Dynamics of the genome compaction in the cell nucleus

2013 Fiscal Year Final Research Report

• Project Area: The physicochemical field for genetic activities
• Project/Area Number: 20114003
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Waseda University
• Principal Investigator: OHYAMA Takashi 早稲田大学, 教育・総合科学学術院, 教授 (60268513)
• Project Period (FY): 2008-11-13 – 2013-03-31
• Keywords: 遺伝情報の収納 / 細胞核 / クロマチン / 染色体 / 核内局在 / 遺伝子発現 / DNAメチル化 / 細胞分化

Research Abstract

We explored the principle that governs the packaging of DNA in the cell nucleus. The biggest finding was as follows: in yeast, the paths of nucleosomal arrays and the chromatin architectures are determined principally by the physical properties of genomic DNA and the size of the nucleus. The second biggest finding was that DNA sequence-based selective association occurs between nucleosomes with identical DNA sequences. Thus, physical properties of DNA, DNA sequence-based selective association between nucleosomes and the nucleus size are critical determinants in the genome compaction in the nucleus. Furthermore, we also found that most of the methylation introduced into DNA induces changes in conformation or physical-properties of the methylated sites, indicating some role of DNA methylation in the genome compaction in the nucleus.

Research Products

• [Journal Article] Positions of pluripotency genes and hepatocyte-specific genes in the nucleus before and after mouse ES cell differentiation (2014)
  • Author(s): Udagawa, K. and Ohyama, T.
  • Journal Title: Genet. Mol. Res Volume: 13 Pages: 1979-1988
  • DOI: 10.4238/2014.March.24.2
  • Peer Reviewed
• [Journal Article] Selective association between nucleosomes with identical DNA sequences (2013)
  • Author(s): Nishikawa, J. and Ohyama, T.
  • Journal Title: Nucleic Acids Res Volume: 41 Pages: 1544-1554
  • DOI: 10.1093/nar/gks1269
  • Peer Reviewed
• [Journal Article] S-like ribonuclease gene expression in carnivorous plants (2013)
  • Author(s): Nishimura, E., Kawahara, M., Kodaira, R., Kume, M., Arai, N., Nishikawa, J. and Ohyama, T.
  • Journal Title: Planta Volume: 238 Pages: 955-967
  • DOI: 10.1007/s00425-013-1945-6
  • Peer Reviewed
• [Journal Article] Most methylation-susceptible DNA sequences in human embryonic stem cells undergo a change in conformation or flexibility upon methylation (2013)
  • Author(s): Shimooka, Y., Nishikawa, J. and Ohyama, T.
  • Journal Title: Biochemistry Volume: 52 Pages: 1344-1354
  • DOI: 10.1021/bi301319y
  • Peer Reviewed
• [Journal Article] Regions with unusually high flexibility occur frequently in human genomic DNA (2013)
  • Author(s): Kimura, H., Kageyama, D., Furuya, M., Sugiyama, S., Murata, N. and Ohyama, T.
  • Journal Title: Biosci. Biotechnol. Biochem Volume: 77 Pages: 612-617
  • DOI: 10.1271/bbb.120850
  • Peer Reviewed
• [Journal Article] The genome folding mechanism in yeast (2013)
  • Author(s): Kimura, H., Shimooka, Y., Nishikawa, J., Miura, O., Sugiyama, S., Yamada, S. and Ohyama, T.
  • Journal Title: J. Biochemistry Volume: 154 Pages: 137-147
  • DOI: 10.1093/jb/mvt033
  • Peer Reviewed
• [Journal Article] Intrinsic homology-sensing and assembling property of chromatin fiber (2013)
  • Author(s): Nishikawa, J., Shimooka, Y. and Ohyama, T.
