Hitoshi Kurumizaka

Summary

Affiliation: Waseda University
Country: Japan

Publications

  1. pmc Biochemical analysis of the N-terminal domain of human RAD54B
    Naoyuki Sarai
    Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Nucleic Acids Res 36:5441-50. 2008
  2. pmc Stimulation of Dmc1-mediated DNA strand exchange by the human Rad54B protein
    Naoyuki Sarai
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Nucleic Acids Res 34:4429-37. 2006
  3. doi request reprint Current progress on structural studies of nucleosomes containing histone H3 variants
    Hitoshi Kurumizaka
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Curr Opin Struct Biol 23:109-15. 2013
  4. doi request reprint Human tNASP promotes in vitro nucleosome assembly with histone H3.3
    Daiki Kato
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo, 162 8480, Japan
    Biochemistry 54:1171-9. 2015
  5. ncbi request reprint Structural basis for octameric ring formation and DNA interaction of the human homologous-pairing protein Dmc1
    Takashi Kinebuchi
    Protein Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Mol Cell 14:363-74. 2004
  6. pmc Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein
    Norie Fujikawa
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Nucleic Acids Res 32:82-92. 2004
  7. pmc Histone chaperone activity of Fanconi anemia proteins, FANCD2 and FANCI, is required for DNA crosslink repair
    Koichi Sato
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
    EMBO J 31:3524-36. 2012
  8. ncbi request reprint Human centromere protein B induces translational positioning of nucleosomes on alpha-satellite sequences
    Yoshinori Tanaka
    Protein Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 280:41609-18. 2005
  9. ncbi request reprint Stimulation of DNA strand exchange by the human TBPIP/Hop2-Mnd1 complex
    Rima Enomoto
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 281:5575-81. 2006
  10. pmc Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2
    Naoki Horikoshi
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Acta Crystallogr D Biol Crystallogr 69:2431-9. 2013

Collaborators

Detail Information

Publications82

  1. pmc Biochemical analysis of the N-terminal domain of human RAD54B
    Naoyuki Sarai
    Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Nucleic Acids Res 36:5441-50. 2008
    ..Thus, RAD54B binding may affect the quaternary structure of DMC1. These observations suggest that the N-terminal domain of RAD54B plays multiple roles of in homologous recombination...
  2. pmc Stimulation of Dmc1-mediated DNA strand exchange by the human Rad54B protein
    Naoyuki Sarai
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Nucleic Acids Res 34:4429-37. 2006
    ..Therefore, Rad54B may stimulate the Dmc1-mediated DNA strand exchange by stabilizing the nucleoprotein filament, which is formed on the ssDNA tails produced at DSB sites during homologous recombination...
  3. doi request reprint Current progress on structural studies of nucleosomes containing histone H3 variants
    Hitoshi Kurumizaka
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Curr Opin Struct Biol 23:109-15. 2013
    ..In this review, we survey the current progress in the studies of nucleosomes containing H3 variants, and discuss their implications for the architecture and dynamics of chromatin domains...
  4. doi request reprint Human tNASP promotes in vitro nucleosome assembly with histone H3.3
    Daiki Kato
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo, 162 8480, Japan
    Biochemistry 54:1171-9. 2015
    ..1-H4 complex. These results provide evidence that tNASP is ubiquitously produced in various types of human tissues and promotes in vitro nucleosome assembly with H3 variant specificity. ..
  5. ncbi request reprint Structural basis for octameric ring formation and DNA interaction of the human homologous-pairing protein Dmc1
    Takashi Kinebuchi
    Protein Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Mol Cell 14:363-74. 2004
    ..The inner patch binds both single-stranded and double-stranded DNAs, while the outer one binds single-stranded DNA. Based on these results, we propose a model for the interaction of the Dmc1 rings with DNA...
