Epigenomic variation and its relationship with genetic and phenotypic variations in the mouse

• Project/Area Number: 21200037
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research a proposed research project)
• Allocation Type: Single-year Grants
• Research Field: 基礎ゲノム科学; Genetics/Genome dynamics
• Research Institution: Kyushu University (2010-2011); National Institute of Genetics (2009)
• Principal Investigator: ICHIYANAGI Kenji 九州大学, 生体防御医学研究所, 助教 (70401560)
• Project Period (FY): 2009 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥30,940,000 (Direct Cost: ¥23,800,000、Indirect Cost: ¥7,140,000); Fiscal Year 2011: ¥10,010,000 (Direct Cost: ¥7,700,000、Indirect Cost: ¥2,310,000); Fiscal Year 2010: ¥10,010,000 (Direct Cost: ¥7,700,000、Indirect Cost: ¥2,310,000); Fiscal Year 2009: ¥10,920,000 (Direct Cost: ¥8,400,000、Indirect Cost: ¥2,520,000)
• Keywords: ゲノム多様性 / ゲノム機能・発現 / エピゲノム多様性 / エピゲノム / DNAメチル化 / 表現型分離 / 種分化 / レトロトランスポゾン

Research Abstract

Phenotypic variations within ａ population of ａ species can lead to speciation. Besides genetic variations, variations of epigenetic regulation, such as DNA methylation and histon post-translational modifications, among the individuals could be a source of such phenotypic variation. In this study, we first established ａ method to collect methylated genomic DNA regions, then utilized ａ next generation sequencer to compare DNA methylation between mouse strains of the identical species but different subspecies, which identified about 1500 and 4000 regions showing difference in DNA methylation levels between the strains in liver and sperm, respectively. Interestingly, about half of the regions identified in liver showed methylation difference in sperm as well. Together with a F1 hybrid analysis, the results suggest that majority of intraspecific epigenetic variations are due to cis-sequences of these regions.

Research Products

• [Journal Article] Inhibition of MspI cleavage activity by hydroxymethylation of the CpG site : A concern for DNA modification studies using restriction endonucleases (2012)
  • Author(s): Ichiyanagi, K.
  • Journal Title: Epigenetics Volume: 7 Issue: 2 Pages: 131-136
  • DOI: 10.4161/epi.7.2.18909
  • Peer Reviewed
• [Journal Article] Locus- and domain-dependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development (2011)
  • Author(s): Ichiyanagi, K., Li, Y., Watanabe, T., Ichiyanagi, T., Fukuda, K., Kitayama, J., Yamamoto, Y., Kuramochi-Miyagawa, S., Nakano, T., Yabuta, Y., Seki, Y., Saitou, M., Sasaki, H.
  • Journal Title: Genome Research Volume: 21 Issue: 10 Pages: 2058-2066
  • DOI: 10.1101/gr.
  • Peer Reviewed
• [Journal Article] Role for piRNAs and non-coding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus (2011)
  • Author(s): Watanabe, T., Tomizawa, S., Mitsuya, K., Totoki, Y., Yamamoto, Y., Kuramochi-Miyagawa, S., Iida, N., Hoki, Y., Murphy, P.J., Toyoda, A., Gotoh, K., Hiura, H., Arima, T., Fujiyama, A., Sado, T., Shibata, T., Nakano, T., Lin, H., Ichiyanagi, K., Soloway, P.D., Sasaki, H
  • Journal Title: Science Volume: 332 Issue: 6031 Pages: 848-52
  • DOI: 10.1126/science.1203919
  • Peer Reviewed
• [Journal Article] Role for piRNAs and non-coding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus. (2011)
  • Author(s): Watanabe, T., Tomizawa, S., Mitsuya, K., Totoki, Y., Yamamoto, Y., Kuramochi-Miyagawa, S., Iida, N., Hoki, Y., Murphy, P.J., Toyoda, A., Gotoh, K., Hiura, H., Arima, T., Fujiyama, A., Sado, T., Shibata, T., Nakeno, T., Lin, H., Ichiyanagi, K., Soloway, P.D., Sasaki
  • Journal Title: Science Volume: (印刷中)
  • Peer Reviewed
• [Journal Article] ゲノムワイドなＤＮＡメチル化解析 (2009)
  • Author(s): 一柳健司, 佐々木裕之
  • Journal Title: 分子細胞治療8 Pages: 372-376
• [Presentation] Epigenetic differences between mouse subspecies in somatic and germ cells (2011)
  • Author(s): Ichiyanagi, T, Toh, H., Ohkawa, Y., Sasaki, H., Ichiyanagi, K.
  • Organizer: Gordon Research Conference
  • Place of Presentation: 米国マサチュセッツ州
  • Year and Date: 2011-08-07
• [Presentation] Epigenetic differences between mouse subspecies in somatic and germ cells. (2011)
  • Author(s): Ichiyanagi, T., Toh, H., Ohkawa, Y., Sasakil, H., and Ichiyanagi, K.
  • Organizer: Gordon Research Conference
  • Place of Presentation: USA, MA
• [Presentation] マウス亜種間における体細胞および生殖細胞でのDNAメチル化の違い (2011)
  • Author(s): 一柳朋子, 藤英博, 大川恭行, 佐々木裕之, 一柳健司
  • Organizer: 第34回日本分子生物学会
  • Place of Presentation: 横浜
• [Presentation] piRNA-independent, but genomic-location-dependent control of DNA methylation of mouse B1 retrotransposon during male germ-line development. (2010)
  • Author(s): 一柳健司、李玉鳳、北山淳子、渡部聡朗、山本耕裕、佐々木裕之
  • Organizer: 第33回日本分子生物学会年会
  • Place of Presentation: 神戸
  • Year and Date: 2010-12-08
• [Presentation] マウス精子形成過程におけるB1レトロトランスポゾンのDNAメチル化はpiRNAに依存せず、ローカス特異的に制御されている (2010)
  • Author(s): 一柳健司、李玉鳳、北山淳子、渡部聡朗、山本耕裕、佐々木裕之
  • Organizer: 日本遺伝学会第82回札幌大会
  • Place of Presentation: 札幌
  • Year and Date: 2010-09-21
• [Remarks]
  • URL: http://www.bioreg.kyushu-u.ac.jp/labo/epigenome/index.html