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Yi-Hsien Su's LAB｜Institute of Cellular and Organismic Biology, Academia Sinica

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Yi-Hsien Su's LAB

  • Yi-Hsien Su
    Research Fellow
    • SpecialtyDevelopmental Biology, Gene Regulatory Networks, Systems Biology
    • E-mailyhsu@gate.sinica.edu.tw
    • Tel02-2789-9511
    • LabR410/ICOB
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Lab IntroductionOpenClose
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Development of animal body plans is controlled by large networks of regulatory genes. Gene regulatory networks (GRNs) describe signaling pathways leading to the activation of DNA-recognizing regulatory proteins (transcription factors) and the interactions between the transcription factors and the modular DNA sequence elements that control spatial and temporal expression of regulatory genes. A given set of regulatory genes expressed in certain cells at a certain time during development specifies cell differentiation, organogenesis, and body plan formation.

My research has been focused on understanding the causal links between regulatory factors including signaling molecules and transcription factors that constitute developmental gene GRNs. My lab is especially interested in molecular mechanisms regulating animal body plan formation and axial pattering. We use sea urchins as a model organism because their embryos are easy to observe and the organization of the embryo is relatively simple. The available genomic resources and microinjection technique also make them an ideal model for GRN analysis. In addition, during sea urchin development, their body plans change several times from a radial blastula to a bilateral gastrula, via a left-right asymmetric larva stage, and eventually form a peculiar penta-symmetric body plan that is characteristic to the phylum Echinodermata. In the past few years, our main focus is to understand how BMP signals pattern dorsal-ventral and left-right axis in the sea urchin embryo. Several research projects have been developed following this direction. In addition, we have also been working on acorn worm Ptychodera flava collected in Taiwan for comparison studies. Acorn worms belong to Hemichordate, which is a sister group to Echinoderms including sea urchins. The acorn worm studies will shed light on the evolution of developmental mechanisms in deuterostomes.

 

Sea Urchin: ICOB Open House

Honor and AwardOpenClose

2020 Outstanding Research Award from Ministry of Science and Technology, Taiwan (科技部傑出研究獎)

2014 The Academia Sinica Research Award for Junior Research Investigators (中央研究院年輕學者研究著作獎)

2014 Ta-You Wu Memorial Award for Junior Research Investigators from Ministry of Science and Technology, Taiwan (科技部吳大猷先生紀念獎)