  6. pmc Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein
    Norie Fujikawa
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Nucleic Acids Res 32:82-92. 2004
    ..This electron density, which may be due to a water molecule or a metal ion, can exist in the hemimethylated state, but not in the fully methylated state, because of steric clash with the additional methyl group...
  7. pmc Histone chaperone activity of Fanconi anemia proteins, FANCD2 and FANCI, is required for DNA crosslink repair
    Koichi Sato
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
    EMBO J 31:3524-36. 2012
    ..Although FANCI by itself lacked nucleosome-assembly activity, it significantly stimulated FANCD2-mediated nucleosome assembly. These observations suggest that FANCD2-FANCI may regulate chromatin dynamics during DNA repair...
  8. ncbi request reprint Human centromere protein B induces translational positioning of nucleosomes on alpha-satellite sequences
    Yoshinori Tanaka
    Protein Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 280:41609-18. 2005
    ..Therefore, CENP-B may be a determinant for translational positioning of the centromere-specific nucleosomes through its binding to the nucleosomal CENP-B box...
  9. ncbi request reprint Stimulation of DNA strand exchange by the human TBPIP/Hop2-Mnd1 complex
    Rima Enomoto
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 281:5575-81. 2006
    ..Therefore, the human TBPIP/Hop2-Mnd1 complex may ensure proper pairing between homologous chromosomes through its stimulation of strand exchange during meiosis...
  10. pmc Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2
    Naoki Horikoshi
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Acta Crystallogr D Biol Crystallogr 69:2431-9. 2013
    ..Z.1 and H2A.Z.2. These findings provide important new information for understanding the differences in the regulation and functions of H2A.Z.1 and H2A.Z.2 in cells. ..
  11. pmc Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T
    Hiroaki Tachiwana
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku ku, Tokyo 162 8480, Japan
    Proc Natl Acad Sci U S A 107:10454-9. 2010
    ..These physical and structural properties of the H3T-containing nucleosome may provide the basis of chromatin reorganization during spermatogenesis...
  12. doi request reprint Crystal structure of the human centromeric nucleosome containing CENP-A
    Hiroaki Tachiwana
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Nature 476:232-5. 2011
    ..The structure provides the first atomic-resolution picture of the centromere-specific nucleosome...
  13. pmc Preferential binding to branched DNA strands and strand-annealing activity of the human Rad51B, Rad51C, Rad51D and Xrcc2 protein complex
    Hiroshi Yokoyama
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Nucleic Acids Res 32:2556-65. 2004
    ..2 kb in length) and its complementary circular ssDNA. These properties of the BCDX2 complex may be important for its roles in the maintenance of chromosomal integrity...
  14. ncbi request reprint Mutational analyses of the human Rad51-Tyr315 residue, a site for phosphorylation in leukaemia cells
    Yoshimasa Takizawa
    Graduate School of Integrated Science, Yokohama City University, 1 7 29 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Genes Cells 9:781-90. 2004
    ..Therefore, the Rad51-Tyr315 residue plays important roles in ssDNA binding and filament formation...
  15. pmc Identification of a second DNA binding site in the human Rad52 protein
    Wataru Kagawa
    RIKEN Systems and Structural Biology Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama, Japan
    J Biol Chem 283:24264-73. 2008
    ..Our findings suggest that Rad52 aligns two recombining DNA molecules within the first and second DNA binding sites to stimulate the homology search and strand invasion processes...
  16. ncbi request reprint Roles of the human Rad51 L1 and L2 loops in DNA binding
    Yusuke Matsuo
    Graduate School of Science and Engineering, Waseda University, Tokyo, Japan
    FEBS J 273:3148-59. 2006
    ..However, the fluorescence intensity of the tryptophan replacing the Rad51-Phe279 residue was strongly reduced upon DNA binding, indicating that the L2 loop is also close to the DNA-binding site...
  17. doi request reprint Purification of the human SMN-GEMIN2 complex and assessment of its stimulation of RAD51-mediated DNA recombination reactions
    Motoki Takaku
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Biochemistry 50:6797-805. 2011
    ..These results provide the first evidence that the SMN-GEMIN2 complex plays a role in homologous recombination, in addition to spliceosomal snRNP assembly...
