脊索動物胚発生の分子発生システムゆらぎ測定と進化的保存性

• Project Area: Evolutionary theory for constrained and directional diversities
• Project/Area Number: 17H06387
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: The University of Tokyo
• Principal Investigator: 入江 直樹 東京大学, 大学院理学系研究科(理学部), 准教授 (10536121)
• Co-Investigator(Kenkyū-buntansha): 上坂 将弘 国立研究開発法人理化学研究所, 生命機能科学研究センター, 研究員 (20756499)
• Project Period (FY): 2017-06-30 – 2022-03-31
• Project Status: Granted (Fiscal Year 2021)
• Budget Amount: ¥145,340,000 (Direct Cost: ¥111,800,000、Indirect Cost: ¥33,540,000); Fiscal Year 2021: ¥22,880,000 (Direct Cost: ¥17,600,000、Indirect Cost: ¥5,280,000); Fiscal Year 2020: ¥24,830,000 (Direct Cost: ¥19,100,000、Indirect Cost: ¥5,730,000); Fiscal Year 2019: ¥26,520,000 (Direct Cost: ¥20,400,000、Indirect Cost: ¥6,120,000); Fiscal Year 2018: ¥29,380,000 (Direct Cost: ¥22,600,000、Indirect Cost: ¥6,780,000); Fiscal Year 2017: ¥41,730,000 (Direct Cost: ¥32,100,000、Indirect Cost: ¥9,630,000)
• Keywords: 進化 / 発生 / バイオインフォマティクス / EvoDevo / 進化発生生物学 / 反復説 / 砂時計モデル / 比較発生 / ゲノム / エピジェネティクス / 進化可能性 / 発生拘束 / 進化発生学

Outline of Annual Research Achievements

生物の表現型は進化を通して完全に変幻自在ではない。例えば動物のボディプラン（基本的な解剖宅的特徴）は、５億年以上前のカンブリア爆発期あるいはそれ以前に成立してから大きく変更された形跡がなく、強固に保存されてきた。このように進化的に強固に保存された形質は、系統慣性、あるいは系統拘束といった概念で説明されることが多く、進化しにくい性質があると予想されている。しかし、実際にそうした形質を進化的な多様化から拘束する何らかの仕組みがあるのか、あるいは単に適応的な形質だったために保存されたのか、それとも偶然の産物として保存されているのかについては明らかになっておらず、本課題ではこの問題に取り組んでいる。
発生砂時計モデルによれば、ボディプランが進化を通して保存されるのは、発生過程の保存された器官形成期が保存されるためだとしており、独立した複数の研究がこのモデル成立を支持している。しかし、すでに胚致死による負の選択圧ではこの器官形成期の保存性が説明できないことを明らかにしており、本課題では頑健性（非遺伝的な表現型揺らぎの小ささ）という観点に着目して研究を行っている。これまで、メダカ近交系を用いた器官形成期の揺らぎを測定し、発生初期や後期よりも揺らぎが小さいというデータが得られつつあるものの、技術誤差によるノイズの影響や発現量の影響など、様々な交絡要因が考えられたため、それらを緻密に除去する実験データの追加、再検証を行っている。結果として、やはり揺らぎと進化的保存正の相関を示唆する結果が得られつつある。また、多面的に発現する遺伝子と揺らぎの相関もみられつつある状況にあり、ボディプラン保存の背景にある進化メカニズムに寄与している可能性が濃厚となってきた。

Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

計画当初に想定していた揺らぎの測定系構築に成功した他、揺らぎと進化的保存性の相関もみえつつあるなど、順調に進展している。

Strategy for Future Research Activity

新型コロナ感染症の影響で思うように実験ができていない状況が続いているものの、概ねデータは揃いつつあり、最終的な解析を詰める予定である。また、技術発展もあり、細胞レベルでのボディプランの保存性解明という問題にも今年度は取り組む予定である。