Lab MemberOpenClose
Name Job Title Telephone Email Remark
Han-Ru Li Research Assistant 02-2789-9517 -
Yi-Chih Chen Project Technician 02-2789-9517 -
Tzu-Pei Fan Postdoctoral Fellow 02-2789-9517 -
Yi-Hsien Su Research Fellow 02-2789-9511 yhsu@gate.sinica.edu.tw
PublicationOpenClose
  1. Chang, W.L. and Su, Y.H.* (2022) Zygotic hypoxia-inducible factor alpha regulates spicule elongation in the sea urchin embryo, Developmental Biology, 484, 63-74.
  2. Gil-Gálvez, A., Jiménez-Gancedo, S., Pérez-Posada, A., Franke, M., Acemel, R.D., Lin, C.Y., Chou, C., Su, Y.H., Yu, J.K., Bertrand, S., Schubert, M., Escrivá, H., Tena, J.J.*, Gómez-Skarmeta, J.L. (2022) Gain of gene regulatory network interconnectivity at the origin of vertebrates. Proceedings of the National Academy of Sciences of the United States of America, 119(11): e2114802119.
  3. Su, Y.H.* (2022) Dorsal-ventral axis formation in sea urchin embryos, Current Topics in Developmental Biology issue “Gene Regulatory Mechanisms in Development and Evolution: Insights from Echinoderms”, 146, 183-210  (invited book chapter).
  4. Lin, C.Y., Yu, J.K.*, Su, Y.H.* (2021) Evidence for BMP-mediated specification of primordial germ cells in the indirect-developing hemichordate, Evolution & Development, 23, 28-45
  5. Lin, C.Y., Lu, M.Y.J., Yue, J.X., Li, K.L., Le Petillon, Y., Yong, L.W., Chen, Y.H., Tsai, F.Y., Lyu, Y.F., Chen, C.Y., Hwang, S.P.L., Su, Y.H.*, Yu, J.K.* (2020) Single-blastomere transcriptome profiling reveals molecular asymmetry in the early amphioxus embryo, PLOS Genetics, 16(12): e1009294.
  6. Su, Y.H.*, Ota, K.G. (2020) Editorial: EvoDevo research in Asia, Evolution & Development, 22, 407-408.
  7. Yu, J.K.*, Su, Y.H. (2020) The evolution of the neural border and peripheral nervous system-Insights from invertebrate deuterostome animals (Book Chapter). Chapter 3 of Evolving Neural Crest Cells, edited by Brain Frank Eames, Danial Meulemans Medeiros, and Igor Adameyko, CRC Press.
  8. Li, Q., Zhang, P., Li, J., Yu, H., Zhan, X., Zhu, Y., Guo, Q., Tan, H., Lundholm, N., Garcia, L., Martin, M.D., Subirats, M.A., Su, Y.H., Ruiz-Trillo, I., Martindale, M.Q., Yu, J.K., Gilbert, M.T.P., Zhang, G., 2020. On the origin and evolution of RNA editing in metazoans. bioRxiv doi: https://doi.org/10.1101/2020.01.19.911685.
  9. Wang, Y.T., Tseng, T.L., Kuo, Y.C., Yu, J.K., Su, Y.H., Poss, K.D., Chen, C.H.* (2019) Genetic reprogramming of positional memory in a regenerating appendage. Current Biology, 29, 4193-4207.
  10. Coffman J.A.*, Su, Y.H.* (2019) Redox regulation of development and regeneration. Current Opinion in Genetics & Development: Developmental mechanisms, patterning and evolution, 57, 9-15 (invited review).
  11. Su, Y.H.*, Chen, Y.C., Ting, H.C., Fan, T.P., Lin, C.Y., Wang, K.T., Yu, J.K.* (2019) BMP controls dorsoventral and neural patterning in indirect-developing hemichordates providing insights into a possible origin of chordates. Proceedings of the National Academy of Sciences of the United States of America, 116, 12925-12932.
  12. Lin, C.Y., Oulhen, N., Wessel, G., Su, Y.H.* (2019) CRISPR/Cas9-mediated genome editing in sea urchins. Methods in Cell Biology, 151, 305-321 (Book Chapter).
  13. Campanale, J.P., Hamdoun, A., Wessel, G.M., Su, Y.H., Oulhen, N. (2019) Methods to label, isolate, and image sea urchin small micromeres, the primordial germ cells (PGCs). Methods in Cell Biology, 150, 269-292 (Book Chapter).
  14. Fan, T.P., Ting, H.C., Yu, J.K., Su, Y.H.* (2018) Reiterative use of FGF signaling in mesoderm development during embryogenesis and metamorphosis in the hemichordate Ptychodera flava. BMC Evolutionary Biology, 18, 120.
  15. Luttrell, S.M., Su, Y.H., Swalla, B.J.* (2018) Getting a head with Ptychodera flava larval regeneration. Biological Bulletin, 234, 152-164.
  16. Hu, M., Tseng, Y.C., Su, Y.H., Lein, E., Lee, H.G., Lee, J.R., Dupont, S., Stumpp, M.* (2017) Variability in larval gut pH regulation defines sensitivity to ocean acidification in six species of the Ambulacraria superphylum. Proceedings of the Royal Society B-Biological Sciences, 284, 20171066.
  17. Chang, W.L.#, Chang, Y.C.#, Lin, K.T., Li, H.R., Pai, C.Y., Chen, J.H., Su, Y.H.* (2017) Asymmetric distribution of hypoxia-inducible factor α regulates dorsoventral axis in the early sea urchin embryo. Development, 144, 2940-2950 (#contributed equally; cover and feature article).
