Takehiko Shibata

Summary

Affiliation: RIKEN Brain Science Institute
Country: Japan

Publications

  1. ncbi Homologous genetic recombination as an intrinsic dynamic property of a DNA structure induced by RecA/Rad51-family proteins: a possible advantage of DNA over RNA as genomic material
    T Shibata
    Cellular and Molecular Biology Laboratory, RIKEN, The Institute of Physical and Chemical Research, Hirosawa 2 1, Wako Shi, Saitama 351 0198, Japan
    Proc Natl Acad Sci U S A 98:8425-32. 2001
  2. ncbi DNA recombination protein-dependent mechanism of homoplasmy and its proposed functions
    Takehiko Shibata
    Cellular and Molecular Biology Laboratory, RIKEN The Institute of Physical and Chemical Research, Hirosawa 2 1, Wako Shi, Saitama 351 0198, Japan
    Mitochondrion 7:17-23. 2007
  3. ncbi [Mitochondrial inheritance in yeast: mtDNA recombination and homoplasmy]
    Takehiko Shibata
    Tanpakushitsu Kakusan Koso 50:1822-6. 2005
  4. ncbi Distinct chromatin modulators regulate the formation of accessible and repressive chromatin at the fission yeast recombination hotspot ade6-M26
    Kouji Hirota
    Shibata Distinguished Senior Scientist Laboratory, RIKEN Discovery Research Institute, Wako Shi, Saitama 351 0198, Japan
    Mol Biol Cell 19:1162-73. 2008
  5. ncbi Targeted induction of meiotic double-strand breaks reveals chromosomal domain-dependent regulation of Spo11 and interactions among potential sites of meiotic recombination
    Tomoyuki Fukuda
    Shibata Distinguished Senior Scientist Laboratory, RIKEN, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    Nucleic Acids Res 36:984-97. 2008
  6. ncbi DNA recombination-initiation plays a role in the extremely biased inheritance of yeast [rho-] mitochondrial DNA that contains the replication origin ori5
    Feng Ling
    RIKEN Discovery Research Institute, Hirosawa 2 1, Wako Shi, Saitama 351 0198, Japan
    Mol Cell Biol 27:1133-45. 2007
  7. ncbi Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs
    Kouji Hirota
    Cellular and Molecular Biology Laboratory, RIKEN Advanced Science Institute, Wako Shi, Saitama 351 0198, Japan
    Nature 456:130-4. 2008
  8. ncbi Reactive oxygen species regulate DNA copy number in isolated yeast mitochondria by triggering recombination-mediated replication
    Akiko Hori
    Chemical Genetics Laboratory, RIKEN Advanced Science Institute, Hirosawa 2 1, Wako Shi, Saitama 351 0198, Japan
    Nucleic Acids Res 37:749-61. 2009
  9. ncbi Roles of histone acetylation and chromatin remodeling factor in a meiotic recombination hotspot
    Takatomi Yamada
    Genetic Dynamics Research Unit Laboratory, RIKEN, Wako, Saitama, Japan
    EMBO J 23:1792-803. 2004
  10. ncbi Fission yeast global repressors regulate the specificity of chromatin alteration in response to distinct environmental stresses
    Kouji Hirota
    Genetic Dynamics Research Unit Laboratory, RIKEN Institute of Physical and Chemical Research, Wako Shi, Saitama 351 0198, Japan
    Nucleic Acids Res 32:855-62. 2004

Collaborators

Detail Information

Publications57

  1. ncbi Homologous genetic recombination as an intrinsic dynamic property of a DNA structure induced by RecA/Rad51-family proteins: a possible advantage of DNA over RNA as genomic material
    T Shibata
    Cellular and Molecular Biology Laboratory, RIKEN, The Institute of Physical and Chemical Research, Hirosawa 2 1, Wako Shi, Saitama 351 0198, Japan
    Proc Natl Acad Sci U S A 98:8425-32. 2001
    ..e., protein-segment shuffling). These properties may give an extensive evolutionary advantage to DNA...
