Development and application of methods for identifying protein-DNA interactions in a tissue-specific manner

• Project/Area Number: 15K14527
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Developmental biology
• Research Institution: Kochi University of Technology
• Principal Investigator: Kamachi Yusuke 高知工科大学, 環境理工学群, 教授 (90263334)
• Project Period (FY): 2015-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000); Fiscal Year 2016: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000); Fiscal Year 2015: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
• Keywords: 転写因子 / クロマチン免疫沈降 / エピトープタグ / クロマチン免疫沈降法

Outline of Final Research Achievements

Analysis of the interaction between protein and genomic DNA in cells is important for understanding gene regulatory mechanism. A technique called chromatin immunoprecipitation is used for this purpose, but there are various technical limitations such as the requirement of high quality antibodies. This research aims to develop a versatile method that detects protein-DNA interactions in specific tissues of animal embryos with high sensitivity by introducing a specific short amino acid sequence such as a biotin tag to the target protein.

Research Products

• [Journal Article] Cooperation of Sall4 and Sox8 transcription factors in the regulation of the chicken Sox3 gene during otic placode development (2018)
  • Author(s): Okamoto Yu、Nishimura Naoko、Matsuda Kazunari、Ranawakage Deshani C.、Kamachi Yusuke、Kondoh Hisato、Uchikawa Masanori
  • Journal Title: Development, Growth & Differentiation Volume: 60 Issue: 3 Pages: 133-145
  • DOI: 10.1111/dgd.12427
  • Peer Reviewed / Open Access
• [Journal Article] Regulation of trunk neural crest delamination by δEF1 and Sip1 in the chicken embryo (2016)
  • Author(s): Yasumi, T., Inoue, M., Maruhashi, M., Kamachi, Y., Higashi, Y., Kondoh, H., Uchikawa, M.
  • Journal Title: Dev. Growth. Differ. Volume: 58 Issue: 2 Pages: 205-214
  • DOI: 10.1111/dgd.12256
  • Peer Reviewed
• [Presentation] Optimization of epitope tagging for robust chromatin immunoprecipitation (2017)
  • Author(s): Deshani C. Ranawakage, Yusuke Kamachi
  • Organizer: The 6th International Symposium on Frontier Technology
  • Int'l Joint Research
• [Book] Sox2: Biology and Role in Development and Disease (Editors : Kondoh & Lovell-Badge) (2015)
  • Author(s): Y. Kamachi (Chapter 6: Evolution of Sox2 and Functional Redundancy in Relation to Other SoxB1 Genes)
  • Total Pages: 344
  • Publisher: Elsevier
• [Book] Sox2: Biology and Role in Development and Disease (Editors : Kondoh & Lovell-Badge) (2015)
  • Author(s): H. Kondoh and Y. Kamachi (Chapter 8: SOX2-Partner Factor Interactions and Enhancer Regulation)
  • Total Pages: 344
  • Publisher: Elsevier