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Experimental verification of genomic changes which caused human-specific characters

Research Project

Project/Area Number 23370101
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Physical anthropology
Research InstitutionNational Institute of Genetics

Principal Investigator

SAITOU Naruya  国立遺伝学研究所, 集団遺伝研究系, 教授 (30192587)

Co-Investigator(Kenkyū-buntansha) SUMIYAMA Kenta  国立遺伝学研究所, 集団遺伝研究系, 客員研究員 (00370114)
Project Period (FY) 2011-04-01 – 2014-03-31
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥20,150,000 (Direct Cost: ¥15,500,000、Indirect Cost: ¥4,650,000)
Fiscal Year 2013: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000)
Fiscal Year 2012: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
Fiscal Year 2011: ¥8,060,000 (Direct Cost: ¥6,200,000、Indirect Cost: ¥1,860,000)
Keywords分子・遺伝 / ホミニゼーション / CNS / 非コード領域 / 発生制御 / 比較ゲノム / 生物進化 / 人類進化 / 組織特異的エンハンサー / トランスジェニックマウス / 進化発生 / 転写制御
Research Abstract

We used transgenic mice experiment for inferring function of particular DNA fragments as well as comparative genomics. Some USA researchers proposed that positive selection on short non-coding DNA created new human-specific phenotype, while Sumiyama & Saitou (2012) found same phenotype by eliminating that DNA fragment. Therefore, it is possible that phenotype emerged by loss-of-function mutations which were selectively neutral. Babarinde & Saitou (2013) conducted genome comparison and found that primate specific conserved non-coding regions are far more abundant than three other mammalian lineages (rodents, carnivores, and cetariodactyla).

Report

(4 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • Research Products

    (41 results)

All 2014 2013 2012 2011 Other

All Journal Article (20 results) (of which Peer Reviewed: 20 results,  Open Access: 1 results,  Acknowledgement Compliant: 1 results) Presentation (13 results) (of which Invited: 5 results) Book (3 results) Remarks (5 results)

  • [Journal Article] Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders2013

    • Author(s)
      Babarinde I. and Saitou N
    • Journal Title

      Genome Biology and Evolution

      Volume: vol.5 Pages: 2330-2343

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] The African coelacanth genome provides insights into tetrapod evolution2013

    • Author(s)
      Amemiya C. T., Alföldi J., Lee A. P., Fan S., Philippe H., Maccallum I., Braasch I., Manousaki T., Schneider I., Rohner N., Organ C., Chalopin D., Smith J. J, Robinson M., Dorrington R. A., Gerdol M., Aken B., Biscotti M. A., Barucca M., Baurain D., Berlin A. M., Blatch G. L., Buonocore F., Burmester T., Campbell M. S., Canapa A., Cannon J. P., Christoffels A., De Moro G., Edkins A. L., Fan L., Fausto A. M., Feiner N., Forconi M., Gamieldien J., Gnerre S., Gnirke A., Goldstone J. V., Haerty W., Hahn M. E., Hesse U., Hoffmann S., Johnson J., Karchner S. I., Kuraku S., Lara M., Levin J. Z., Litman G. W., Mauceli E., Miyake T., Mueller M. G., Nelson D. R., Nitsche A., Olmo E., Ota T., Pallavicini A., Panji S., Picone B., Ponting C. P., Prohaska S. J., Przybylski D., Saha N. R., Ravi V., Ribeiro F. J. Sauka Spengler T., Scapigliati G., Searle S. M., Sharpe T., Simakov O., Stadler P. F., Stegeman J. J., Sumiyama K., Tabbaa D., Tafer H., Turner-Maier J., van Heusden P., White S., Williams L., Yandell M., Brinkmann H., Volff J. N., Tabin C. J., Shubin N., Schartl M., Jaffe D. B., Postlethwait J. H., Venkatesh B., Di Palma F., Lander E. S., Meyer A., Lindblad-Toh K
    • Journal Title

      Nature

      Volume: vol.496 Pages: 311-316

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] GDNF and endothelin 3 regulate migration of enteric neur crest-derived cells via protein kinase A and Rac12013

