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
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