  • Journal Title: Meiosis (Bernstein, H. and Bernstein, C. (eds.)) (InTech)
  • DOI: 10.5772/56548
• [Journal Article] Nuclear localization of reporter genes activated by curved DNA (2012)
  • Author(s): Udagawa, K., Kimura, H., Tanabe, H. and Ohyama, T.
  • Journal Title: J. Biosci. Bioeng Volume: 113 Pages: 431-437
  • DOI: 10.1016/j.jbiosc.2011.11.022
  • Peer Reviewed
• [Journal Article] Competence of an artificial bent DNA as a transcriptional activator in mouse ES cells (2011)
  • Author(s): Tanase, J., Mitani, T., Udagawa, K., Nishikawa, J. and Ohyama, T.
  • Journal Title: Mol. Biol. Rep Volume: 38 Pages: 37-47
  • DOI: 10.1007/s11033-010-0075-5
  • Peer Reviewed
• [Journal Article] Highly efficient chromatin transcription induced by superhelically curved DNA segments: the underlying mechanism revealed by a yeast system (2010)
  • Author(s): Tanase, J., Morohashi, N., Fujita, M., Nishikawa, J., Shimizu, M. and Ohyama, T.
  • Journal Title: Biochemistry Volume: 49 Pages: 2351-2358
  • DOI: 10.1021/bi901950w
• [Journal Article] ゲノムDNAはいかにして折り畳まれるか-DNA物性とゲノム収納- (2009)
  • Author(s): 大山隆, 木村元, 下岡保俊
  • Journal Title: 実験医学増刊号「細胞核-遺伝情報制御と疾患」 Volume: 27 Pages: 2715-2722
• [Journal Article] The human actin-related protein hArp5 : nucleo-cytoplasmic shuttling and involvement in DNA repair (2009)
  • Author(s): Kitayama, K., Kamo, M., Oma, Y., Matsuda, R., Uchida, T., Ikura, T., Tashiro, S., Ohyama,T., Winsor, B. and Harata, M.
  • Journal Title: Exp. Cell Res Volume: 315 Pages: 206-217
  • DOI: 10.1016/j.yexcr.2008.10.028
  • Peer Reviewed
• [Journal Article] A common mechanical property shared by yeast nucleosomal DNAs (2008)
  • Author(s): Kimura, H. and Ohyama, T.
  • Journal Title: J. Adv. Sci Volume: 20 Pages: 37-40
  • DOI: 10.2978/jsas.20.37
  • Peer Reviewed
• [Journal Article] DNAの高次構造と物理的特性に印された遺伝情報 (2008)
  • Author(s): 大山隆
  • Journal Title: 蛋白質核酸酵素 Volume: 53 Pages: 1-11
• [Journal Article] Structural and functional characteristics of S-like ribonucleases from carnivorous plants
  • Author(s): Nishimura, E., Jumyo, S., Arai, N., Kanna, K., Kume, M., Nishikawa, J., Tanase, J. and Ohyama, T.
  • Journal Title: Planta Volume: (in press)
  • Peer Reviewed
• [Presentation] DNA sequence-dependent self-assembling property of chromatin fiber (2013)
  • Author(s): Nishikawa J., Shimooka Y. and Ohyama T.
  • Organizer: The 2013 ASCB annual meeting
  • Place of Presentation: New Orleans
  • Year and Date: 20131200
• [Presentation] Intrinsic homology-sensing and assembling property of chromatin (2013)
  • Author(s): Ohyama T.
  • Organizer: 23^<rd> Wilhelm Bernhard Workshop on the cell nucleus
  • Place of Presentation: Debrecen
  • Year and Date: 20130800
• [Presentation] Self-organizing and self-assembling properties of chromatin fiber (2013)
  • Author(s): Ohyama T.
  • Organizer: 1st Singapore-Japan-India Joint Symposium on Protein-DNA interactions in prokaryotic nucleoid and eukaryotic chromatin
  • Place of Presentation: Singapore
  • Year and Date: 20130700
  • Invited
• [Presentation] Characteristics of DNA in meiotic recombination hotspots (2012)
  • Author(s): Miura O., Kimura H., Ogake T. and Ohyama T.
  • Organizer: 2012 Annual Meeting of the American Society for Cell Biology