  18. doi request reprint Biochemical analysis of the human DMC1-I37N polymorphism
    Juri Hikiba
    Laboratory of Structural Biology, Waseda University, Tokyo, Japan
    FEBS J 276:457-65. 2009
    ..These biochemical differences between the DMC1 and DMC1-I37N proteins suggest that the DMC1-I37N polymorphism may be a source of improper meiotic recombination, causing meiotic defects in humans...
  19. ncbi request reprint Role of the N-terminal domain of the human DMC1 protein in octamer formation and DNA binding
    Takashi Kinebuchi
    Protein Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    J Biol Chem 280:28382-7. 2005
    ..Therefore, the N-terminal domain of DMC1 is required for the formation of the octamer, which may support the proper DNA binding activity of the DMC1 protein...
  20. pmc Structural basis of replication origin recognition by the DnaA protein
    Norie Fujikawa
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Nucleic Acids Res 31:2077-86. 2003
    ..These base-specific interactions explain how DnaA exhibits higher affinity for the strong DnaA boxes (R1, R2 and R4) than the weak DnaA boxes (R3 and M) in the replication origin...
  21. doi request reprint From meiosis to postmeiotic events: uncovering the molecular roles of the meiosis-specific recombinase Dmc1
    Wataru Kagawa
    Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku ku, Tokyo, Japan
    FEBS J 277:590-8. 2010
    ..Recent structural, biochemical, and genetic findings are now revealing the molecular mechanisms of Dmc1-mediated homologous recombination and its regulation by various recombination mediators...
  22. doi request reprint Comprehensive structural analysis of mutant nucleosomes containing lysine to glutamine (KQ) substitutions in the H3 and H4 histone-fold domains
    Wakana Iwasaki
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku ku, Tokyo 162 8480, Japan
    Biochemistry 50:7822-32. 2011
    ..These results provide an important structural basis for understanding how histone modifications and mutations affect chromatin structure and function...
  23. pmc Nucleosome formation activity of human somatic nuclear autoantigenic sperm protein (sNASP)
    Akihisa Osakabe
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku ku, Tokyo 162 8480, Japan
    J Biol Chem 285:11913-21. 2010
    ..These experiments are the first demonstration that human NASP directly promotes nucleosome assembly and provide compelling evidence that sNASP is a bona fide histone chaperone for H3.H4...
  24. pmc Nap1 regulates proper CENP-B binding to nucleosomes
    Hiroaki Tachiwana
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Nucleic Acids Res 41:2869-80. 2013
    ..We therefore propose a novel mechanism of CENP-B regulation by Nap1...
  25. pmc Stable complex formation of CENP-B with the CENP-A nucleosome
    Risa Fujita
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Nucleic Acids Res 43:4909-22. 2015
    ..Our in vivo assay also revealed that CENP-B binding in the vicinity of the CENP-A nucleosome substantially stabilizes the CENP-A nucleosome on alphoid DNA in human cells. ..
  26. ncbi request reprint Positive role of the mammalian TBPIP/HOP2 protein in DMC1-mediated homologous pairing
    Rima Enomoto
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 279:35263-72. 2004
    ..Therefore, these results suggest that TBPIP/HOP2 directly binds to DNA and functions as an activator for DMC1 during the homologous pairing step in meiosis...
  27. doi request reprint Structures of human nucleosomes containing major histone H3 variants
    Hiroaki Tachiwana
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 162 8480, Japan
    Acta Crystallogr D Biol Crystallogr 67:578-83. 2011
    ..1 nucleosome. Since the amino-acid residues specific for H3.2 and H3.3 are located on the accessible surface of the H3/H4 tetramer, they may be potential interaction sites for H3.2- and H3.3-specific chaperones...