    • Author(s)
      Goto A., Sumiyama K., Kamioka Y., Nakasyo E., Ito K., Iwasaki M., Enomoto H.,and Matsuda M
    • Journal Title

      Journal of Neuroscience

      Volume: vol.33 Pages: 4901-4912

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] A SINE-derived element constitutes a unique modular enhancer for mammalian diencephalic Fgf82013

    • Author(s)
      Nakanishi A., Kobayashi N., Suzuki-HiranoA., Nishihara H., Sasaki T., Hirakawa M., Sumiyama K., Shimogori T., and Okada N
    • Journal Title

      PLOS ONE

      Volume: vol.7,no.8

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Vertebrate paralogous conserved non-coding sequences may be related to gene expressions in brain2013

    • Author(s)
      Matsunami M. and Saitou N
    • Journal Title

      Genome Biology and Evolution

      Volume: vol.5 Pages: 140-150

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders2013

    • Author(s)
      Babarinde I. and Saitou N.
    • Journal Title

      Genome Biology and Evolution

      Volume: 5 Issue: 12 Pages: 2330-2343

    • DOI

      10.1093/gbe/evt177

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The African coelacanth genome provides insights into tetrapod evolution2013

    • Author(s)
      Amemiya C.T., Alfoldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Sumiyama K, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K., et al.
    • Journal Title

      Nature

      Volume: 496 Issue: 7445 Pages: 311-316

    • DOI

      10.1038/nature12027

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] GDNF and endothelin 3 regulate migration of enteric neural crest-derived cells via PKA and Rac12013

    • Author(s)
      Goto A, Sumiyama K, Kamioka Y, Nakasho E, Ito K, Iwasaki M, Enomoto H, Matsuda M.
    • Journal Title

      Journal of Neuroscience

      Volume: 33 Issue: 11 Pages: 4901-4912

    • DOI

      10.1523/jneurosci.4828-12.2013

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Vertebrate Paralogous Conserved Noncoding Sequences May Be Related to Gene Expressions in Brain2013

    • Author(s)
      Masatoshi Matsunami, Naruya Saitou
    • Journal Title

      Genome Biology and Evolution

      Volume: 5 Issue: 1 Pages: 140-150

    • DOI

      10.1093/gbe/evs128

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identification and characterization of lineage-specific highly conserved noncoding sequences in mammalian genomes2012

    • Author(s)
      Takahashi M. and Saitou N
    • Journal Title

      Genome Biology and Evolution

      Volume: vol.4 Pages: 641-657

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Theria-specific homeodomain and cis-regulatory element evolution of the Dlx3-4 bigene cluster in 12 different mammalian species2012

    • Author(s)
      Sumiyama K., Miyake T., Grimwood J., Stuart A., Dickson M., Schmutz J., Ruddle F. H., Myers R. M., and Amemiya C. T
    • Journal Title

      Journal of Experimental Zoology Part B : Molecular and Developmental Evolution

      Volume: vol.318,no.8 Pages: 639-650

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Live Imaging of Protein Kinase Activities in Transgenic Mice Expressing FRET Biosensors2012

    • Author(s)
      Kamioka Y., Sumiyama K., Mizuno R., Sakai Y., Hirata E., Kiyokawa E., and Matsuda M., co-first authors
    • Journal Title

      Cell Structure and Function

      Volume: vol.37,no.1 Pages: 65-73

    • NAID

      40019581951

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] A SINE-Derived Element Constitutes a Unique Modular Enhancer for Mammalian Diencephalic Fgf8.2012

    • Author(s)
      Akiko Nakanishi, Naoki Kobayashi, Asuka Suzuki-Hirano, Hidenori Nishihara, Takeshi Sasaki, Mika Hirakawa, Kenta Sumiyama, Tomomi Shimogori, Norihiro Okada.
    • Journal Title