Research Products

• [Int'l Joint Research] Boston University/California Institute of Technology/Brown University(米国)
• [Int'l Joint Research] Kunming Institute of Zoology/Yunnan Agricultural University/Chinese Academy of Sciences(中国)
• [Int'l Joint Research] BGI/PICB(中国)
• [Int'l Joint Research] Boston University(米国)
• [Int'l Joint Research] 昆明動物学研究所(中国)
• [Int'l Joint Research] ボストン大学/ブラウン大学(米国)
• [Journal Article] The developmental hourglass model and recapitulation: An attempt to integrate the two models. (2021)
  • Author(s): Uesaka, M., Kuratani, S., and Irie, N.
  • Journal Title: J Exp Zool B Mol Dev Evol. Volume: in press Issue: 1-2 Pages: 1-11
  • DOI: 10.1002/jez.b.23027
  • Peer Reviewed / Open Access
• [Journal Article] How can recapitulation be reconciled with modern concepts of evolution? (2021)
  • Author(s): Kuratani S, Uesaka M, Irie N.
  • Journal Title: J Exp Zool B Mol Dev Evol. Volume: in press Issue: 1-2 Pages: 1-8
  • DOI: 10.1002/jez.b.23020
  • Peer Reviewed / Open Access
• [Journal Article] Genomic insights of body plan transitions from bilateral to pentameric symmetry in Echinoderms (2020)
  • Author(s): Yongxin Li, et al. (35名中 35番目 Naoki Irie*)
  • Journal Title: Communications Biology Volume: 3:371 Issue: 1 Pages: 371-371
  • DOI: 10.1038/s42003-020-1091-1
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Toward understanding of evolutionary constraints: experimental and theoretical approaches (2020)
  • Author(s): Chikara Furusawa*, Naoki Irie*
  • Journal Title: Biophysical Reviews Volume: 12 Issue: 5 Pages: 1155-1161
  • DOI: 10.1007/s12551-020-00708-2
  • Peer Reviewed / Open Access
• [Journal Article] The developmental transcriptome for Lytechinus variegatus exhibits temporally punctuated gene expression changes (2020)
  • Author(s): John D. Hogan, et al. (Naoki Irie 19名中16番目)
  • Journal Title: Developmental Biology Volume: 460:2 Issue: 2 Pages: 139-154
  • DOI: 10.1016/j.ydbio.2019.12.002
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Recapitulation-like developmental transitions of chromatin accessibility in vertebrates (2019)
  • Author(s): Uesaka Masahiro、Kuratani Shigeru、Takeda Hiroyuki、Irie Naoki
  • Journal Title: Zoological Letters Volume: 5 Issue: 1 Pages: 33-33
  • DOI: 10.1186/s40851-019-0148-9
  • Peer Reviewed / Open Access
• [Journal Article] The phylum Vertebrata: a case for zoological recognition. (2018)
  • Author(s): Irie, N., Kuratani, S., and Satoh, N.
  • Journal Title: Zoological Lett Volume: 4 Issue: 1 Pages: 32-32
  • DOI: 10.1186/s40851-018-0114-y
  • Peer Reviewed / Open Access
• [Journal Article] Embryonic lethality is not sufficient to explain hourglass-like conservation of vertebrate embryos (2018)
  • Author(s): Yui Uchida, Masahiro Uesaka, Takayoshi Yamamoto, Hiroyuki Takeda and Naoki Irie
  • Journal Title: EvoDevo Volume: 9:7 Issue: 1 Pages: 1-11
  • DOI: 10.1186/s13227-018-0095-0
  • Peer Reviewed / Open Access
• [Journal Article] Centromere evolution and CpG methylation during vertebrate speciation (2017)
  • Author(s): Kazuki Ichikawa, Shingo Tomioka, Yuta Suzuki, Ryohei Nakamura, Koichiro Doi, Jun Yoshimura, Masahiko Kumagai, Yusuke Inoue, Yui Uchida, Naoki Irie, Hiroyuki Takeda* & Shinich Morishita*
  • Journal Title: Nature Communications Volume: 1833 Issue: 1 Pages: 1722-1730
  • DOI: 10.1038/s41467-017-01982-7
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Weighted gene co-expression network analysis reveals potential genes involved in early metamorphosis process in sea cucumber Apostichopus japonicus (2017)
  • Author(s): Yongxin Li, Mani Kikuchi, Xueyan Li, Qionghua Gao, Zijun Xiong, Yandong Ren, Ruoping Zhao, Bingyu Mao, Mariko Kondo, Naoki Irie, Wen Wang*
  • Journal Title: BBRC Volume: 495:1 Issue: 1 Pages: 1395-1402
  • DOI: 10.1016/j.bbrc.2017.11.154
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Constrained vertebrate evolution by pleiotropic genes. (2017)
  • Author(s): Hu H, Uesaka M, Guo S, Shimai K, Lu TM, Li F, Fujimoto S, Ishikawa M, Liu S, Sasagawa Y, Zhang G, Kuratani S, Yu JK, Kusakabe TG, Khaitovich P, Irie N; EXPANDE Consortium.