  28. doi request reprint Vertebrate Spt2 is a novel nucleolar histone chaperone that assists in ribosomal DNA transcription
    Akihisa Osakabe
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    J Cell Sci 126:1323-32. 2013
    ..Based on these results, we conclude that vertebrate Spt2 is a novel histone chaperone with a separate DNA-binding domain that facilitates ribosomal DNA transcription through chromatin remodeling during transcription...
  29. doi request reprint Holliday junction-binding activity of human SPF45
    Naoki Horikoshi
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Genes Cells 15:373-83. 2010
    ..These biochemical results support the idea that human SPF45 functions in DNA repair by homologous recombination...
  30. pmc Recombination activator function of the novel RAD51- and RAD51B-binding protein, human EVL
    Motoki Takaku
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, and Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    J Biol Chem 284:14326-36. 2009
    ..These results suggest that the EVL protein is a novel recombination factor that may be required for repairing specific DNA lesions, and that may cause tumor malignancy by its inappropriate expression...
  31. pmc Single-stranded DNA catenation mediated by human EVL and a type I topoisomerase
    Motoki Takaku
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Nucleic Acids Res 38:7579-86. 2010
    ....
  32. doi request reprint Biochemical analysis of the human EVL domains in homologous recombination
    Motoki Takaku
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
    FEBS J 276:5841-8. 2009
    ..Structured digital abstract: * MINT-7239394: EVL (uniprotkb:Q9UI08) binds (MI:0407) to RAD51 (uniprotkb:Q06609) by pull down (MI:0096)...
  33. ncbi request reprint Crystal structure of the human centromere protein B (CENP-B) dimerization domain at 1.65-A resolution
    Maki S Tawaramoto
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 278:51454-61. 2003
    ..This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation...
  34. pmc The centromeric nucleosome-like CENP-T-W-S-X complex induces positive supercoils into DNA
    Kozo Takeuchi
    Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411 8540, Japan, The Graduate University for Advanced Studies Sokendai, Mishima, Shizuoka 411 8540, Japan, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812 8581, Japan, JST, PRESTO, Fukuoka 812 8582, Japan and Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku ku, Tokyo 162 8480, Japan
    Nucleic Acids Res 42:1644-55. 2014
    ..In summary, our work reveals the structural features and properties of the CENP-T-W-S-X complex for its localization to centromeres...
  35. ncbi request reprint Holliday junction binding activity of the human Rad51B protein
    Hiroshi Yokoyama
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 278:2767-72. 2003
    ..Therefore, the Rad51B protein may have a specific function in Holliday junction processing in the homologous recombinational repair pathway in humans...
  36. ncbi request reprint Comparison between the CENP-A and histone H3 structures in nucleosomes
    Hiroaki Tachiwana
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
    Nucleus 3:6-11. 2012
    ..In this Extra View article, we provide a detailed structural comparison between CENP-A and H3 in nucleosomes and describe their distinctions and similarities...
  37. doi request reprint The putative nuclear localization signal of the human RAD52 protein is a potential sumoylation site
    Kengo Saito
    Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    J Biochem 147:833-42. 2010
    ..These results suggest the possibility of sumoylation playing an important role in the nuclear transport of RAD52...
  38. pmc Human PSF concentrates DNA and stimulates duplex capture in DMC1-mediated homologous pairing
    Yuichi Morozumi
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Nucleic Acids Res 40:3031-41. 2012
    ..These results suggested that PSF may function as an activator for the meiosis-specific recombinase DMC1 in higher eukaryotes...
  39. ncbi request reprint [Structural and biochemical aspects of homologous genetic (DNA) recombination]
    Hitoshi Kurumizaka
    Graduate School of Science and Engineering, Waseda University, 2 2 Wakamatsu, Shinjuku ku, Tokyo 162 8480, Japan
    Seikagaku 80:511-20. 2008
  40. doi request reprint Structural analysis of the hexasome, lacking one histone H2A/H2B dimer from the conventional nucleosome
    Yasuhiro Arimura
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Biochemistry 51:3302-9. 2012
    ..Our studies suggest that octasomes can be converted into hexasomes by the eviction of one of the H2A/H2B dimers, and the release of about 40 base-pairs of DNA, without involving large structural changes in the nucleosome core particle...