  • Place of Presentation: San Francisco
  • Year and Date: 20121200
• [Presentation] The genome folding principle as revealed by modelling of yeast interphase chromosomes (2011)
  • Author(s): Ohyama T.
  • Organizer: The 22ndWilhelm Bernhard Workshop
  • Place of Presentation: Latvia
  • Year and Date: 20110800
• [Presentation] The genome folding principle in yeast (2011)
  • Author(s): Kimura H., Shimooka Y., Nishikawa J., Miura O., Sugiyama S., Yamada S. and Ohyama T.
  • Organizer: The 22nd Wilhelm Bernhard Workshop
  • Place of Presentation: Latvia
  • Year and Date: 20110800
• [Presentation] Structural and physical properties of methylated DNA (2011)
  • Author(s): Shimooka Y. and Ohyama T.
  • Organizer: The 22ndWilhelm Bernhard Workshop
  • Place of Presentation: Latvia
  • Year and Date: 20110800
• [Presentation] Three-dimensional architecture of chromatin fibers in the interphase nucleus (2010)
  • Author(s): Kimura H., Shimooka Y., Nishikawa J., Miura O., Yamada S. and Ohyama T.
  • Organizer: The American Society for Cell Biology 50th Annual Meeting
  • Place of Presentation: Philadelphia
  • Year and Date: 20101200
• [Presentation] Self-assembly of nucleosomes (2010)
  • Author(s): Nishikawa J. and Ohyama T.
  • Organizer: The American Society for Cell Biology 50th Annual Meeting
  • Place of Presentation: Philadelphia
  • Year and Date: 20101200
• [Presentation] S-like RNase gene expression in carnivorous plants (2010)
  • Author(s): Nishimura E., Horiuchi S., Nozaki N. and Ohyama T.
  • Organizer: The American Society for Cell Biology 50th Annual Meeting
  • Place of Presentation: Philadelphia
  • Year and Date: 20101200
• [Presentation] How genomic DNA is functionally folded in a nucleus (2009)
  • Author(s): Ohyama T., Kimura H., Shimooka Y., Kageyama D., Furuya M., Udagawa K. and Tanase J.
  • Organizer: TheWilhelm Bernhard Workshop 21st InternationalWorkshop on the Cell Nucleus
  • Place of Presentation: Ustron, Poland
  • Year and Date: 20090800
• [Presentation] 3D structure of 10 nm chromatin fiber deduced from DNA flexibility (2009)
  • Author(s): Kimura H., Shimooka Y., Sugiyama S. and Ohyama T.
  • Organizer: TheWilhelm Bernhard Workshop 21st InternationalWorkshop on the Cell Nucleus
  • Place of Presentation: Ustron, Poland
  • Year and Date: 20090800
• [Presentation] Localization of transgenes activated by an artificial curved DNA (2009)
  • Author(s): Udagawa K., Yamamoto T., Fukagawa T. and Ohyama T.
  • Organizer: TheWilhelm Bernhard Workshop 21st InternationalWorkshop on the Cell Nucleus
  • Place of Presentation: Ustron, Poland
  • Year and Date: 20090800
• [Presentation] Stable transgene expression based on chromatin engineering (2009)
  • Author(s): Tanase J., Udagawa K. and Ohyama T.
  • Organizer: TheWilhelm Bernhard Workshop 21st InternationalWorkshop on the Cell Nucleus
  • Place of Presentation: Ustron, Poland
  • Year and Date: 20090800
• [Presentation] How genomic DNA is functionally folded in a nucleus (2009)
  • Author(s): Ohyama T., Kimura H., Kageyama D., Furuya M., Shimooka Y., Udagawa K. and Tanase J.
  • Organizer: 18th Lake Shirakaba Conference
  • Place of Presentation: Copenhagen
  • Year and Date: 20090600
  • Invited