Structural basis for regulation of chromatin structure by DNA methylation

• Project/Area Number: 13480230
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Molecular biology
• Research Institution: Yokohama City University
• Principal Investigator: SHIRAKAWA Masahiro Yokohama City University, Graduate School of Integrated Science, Professer (00202119)
• Project Period (FY): 2001 – 2003
• Project Status: Completed (Fiscal Year 2003)
• Budget Amount: ¥12,800,000 (Direct Cost: ¥12,800,000); Fiscal Year 2003: ¥3,800,000 (Direct Cost: ¥3,800,000); Fiscal Year 2002: ¥4,000,000 (Direct Cost: ¥4,000,000); Fiscal Year 2001: ¥5,000,000 (Direct Cost: ¥5,000,000)
• Keywords: DNA methylation / ubiquitination / DNA repair / NMR / クロマチン / 動的構造 / ヒストン メチル / メチル化DNA結合蛋白質 / クロマチン構造 / エピジェネティックス / 転写 / ヒストン メチル化 / メチル化DNA / メチル化DNA結合ドメイン / 立体構造 / ミスマッチDNA

Research Abstract

The purpose of this study was to clarify the regulation of chromatin structures mediated by genome DNA methylation, and to investigate post-translational modifications of nuclear proteins by ubiquitin-like modifier proteins. We proceeded structural and functional analyses of the methylated DNA binding domain (MBD) of MBD1, the ubiquitin-like domain of human HR23B, and the ubiquitin-associated (UBA) domain of Saccharomyces cerevisae Rad23 and Lys 48- or Lys 63-linked di- or tetra-ubiquitin.
We analyzed the dynamic property of the complex between MBD1 MBD and a methylated DNA by using NMR, SPR and isothermal calorimetry. We have determined solution structure of ubiquitin-like domain of human HR23B in complex with a ubiquitin interacting motif of proteasomal S5a subunit by NMR. We also determined solution structure of the complex between the UBA domain of yeast DSK2 and ubiquitin. In addition, we showed that show the difference in structural properties of Lys 48- or Lys 63-linked ubiquitin chains by isotope-aided NMR and small angle X-ray scattering.