  41. pmc GEMIN2 promotes accumulation of RAD51 at double-strand breaks in homologous recombination
    Yoshimasa Takizawa
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
    Nucleic Acids Res 38:5059-74. 2010
    ..These observations and our biochemical analyses reveal that GEMIN2 regulates HR as a novel RAD51 mediator...
  42. ncbi request reprint Crystal structure of the homologous-pairing domain from the human Rad52 recombinase in the undecameric form
    Wataru Kagawa
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama, Japan
    Mol Cell 10:359-71. 2002
    ..A mutational analysis revealed that the amino acid residues located between the beta-beta-beta-alpha fold and the characteristic hairpin loop are essential for ssDNA and dsDNA binding...
  43. ncbi request reprint In vivo and in vitro footprinting of nucleosomes and transcriptional activators using an infrared-fluorescence DNA sequencer
    Nobuyuki Morohashi
    Department of Chemistry, Graduate School of Science and Engineering, Meisei University, Hino, Tokyo, Japan
    Biol Pharm Bull 31:187-92. 2008
    ..Thus, the footprinting procedure established in this study will be useful to researchers studying DNA-protein interactions and chromatin structure in vivo and in vitro...
  44. pmc Homologous pairing activities of two rice RAD51 proteins, RAD51A1 and RAD51A2
    Yuichi Morozumi
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku, Tokyo, Japan
    PLoS ONE 8:e75451. 2013
    ..These findings suggest that although both RAD51A1 and RAD51A2 have the potential to catalyze homologous pairing, RAD51A2 may be the major recombinase in rice. ..
  45. pmc Region and amino acid residues required for Rad51C binding in the human Xrcc3 protein
    Hitoshi Kurumizaka
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Nucleic Acids Res 31:4041-50. 2003
    ..Superposition of the Xrcc3 Tyr139 and Phe249 residues on the RecA structure suggested that Tyr139 may function to ensure proper folding and Phe249 may be important to constitute the Rad51C-binding interface in Xrcc3...
  46. ncbi request reprint Homologous pairing and ring and filament structure formation activities of the human Xrcc2*Rad51D complex
    Hitoshi Kurumizaka
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 277:14315-20. 2002
    ..In the presence of ssDNA, Xrcc2*Rad51D formed a filamentous structure, which is commonly observed among the human homologous pairing proteins, Rad51, Rad52, and Xrcc3*Rad51C...
  47. doi request reprint The Lys313 residue of the human Rad51 protein negatively regulates the strand-exchange activity
    Takako Ishida
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 3 4 1 Okubo, Shinjuku ku, Tokyo 169 8555, Japan
    Genes Cells 13:91-103. 2008
    ..These results suggest that the electrostatic environment around position 313 is important for the regulation of the HsRad51 recombinase activity...
  48. ncbi request reprint CpG methylation of the CENP-B box reduces human CENP-B binding
    Yoshinori Tanaka
    Protein Research Group, RIKEN Genomic Sciences Center, Suehiro cho, Tsurumi, Yokohama, Japan
    FEBS J 272:282-9. 2005
    ..Competition analyses revealed that the affinity of CENP-B for the CENP-B box DNA is reduced nearly to the level of nonspecific DNA binding by CpG methylation...
  49. doi request reprint Compensatory functions and interdependency of the DNA-binding domain of BRCA2 with the BRCA1-PALB2-BRCA2 complex
    Muthana Al Abo
    Authors Affiliations Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Sakyo ku and Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku ku, Tokyo, Japan
    Cancer Res 74:797-807. 2014
    ..This knowledge adds to our ability to accurately predict the efficacy of antimalignant therapies for patients carrying mutations in the BRCA2 gene...