  2. ncbi DNA recombination protein-dependent mechanism of homoplasmy and its proposed functions
    Takehiko Shibata
    Cellular and Molecular Biology Laboratory, RIKEN The Institute of Physical and Chemical Research, Hirosawa 2 1, Wako Shi, Saitama 351 0198, Japan
    Mitochondrion 7:17-23. 2007
    ..Conversely, within the nuclear genome, homologous DNA recombination causes genetic diversity. Considering these contradictory roles of this key reaction in DNA recombination, possible functions of homoplasmy are discussed...
  3. ncbi [Mitochondrial inheritance in yeast: mtDNA recombination and homoplasmy]
    Takehiko Shibata
    Tanpakushitsu Kakusan Koso 50:1822-6. 2005
  4. ncbi Distinct chromatin modulators regulate the formation of accessible and repressive chromatin at the fission yeast recombination hotspot ade6-M26
    Kouji Hirota
    Shibata Distinguished Senior Scientist Laboratory, RIKEN Discovery Research Institute, Wako Shi, Saitama 351 0198, Japan
    Mol Biol Cell 19:1162-73. 2008
    ..Thus, we propose that multiple chromatin modulators regulate chromatin structure reversibly and participate in the regulation of both meiotic recombination and stress-induced transcription around CRE-like sequences...
  5. ncbi Targeted induction of meiotic double-strand breaks reveals chromosomal domain-dependent regulation of Spo11 and interactions among potential sites of meiotic recombination
    Tomoyuki Fukuda
    Shibata Distinguished Senior Scientist Laboratory, RIKEN, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    Nucleic Acids Res 36:984-97. 2008
    ..Thus, potential sites for Spo11-mediated DSB are subject to domain-specific and local competitive regulations during and after DSB formation...
  6. ncbi DNA recombination-initiation plays a role in the extremely biased inheritance of yeast [rho-] mitochondrial DNA that contains the replication origin ori5
    Feng Ling
    RIKEN Discovery Research Institute, Hirosawa 2 1, Wako Shi, Saitama 351 0198, Japan
    Mol Cell Biol 27:1133-45. 2007
    ....
  7. ncbi Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs
    Kouji Hirota
    Cellular and Molecular Biology Laboratory, RIKEN Advanced Science Institute, Wako Shi, Saitama 351 0198, Japan
    Nature 456:130-4. 2008
    ..Our results demonstrate that transcription through the promoter region is required to make DNA sequences accessible to transcriptional activators and to RNAPII...
  8. ncbi Reactive oxygen species regulate DNA copy number in isolated yeast mitochondria by triggering recombination-mediated replication
    Akiko Hori
    Chemical Genetics Laboratory, RIKEN Advanced Science Institute, Hirosawa 2 1, Wako Shi, Saitama 351 0198, Japan
    Nucleic Acids Res 37:749-61. 2009
    ..We therefore propose that ROS act as a regulator of mtDNA copy number, acting through the Mhr1-dependent initiation of rolling-circle replication promoted by Ntg1-induced DSB in the single-stranded regions at ori5...
  9. ncbi Roles of histone acetylation and chromatin remodeling factor in a meiotic recombination hotspot
    Takatomi Yamada
    Genetic Dynamics Research Unit Laboratory, RIKEN, Wako, Saitama, Japan
    EMBO J 23:1792-803. 2004
    ..These results suggest that HATs and ADCRs cooperatively alter local chromatin structure, as in selective transcription activation, to activate meiotic recombination at M26 in a site-specific manner...
  10. ncbi Fission yeast global repressors regulate the specificity of chromatin alteration in response to distinct environmental stresses
    Kouji Hirota
    Genetic Dynamics Research Unit Laboratory, RIKEN Institute of Physical and Chemical Research, Wako Shi, Saitama 351 0198, Japan
    Nucleic Acids Res 32:855-62. 2004
    ..Such a role for these proteins may serve as a paradigm for the regulation of stress response in higher eukaryotes...
  11. ncbi A fluorescent antibiotic resistance marker for rapid production of transgenic rice plants
    Tetsuko Ochiai-Fukuda
    Laboratory for Remediation Research, Plant Science Center (PSC1) and Discovery Research Institute (DRI, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
    J Biotechnol 122:521-7. 2006
    ..In addition, the small size (1.1 kb) of gfbsd is preferable for construction of transformation vectors. This new marker gene will make a significant contribution in molecular genetic studies of rice plants...
