Structural analysis of nucleosome containing methylated DNA

• Project/Area Number: 26840025
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Structural biochemistry
• Research Institution: Waseda University
• Principal Investigator: Osakabe Akihisa 早稲田大学, 理工学術院, 助教 (70632107)
• Project Period (FY): 2014-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000); Fiscal Year 2015: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2014: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000)
• Keywords: メチル化DNA / ペリセントロメア / ヘテロクロマチン / ヒストン / ヌクレオソーム / クロマチン / DNAメチル化 / エピジェネティクス / CpGダイヌクレオチド

Outline of Final Research Achievements

The aim of this study is to understand the mechanism how DNA methylation affects the chromatin structure. To this end, we reconstituted the nucleosome containing methylated DNA, and performed the biochemical and structural analyses of reconstituted nucleosomes. We determined the crystal structure of the nucleosome containing methylated DNA, and found that DNA methylation does not affect the intrinsic DNA wrapping property of the nucleosome. Furthermore, we found that the DNA methylation affects the translational position of the nucleosome and the flexibility of DNA ends of the nucleosome.

Research Products

• [Int'l Joint Research] National Institutes of Health(米国)
• [Int'l Joint Research] Friedrich Miescher Institute(スイス)
• [Journal Article] Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis. (2016)
  • Author(s): Urahama T, Harada A, Maehara K, Horikoshi N, Sato K, Sato Y, Shiraishi K, Sugino N, Osakabe A, Tachiwana H, Kagawa W, Kimura H, Ohkawa Y, Kurumizaka H.
  • Journal Title: Epigenetics Chromatin Volume: 9 Issue: 1 Pages: 1-16
  • DOI: 10.1186/s13072-016-0051-y
  • Peer Reviewed / Open Access
• [Journal Article] Crystal structure of the nucleosome containing ultraviolet light-induced cyclobutane pyrimidine dimer. (2016)
  • Author(s): Horikoshi N, Tachiwana H, Kagawa W, Osakabe A, Matsumoto S, Iwai S, Sugasawa K, Kurumizaka H.
  • Journal Title: Biochem Biophys Res Commun. Volume: 471 Issue: 1 Pages: 117-122
  • DOI: 10.1016/j.bbrc.2016.01.170
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] The C-terminal acidic domain of histone chaperone human NAP1 is an efficient binding-assistant for histone H2A-H2B but not H3-H4. (2016)
  • Author(s): Ohtomo, H., Akashi, S., Moriwaki, Y., Okuwaki, M., Osakabe, A., Nagata, K., Kurumizaka, H., Nishimura, Y.
  • Journal Title: Genes Cells Volume: 21 Issue: 3 Pages: 252-264
  • DOI: 10.1111/gtc.12339
  • NAID: 120007135590
  • Peer Reviewed / Open Access
• [Journal Article] Structure and function of human histone H3.Y nucleosome. (2016)
  • Author(s): Kujirai, T., Horikoshi, N., Sato, K., Maehara, K., Machida, S., Osakabe, A., Kimura, H., Ohkawa, Y. and Kurumizaka, H.
  • Journal Title: Nucleic Acids Research Volume: 1 Issue: 13 Pages: 1-15
  • DOI: 10.1093/nar/gkw202
  • Peer Reviewed / Open Access
• [Journal Article] Stable complex formation of CENP-B with the CENP-A nucleosome. (2015)
  • Author(s): Fujita R, Otake K, Arimura Y, Horikoshi N, Miya Y, Shiga T, Osakabe A, Tachiwana H, Ohzeki JI, Larionov V, Masumoto H, Kurumizaka H.
  • Journal Title: Nucleic Acids Res. Volume: in press Issue: 10 Pages: 4949-4922