  50. ncbi request reprint Structure of the CENP-A nucleosome and its implications for centromeric chromatin architecture
    Hiroaki Tachiwana
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku ku, Tokyo, Japan
    Genes Genet Syst 86:357-64. 2011
    ..In this review, we describe the structure and the physical properties of the CENP-A nucleosome, and discuss their implications for centromeric chromatin architecture...
  51. pmc Functional analyses of the C-terminal half of the Saccharomyces cerevisiae Rad52 protein
    Wataru Kagawa
    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, Department of Applied Biological Science, Nihon University College of Bioresource Sciences, Fujisawa shi, Kanagawa 252 0880, Japan, Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan and Cellular and Molecular Biology Laboratory, RIKEN, Wako Shi, Saitama 351 0198, Japan
    Nucleic Acids Res 42:941-51. 2014
    ..Our studies suggested that phenylalanine-349 and tyrosine-409 are key residues in the C-terminal half of Rad52 and probably play an important role in the mediator activity. ..
  52. ncbi request reprint Identification of functional domains of the Escherichia coli SeqA protein
    Norie Fujikawa
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Biochem Biophys Res Commun 300:699-705. 2003
    ..Therefore, two essential SeqA activities, self-association and DNA-binding, are independently performed by the structurally distinct N-terminal and C-terminal domains, respectively...
  53. ncbi request reprint Expression and purification of recombinant human histones
    Yoshinori Tanaka
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Methods 33:3-11. 2004
    ..coli. A new CENP-A gene optimized for the E. coli expression system was also constructed, and we found that the purified recombinant CENP-A protein formed a nucleosome-like structure with histones H2A, H2B, and H4...
  54. ncbi request reprint Altered DNA binding by the human Rad51-R150Q mutant found in breast cancer patients
    Takako Ishida
    Laboratory of Structural Biology, Graduate School of Science and Engineering, Waseda University, 3 4 1 Okubo, Shinjuku ku, Tokyo 169 8555, Japan
    Biol Pharm Bull 30:1374-8. 2007
    ..These differences in the DNA-binding properties between HsRad51(R150Q) and HsRad51 may be important to account for the tumorigenesis in breast cancer patients with the HsRad51(R150Q) mutation...
  55. pmc Crystal structure and stable property of the cancer-associated heterotypic nucleosome containing CENP-A and H3.3
    Yasuhiro Arimura
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Sci Rep 4:7115. 2014
    ....
  56. pmc Structural basis of a nucleosome containing histone H2A.B/H2A.Bbd that transiently associates with reorganized chromatin
    Yasuhiro Arimura
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Sci Rep 3:3510. 2013
    ..These results suggested that H2A.B rapidly and transiently forms nucleosomes with short DNA segments during chromatin reorganization. ..
  57. doi request reprint Purification and characterization of the fission yeast telomere clustering factors, Bqt1 and Bqt2
    Yuichi Ichikawa
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Protein Expr Purif 88:207-13. 2013
    ..The expression and purification procedures established here will facilitate further biophysical studies of the Bqt1-Bqt2 complex...
  58. doi request reprint Biochemical analysis of the human ENA/VASP-family proteins, MENA, VASP and EVL, in homologous recombination
    Motoki Takaku
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo, Japan
    J Biochem 149:721-9. 2011
    ..These results support the ideas that the ENA/VASP-family proteins are functionally redundant in homologous recombination, and that all three may be involved in the DSB repair pathway in humans...
  59. doi request reprint Crystal structure of the nucleosome containing ultraviolet light-induced cyclobutane pyrimidine dimer
    Naoki Horikoshi
    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
    Biochem Biophys Res Commun 471:117-22. 2016
    ..These results provide important structural and biochemical information for understanding how the CPD is accommodated and recognized in chromatin. ..
