Evolutionary analysis on regulatory mechanism of the Dlx3-7 gene cluster regarding evolution of morphological novelty.

• Project/Area Number: 18570007
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Genetics/Genome dynamics
• Research Institution: National Institute of Genetics
• Principal Investigator: SUMIYAMA Kenta National Institute of Genetics, Department of Population Genetics, Assistant professor (00370114)
• Project Period (FY): 2006 – 2007
• Project Status: Completed (Fiscal Year 2007)
• Budget Amount: ¥3,910,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥210,000); Fiscal Year 2007: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2006: ¥3,000,000 (Direct Cost: ¥3,000,000)
• Keywords: Development / Differentiation / Regulation of gene expression / Evolution / Gene / Genome / Transgenic mice / Evo-devo / cis-element

Research Abstract

The mammalian D1×3 and D1×7 genes are organized as a bigene cluster, and their respective expression patterns are controlled temporally and spatially by cis-elements that have been identified in the intergenic region of the cluster. Previous work showed that one of the conserved elements (137-2) was indeed a visceral arch enhancer that was able to recapitulate the nested expression pattern. We have extended these analyses to include twelve additional mammalian taxa (including a marsupial and a monotreme) in order to study evolution of the non-coding functional elements in mammals. Large-scale sequence comparisons and subsequent conservative motif extraction by the evolutionary rigidity assay (ERA) showed that each cis-element motif exhibited different degrees of evolutionary conservation among mammalian species. 137-1 harbored IL very old conservative motif that was shared by amphioxus distal-less gene. On the other hand, 137-2 exhibited less conservation between monotreme and marsupial/eutherian ancestor despite being highly conserved among marsupial/eutherian species. Since 137-2 has been shown to be important for the craniofacial expression, this intermittent evolution of 137-2 element may possibly be related to craniofacial innovation of mammals.

