July 2017

Synthetic Posttranslational Modifications: Chemical Catalyst-Driven Regioselective Histone Acylation of Native Chromatin.

J Am Chem Soc 2017 06 23;139(22):7568-7576. Epub 2017 May 23.

Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

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http://dx.doi.org/10.1021/jacs.7b02138DOI Listing
June 2017

Identification of the amino acid residues responsible for stable nucleosome formation by histone H3.Y.

Nucleus 2017 05 24;8(3):239-248. Epub 2017 Jan 24.

a Laboratory of Structural Biology , Graduate School of Advanced Science and Engineering , Shinjuku-ku, Tokyo , Japan.

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http://dx.doi.org/10.1080/19491034.2016.1277303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499910PMC
May 2017

Influence of polynucleosome preparation methods on sedimentation velocity analysis of chromatin.

J Biochem 2017 Apr;161(4):381-388

Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.

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http://dx.doi.org/10.1093/jb/mvw081DOI Listing
April 2017

Structure and function of human histone H3.Y nucleosome.

Nucleic Acids Res 2017 04;45(6):3612

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

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http://dx.doi.org/10.1093/nar/gkw1219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389699PMC
April 2017

Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8.

Biochemistry 2017 04 10;56(16):2184-2196. Epub 2017 Apr 10.

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Research Institute for Science and Engineering, and Institute for Medical-oriented Structural Biology, Waseda University , 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

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http://dx.doi.org/10.1021/acs.biochem.6b01098DOI Listing
April 2017

Crystal structure of the overlapping dinucleosome composed of hexasome and octasome.

Science 2017 04;356(6334):205-208

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

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http://dx.doi.org/10.1126/science.aak9867DOI Listing
April 2017

Xeroderma pigmentosum group C protein interacts with histones: regulation by acetylated states of histone H3.

Genes Cells 2017 Mar 24;22(3):310-327. Epub 2017 Feb 24.

Division of Genomic Functions and Dynamics, Biosignal Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.

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http://dx.doi.org/10.1111/gtc.12479DOI Listing
March 2017

In vitro reconstitution and biochemical analyses of the Schizosaccharomyces pombe nucleosome.

Biochem Biophys Res Commun 2017 Jan 24;482(4):896-901. Epub 2016 Nov 24.

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Research Institute for Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2016.11.130DOI Listing
January 2017

Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis.

Cell Rep 2017 01;18(3):593-600

Center for Genetic Analysis of Biological Responses, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.12.065DOI Listing
January 2017

Polymorphism of apyrimidinic DNA structures in the nucleosome.

Sci Rep 2017 01 31;7:41783. Epub 2017 Jan 31.

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

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http://dx.doi.org/10.1038/srep41783DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5282573PMC
January 2017

FANCI-FANCD2 stabilizes the RAD51-DNA complex by binding RAD51 and protects the 5'-DNA end.

Nucleic Acids Res 2016 12 30;44(22):10758-10771. Epub 2016 Sep 30.

Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan

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http://dx.doi.org/10.1093/nar/gkw876DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5159555PMC
December 2016

A Genetically Encoded Probe for Live-Cell Imaging of H4K20 Monomethylation.

J Mol Biol 2016 10 14;428(20):3885-3902. Epub 2016 Aug 14.

Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2016.08.010DOI Listing
October 2016

Structure of the human DNA-repair protein RAD52 containing surface mutations.

Acta Crystallogr F Struct Biol Commun 2016 08 13;72(Pt 8):598-603. Epub 2016 Jul 13.

Department of Interdisciplinary Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino-shi, Tokyo 191-8506, Japan.

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http://dx.doi.org/10.1107/S2053230X1601027XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973300PMC
August 2016

Structure and function of human histone H3.Y nucleosome.

Nucleic Acids Res 2016 07 25;44(13):6127-41. Epub 2016 Mar 25.

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan Research Institute for Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan

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http://dx.doi.org/10.1093/nar/gkw202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5291245PMC
July 2016

Sequence-directed nucleosome-depletion is sufficient to activate transcription from a yeast core promoter in vivo.

Biochem Biophys Res Commun 2016 07 18;476(2):57-62. Epub 2016 May 18.

Program in Chemistry and Life Science, School of Science and Engineering, Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2016.05.063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4902108PMC
July 2016

Structural and biochemical analyses of monoubiquitinated human histones H2B and H4.

Open Biol 2016 06;6(6)

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan Research Institute for Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan

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http://dx.doi.org/10.1098/rsob.160090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4929944PMC
June 2016

Crystal structures of heterotypic nucleosomes containing histones H2A.Z and H2A.

Open Biol 2016 06;6(6)

Research Institute for Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan

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http://dx.doi.org/10.1098/rsob.160127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4929947PMC
June 2016

Chromatin architecture may dictate the target site for DMC1, but not for RAD51, during homologous pairing.

Sci Rep 2016 Apr 7;6:24228. Epub 2016 Apr 7.

Laboratory of Structural Biology, Graduate School of Advanced Science &Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

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http://dx.doi.org/10.1038/srep24228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4823753PMC
April 2016

C-terminal acidic domain of histone chaperone human NAP1 is an efficient binding assistant for histone H2A-H2B, but not H3-H4.

Genes Cells 2016 Mar 4;21(3):252-63. Epub 2016 Feb 4.

Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.