  • Journal Title: Nat Ecol Evol Volume: 1 Issue: 11 Pages: 1722-1730
  • DOI: 10.1038/s41559-017-0318-0
  • Peer Reviewed / Int'l Joint Research
• [Presentation] Developmental robustness may bias macroevolutionary outcome (2020)
  • Author(s): Naoki Irie
  • Organizer: 17th Spanish Society for Developmental Biology Meeting (Spain, online)
  • Int'l Joint Research / Invited
• [Presentation] 動物表現型進化の予測にむけて (2020)
  • Author(s): 入江直樹
  • Organizer: ExCELLS シンポジウム
  • Invited
• [Presentation] 動物ボディプランにみられる進化的慣性力の仕組みは？ (2020)
  • Author(s): 入江直樹
  • Organizer: 日本進化学会
  • Invited
• [Presentation] 遺伝子の使い回しは多様化にとって諸刃の剣か (2020)
  • Author(s): 入江直樹
  • Organizer: 日本分子生物学会
  • Invited
• [Presentation] Potential double-edged sword effect of gene re-usage toward evolutionary diversification (2019)
  • Author(s): Naoki Irie
  • Organizer: Molecular Biology Society of Japan
• [Presentation] Possible bias toward micro- and macro-evolutionary conservation by developmental systems (2019)
  • Author(s): Naoki Irie
  • Organizer: Workshoo reconciling micro-macro evolution (Oslo)
  • Int'l Joint Research / Invited
• [Presentation] Do echinoderm embryos follow hourglass-like divergence? (2019)
  • Author(s): Naoki Irie
  • Organizer: ICG-Ocean 2019
  • Int'l Joint Research / Invited
• [Presentation] What makes animal embryos to follow the hourglass model? (2019)
  • Author(s): Naoki Irie
  • Organizer: 日本生物物理学会
  • Invited
• [Presentation] Could have “small phenotypic fluctuation” contributed to the evolutionary conservation in vertebrate embryogenesis? (2019)
  • Author(s): Yui Uchida, Naoki Irie
  • Organizer: 21st Annual Meeting of the Society of Evolutionary Studies, Japan
• [Presentation] Development and Evolution (2019)
  • Author(s): Naoki Irie
  • Organizer: SERB School in Evolutionary Biology
  • Int'l Joint Research / Invited
• [Presentation] The developmental hourglass model in animal embryogenesis (2018)
  • Author(s): Naoki Irie
  • Organizer: Developmental Biology of Sea Urchin and other Marine Invertebrates
  • Int'l Joint Research / Invited
• [Presentation] Cost of complexity” contributed to the vertebrate bodyplan conservation? (2018)
  • Author(s): Naoki Irie
  • Organizer: Euro EvoDevo
  • Int'l Joint Research / Invited
• [Presentation] Gene re-usages constrained the evolvability of animal bodyplan? (2018)
  • Author(s): Naoki Irie
  • Organizer: EvoDevo Seminar series, Cambridge University
  • Invited
• [Presentation] “Cost of complexity” hypothesis supported in animal embryonic evolution? (2018)
  • Author(s): Naoki Irie
  • Organizer: The 1st AsiaEvo conference
  • Int'l Joint Research
• [Presentation] 遺伝子の使い回しは進化にとって諸刃の剣か？ (2018)
  • Author(s): 入江直樹
  • Organizer: 再生学異分野融合研究会
  • Invited
• [Presentation] 表現型揺らぎから探る進化の方向性と拘 (2018)
  • Author(s): 入江直樹
  • Organizer: 日本進化学会
• [Presentation] 複雑な遺伝子制御を持つ動物ほど進化可能性が低いかもしれない (2018)
  • Author(s): 入江直樹
  • Organizer: 生命の起源および進化学会
  • Invited
• [Presentation] In search for a general law of animal embryonic evolution? (2017)
  • Author(s): Naoki Irie
  • Organizer: he 12th International Workshop on Advanced Genomics [12AGW]
  • Int'l Joint Research / Invited
• [Presentation] What are the potential mechanisms that made vertebrates’ bodyplan conserved? (2017)
  • Author(s): Naoki Irie
  • Organizer: 50th Anniversary Meeting of Japanese Society of Developmental Biologists
• [Presentation] The developmental hourglass model: the law of embryonic evolution? (2017)
  • Author(s): Naoki Irie
  • Organizer: From Genetic Networks to a Cellular Wiring Diagram
  • Int'l Joint Research / Invited
• [Presentation] 複雑な遺伝子制御を持つ動物ほど進化可能性が低いかもしれない (2017)
  • Author(s): Naoki Irie
  • Organizer: 生命の起源および進化学会
  • Invited
• [Remarks] 入江直樹研究室
  • URL: http://www.bs.s.u-tokyo.ac.jp/~hassei/irie/index.html#home
• [Remarks] 新学術領域 進化制約方向性
  • URL: http://constrained-evo.org/
• [Remarks] 研究室ウェブサイト
  • URL: http://www.bs.s.u-tokyo.ac.jp/~hassei/irie/index.html#home
• [Funded Workshop] CDE Open Online Seminar series(1 ~ 3回) (2020)