Robustness, flexibility and phase transitions of the gene regulatory network.

• Project/Area Number: 15KT0074
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Multi-year Fund
• Section: 特設分野
• Research Field: Constructive Systems Biology
• Research Institution: University of Tsukuba
• Principal Investigator: Wada Hiroshi 筑波大学, 生命環境系, 教授 (60303806)
• Co-Investigator(Kenkyū-buntansha): 矢田 哲士 九州工業大学, 大学院情報工学研究院, 教授 (10322728) ; 市瀬 夏洋 京都大学, 情報学研究科, 助教 (70302750)
• Project Period (FY): 2015-07-10 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥17,940,000 (Direct Cost: ¥13,800,000、Indirect Cost: ¥4,140,000); Fiscal Year 2018: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000); Fiscal Year 2017: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000); Fiscal Year 2016: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000); Fiscal Year 2015: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
• Keywords: 遺伝子制御ネットワーク / 形態進化 / 棘皮動物 / 軟体動物 / ネットワーク理論 / 発生システム浮動 / 遺伝子ネットワーク / ヒトデ / ウニ / 幼生骨片 / SPILE遺伝子群 / 新規遺伝子 / 砂時計モデル / 転写制御ネットワーク / 新規細胞タイプ

Outline of Final Research Achievements

Morphological evolution of animals was brought about by genetic changes. The genes responsible for morphogenesis function in the form of a gene regulatory network. We clarified how the characteristics of this network have been shaped by the need for robustness against mutations and environmental changes. The study of the early developmental processes of molluscs and echinoderms also revealed that this transcriptional regulatory network is much more diverse than previously thought. Network diversity that does not bring about many changes in developmental processes may have been linked to the creation of diverse forms of animals.

Academic Significance and Societal Importance of the Research Achievements

生物の進化は人が人生よりもはるかに長いスケールで進行する現象なので、一般社会に理解が浸透しにくい。自然選択の概念は比較的受け入れ安いが、選択の素材となる形態の多様性が遺伝子の書き換えからどのようにもたらされるかについて、わかりやすく説明することが求められている。本研究は、そのような形態の多様性の創造プロセスに、遺伝子制御機構のネットワークとしての性質が深くかかわることを示したものであり、社会の進化という現象の理解の増進に貢献した。

