Mitsuhiro Shimizu

Summary

Affiliation: Meisei University
Country: Japan

Publications

  1. pmc Yeast Ume6p repressor permits activator binding but restricts TBP binding at the HOP1 promoter
    Mitsuhiro Shimizu
    Department of Chemistry, Meisei University, Hino, Tokyo 191 8506, Japan
    Nucleic Acids Res 31:3033-7. 2003
  2. ncbi request reprint A C-terminal segment with properties of alpha-helix is essential for DNA binding and in vivo function of zinc finger protein Rme1p
    M Shimizu
    Department of Chemistry, Meisei University, 2 1 1 Hodokubo, Hino, Tokyo, 191 8506 Japan
    J Biol Chem 276:37680-5. 2001
  3. pmc Destabilization of nucleosomes by an unusual DNA conformation adopted by poly(dA) small middle dotpoly(dT) tracts in vivo
    M Shimizu
    Department of Chemistry, Meisei University, Hino, Tokyo 191 8506 and School of Pharmacy, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192 0392, Japan
    EMBO J 19:3358-65. 2000
  4. pmc Effect of sequence-directed nucleosome disruption on cell-type-specific repression by alpha2/Mcm1 in the yeast genome
    Nobuyuki Morohashi
    Department of Chemistry, Meisei University, 2 1 1 Hodokubo, Hino, Tokyo 191 8506, Japan
    Eukaryot Cell 5:1925-33. 2006
  5. ncbi request reprint Hap1p photofootprinting as an in vivo assay of repression mechanism in Saccharomyces cerevisiae
    Mitsuhiro Shimizu
    Department of Chemistry, Meisei University, Tokyo 191 8506, Japan
    Methods Enzymol 370:479-87. 2003
  6. pmc A nucleosome positioned by alpha2/Mcm1 prevents Hap1 activator binding in vivo
    Nobuyuki Morohashi
    Department of Chemistry, Meisei University, 2 1 1 Hodokubo, Hino, Tokyo 191 8506, Japan
    Biochem Biophys Res Commun 364:583-8. 2007
  7. 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
  8. pmc The linker histone homolog Hho1p from Saccharomyces cerevisiae represents a winged helix-turn-helix fold as determined by NMR spectroscopy
    Katsuki Ono
    School of Life Science, Tokyo University of Pharmacy and Life Science, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    Nucleic Acids Res 31:7199-207. 2003
  9. pmc Genomic footprinting of the yeast zinc finger protein Rme1p and its roles in repression of the meiotic activator IME1
    M Shimizu
    School of Pharmacy, Tokyo University of Pharmacy and Life Science, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    Nucleic Acids Res 26:2329-36. 1998
  10. 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