  12. ncbi A DNA-binding surface of SPO11-1, an Arabidopsis SPO11 orthologue required for normal meiosis
    Yoshinori Shingu
    Cellular and Molecular Biology Laboratory, RIKEN Advanced Science Institute, Wako Shi, Saitama, Japan
    FEBS J 277:2360-74. 2010
    ..Thus, the Gly215, Arg222 and Arg223 residues of SPO11-1 form a DNA-binding surface that is functional in meiosis...
  13. ncbi Concordant evolution of trichothecene 3-O-acetyltransferase and an rDNA species phylogeny of trichothecene-producing and non-producing fusaria and other ascomycetous fungi
    Takeshi Tokai
    Laboratory for Remediation Research, Plant Science Center, RIKEN, Wako, Saitama 351-0198, and Yokohama, Kanagawa 230-0045, Japan
    Microbiology 151:509-19. 2005
    ..The phylogeny of the 3-O-acetyltransferase was mostly concordant with the rDNA species phylogeny of these ascomycetous fungi...
  14. ncbi Recombination-dependent mtDNA partitioning: in vivo role of Mhr1p to promote pairing of homologous DNA
    Feng Ling
    Cellular and Molecular Biology Laboratory, RIKEN, Hirosawa 2 1, Wako Shi, Saitama 351 0198, Japan
    EMBO J 21:4730-40. 2002
    ..These results suggest a mechanism for mtDNA inheritance similar to that operating in the replication and packaging of phage DNA...
  15. ncbi The double-stranded break-forming activity of plant SPO11s and a novel rice SPO11 revealed by a Drosophila bioassay
    Yoshinori Shingu
    Cellular and Molecular Biology Laboratory, RIKEN Advanced Science Institute, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    BMC Mol Biol 13:1. 2012
    ..In addition, plants have multiple SPO11-homologues...
  16. ncbi Screening of putative oxygenase genes in the Fusarium graminearum genome sequence database for their role in trichothecene biosynthesis
    Takeshi Tokai
    Laboratory for Remediation Research, and Plant and Microbial Metabolic Engineering Unit-Laboratory, Plant Science Center (PSC1) and Discovery Research Institute, RIKEN, Wako, Saitama 351-0198, Japan
    FEMS Microbiol Lett 251:193-201. 2005
    ..asiaticum. The results are discussed in relation to the presence of as-yet-unidentified oxygenation genes that are necessary for the biosynthesis of trichothecenes...
  17. ncbi RecR forms a ring-like tetramer that encircles dsDNA by forming a complex with RecF
    Masayoshi Honda
    RIKEN Advanced Science Institute, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    Nucleic Acids Res 36:5013-20. 2008
    ..Thus, we propose that the ring-like ttRecR tetramer has a key role in tethering the ttRecFR complex onto dsDNA and that the ring structure may function as a clamp protein...
  18. ncbi Mhr1p-dependent concatemeric mitochondrial DNA formation for generating yeast mitochondrial homoplasmic cells
    Feng Ling
    Cellular and Molecular Biology Laboratory, RIKEN, Saitama 351 0198, Japan
    Mol Biol Cell 15:310-22. 2004
    ....
  19. ncbi New TAXI-type xylanase inhibitor genes are inducible by pathogens and wounding in hexaploid wheat
    Tomoko Igawa
    Laboratory for Remediation Research, Plant Science Center, RIKEN, 1 7 22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230 0045, Japan
    Plant Cell Physiol 45:1347-60. 2004
    ..xylanases: it was also active against some spelt xylan-induced xylanases of F. graminearum. These features suggest that some, but not all, TAXI-type xylanase inhibitors have a role in plant defense...
  20. ncbi Meiotic association between Spo11 regulated by Rec102, Rec104 and Rec114
    Hiroyuki Sasanuma
    Genetic System Regulation Laboratory, RIKEN Discovery Research Institute, Hirosawa 2 1, Wako, Saitama 351 0198, Japan
    Nucleic Acids Res 35:1119-33. 2007
    ..Together, these results suggest that in vivo self-association of Spo11 during meiosis is genetically regulated. The results are discussed in relation to possible roles of Spo11 self-interaction in the control of the cleavage activity...