Research Products

• [Journal Article] Identification of a unique lamprey gene with tandemly repeated sequences and pharyngeal chondrocyte-specific expression (2019)
  • Author(s): Yokoyama Hiromasa、Morino Yoshiaki、Wada Hiroshi
  • Journal Title: Gene Volume: 701 Pages: 9-14
  • DOI: 10.1016/j.gene.2019.02.094
  • NAID: 120007133617
  • Peer Reviewed
• [Journal Article] The role of retinoic acid signaling in starfish metamorphosis (2018)
  • Author(s): Yamakawa Shumpei、Morino Yoshiaki、Honda Masanao、Wada Hiroshi
  • Journal Title: EvoDevo Volume: 9 Issue: 1 Pages: 1-11
  • DOI: 10.1186/s13227-018-0098-x
  • NAID: 120007134132
  • Peer Reviewed / Open Access
• [Journal Article] Asymmetry in indegree and outdegree distributions of gene regulatory networks arising from dynamical robustness (2018)
  • Author(s): Natsuhiro Ichinose, Tetsushi Yada, and Hiroshi Wada
  • Journal Title: Phys. Rev. E Volume: 97 Issue: 6 Pages: 062315-062315
  • DOI: 10.1103/physreve.97.062315
  • NAID: 120007133990
• [Journal Article] Regeneration of the acorn worm pygochord with the implication for its convergent evolution with the notochord (2018)
  • Author(s): Yoshimura Koji、Morino Yoshiaki、Wada Hiroshi
  • Journal Title: Development, Growth & Differentiation Volume: 61 Issue: 2 Pages: 158-165
  • DOI: 10.1111/dgd.12581
  • NAID: 120007128047
  • Peer Reviewed
• [Journal Article] Hemichordate nervous system (2018)
  • Author(s): Norio Miyamoto and Hiroshi Wada
  • Journal Title: Oxford Research Encyclopedia of Neuroscience. Volume: in press
  • Peer Reviewed
• [Journal Article] Hidden genetic history of the Japanese sand dollar Peronella (Echinoidea: Laganidae) revealed by nuclear intron sequences. (2018)
  • Author(s): Megumi Endo, Mamiko Hirose, Masanao Honda, Hiroyuki Koga, Yoshiaki Morino, Masato Kiyomoto and Hiroshi Wada
  • Journal Title: Gene Volume: in press
  • NAID: 120007134027
  • Peer Reviewed
• [Journal Article] Estimating optimal sparseness of developmental gene networks using a semi-quantitative model. (2017)
  • Author(s): Ichinose N, Yada T, Wada H.
  • Journal Title: PLoS One Volume: 12 Issue: 4 Pages: e0176492-e0176492
  • DOI: 10.1371/journal.pone.0176492
  • NAID: 120006309309
  • Peer Reviewed / Open Access
• [Journal Article] Expansion of TALE homeobox genes and the evolution of spiralian development (2017)
  • Author(s): Yoshiaki Morino, Naoki Hashimoto, and Hiroshi Wada
  • Journal Title: Nature, Ecology and Evolution Volume: 1 Issue: 12 Pages: 1942-1949
  • DOI: 10.1038/s41559-017-0351-z
  • Peer Reviewed
• [Journal Article] Reiterative expression of pax1 directs pharyngeal pouch segmentation in medaka (Oryzias latipes) (2016)
  • Author(s): Kazunori Okada, Keiji Inohaya, Takeshi Mise, Akira Kudo, Shinji Takada, and Hiroshi Wada
  • Journal Title: Development Volume: 143 Pages: 1800-1810
  • DOI: 10.1242/dev.130039
  • Peer Reviewed
• [Journal Article] Comparative morphology and development of extra-ocular muscles in the lamprey and gnathostomes reveal the ancestral state and developmental patterns of the vertebrate head. (2016)
  • Author(s): Suzuki D*, Fukumoto Y, Yoshimura M, Yamazaki Y, Kosaka J, Kuratani S, Wada H.
  • Journal Title: Zoological Letters Volume: 2 Issue: 1 Pages: 10-10
  • DOI: 10.1186/s40851-016-0046-3
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] The diversity of nanos expression in echinoderm embryos supports different mechanisms in germ cell specification (2016)
  • Author(s): Tara Fresques, Steven Zachary Swartz, Celina Juliano, Yoshiaki Morino, Mani Kikuchi, Koji Akasaka, Hiroshi Wada, Mamiko Yajima, and Gary M. Wessel
  • Journal Title: Evolutiona and Development Volume: 18 Issue: 4 Pages: 267-278
  • DOI: 10.1111/ede.12197
  • Int'l Joint Research
• [Journal Article] The conserved genetic background for pluteus arm development in brittlestars and sea urchin. (2016)
  • Author(s): Yoshiaki Morino, Hiroyuki Koga and Hiroshi Wada
  • Journal Title: Evolution and Development Volume: 18 Issue: 2 Pages: 89-95
  • DOI: 10.1111/ede.12174
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Experimental approach reveals the role of alx1 in the evolution of the echinoderm larval skeleton. (2016)
  • Author(s): Hiroyuki Koga, Haruka Fujitani, Yoshiaki Morino, Norio Miyamoto, Jun Tsuchimoto, Tomoko F. Shibata, Masafumi Nozawa, Shuji Shigenobu, Atsushi Ogura, Kazunori Tachibana, Masato Kiyomoto, Shonan Amemiya, Hiroshi Wada
  • Journal Title: Plos One Volume: 11 Issue: 2 Pages: e0149067-e0149067
  • DOI: 10.1371/journal.pone.0149067
  • NAID: 120007129678
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] ドメインシャッフリングは脊椎動物の新規形質に貢献したか (2019)
  • Author(s): 仮屋山博文、和田洋
  • Organizer: 動物学会関東支部71回大会
• [Presentation] Title of Presentation: Increased number of spiralian TALE homeobox genes in bivalve lineage and evolution of cell fate segregation program in the early development (2018)
  • Author(s): Supanat Phuangphong, Jumpei Tsunoda, Hiroshi Wada and Yoshiaki Morino
  • Organizer: 第70回細胞生物学会・第51回発生生物学会合同大会
  • Int'l Joint Research