Research Products

• [Journal Article] Structure of the ubiquitin-interacting motif of S5a bound to the ubiquitin-like domain of HR23B. (2004)
  • Author(s): Fujiwara,K., Tenno,T., Sugasawa,K., Jee,J.-G., Ohki,I., Kojima,C., Tochio,H., Hiroaki,H., Hanaoka,F., shirakawa,M.
  • Journal Title: Journal of Biological Chemistry 279 Pages: 4760-4767
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Structure of the ubiquitin-interacting motif of S5a bound to the ubiquitin-like domain of HR23B (2004)
  • Author(s): Fujiwara, K., Tenno, T., Sugasawa, K., Jee, J.-G., Ohki, I., Kojima, C., Tochio, H., Hiroaki, H., Hanaoka, F., Shirakawa, M.
  • Journal Title: Journal of Biological Chemistry 279 Pages: 4760-4767
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The structure and binding mode of interleukin-18. (2003)
  • Author(s): Kato,Z, Jee,J.-G., Shikano,H., Mishima,M., Ohki,I., Ohnishi,H., Li,A., Hashimoto,K., Matsukuma,E., Omoya,K., Yamamoto,Y., Yoneda,T., Hara,T., Kondo,N., Shirakawa,M.
  • Journal Title: Nature Structural Biology 10 Pages: 966-971
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Structure of the male determinant factor for Brassica self-incompatibility. (2003)
  • Author(s): Mishima,M., Takayama,S., Saski,K., Jee,J.G., Kojima,C., Iogai,A., Shirakawa,M.
  • Journal Title: Journal of Biological Chemistry 278 Pages: 36389-36395
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Methylated DNA-binding domain 1 and methylpurine-DNA glycosylase link transcriptional repression and DNA repair in chromatin. (2003)
  • Author(s): Watanabe,S., Ichimura,T., Fujita,N., Tsuruzoe,S., Ohki,I., Shirakawa,M., Kawasuji,M., Nakao,M.
  • Journal Title: Proceedings of Natural Academy of Sciences USA 100 Pages: 12859-12864
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] The structure and binding modeof interleukin-18 (2003)
  • Author(s): Kato, Z, Jee, J.-G., Shikano, H., Mishima, M., Ohki, I., Ohnishi, H., Li, A., Hashimoto, K., Matsukuma, E., Omoya, K., Yamamoto, Y., Yoneda, T., Hara, T., Kondo, N., Shirakawa, M.
  • Journal Title: Nature Structural Biology 10 Pages: 966-971
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structure of the male determinant factor for Brassica self-incompatibility (2003)
  • Author(s): Mishima, M., Takayama, S., Sasaki, K., Jee, J.G., Kojima, C., Isogai, A., Shirakawa, M.
  • Journal Title: Journal of Biological Chemistry 278 Pages: 36389-36395
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Methylated DNA-binding domain 1 and methylpurine-DNA glycosylase link transcriptional repression and DNA repair in chromatin (2003)
  • Author(s): Watanabe, S., Ichimura, T., Fujita, N., Tsuruzoe, S., Ohki, I., Shirakawa, M., Kawasuji, M., Nakao, M.
  • Journal Title: Proceedings of Natural Academy of Sciences USA 100 Pages: 12859-12864
  • Description: 「研究成果報告書概要(欧文)」より
• [Publications] Auesukaree, C., Homma, T., Tochio, K., Shirakawa, M., Kaneko, Y., Harashima, S.: "Intracellular phosphate serves as a signal for the regulation of the PHO pathway in Saccaromyces cerevisiae"Journal of Biological Chemistry. (In press).
• [Publications] Fujiwara, K., Tenno, T., Sugasawa, K., Jee, J.-G., Ohki, I., Kojima, C., Tochio, H., Hiroaki, H., Hanaoka, F., Shirakawa, M.: "Structure of the ubiquitin-interacting motif of S5a bound to the ubiquitin-like domain of HR23B"Journal of Biological Chemistry. 279. 4760-4767 (2004)
• [Publications] Kato, Z, 他(全15名中15番目): "The structure and binding mode of interleukin-18"Nature Structural Biology. 10. 966-971 (2003)
• [Publications] Mishima, M., Takayama, S., Sasaki, K., Jee, J.G., Kojima, C., Isogai, A., Shirakawa, M.: "Structure of the male determinant factor for Brassica self-incompatibility"Journal of Biological Chemistry. 278. 36389-36395 (2003)
• [Publications] Takahashi, M., Maraboeuf, F., Sakai, Y., Yakushiji, H., Mishima, M., 他: "Role of tryptophan residues in the recognition of nutagenic oxidized nucleotides by human antimutator MTH1 protein"Journal of Molecular Biology. 319. 129-139 (2002)
• [Publications] Sakai, Y., Furuichi, M., Takahashi, M., Mishima, M., Iwai, S., 他: "A molecular basis for the selective recognition of 2-hydroxy-dATP and 8-oxo-dGTP by human MTH1"Journal of Biological Chemistry. 319. 8579-8587 (2002)
• [Publications] Kouno, T., Miura, K., Kanematsu, T., Shirakawa, M., Hirata, M., 他: "1H, 13C and 15N resonance assignments of GABARAP, GABAA receptor associated protein"Journal of Biomolecular NMR. 22. 97-98 (2002)
• [Publications] Takahashi, M., Maraboeuf, F., Sakai, Y.他: "Role of tryptophan resideus in recogrition of mutagenic oxdized nucleotides by human antimutator MTH1 protein"Journal of Molecular Biology. (印刷中).
• [Publications] Sakai, Y., Furuichi, M., Takahashi, M.他: "A molecular basis for the selective recognition of 2-hydroxy-dATP and 8-Oxo-dGTP by human MTH1"Journal of Biological Chemistry. (印刷中).
• [Publications] Kouno, T., Miura, K., Kanematsu, T.他: "1H, 13C and 15N resonance assignments of GABARAP, GABAA receptor associated protein"J. biomol. NMR. (印刷中).
• [Publications] Jee, J.-G., Ikegami, T., Hashimoto, M.他: "Solution Structure of the Fibronection TypeIII Domain from Bacillus cirulans WL-12 Chitinose A1"Journal of Biological Chemistry. 277. 1388-1397 (2002)
• [Publications] Ohki, I., Shimotake, N., Fujita, N.他: "Solution Structure of the Methyl-CpG-binding Domain of Human MBD1 in Complex with Methylated DNA"Cell. 105. 487-497 (2001)