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Mechanisms of chromatin organization in genome dictated by DNA structural properties.

Research Project

Project/Area Number 14572079
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Biological pharmacy
Research InstitutionMeisei University

Principal Investigator

SHIMIZU Mitsuhiro  Meisei University, Faculty of Physical Sciences and Engineering, Associate Professor, 理工学部, 助教授 (80231364)

Project Period (FY) 2002 – 2003
Project Status Completed (Fiscal Year 2003)
Budget Amount *help
¥3,500,000 (Direct Cost: ¥3,500,000)
Fiscal Year 2003: ¥1,300,000 (Direct Cost: ¥1,300,000)
Fiscal Year 2002: ¥2,200,000 (Direct Cost: ¥2,200,000)
Keywordschromatin / nucleosome / DNA structure / transcriptional regulation / repetitive sequences / budding yeast / genome
Research Abstract

Gene expression in eukaryotic cells involves the interaction of proteins with DNA packaged into nucleosomes. Nucleosomes are often located at distinct positions in promoter regions to regulate transcription. Thus, the factors that influence the nucleosome positioning are essential to elucidating the mechanism of gene expression. In this project, we have examined the role of DNA structures in chromatin organization and its effect on gene expression in vivo.
1.Effect of DNA structures on nucleosome positioning in vivo.
We have examined effect of simple repeating sequences that can form alternative DNA conformations on nucleosome positioning using yeast minichromosome system. The repeating sequences are categorized into 4 groups in terms of nucleosome-promoting and nucleosome-disrupting properties.
2.Effect of chromatin alteration through DNA structures on repression in yeast genome.
In Saccharomyces cerevisiae, nucleosomes are precisely positioned in the promoters of a cell-specific genes such as STE6 and BAR1. Here, we have demonstrated that chromatin alteration by intrinsic DNA structures disrupts repression of BAR1 in genome and of STE6-lacZ reporter plasmids in a cells. Therefore, proper nucleosome positioning is essential for regulation of cell type-specific transcription and cell type identity.
3.Effect of triplet repeat sequences on chromatin organization.
We have shown that triplet repeat sequences that cause human hereditary diseases affect nucleosome organization in yeast minichromosomes. Their effect on gene expression is associated with their features on chromatin structure. The sticky DNA formation at longer GAA repeats from Friedreich's ataxia was also investigated in yeast minichromosomes.
In summary, intrinsic DNA structures play important roles in nucleosome organization in vivo. Our studies also emphasizes that chromatin alteration through DNA structures would make it possible to modulate gene expression artificially in eukaryotes.

Report

(3 results)
  • 2003 Annual Research Report   Final Research Report Summary
  • 2002 Annual Research Report
  • Research Products

    (24 results)

All 2003 2002 Other

All Journal Article (15 results) Book (1 results) Publications (8 results)

  • [Journal Article] Yeast Ume6p repressor permits activator binding but restricts TATA-box binding protein association with the HOP1 promoter.2003

    • Author(s)
      Mituhiro Shimizu
    • Journal Title

      Nucleic Acids Res. 31・12

      Pages: 3033-3037

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Purification of single-strand DNA binding protein from an Escherichia coli lysate using counter-current chromatography, partition and precipitation2003

    • Author(s)
      Yoichi Shibusawa
    • Journal Title

      J.Chromatogr.B 793・2

      Pages: 275-279

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Separation and recovery of DNA fragments by electrophoresis through a thermoreversible hydrogel of multiplied block copolymers composed of poly(ethylene oxide) and poly (propylene oxide)2003

    • Author(s)
      Hiroshi Yoshioka
    • Journal Title

      Anal.Biochem. 323・2

      Pages: 218-223

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] The linker histone homolog Hho1p from Saccharomyces cerevisiae represents a winged helix-turn-helix fold as determined by NMR spectroscopy2003

    • Author(s)
      Katsuki Ono
    • Journal Title

      Nucleic Acids Res. 31・24

      Pages: 7199-7207

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Yeast Ume6p repressor permits activator binding but restricts TATA-box binding protein association with the HOP1 promoter.2003

    • Author(s)
      Mitsuhiro Shimizu, Keiko Takahashi, Teresa Lamb, Heisaburo Shindo, Aaron P.Mitchell
    • Journal Title

      Nucleic Acids Res. 31

      Pages: 3033-3037

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Purification of single-strand DNA binding protein from anEscherichia coli lysate using counter-current chromatography, partition and precipitation.2003

    • Author(s)
      Yoichi Shibusawa, Yohko Ino, Takashi Kinebuchi, Mitsuhiro Shimizu, Heisaburo Shindo, Yoichiro Ito
    • Journal Title

      J.Chromatogr.B 793

      Pages: 275-279

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Separation and recovery of DNA fragments by electrophoresisthrough a thermoreversible hydrogel of multipliedblock copolymers composed of poly(ethylene oxide) and poly(propylene oxide).2003