• [Presentation] The increasing of spiralian TALE homeobox gene number and the modification of cell fate segregation pattern in bivalve early development (2018)
  • Author(s): Supanat Phuangphong, Jumpei Tsunoda, Hiroshi Wada and Yoshiaki Morino
  • Organizer: 日本動物学会 第89回大会
• [Presentation] Expansion of lineage-specific homeobox genes and the evolution of spiralian development (2018)
  • Author(s): Yoshiaki Morino and Hiroshi Wada
  • Organizer: 第70回細胞生物学会・第51回発生生物学会合同大会
  • Int'l Joint Research
• [Presentation] Evolution of the spiralian development: insights from lineage specific homeobox genes (2018)
  • Author(s): Yoshiaki Morino and Hiroshi Wada
  • Organizer: 7th Meeting of the European Society for European Developmental Biology
  • Int'l Joint Research
• [Presentation] 冠輪動物の割球特異化機構における発生システム浮動 (2018)
  • Author(s): 守野孔明、和田洋
  • Organizer: 日本進化学会第20回大会
  • Invited
• [Presentation] Lineage specific expansion of homeobox genes and evolution of spiralian development (2018)
  • Author(s): Yoshiaki Morino and Hiroshi Wada
  • Organizer: Developmental Biology of the Sea Urchin XXV
  • Int'l Joint Research / Invited
• [Presentation] The role of retinoic acid signaling in starfish metamorphosis (2018)
  • Author(s): Shumpei Yamakawa, Yoshiaki Morino, Masanao Honda and Hiroshi Wada,
  • Organizer: Developmental Biology of the Sea Urchin XXV
  • Int'l Joint Research
• [Presentation] The role of retinoic acid signaling in starfish metamorphosis (2018)
  • Author(s): Shumpei Yamakawa, Yoshiaki Morino, Masanao Honda and Hiroshi Wada
  • Organizer: 7th EURO EVO DEVO
  • Int'l Joint Research
• [Presentation] The role of retinoic acid signaling in starfish metamorphosis, (2018)
  • Author(s): Shumpei Yamakawa, Yoshiaki Morino, Masanao Honda and Hiroshi Wada
  • Organizer: International Echioderm Conference
  • Int'l Joint Research
• [Presentation] The role of retinoic acid signaling in starfish metamorphosis (2018)
  • Author(s): Shumpei Yamakawa, Yoshiaki Morino, Masanao Honda and Hiroshi Wada
  • Organizer: 第70 回日本細胞生物学会・第51 回日本発生生物学会合同大会
  • Int'l Joint Research
• [Presentation] イトマキヒトデにおけるレチノイン酸シグナル経路の役割 (2017)
  • Author(s): 山川隼平, 守野孔明, 和田洋
  • Organizer: 日本動物学会 第88回富山大会
• [Presentation] ヒトデ類におけるレチノイン酸シグナル経路の役割 (2017)
  • Author(s): 山川隼平, 守野孔明, 和田洋
  • Organizer: 2017年度生命科学系学会合同年次大会(Conbio2017)
• [Presentation] 棘皮動物の骨の進化を探る：NGSによる骨形成調節遺伝子の探索 (2017)
  • Author(s): 山嵜敦子、守野孔明、和田洋
  • Organizer: NGS現場の会 第五回研究会
• [Presentation] 冠輪動物特異的Homeobox 遺伝子と割球特異化機構に見られる発生システム浮動 (2017)
  • Author(s): 守野孔明, 和田洋
  • Organizer: 2017年度生命科学系学会合同年次大会(Conbio2017)
• [Presentation] 冠輪動物の初期発生に見られる発生システム浮動 (2017)
  • Author(s): 守野孔明, 和田洋
  • Organizer: 日本動物学会 第88回富山大会
• [Presentation] 軟体動物の割球特異化システムに見られる発生システム浮動 (2017)
  • Author(s): 守野孔明, 和田洋
  • Organizer: NGS現場の会 第五回研究会
• [Presentation] ワレカラ類における歩脚の消失と再獲得 (2017)
  • Author(s): 梶野瑞貴 和田洋
  • Organizer: 日本動物学会関東支部 第69回大会
  • Place of Presentation: 東京都港区 東京海洋大学
• [Presentation] イトマキヒトデにおける五放射相称の発生機構について (2017)
  • Author(s): 山川隼平, 守野孔明, 和田洋
  • Organizer: 日本動物学会関東支部 第69回大会
  • Place of Presentation: 東京都港区 東京海洋大学
• [Presentation] Expansion of TALE homeobox genes and the evolution of spiralian development (2016)
  • Author(s): Yoshiaki Morino, Naoki Hashimoto, Hiroshi Wada
  • Organizer: 22nd International Congress of Zoology & the 87th meeting of the ZSJ
  • Place of Presentation: Okinawa, Okinawa Institute of Science and Technology, Onna-son
  • Year and Date: 2016-11-14
  • Int'l Joint Research
• [Presentation] Acquisition of brachiolaria arms by co-option of regulatory module of tube feet (2016)
  • Author(s): Mao Nitobe, Yoshiaki Morino, Atsuko Yamazaki, Hiroshi Wada
  • Organizer: 22nd International Congress of Zoology & the 87th meeting of the ZSJ
  • Place of Presentation: Okinawa, Okinawa Institute of Science and Technology, Onna-son
  • Year and Date: 2016-11-14
  • Int'l Joint Research
• [Presentation] The screening of adult skeletogenic genes in a starfish Patiria pectinifera: Implications for innovation of larval skeletons in echinoderm (2016)
  • Author(s): Atsuko Yamazaki, Yoshiaki Morino, Mao Nitobe, Hiroshi Wada
  • Organizer: 22nd International Congress of Zoology & the 87th meeting of the ZSJ
  • Place of Presentation: Okinawa, Okinawa Institute of Science and Technology, Onna-son
  • Year and Date: 2016-11-14
  • Int'l Joint Research
• [Presentation] Characterization of gene regulatory network for adult skeletogenesis in a starfish Patiria pectinifera: Implications for innovation of larval skeletons in echinoderm (2016)
  • Author(s): Atsuko Yamazaki, Yoshiaki Morino, Mao Nitobe, Hiroshi Wada
  • Organizer: The European Society for Evolutionary Developmental Biology
  • Place of Presentation: Uppsala, Sweden
  • Year and Date: 2016-07-26
  • Int'l Joint Research
• [Presentation] イトマキヒトデの成体骨片形成メカニズムの解析：幼生骨片の「起源」を探る (2016)
  • Author(s): 山嵜敦子、守野孔明、山川隼平、仁戸部真生、和田洋
  • Organizer: 第13回棘皮動物研究集会
  • Place of Presentation: 東京都港区 東京海洋大学
• [Remarks] 研究成果は以下のHPにて公表している
  • URL: http://www.biol.tsukuba.ac.jp/~hwada/index.html