  • DOI: 10.1093/nar/gkv405
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Dynamic changes in CCAN organization through CENP-C during cell-cycle progression. (2015)
  • Author(s): Nagpal H, Hori T, Furukawa A, Sugase K, Osakabe A, Kurumizaka H, Fukagawa T
  • Journal Title: Molecular biology of the cell Volume: 26 Issue: 21 Pages: 3768-3776
  • DOI: 10.1091/mbc.e15-07-0531
  • Peer Reviewed / Open Access
• [Journal Article] Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA. (2015)
  • Author(s): Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y, Kurumizaka H.
  • Journal Title: Open Biol. Volume: 5 Issue: 10 Pages: 150128-150128
  • DOI: 10.1098/rsob.150128
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome. (2015)
  • Author(s): Osakabe, A., Tachiwana, H., Kagawa, W., Horikoshi, N., Matsumoto, S., Hasegawa, M., Matsumoto, N., Toga, T., Yamamoto, J., Hanaoka, F., Thoma, N.H., Sugasawa, K., Iwai, S., Kurumizaka, H.
  • Journal Title: Scientific Reports Volume: 5 Issue: 1 Pages: 16330-16330
  • DOI: 10.1038/srep16330
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] N-terminal phosphorylation of HP1α increases its nucleosome-binding specificity. (2014)
  • Author(s): Nishibuchi G, Machida S, Osakabe A, Murakoshi H, Hiragami-Hamada K, Nakagawa R, Fischle W, Nishimura Y, Kurumizaka H, Tagami H, Nakayama JI.
  • Journal Title: Nucleic Acids Res. Volume: 42 Issue: 20 Pages: 12498-12511
  • DOI: 10.1093/nar/gku995
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Crystal structure of human nucleosome containing the testis-specific histone variant TSH2B. (2014)
  • Author(s): Urahama, T., Horikoshi, N., Osakabe, A., Tachiwana, H., and Kurumizaka, H.
  • Journal Title: Acta Cryst. Volume: F70 Issue: 4 Pages: 444-449
  • DOI: 10.1107/s2053230x14004695
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] クロマチンにおける紫外線損傷DNA認識機構の解析 (2016)
  • Author(s): 越阪部晃永、立和名博昭、堀越直樹、香川亘、松本翔太、山元淳平、花岡文雄、菅澤薫、岩井成憲、胡桃坂仁志
  • Organizer: 第33回染色体ワークショップ・第14回核ダイナミクス研究会
  • Place of Presentation: 松島
  • Year and Date: 2016-01-12
• [Presentation] Structural and biochemical analyses for accommodation and recognition of UV-damaged bases within nucleosome (2015)
  • Author(s): Akihisa Osakabe, Hiroaki Tachiwana, Wataru Kagawa, Naoki Horikoshi, Syota Matsumoto, Junpei Yamamoto, Fumio Hanaoka, Kaoru Sugasawa, Shigenori Iwai, Hitoshi Kurumizaka
  • Organizer: International Symposium on Chromatin Structure, Dynamics, and Function
  • Place of Presentation: 淡路島
  • Year and Date: 2015-08-23
  • Int'l Joint Research
• [Presentation] Biochemical and structural analyses of the nucleosome containing methylated DNA (2014)
  • Author(s): Akihisa Osakabe, Fumiya Adachi, Yasuhiro Arimura, Naoki Horikoshi, Yasuyuki Ohkawa, Hitoshi Kurumizaka
  • Organizer: EMBO Workshop: Histone Variants
  • Place of Presentation: Strasbourg
  • Year and Date: 2014-06-02 – 2014-06-04
• [Presentation] メチル化DNAを含むヌクレオソームの生化学的・構造生物学的機能解析 (2014)
  • Author(s): 越阪部晃永、足立風水也、有村泰宏、堀越直樹、大川恭行、胡桃坂仁志
  • Organizer: 第8回日本エピジェネティクス研究会年会
  • Place of Presentation: 東京
  • Year and Date: 2014-05-25 – 2014-05-27
• [Remarks] 研究代表者が所属する研究室のホームページ
  • URL: http://www.eb.waseda.ac.jp/kurumizaka/