      PLoS ONE

      Volume: 7 Issue: 8 Pages: e43785-e43785

    • DOI

      10.1371/journal.pone.0043785

    • Related Report
      2013 Annual Research Report 2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identification and characterization of lineage-specific highly conserved noncoding sequences in mammalian genomes. Genome Biology and Evolution2012

    • Author(s)
      Takahashi M, Saitou N
    • Journal Title

      Genome Biology and Evolution

      Volume: (In press) Issue: 5 Pages: 641-657

    • DOI

      10.1093/gbe/evs035

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Loss-of-function mutation in a repressor module of human-specifically activated enhancer HACNS12011

    • Author(s)
      Sumiyama K. and Saitou N
    • Journal Title

      Molecular Biology and Evolution

      Volume: vol.28 Pages: 3005-3007

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Exploration for functional nucleotide sequence candidates within coding regions of mammalian genes2011

    • Author(s)
      Suzuki R. and Saitou N
    • Journal Title

      DNA Research

      Volume: vol.18,no.3 Pages: 177-183

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] A Mammalian Conserved Element Derived from SINE Displays Enhancer Properties Recapitulating Satb2 Expression in Early-Born Callosal Projection Neurons2011

    • Author(s)
      Tashiro K., Teissier A., Kobayashi N., Nakanishi A., Sasaki T., Yan K., Tarabykin V., Vigier L., Sumiyama K., Hirakawa M., Nishihara H., Pierani A., and Okada N
    • Journal Title

      PLOS ONE

      Volume: vol.6,no.12

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Loss-of-function mutation in a repressor module of human-specifically activated enhancer HACNS12011

    • Author(s)
      Kenta Sumiyama
    • Journal Title

      Molecular Biology and Evolution

      Volume: 28 Pages: 3005-3007

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Evolutionary patterns of recently emerged animal duplogs2011

    • Author(s)
      Kiyoshi Ezawa
    • Journal Title

      Genome Biology and Evolution

      Volume: 3 Pages: 1119-1135

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Exploration for functional nucleotide sequence candidates within coding regions of mammalian genes2011

    • Author(s)
      Rumiko Suzuki
    • Journal Title

      DNA Research

      Volume: 18 Pages: 177-183

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Presentation] 中立進化してきたホモ・サピエンス2013

    • Author(s)
      斎藤成也
    • Organizer
      日本環境変異原学会第42回大会
    • Place of Presentation
      岡山コンベンションセンター
    • Year and Date
      2013-11-29
    • Related Report
      2013 Final Research Report
    • Invited
  • [Presentation] Neutral mutations and purifying selection dominate genome evolution2013

    • Author(s)
      Saitou N
    • Organizer
      Commemorative Symposium for the 29th International Prize for Biology
    • Place of Presentation
      九州大学馬出キャンパス医学部百年講堂 大ホール
    • Year and Date
      2013-11-22
    • Related Report
      2013 Final Research Report
    • Invited
  • [Presentation] 霊長類レベルと現代人レベルの人類ゲノム学研究の紹介2013

    • Author(s)
      斎藤成也
    • Organizer
      第67回日本人類学会大会
    • Place of Presentation
      国立科学博物館上野本館
    • Year and Date
      2013-11-01
    • Related Report
      2013 Final Research Report
  • [Presentation] 人類進化におけるゲノム非コード領域転写調節機能進化解析の試み2012

    • Author(s)
      隅山 健太, 斎藤 成也
    • Organizer
      第66回日本人類学会大会
    • Place of Presentation
      慶應義塾大学日吉キャンパス
    • Year and Date
      2012-11-02
    • Related Report
      2013 Final Research Report
  • [Presentation] Toolkit genes, cis-regulatory modules, turnover, and evolvability2011

    • Author(s)
      隅山健太
    • Organizer
      第1回Tokyo Vertebrate Morphology Meeting
    • Place of Presentation
      東京(招待講演)
    • Year and Date
      2011-12-10
    • Related Report
      2011 Annual Research Report
  • [Presentation] 哺乳類ゲノムにおいて系統特異的に高度に保存された非コード塩基配列の同定とそれらの特性2011