  60. pmc Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis
    Takashi Urahama
    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
    Epigenetics Chromatin 9:2. 2016
    ..Human histone H3.5 is a non-allelic H3 variant evolutionally derived from H3.3. The H3.5 mRNA is highly expressed in human testis. However, the function of H3.5 has remained poorly understood...
  61. doi request reprint Relaxed Chromatin Formation and Weak Suppression of Homologous Pairing by the Testis-Specific Linker Histone H1T
    Shinichi Machida
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Biochemistry 55:637-46. 2016
    ..These results suggested that the testis-specific linker histone, H1T, possesses a specific function to produce the chromatin architecture required for proper chromosome regulation, such as homologous recombination. ..
  62. doi request reprint Expression and purification of human FANCI and FANCD2 using Escherichia coli cells
    Daisuke Takahashi
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Protein Expr Purif 103:8-15. 2014
    ..Therefore, these purification methods for human FANCI and FANCD2 provide novel procedures to facilitate structural and biochemical studies of human FANCI and FANCD2. ..
  63. pmc Nap1 stimulates homologous recombination by RAD51 and RAD54 in higher-ordered chromatin containing histone H1
    Shinichi Machida
    1 Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan 2
    Sci Rep 4:4863. 2014
    ..We determined that Nap1 binds to RAD54, enhances the RAD54-mediated nucleosome remodeling by evicting histone H1, and eventually stimulates the RAD51-mediated homologous pairing in higher-ordered chromatin containing histone H1. ..
  64. pmc Filament formation and robust strand exchange activities of the rice DMC1A and DMC1B proteins
    Isao Sakane
    Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, 513 Wasedatsurumaki cho, Shinjuku ku, Tokyo 162 0041, Japan
    Nucleic Acids Res 36:4266-76. 2008
    ..These biochemical differences between the DMC1A and DMC1B proteins may provide important insight into their functional differences during meiosis in rice...
  65. doi request reprint Structural and biochemical analyses of the human PAD4 variant encoded by a functional haplotype gene
    Naoki Horikoshi
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjyuku ku, Tokyo 162 8480, Japan
    Acta Crystallogr D Biol Crystallogr 67:112-8. 2011
    ....
  66. pmc Defective FANCI binding by a fanconi anemia-related FANCD2 mutant
    Koichi Sato
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
    PLoS ONE 9:e114752. 2014
    ..In addition, the histone chaperone activity of cFANCD2 L234R was also defective. These findings may explain some aspects of Fanconi anemia pathogenesis by a FANCD2 missense mutation. ..
  67. pmc DIDS, a chemical compound that inhibits RAD51-mediated homologous pairing and strand exchange
    Takako Ishida
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Nucleic Acids Res 37:3367-76. 2009
    ..A gel mobility shift assay showed that DIDS significantly inhibited the DNA-binding activity of RAD51. Therefore, DIDS may bind near the DNA binding site(s) of RAD51 and compete with DNA for RAD51 binding...
  68. pmc Telomeric repeats act as nucleosome-disfavouring sequences in vivo
    Yuichi Ichikawa
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering RISE, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8640, Japan, 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 and Graduate School of Medical Life Science, Yokohama City University, 1 7 29 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Nucleic Acids Res 42:1541-52. 2014
    ..Thus, our results suggest that this inherent structural feature of the telomeric repeat sequences is involved in the functional dynamics of the telomeric chromatin structure. ..
  69. doi request reprint Halenaquinone, a chemical compound that specifically inhibits the secondary DNA binding of RAD51
    Motoki Takaku
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku ku, Tokyo 162 8480, Japan
    Genes Cells 16:427-36. 2011
    ..In vivo, halenaquinone significantly inhibited the retention of RAD51 at double-strand break sites. Therefore, halenaquinone is a novel type of RAD51 inhibitor that specifically inhibits the RAD51-dsDNA binding...