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http://dx.doi.org/10.1111/gtc.12339DOI Listing
March 2016

Two arginine residues suppress the flexibility of nucleosomal DNA in the canonical nucleosome core.

PLoS One 2015 18;10(3):e0120635. Epub 2015 Mar 18.

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0120635PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365049PMC
February 2016

Relaxed Chromatin Formation and Weak Suppression of Homologous Pairing by the Testis-Specific Linker Histone H1T.

Biochemistry 2016 Feb 22;55(4):637-46. Epub 2016 Jan 22.

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University , 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

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http://dx.doi.org/10.1021/acs.biochem.5b01126DOI Listing
February 2016

Crystal structure of the nucleosome containing ultraviolet light-induced cyclobutane pyrimidine dimer.

Biochem Biophys Res Commun 2016 Feb 2;471(1):117-22. Epub 2016 Feb 2.

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Research Institute for Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2016.01.170DOI Listing
February 2016

GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler.

Genome Biol 2016 Feb 27;17:36. Epub 2016 Feb 27.

Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.

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http://dx.doi.org/10.1186/s13059-016-0897-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4769547PMC
February 2016

Crystal structure of the nucleosome containing histone H3 with crotonylated lysine 122.

Biochem Biophys Res Commun 2016 Jan 13;469(3):483-9. Epub 2015 Dec 13.

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2015.12.041DOI Listing
January 2016

Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis.

Epigenetics Chromatin 2016 15;9. Epub 2016 Jan 15.

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan.

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http://dx.doi.org/10.1186/s13072-016-0051-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4714512PMC
January 2016

Defective FANCI binding by a fanconi anemia-related FANCD2 mutant.

PLoS One 2014 9;9(12):e114752. Epub 2014 Dec 9.

Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, Tokyo, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114752PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260917PMC
December 2015

Dynamic changes in CCAN organization through CENP-C during cell-cycle progression.

Mol Biol Cell 2015 Nov 9;26(21):3768-76. Epub 2015 Sep 9.

Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan Department of Molecular Genetics, National Institute of Genetics and Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan

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http://dx.doi.org/10.1091/mbc.E15-07-0531DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4626062PMC
November 2015

Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome.

Sci Rep 2015 Nov 17;5:16330. Epub 2015 Nov 17.

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

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http://dx.doi.org/10.1038/srep16330DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4648065PMC
November 2015

Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA.

Open Biol 2015 Oct;5(10)

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan

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http://dx.doi.org/10.1098/rsob.150128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632512PMC
October 2015

Human FAN1 promotes strand incision in 5'-flapped DNA complexed with RPA.

J Biochem 2015 Sep 27;158(3):263-70. Epub 2015 Apr 27.

Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan and

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http://dx.doi.org/10.1093/jb/mvv043DOI Listing
September 2015

hCAS/CSE1L regulates RAD51 distribution and focus formation for homologous recombinational repair.

Genes Cells 2015 Sep 30;20(9):681-94. Epub 2015 Jun 30.

Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 734-8551, Japan.

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http://dx.doi.org/10.1111/gtc.12262DOI Listing
September 2015

Structure of RizA, an L-amino-acid ligase from Bacillus subtilis.

Acta Crystallogr F Struct Biol Commun 2015 Sep 25;71(Pt 9):1125-30. Epub 2015 Aug 25.

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

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http://journals.iucr.org/f/issues/2015/09/00/hv5300/hv5300.p
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http://scripts.iucr.org/cgi-bin/paper?S2053230X15012698
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http://dx.doi.org/10.1107/S2053230X15012698DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4555917PMC
September 2015

Charge-neutralization effect of the tail regions on the histone H2A/H2B dimer structure.

Protein Sci 2015 Aug 3;24(8):1224-31. Epub 2015 Apr 3.

Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1002/pro.2673DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4534173PMC
August 2015

Cdt1-binding protein GRWD1 is a novel histone-binding protein that facilitates MCM loading through its influence on chromatin architecture.

Nucleic Acids Res 2015 Jul 18;43(12):5898-911. Epub 2015 May 18.

Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan

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http://dx.doi.org/10.1093/nar/gkv509DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499137PMC
July 2015

Stable complex formation of CENP-B with the CENP-A nucleosome.

Nucleic Acids Res 2015 May 27;43(10):4909-22. Epub 2015 Apr 27.

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan

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http://nar.oxfordjournals.org/content/43/10/4909.full.pdf
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv405
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http://dx.doi.org/10.1093/nar/gkv405DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4446444PMC
May 2015

Mass spectrometric approach for characterizing the disordered tail regions of the histone H2A/H2B dimer.

Anal Chem 2015 Feb 29;87(4):2220-7. Epub 2015 Jan 29.

Graduate School of Medical Life Science, Yokohama City University , 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1021/ac503689wDOI Listing
February 2015

Human tNASP promotes in vitro nucleosome assembly with histone H3.3.

Biochemistry 2015 Feb 30;54(5):1171-9. Epub 2015 Jan 30.

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University , 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.

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http://dx.doi.org/10.1021/bi501307gDOI Listing
February 2015

Crystal structure and stable property of the cancer-associated heterotypic nucleosome containing CENP-A and H3.3.

Sci Rep 2014 Nov 19;4:7115. Epub 2014 Nov 19.

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

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http://dx.doi.org/10.1038/srep07115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236741PMC
November 2014