Collaborators

Detail Information

Publications20

  1. pmc Yeast Ume6p repressor permits activator binding but restricts TBP binding at the HOP1 promoter
    Mitsuhiro Shimizu
    Department of Chemistry, Meisei University, Hino, Tokyo 191 8506, Japan
    Nucleic Acids Res 31:3033-7. 2003
    ..We suggest that TBP binding is inhibited through chromatin modification by the Sin3p-Rpd3p and Isw2p complexes recruited by Ume6p...
  2. ncbi request reprint A C-terminal segment with properties of alpha-helix is essential for DNA binding and in vivo function of zinc finger protein Rme1p
    M Shimizu
    Department of Chemistry, Meisei University, 2 1 1 Hodokubo, Hino, Tokyo, 191 8506 Japan
    J Biol Chem 276:37680-5. 2001
    ..Thus, the C-terminal segment is essential and acts as a novel accessory domain for DNA binding by zinc fingers...
  3. pmc Destabilization of nucleosomes by an unusual DNA conformation adopted by poly(dA) small middle dotpoly(dT) tracts in vivo
    M Shimizu
    Department of Chemistry, Meisei University, Hino, Tokyo 191 8506 and School of Pharmacy, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192 0392, Japan
    EMBO J 19:3358-65. 2000
    ..Our results support a mechanism in which a unique poly(dA) small middle dot poly(dT) conformation presets chromatin structure to which transcription factors are accessible...
  4. pmc Effect of sequence-directed nucleosome disruption on cell-type-specific repression by alpha2/Mcm1 in the yeast genome
    Nobuyuki Morohashi
    Department of Chemistry, Meisei University, 2 1 1 Hodokubo, Hino, Tokyo 191 8506, Japan
    Eukaryot Cell 5:1925-33. 2006
    ..Our results illustrate a useful paradigm for analysis of chromatin structural effects at genomic loci...
  5. ncbi request reprint Hap1p photofootprinting as an in vivo assay of repression mechanism in Saccharomyces cerevisiae
    Mitsuhiro Shimizu
    Department of Chemistry, Meisei University, Tokyo 191 8506, Japan
    Methods Enzymol 370:479-87. 2003
  6. pmc A nucleosome positioned by alpha2/Mcm1 prevents Hap1 activator binding in vivo
    Nobuyuki Morohashi
    Department of Chemistry, Meisei University, 2 1 1 Hodokubo, Hino, Tokyo 191 8506, Japan
    Biochem Biophys Res Commun 364:583-8. 2007
    ..These results support the mechanism in which alpha2/Mcm1-dependent nucleosome positioning has a regulatory function to limit the access of transcription factors...
  7. 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...
  8. pmc The linker histone homolog Hho1p from Saccharomyces cerevisiae represents a winged helix-turn-helix fold as determined by NMR spectroscopy
    Katsuki Ono
    School of Life Science, Tokyo University of Pharmacy and Life Science, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    Nucleic Acids Res 31:7199-207. 2003
    ..The above results suggested that Hho1p possesses properties similar to those of linker histones in higher eukaryotes in terms of the structure and binding preference towards supercoiled DNA...
  9. pmc Genomic footprinting of the yeast zinc finger protein Rme1p and its roles in repression of the meiotic activator IME1
    M Shimizu
    School of Pharmacy, Tokyo University of Pharmacy and Life Science, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    Nucleic Acids Res 26:2329-36. 1998
    ..These results suggest that Rme1p functions directly as a repressor of IME1 and that Rgr1p and Sin4p are required for DNA-bound Rme1p to exert repression...
  10. 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. ..
  11. pmc Transcriptional repression at a distance through exclusion of activator binding in vivo
    M Shimizu
    School of Pharmacy, Tokyo University of Pharmacy and Life Science, Hachioji, Japan
    Proc Natl Acad Sci U S A 94:790-5. 1997
    ..Thus Rme1p may alter chromatin to prevent binding of transcriptional activators to distant DNA sequences...
  12. ncbi request reprint Purification of single-strand DNA binding protein from an Escherichia coli lysate using counter-current chromatography, partition and precipitation
    Yoichi Shibusawa
    Department of Analytical Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Science, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    J Chromatogr B Analyt Technol Biomed Life Sci 793:275-9. 2003
    ..The identities of the proteins in the fractions and in the precipitate were confirmed by SDS-polyacrylamide gel electrophoresis with Coomassie Brilliant Blue staining...
  13. ncbi request reprint Functional domains of Escherichia coli single-stranded DNA binding protein as assessed by analyses of the deletion mutants
    T Kinebuchi
    School of Pharmacy, Tokyo University of Pharmacy and Life Science, Hachioji, Japan
    Biochemistry 36:6732-8. 1997
    ..1985) J. Biol. Chem. 260, 3594-3603; Bujalowski, W., & Lohman, T. M. (1986) Biochemistry 25, 7799-7802], occurred at lower and higher SSB concentrations, respectively. A functional map for SSB molecule was presented and discussed...
  14. pmc Dynamics in the isomerization of intramolecular DNA triplexes in supercoiled plasmids
    H Shindo
    School of Pharmacy, Tokyo University of Pharmacy and Life Science, 1432 1 Horinouchi, Hachioji, Tokyo 192 03, Japan
    Nucleic Acids Res 25:4786-91. 1997
    ..Therefore, H-y3 is kinetically inferior but thermodynamically favored at higher supercoil levels in plasmids. The presence of Mg2+ resulted in both a kinetic and a thermodynamic preference for H-y5 formation, relative to the H-y3 form...
  15. ncbi request reprint Protein phylogeny of translation elongation factor EF-1 alpha suggests microsporidians are extremely ancient eukaryotes
    T Kamaishi
    Department of Medical Biology, Showa University, Tokyo, Japan
    J Mol Evol 42:257-63. 1996
    ..plecoglossi is likely to represent the earliest offshoot of eukaryotes. Microsporidians might be the extremely ancient eukaryotes which have diverged before an occurrence of mitochondrial symbiosis...
  16. ncbi request reprint Proteolytic activation of SREBPs during adipocyte differentiation
    J Inoue
    Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113 8657, Japan
    Biochem Biophys Res Commun 283:1157-61. 2001
    ..These results demonstrate that SREBP-2 appears to promote adipocyte differentiation as well as SREBP-1 and that the proteolytic activation of SREBPs may be induced by an as-yet unidentified mechanism in lipid loaded adipocytes...
  17. ncbi request reprint Genetic analysis of the capsid region of astroviruses
    Q H Wang
    Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
    J Med Virol 64:245-55. 2001
    ..To our knowledge, this is the first comparative sequence analysis of the capsid protein precursors of eight serotypes of HAstVs as well as two animal astroviruses (FAstV and PAstV)...
  18. pmc Transcriptional repression by the Pho4 transcription factor controls the timing of SNZ1 expression
    Masafumi Nishizawa
    Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo 160 8582, Japan
    Eukaryot Cell 7:949-57. 2008
    ..These results imply that Pho4 plays positive and negative roles in transcriptional regulation, with both cases involving structural changes in its target chromatin...
  19. doi request reprint 5-Bromouracil disrupts nucleosome positioning by inducing A-form-like DNA conformation in yeast cells
    Kensuke Miki
    International Graduate School of Arts and Sciences, Yokohama City University, Seto 22 2, Kanazawa Ku, Yokohama, Kanagawa 236 0027, Japan
    Biochem Biophys Res Commun 368:662-9. 2008
    ..Since this property is indicative of a rigid conformation of DNA, our results suggest that 5-bromouracil disrupts nucleosome positioning by inducing A-form-like DNA...
  20. ncbi request reprint Distorted DNA structures induced by HMGB2 possess a high affinity for HMGB2
    Yasuyuki Nakamura
    Department of Biological Science and Technology, Science University of Tokyo Yamazaki, Noda, Chiba 278 8510, Japan
    J Biochem 131:153-60. 2002
    ..Thus, the distorted structures present in alpha-DNA and beta-DNA should be important in considering the functional mechanisms in which HMGB2 participates...