  70. pmc Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome
    Akihisa Osakabe
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Sci Rep 5:16330. 2015
    ..We present the first atomic-resolution pictures of the detrimental DNA cross-links of neighboring pyrimidine bases within the nucleosome, and provide the mechanistic framework for lesion recognition by UV-DDB in chromatin. ..
  71. doi request reprint Human FAN1 promotes strand incision in 5'-flapped DNA complexed with RPA
    Daisuke Takahashi
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan and
    J Biochem 158:263-70. 2015
    ..We found that FAN1 efficiently promoted DNA incision at the proper site of RPA-coated 5'-flapped DNA. Therefore, FAN1 possesses the ability to promote the ICL repair of 5'-flapped DNA covered by RPA. ..
  72. pmc Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro
    Hiroaki Tachiwana
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 3 4 1 Okubo, Shinjuku ku, Tokyo 169 8555, Japan
    Nucleic Acids Res 36:2208-18. 2008
    ..1, H3.2 and H3.3, but not in H3t, is the essential residue for the hNap1-mediated nucleosome assembly. These results suggest that H3t may be incorporated into chromatin by a specific chaperone-mediated pathway...
  73. pmc Human PSF binds to RAD51 and modulates its homologous-pairing and strand-exchange activities
    Yuichi Morozumi
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 162 8480, Japan
    Nucleic Acids Res 37:4296-307. 2009
    ..These results suggest that PSF may have dual functions in homologous recombination and RNA processing through its N-terminal and central regions, respectively...
  74. pmc DNA binding properties of the actin-related protein Arp8 and its role in DNA repair
    Akihisa Osakabe
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
    PLoS ONE 9:e108354. 2014
    ..Together with the previous observation that Arp8, but not γ-H2AX, is indispensable for recruiting INO80 complex to DSB in human, results of our study suggest an individual role for Arp8 in DNA repair. ..
  75. doi request reprint A method for evaluating nucleosome stability with a protein-binding fluorescent dye
    Hiroyuki Taguchi
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Methods 70:119-26. 2014
    ..In this report, we describe a convenient assay for evaluating the thermal stability of nucleosomes in vitro. ..
  76. pmc Structure of human nucleosome containing the testis-specific histone variant TSH2B
    Takashi Urahama
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Acta Crystallogr F Struct Biol Commun 70:444-9. 2014
    ..These findings may provide important information for understanding how testis-specific histone variants form nucleosomes during spermatogenesis. ..
  77. doi request reprint Crystal structure of the nucleosome containing histone H3 with crotonylated lysine 122
    Yuya Suzuki
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Biochem Biophys Res Commun 469:483-9. 2016
    ..Consistently, thermal stability assays revealed that the H3 Lys122 crotonylation, as well as the H3 Lys122 acetylation, clearly reduced the histone-DNA association. ..
  78. doi request reprint Green fluorescent protein fused to the C terminus of RAD51 specifically interferes with secondary DNA binding by the RAD51-ssDNA complex
    Wataru Kobayashi
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University
    Genes Genet Syst 89:169-79. 2014
    ..Therefore, GFP fused to the C terminus of RAD51 abolishes the homologous pairing activity of RAD51 by disrupting secondary DNA binding, but does not affect its DMC1-stimulating activity. ..
  79. pmc Structural and functional analyses of the DMC1-M200V polymorphism found in the human population
    Juri Hikiba
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Nucleic Acids Res 36:4181-90. 2008
    ....
  80. doi request reprint Structural basis for the DNA-binding activity of the bacterial β-propeller protein YncE
    Wataru Kagawa
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Acta Crystallogr D Biol Crystallogr 67:1045-53. 2011
    ....
  81. pmc DNA robustly stimulates FANCD2 monoubiquitylation in the complex with FANCI
    Koichi Sato
    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2 2 Wakamatsu cho, Shinjuku ku, Tokyo 162 8480, Japan
    Nucleic Acids Res 40:4553-61. 2012
    ..Therefore, DNA may be the unidentified factor required for proper FANCD2 monoubiquitylation...