  21. ncbi Heteroduplex joint formation free of net topological change by Mhr1, a mitochondrial recombinase
    Feng Ling
    Chemical Genetics Laboratory, RIKEN Advanced Science Institute, Hirosawa 2 1, Wako City, Saitama 351 0198, Japan
    J Biol Chem 284:9341-53. 2009
    ..We propose a novel topological mechanism wherein Mhr1 induces untwisting without net topological change...
  22. ncbi A mechanism for single-stranded DNA-binding protein (SSB) displacement from single-stranded DNA upon SSB-RecO interaction
    Jin Inoue
    RIKEN Advanced Science Institute, 2 1, Hirosawa, Wako, Saitama 351 0198, Japan
    J Biol Chem 286:6720-32. 2011
    ....
  23. ncbi The process of displacing the single-stranded DNA-binding protein from single-stranded DNA by RecO and RecR proteins
    Jin Inoue
    RIKEN Discovery Research Institute, 2 1, Hirosawa, Wako, Saitama 351 0198, Japan
    Nucleic Acids Res 36:94-109. 2008
    ..Interestingly, the interaction of RecR with RecO affected the ssDNA-binding properties of RecO. These results suggest a model of SSB displacement from the ssDNA by RecF pathway proteins...
  24. ncbi Heteronuclear multidimensional NMR and homology modelling studies of the C-terminal nucleotide-binding domain of the human mitochondrial ABC transporter ABCB6
    Kaori Kurashima-Ito
    Cellular and Molecular Biology Laboratory, RIKEN, Wako, Saitama, 351 0198, Japan
    J Biomol NMR 35:53-71. 2006
    ..Since the Helical domain is the putative interface to the transmembrane domain, this cooperativity may explain the coupled functions between domains in the substrate-transportation cycle...
  25. ncbi Metabolism of zearalenone by genetically modified organisms expressing the detoxification gene from Clonostachys rosea
    Naoko Takahashi-Ando
    Laboratory for Remediation Research, Plant Science Center, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
    Appl Environ Microbiol 70:3239-45. 2004
    ..Environ. Microbiol. 68:3545-3549, 2002). An appropriate combination of a candidate host microbe and the codon-optimized synthetic gene may contribute significantly to establishing a mycotoxin detoxification system for food and feed...
  26. ncbi An NMR study on the interaction of Escherichia coli DinI with RecA-ssDNA complexes
    Masatoshi Yoshimasu
    Cellular and Molecular Biology Laboratory, RIKEN, 2 1 Hirosawa, Wako Shi, Saitama 351 0198, Japan
    Nucleic Acids Res 31:1735-43. 2003
    ....
  27. ncbi Trichothecene nonproducer Gibberella species have both functional and nonfunctional 3-O-acetyltransferase genes
    Makoto Kimura
    Laboratory for Remediation Research, Plant Science Center, RIKEN, Wako, Saitama 351 0198, Japan
    Genetics 163:677-84. 2003
    ..The existence of Tri101 in a trichothecene nonproducer suggests that this gene existed in the fungal genome before the divergence of producers from nonproducers in the evolution of Fusarium species...
  28. ncbi An endoplasmic reticulum stress-specific caspase cascade in apoptosis. Cytochrome c-independent activation of caspase-9 by caspase-12
    Nobuhiro Morishima
    Bioarchitect Research Group, RIKEN The Institute of Physical and Chemical Research, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    J Biol Chem 277:34287-94. 2002
    ..These data suggest that procaspase-9 is a substrate of caspase-12 and that ER stress triggers a specific cascade involving caspase-12, -9, and -3 in a cytochrome c-independent manner...