    • Author(s)
      斎藤成也
    • Organizer
      日本遺伝学会第83回大会
    • Place of Presentation
      京都
    • Year and Date
      2011-09-22
    • Related Report
      2011 Annual Research Report
  • [Presentation] 胎盤形成に関与するDlx4遺伝子の獣亜綱(Theria)特異的なタンパク質コード領域および転写制御領域における分子進化と機能解析2011

    • Author(s)
      隅山健太
    • Organizer
      日本進化学会第13回大会
    • Place of Presentation
      京都
    • Year and Date
      2011-07-30
    • Related Report
      2011 Annual Research Report
  • [Presentation] No distinction of orthology/paralogy among human and chimpanzee Rh blood group genes2011

    • Author(s)
      Naruya Saitou
    • Organizer
      SMBE 2011
    • Place of Presentation
      京都
    • Year and Date
      2011-07-28
    • Related Report
      2011 Annual Research Report
  • [Presentation] Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders

    • Author(s)
      Babarinde I.
    • Organizer
      Society for Molecular Biology and Evolution
    • Place of Presentation
      Chicago, USA
    • Related Report
      2013 Annual Research Report
  • [Presentation] 脊椎動物ボディプラン進化における遺伝子重複によるシス転写調節機構新機能獲得進化の可能性

    • Author(s)
      隅山健太
    • Organizer
      日本遺伝学会第85回大会
    • Place of Presentation
      慶應義塾大学日吉キャンパス
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Heterogeneous mode and tempo of conserved noncoding sequence evolution among mammalian lineages and phylogenetic timescales

    • Author(s)
      Babarinde I.
    • Organizer
      日本遺伝学会第85回大会
    • Place of Presentation
      慶應義塾大学日吉キャンパス
    • Related Report
      2013 Annual Research Report
  • [Presentation] Neutral mutations and purifying selection dominate genome evolution

    • Author(s)
      Saitou N.
    • Organizer
      Commemorative Symposium for the 29th International Prize for Biology
    • Place of Presentation
      九州大学キャンパス
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 霊長類レベルと現代人レベルの人類ゲノム学研究の紹介

    • Author(s)
      斎藤成也
    • Organizer
      第67回日本人類学会大会
    • Place of Presentation
      国立科学博物館筑波分館
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Book] Introduction to Evolutionary Genomics2014

    • Author(s)
      Saitou N
    • Total Pages
      475
    • Publisher
      Springer
    • Related Report
      2013 Final Research Report
  • [Book] Introduction to Evolutionary Genomics2014

    • Author(s)
      Saitou N.
    • Total Pages
      484
    • Publisher
      Springer
    • Related Report
      2013 Annual Research Report
  • [Book] ダーウィン入門2011

    • Author(s)
      斎藤成也
    • Total Pages
      235
    • Publisher
      ちくま新書・東京都
    • Related Report
      2011 Annual Research Report
  • [Remarks] ENCODE 計画論文の問題点.斎藤成也生物の科学 遺伝 67(3) 275-278 2013年

    • Related Report
      2013 Final Research Report
  • [Remarks] 遺伝子図鑑 斎藤成也他編集 悠書館・東京 2013年272頁

    • Related Report
      2013 Final Research Report
  • [Remarks] 生物学辞典 第5版 巌佐庸,倉谷滋,斎藤成也,塚谷裕一編 岩波書店 2013年2192頁

    • Related Report
      2013 Final Research Report
  • [Remarks] 生物学辞典 第5版 巌佐庸,倉谷滋,斎藤成也,塚谷裕一編 岩波書店 2013年2192頁

    • Related Report
      2013 Final Research Report
  • [Remarks] <series モデル動物利用マニュアル>生物機能モデルと新しいリソース・ リサーチツール.隅山健太,川上浩一 (担当:分担執筆, 範囲:第6節 新しい生殖工学技術 第4項 トランスポゾンを使った 新しい高効率トランスジェニックマウス作製法)エル・アイ・シー 2011年674頁(656-658)

    • Related Report
      2013 Final Research Report

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Published: 2011-04-06   Modified: 2019-07-29  

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