System level analysis of epigenomic regulation in mammalian embryo

• Project/Area Number: 22510220
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: System genome science
• Research Institution: Kyoto University (2012); The Institute of Physical and Chemical Research (2010-2011)
• Principal Investigator: KUMAKI Yuichi 京都大学, 医学研究科, 助教 (50455341)
• Project Period (FY): 2010 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2012: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2011: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2010: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
• Keywords: エピゲノム制御 / エピジェネティクス / DNA メチル化 / ヒストン修飾 / システムバイオロジー / バイオインフォマティクス / DNAメチル化 / エピゲノム

Research Abstract

Cytosine methylation at CpG site of genomic DNA is indispensable for mammalian development. However, a direct role of DNA methylation remains unclear. To reveal the effect of DNA methylation, we performed genome-wide analysis of gene expression and histone modifications of ES cells, differentiated me sodermal cells, nuclear transferred TS cells deficient for DNA methyltransferases. We found that the effect of DNA methylation loss on global expression profiles are modest, while global tendency of promoter histone modifications, especially H3K27me3, is sensitive to DNA methylation.

Research Products

• [Journal Article] DNA methylation restricts lineage-specific functions of transcription factor Gata4 during embryonic stem cell differentiation. (2013)
  • Author(s): Oda M, Kumaki Y, Shigeta M, Jakt LM, Matsuoka C, Yamagiwa A, Niwa H, Okano M.
  • Journal Title: PLOS Genetics Volume: 9 Issue: 6 Pages: e1003574-e1003574
  • DOI: 10.1371/journal.pgen.1003574
  • Peer Reviewed / Open Access
• [Journal Article] DNA Methylation Is Dispensable for the Growth and Survival of the Extraembryonic Lineages (2010)
  • Author(s): Morito Sakaue#, Hiroshi Ohta#, Yuichi Kumaki, Masaaki Oda, Yuko Sakaide, Chisa Matsuoka, Akiko Yamagiwa, Hitoshi Niwa, Teruhiko Wakayama and Masaki Okano
  • Journal Title: Current Biology Volume: 20 Issue: 16 Pages: 1452-1457
  • DOI: 10.1016/j.cub.2010.06.050
  • Peer Reviewed
• [Journal Article] DNA Methylation is Dispensable for the Growth and Survival of the Extraembryonic Lineages (2010)
  • Author(s): Morito Sakaue, Hiroshi Ohta, Yuichi Kumaki, Masaaki Oda, Yuko Sakaide, Chisa Matsuoka, Akiko Yamagiwa, Hitoshi Niwa, Teruhiko Wakayama, Masaki Okano
  • Journal Title: Current Biology Volume: 20 Pages: 1452-1457
  • Peer Reviewed
• [Presentation] Genome-wide analysis of histone modification in DNA methylation deficient cells (2011)
  • Author(s): Yuichi Kumaki, Akiko Yamagiwa, Chisa Matsuoka and Masaki Okano
  • Organizer: 第63回日本細胞生物学会大会
  • Place of Presentation: 札幌
  • Year and Date: 2011-06-27
• [Presentation] Genome-wide analysis of histone modification in DNA methylation deficient cells (2011)
  • Author(s): Kumaki, Y., Yamagiwa, A., Matsuoka, C., Okano, M.
  • Organizer: 第63回日本細胞生物学会大会
  • Place of Presentation: 北海道大学(札幌)
  • Year and Date: 2011-06-27
• [Presentation] Dnmt 欠損細胞におけるヒストン修飾の ChIP-chip 法による解析 (2010)
  • Author(s): 熊木勇一、山際晶子、松岡智沙、岡野正樹
  • Organizer: 第33回日本分子生物学会年会・第83回日本生化学会大会 合同大会
  • Place of Presentation: 神戸
  • Year and Date: 2010-12-09
• [Presentation] Dnmt 欠損細胞におけるヒストン修飾の ChIP-chip 法による解析 (2010)
  • Author(s): 熊木勇一、山際晶子、松岡智沙、岡野正樹
  • Organizer: 第4回エピジェネティクス研究会年会
  • Place of Presentation: 米子
  • Year and Date: 2010-05-28
• [Presentation] Dnmt欠損細胞におけるヒストン修飾のChIP-chip法による解析 (2010)
  • Author(s): 熊木勇一・山際晶子・松岡智沙・岡野正樹
  • Organizer: 第4回エピジェネティクス研究会年会
  • Place of Presentation: 米子
  • Year and Date: 2010-05-28
• [Presentation] Dnmt欠損細胞におけるヒストン修飾のChIP-chip法による解析 (2010)
  • Author(s): 熊木勇一・山際晶子・松岡智沙・岡野正樹
  • Organizer: 第33回日本分子生物学会年会・第83回日本生化学会大会 合同大会
  • Place of Presentation: 神戸