    • Author(s)
      Hiroshi Yoshioka Yuichi Mori, Mitsuhiro Shimizu
    • Journal Title

      Anal.Biochem. 323(2)

      Pages: 218-23

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] The linker histone homolog Hholp from Saccharomyces cerevisiae represents a winged helix-turn-helix fold as determined by NMR spectroscopy.2003

    • Author(s)
      Katsuki Ono, Osamu Kusano, Sakurako Shimotakahara, Mitsuhiro Shimizu, Toshimasa Yamazaki, Heisaburo Shindo
    • Journal Title

      Nucleic Acids Res. 31(24)

      Pages: 7199-7207

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Hap1p photofootprinting as an in vivo assay of repression mechanism.2003

    • Author(s)
      Mitsuhiro Shimizu, Aaron P.Mitchell
    • Journal Title

      Methods in Enzymology (RNA polymerases and Associated factors, Part C) (eds.S.L.Adhya, S.Garges) (Elsevier Academic Press) Volume 370

      Pages: 479-487

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Distorted DNA structures induced by HMGB2 possess a high affinity for HMGB2.2002

    • Author(s)
      Yasuyuki Nakamura
    • Journal Title

      J.Biochem 131・1

      Pages: 153-160

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Effects of triplet repeat sequences on nucleosome positioning and gene expression in yeast minichromosomes.2002

    • Author(s)
      Nobuyuki Tomita
    • Journal Title

      Nucleic Acids Res.Supple. 2

      Pages: 231-232

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] The role of nuclosome positioning in repression by the yeast α2/Mcm1p repressor.2002

    • Author(s)
      Shinya Saito
    • Journal Title

      Nucleic Acids Res.Supple. 2

      Pages: 93-94

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Distorted DNA structures induced by HMGB2 possess a high affinity for HMGB2.2002

    • Author(s)
      Yasuyuki Nakamura, Mitsuhiro Shimizu, Michiteru Yoshida
    • Journal Title

      J.Biochem. 131(1)

      Pages: 153-160

    • NAID

      10010645255

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] Effects of triplet repeat sequences on nucleosome positioning and gene expression in yeast minichromosomes.2002

    • Author(s)
      Nobuyuki Tomita, Ryo Fujita, Daichi Kurihara, Heisaburo Shindo, Robert D.Wells, Mitsuhiro Shimizu
    • Journal Title

      Nucleic Acids Res.Supple. 2

      Pages: 231-232

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Journal Article] The role of nucleosome positioning in repression by the yeast α2/Mcm1p repressor.2002

    • Author(s)
      Shinya Saito, Shigeki Miura, Yuichi Yamamoto, Heisaburo Shindo, Mitsuhiro Shimizu
    • Journal Title

      Nucleic Acids Res.Supple. 2

      Pages: 93-94

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Book] Methods in Enzymology, Volume 370,RNA polymerases and Associated factors, Part C(Sanker L.Adhya and Susan Garges(eds))2003

    • Author(s)
      Mitsuhiro Shimizu, Aaron P.Mitchell
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Mitsuhiro Shimizu: "Yeast Ume6p repressor permits activator binding but restricts TATA-box binding protein association with the HOP1 promoter"Nucleic Acids Res.. 31・12. 3033-3037 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Hiroshi Yoshioka: "Separation and recovery of DNA fragments by electrophoresis through a thermoreversible hydrogel of multiplied block copolymers composed of poly (ethylene oxide) and poly (propylene oxide)"Anal.Biochem.. 323・2. 218-223 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Katsuki Ono: "The linker histone homolog Hho1p from Saccharomyces cerevisiae represents a winged helix-turn-helix fold as determined by NMR spectroscopy"Nucleic Acids Res.. 31・24. 7199-7207 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Yoichi Shibusawa: "Purification of single-strand DNA binding protein from an Escherichia coli lysate using counter-current chromatography, partition and precipitation"J.Chromatogr.B. 793・2. 275-279 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Mitsuhiro Shimizu: "Hap1p photofootprinting as an in vivo assay of repression mechanism in Saccharomyces cerevisiae"Methods in Enzymology (S.L.Adhya and S.Garges., eds). 370. 479-487 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Yasuyuki Nakakumra: "Distorted DNA structures induced by HMGB2 possess a high affinity for HMGB2"J. Biochem.. 131. 153-160 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Nobuyuki Tomita: "Effects of triplet repeat sequences on nucleosome positioning and gene expression in yeast minichromosomes"Nucleic Acids Res. Supple.. 2. 231-232 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Shinya Saito: "The role of nuclosome positioning in repression by the yeast α2/Mcm1p repressor"Nucleic Acids Res. Supple.. 2. 93-94 (2002)

    • Related Report
      2002 Annual Research Report

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Published: 2002-04-01   Modified: 2016-04-21  

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