  29. ncbi [Rolling circle replication: a universal model for controlling mechanisms of mitochondrial DNA copy number]
    Feng Ling
    Tanpakushitsu Kakusan Koso 52:886-92. 2007
  30. ncbi RecQ5 Interacts with Rad51 and Is Involved in Resistance of Drosophila to Cisplatin Treatment
    Sayako Maruyama
    Cellular and Molecular Biology Laboratory, RIKEN
    Biol Pharm Bull 35:2017-22. 2012
    ..These data suggest that RecQ5 and Rad51 in Drosophila functioned for survival after the flies had been treated with cisplatin...
  31. ncbi An ex vivo method for rapid generation of monoclonal antibodies (ADLib system)
    Hidetaka Seo
    Chiome Bioscience Inc, RIKEN, 2 1 Hirosawa, Wako Shi, Saitama ken 351 0198, Japan
    Nat Protoc 1:1502-6. 2006
    ..The whole process from selection to screening can be completed in about 1 week. Thus, the ADLib system will accelerate biological studies, including drug discovery and design...
  32. ncbi The possible roles of the DNA helicase and C-terminal domains in RECQ5/QE: complementation study in yeast
    Minoru Nakayama
    Cellular and Molecular Biology Laboratory, RIKEN (The Institute of Physical and Chemical Research, Hirosawa, Wako-shi, Saitama, Japan
    DNA Repair (Amst) 3:369-78. 2004
    ..These results suggested that the RECQ5/QE helicase activity is important for cellular function and that the C-terminal domain has a specific function in the absence of Top3...
  33. ncbi Fission yeast Tup1-like repressors repress chromatin remodeling at the fbp1+ promoter and the ade6-M26 recombination hotspot
    Kouji Hirota
    Genetic Dynamics Research Unit Laboratory, The Institute of Physical and Chemical Research RIKEN, Wako Shi, Saitama 351 0198, Japan
    Genetics 165:505-15. 2003
    ..These observations suggest that these fission yeast Tup1-like corepressors repress chromatin remodeling at CRE-related sequences and that Rst2 antagonizes this function...
  34. ncbi A novel method for the biosynthesis of deuterated proteins with selective protonation at the aromatic rings of Phe, Tyr and Trp
    Sundaresan Rajesh
    Cellular and Molecular Biology Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
    J Biomol NMR 27:81-6. 2003
    ....
  35. ncbi Drosophila melanogaster RECQ5/QE DNA helicase: stimulation by GTP binding
    Katsumi Kawasaki
    Cellular and Molecular Biology Laboratory, RIKEN The Institute of Physical and Chemical Research, 2 1 Hirosawa, Wako Shi, Saitama 351 0198, Japan
    Nucleic Acids Res 30:3682-91. 2002
    ..5) (K(m)) values for the substrates during the DNA helicase reaction. The data collectively suggest that the RECQ5/QE protein is activated upon GTP binding through the ATP-binding site...
  36. ncbi The trichothecene biosynthesis gene cluster of Fusarium graminearum F15 contains a limited number of essential pathway genes and expressed non-essential genes
    Makoto Kimura
    Laboratory for Remediation Research, Plant Science Center, RIKEN, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    FEBS Lett 539:105-10. 2003
    ..In contrast, recombinant TRI8 protein displayed no C-3 deacetylase activity, suggesting that the loss or alteration of function contribute directly to the chemotype difference...
  37. ncbi Translocation of Bim to the endoplasmic reticulum (ER) mediates ER stress signaling for activation of caspase-12 during ER stress-induced apoptosis
    Nobuhiro Morishima
    Bioarchitect Research Group, RIKEN, The Institute of Physical and Chemical Research, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    J Biol Chem 279:50375-81. 2004
    ..These results suggest that translocation of Bim to the ER in response to ER stress is an important step toward activation of caspase-12 and initiation of the ER stress-specific caspase cascade...
  38. ncbi Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus
    Marina N Vassylyeva
    Genomic Sciences Center RIKEN, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    Acta Crystallogr D Biol Crystallogr 58:1497-500. 2002
    ..aquaticus RNA polymerase core enzyme as a search model. The refinement of structure and model building of the sigma(70) subunit is now in progress...
  39. ncbi Association of HSP70 with endonucleases allows the expression of otherwise silent mutations
    Hikaru Mizumura
    Bioarchitect Research Group and Cellular and Molecular Biology Laboratory, RIKEN (The Institute of Physical and Chemical Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
    FEBS Lett 522:177-82. 2002
    ..These results suggest that HSP70 interaction with certain endonucleases allows the expression of otherwise silent mutations in them, causing a change in enzyme cleavage specificity...