Research Products

• [Journal Article] Possible involvement of SINEs in mammalian-specific brain formation (2008)
  • Author(s): Sasaki T, et. al.
  • Journal Title: Proceedings of the National Academy of Sciences of the United States of America 105 Pages: 4220-4225
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Possible involvement of SINEs in mammalian-specific brain formation. (2008)
  • Author(s): Takeshi Sasaki, Hidenori Nishihara, Mika Hirakawa, Koji Fjimura, Mikiko Tanaka, Nobuhiro Kokubo, Chiharu Kimura-Yoshida, Isao Matsuo, Kenta Sumiyama, Naruya Saitou, Tomomi Shimogori, Norihiro Okada.
  • Journal Title: Proceedings of the National Academy of Sciences of the United States of America Peer reviewed 105 Pages: 4220-1225
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] 脊椎動物の比較ゲノム:遺伝子間領域の比較解析 (2007)
  • Author(s): 隅山 健太
  • Journal Title: 細胞工学 別冊 Pages: 50-55
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] A series of ENU-induced single base substitutions in a long-range cis-element altering Sonic hedgehog expression in the developing mouse limb bud (2007)
  • Author(s): Masuya H., et. al.
  • Journal Title: Genomics 89(2) Pages: 207-214
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Members of a novel gene family,Gsdm,are expressed exclusively in the epithelium of the skin and gastrointestinal tract in a highly tissue-specific manner (2007)
  • Author(s): Tamura M., et. al.
  • Journal Title: Genomics 89(5) Pages: 618-629
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Members of a novel gene family, Gsdm, are expressed exclusively in the epithelium of the skin and gastrointestinal tract in a highly tissue-specific manner. (2007)
  • Author(s): Masaru Tamura, Shigekazu Tanaka, Tomoaki Fujii, Aya Aoki, Hiromitu Komiyama, Kiyoshi Ezawa, Kenta Sumiyama, Tomoko Sagai, Toshihiko Shiroshi.
  • Journal Title: Genomics. Peer reviewed(2007) 89(5) Pages: 618-629
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Comparative genomic analysis of intergenic region in vertebrates. (2007)
  • Author(s): Kenta Sumiyama, Naruya Saitou
  • Journal Title: Saibou Kougaku ISBN978-4-87962-360-7 Pages: 50-55
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] 脊椎動物の比較ゲノム:遺伝子間領域の比較解析 (2007)
  • Author(s): 隅山健太
  • Journal Title: 細胞工学 別冊 Pages: 50-55
• [Journal Article] A series of ENU-induced single base substitutions in a long-range cis-element altering Sonic hedgehog expression in the developing mouse limb bud (2007)
  • Author(s): Masuya H., et al.
  • Journal Title: Genomics 89(2) Pages: 207-214
• [Journal Article] Members of a novel gene family, Gsdm, are expressed exclusively in the epithelium of the skin and gastrointestinal tract in a highly tissue-specific manner (2007)
  • Author(s): Tamura M., et al.
  • Journal Title: Genomics 89(5) Pages: 618-629
• [Journal Article] A series of ENU-induced single base substitutions in a long-range cis-element altering Sonic hedgehog expression in the developing mouse limb bud. (2006)
  • Author(s): Hiroshi Masuya, Hideki Sezutsu, Yoshiyuki Sakurba, Tomoko Sagai, Masaki Hosoya, Hideki Kaneda, Ikuo Miura, Kimio Kobayashi, Kenta Sumiyama, Aya Shimizu, Junko Nagano, Haruka Yokoyama, Satoko Kaneko, Noriko Sakurai, Yuka Okagaki, Tetsui Noda, Shigeharu Wakana, Yoichi Gondo, Toshihiki Shiroishi.
  • Journal Title: Genomics. Peer reviewed(2007) 89(2) Pages: 207-14
  • Description: 「研究成果報告書概要(欧文)」より
• [Presentation] Identification and evolutionary origin of a limb enhancer in the Dlx3-7 bigene cluster (2007)
  • Author(s): 隅山 健太
  • Organizer: 日本進化学会第9回大会
  • Place of Presentation: 京都大学
  • Year and Date: 2007-08-31
  • Description: 「研究成果報告書概要(和文)」より
• [Presentation] Identification and evolutionary origin of a limb enhancer in the D1x3-7 bigene cluster. (2007)
  • Author(s): Sumiyama K., Ruddle F.
  • Organizer: 9th annual meeting of Society of Evolutionary Studies, Japan
  • Place of Presentation: Kyoto
  • Year and Date: 2007-08-31
  • Description: 「研究成果報告書概要(欧文)」より
• [Presentation] Identification and evolutionary origin of a limb enhancer in the Dlx3-7 bigene cluster (2007)
  • Author(s): Sumiyama K
  • Organizer: Society for Molecular Biology and Evolution
  • Place of Presentation: Halifax,Canada
  • Year and Date: 2007-06-27
  • Description: 「研究成果報告書概要(和文)」より
• [Presentation] Identification and evolutionary origin of a limb enhancer in the D1x3-7 bigene cluster. (2007)
  • Author(s): Sumiyama K.
  • Organizer: Annual Meeting of the Society for Molecular Biology and Evolution
  • Place of Presentation: Halifax, Nova Scotia, Canada
  • Year and Date: 2007-06-27
  • Description: 「研究成果報告書概要(欧文)」より
• [Presentation] Identification and evolutionary origin of a limb enhancer in the Dlx3-7 bigene cluster. (2007)
  • Author(s): Sumiyama K
  • Organizer: Society for Molecular Biology and Evolution
  • Place of Presentation: Halifax, Canada
  • Year and Date: 2007-06-27
• [Presentation] Dlx3-7遺伝子クラスターの四肢エンハンサーの同定およびその進化的起源 (2007)
  • Author(s): 隅山 健太
  • Organizer: 第40回日本発生生物学会大会
  • Place of Presentation: 福岡国際会議場
  • Year and Date: 2007-05-30
  • Description: 「研究成果報告書概要(和文)」より
• [Presentation] Identification of a limb enhancer of D1x3-7 gene cluster and its evolutionary origin. (2007)
  • Author(s): Sumiyama K., Ruddle F.
  • Organizer: 40th annual meeting of the Japanese Society of Dvelopmental Biologists
  • Place of Presentation: Fukuoka
  • Year and Date: 2007-05-30
  • Description: 「研究成果報告書概要(欧文)」より
• [Presentation] Episodic rapid evolution on regulatory elements of the mammalian Dlx3-7 gene cluster. (2006)
  • Author(s): Sumiyama K.
  • Organizer: 8th annual meeting of Society of Evolutionary Studies, Japan
  • Place of Presentation: Yoyogi
  • Year and Date: 2006-08-29
  • Description: 「研究成果報告書概要(欧文)」より
• [Presentation] ほ乳類Dlx3-7遺伝子クラスター発現調節領域に起きた過去の急速な進化 (2006)
  • Author(s): 隅山 健太
  • Organizer: 第8回進化学会大会
  • Place of Presentation: 国立オリンピック記念青少年総合センター
  • Description: 「研究成果報告書概要(和文)」より