  40. ncbi Cdc7-dependent phosphorylation of Mer2 facilitates initiation of yeast meiotic recombination
    Hiroyuki Sasanuma
    Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3 8 1, Meguro ku, Tokyo 153 8902, Japan
    Genes Dev 22:398-410. 2008
    ..We thus propose that Cdc7, in concert with CDK, regulates Spo11 loading to DSB sites via Mer2 phosphorylation...
  41. ncbi 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
    ....
  42. ncbi 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...
  43. ncbi Heteroduplex joint formation by a stoichiometric complex of Rad51 and Rad52 of Saccharomyces cerevisiae
    Naoto Arai
    Department of Applied Biological Science, Nihon University College of Bioresource Sciences, Fujisawa shi, Kanagawa, Japan
    J Biol Chem 280:32218-29. 2005
    ....
  44. ncbi Correlation between premeiotic DNA replication and chromatin transition at yeast recombination initiation sites
    Hajime Murakami
    Genetic Dynamics Research Unit-Laboratory, RIKEN (The Institute of Physical and Chemical Research, Wako-shi, Saitama 351-0198, Japan
    Nucleic Acids Res 31:4085-90. 2003
    ....
  45. ncbi Multiple modes of chromatin configuration at natural meiotic recombination hot spots in fission yeast
    Kouji Hirota
    Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3 8 1, Meguroku, Tokyo 153 8902, Japan
    Eukaryot Cell 6:2072-80. 2007
    ....
  46. ncbi 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...
  47. ncbi 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...
  48. ncbi 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...
  49. ncbi Rapid generation of specific antibodies by enhanced homologous recombination
    Hidetaka Seo
    Genetic Dynamics Research Unit, RIKEN Discovery Research Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
    Nat Biotechnol 23:731-5. 2005
    ....
  50. ncbi Roles of the HSP70-subunit in a eukaryotic multi-site-specific endonuclease, Endo.SceI: autophosphorylation and heat stability
    Katsumi Kawasaki
    Department of Biochemistry, Faculty of Pharmaceutical Sciences, Setsunan University, 45 1 Nagaotoge cho, Hirakata, Osaka 573 0101, Japan
    Biosci Biotechnol Biochem 68:2557-64. 2004
    ..SceI. These findings suggest that the HSP70-subunit shields Endo.SceI from heat inactivation through ATP/ADP binding...
  51. ncbi Incorporation of DUF/FACT into chromatin enhances the accessibility of nucleosomal DNA
    Hidetaka Seo
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Biochem Biophys Res Commun 303:8-13. 2003
    ..Also we found that DUF has a high affinity for core histones in vitro. We suggest that the function of DUF may be to make the chromatin structure accessible to replication factors...
  52. ncbi 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...
  53. ncbi [Role of homologous DNA recombination in regulation of molecular evolution]
    Takehiko Shibata
    Tanpakushitsu Kakusan Koso 48:704-6. 2003
  54. ncbi [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
  55. ncbi Modulation of immunoglobulin gene conversion frequency and distribution by the histone deacetylase HDAC2 in chicken DT40
    Waka Lin
    Shibata Distinguished Scientist Laboratory, RIKEN Discovery Research Institute, Saitama Ken, Japan
    Genes Cells 13:255-68. 2008
    ..These results underscore the potential participation of HDAC-mediated histone acetylation in Ig diversification, but also suggest a specific role of HDAC2 to control the spatial targeting of Ig gene conversion...
  56. ncbi Overproduction, crystallization and preliminary diffraction data of ADP-ribose pyrophosphatase from Thermus thermophilus HB8
    Sachiko Yoshiba
    Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
    Acta Crystallogr D Biol Crystallogr 59:1840-2. 2003
    ..50 A resolution from the apo form using synchrotron radiation and to 2.0 A resolution from the complexed form. Both crystals belong to space group P3(1)21 or P3(2)21 and contain one molecule in the asymmetric unit...
  57. ncbi 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...