  18. Su, Y.H.* and Yu, J.K.* (2017) EvoDevo: Changes in developmental controls underlying the evolution of animal body plans. Developmental Biology, 427, 177-178 (Editorial for the special issue).
  19. Cui, M. #, Lin, C.Y. #, and Su, Y.H.* (2017) Recent advances in functional perturbation and genome editing techniques in studying sea urchin development. Briefings in Functional Genomics, 16, 309-318 (invited review; #contributed equally).
  20. Chang, Y.C., Pai, C.Y., Chen, Y.C., Ting, H.C., Martinez, P., Telford, M.J., Yu, J.K., and Su, Y.H.* (2016) Regulatory circuit rewiring and functional divergence of the duplicate admp genes in dorsoventral axial patterning. Developmental Biology, 410, 108-118.
  21. Lin, C.Y. and Su, Y.H.* (2016) Genome editing in sea urchin embryos by using a CRISPR/Cas9 system. Developmental Biology, 409, 420-428.
  22. Lin, C.Y., Tung, C.H., Yu, J.K.*, Su, Y.H.* (2016) Reproductive periodicity, spawning induction, and larval metamorphosis of the hemichordate acorn worm Ptychodera flava. J Exp Zool B, 326, 47-60.
  23. Simakov, O.*, Kawashima, T., Marlétaz, F., Jenkins, J., Koyanagi, R., Mitros, T., Hisata, K., Bredeson, J., Shoguchi, E., Gyoja, F., Yue, J.X., Chen Y.C., Freeman, R.M. Jr, Sasaki, A., Hikosaka-Katayama, T., Sato, A., Fujie, M., Baughman, K.W., Levine, J., Gonzalez, P., Cameron, C., Fritzenwanker, J.H., Pani, A.M., Goto, H., Kanda, M., Arakaki, N., Yamasaki, S., Qu, J., Cree, A., Ding, Y., Dinh, H.H., Dugan, S., Holder, M., Jhangiani, S.N., Kovar, C.L., Lee, S.L., Lewis, L.R., Morton, D., Nazareth, L.V., Okwuonu, G., Santibanez, J., Chen, R., Richards, S., Muzny, D.M., Gillis, A., Peshkin, L., Wu, M., Humphreys, T., Su, Y.H., Putnam, N., Schmutz, J., Fujiyama, A., Yu, J.K., Tagawa, K., Worley, K.C., Kirschner, M.W., Lowe, C.J., Satoh, N.*, Rokhsar, D.S.*, Gerhart, J.* (2015) Hemichordate genomes and deuterostome origins. Nature, 527, 459-465.
  24. Andrikou, C., Pai, C.Y., Su, Y.H.*, Arnone, M.I.* (2015) Logics and properties of a genetic regulatory program that drives embryonic muscle development in an echinoderm. eLife, 4:e07343.
  25. Fan, T.P. and Su, Y.H.* (2015) FGF signaling repertoire of the indirect developing hemichordate Ptychodera flava. Marine Genomics, 24, 167-175.
  26. Stumpp, M., Hu, M.Y, Tseng, Y.C., Guh, Y.J., Chen Y.C., Yu, J.K., Su, Y.H., Hwang, P.P.* (2015) Evolution of extreme stomach pH in bilateria inferred from gastric alkalization mechanisms in basal deuterostomes. Scientific Reports, 5:10421.
  27. Satoh, N.*, Tagawa, K., Lowe, C., Yu, J.K., Kawashima, T., Takahashi, H., Ogasawara, M., Kirschner, M., Hisata, K., Su, Y.H., Gerhart, J. (2014) On a possible evolutionary link of the stomochord of hemichordates to pharyngeal organs of chordates. genesis, 52, 925-934.
  28. Chen, S.H., Li, K.L., Lu, I.H., Wang, Y.B., Tung, C.H., Ting, H.C., Lin, C.Y., Lin, C.Y.*, Su, Y.H.*, Yu, J.K.* (2014) Sequencing and analysis of the transcriptome of the acorn worm Ptychodera flava, an indirect developing hemichordate. Marine Genomics, 15, 35-43.
  29. Su Y.H.* (2014) Telling left from right: Left-right asymmetric controls in sea urchins. genesis, 52, 269-278 (invited review).
  30. Tung C.H. #, Cheng Y.R. #, Lin C.Y., Ho J.S., Yu J.K.*, Su Y.H.* (2014) A new copepod with transformed body plan and unique phylogenetic position parasitic in the acorn worm Ptychodera flava. Biological Bulletin, 226, 69-80 (#contributed equally).
  31. Ikuta T.#, Chen Y.C.#, Annunziata R., Ting H.C., Tung C.H., Koyanagi R., Tagawa K., Humphreys T., Fujiyama A., Saiga H., Satoh N., Yu J.K., Arnone M.I., Su Y.H.* (2013) Identification of an intact ParaHox cluster with temporal colinearity but residual spatial colinearity in the hemichordate Ptychodera flava. BMC Evolutionary Biology, 13, 129 (#contributed equally).
  32. Peterson K.J.*, Su Y.H., Arnone M.I., Swalla B.J., King, B. (2013) microRNAs support the monophyly of enteropneust hemichordates. J Experimental Zoology B, 320, 368-374.
  33. Ben-Tabou de-Leon S.*, Su Y.H.*, Lin, K.T., Li, E., Davidson, E.H.* (2013) Gene regulatory control in the sea urchin aboral ectoderm: Spatial initiation, signaling inputs, and cell fate lockdown. Developmental Biology, 374, 245-254.
  34. Luo Y.J., Su Y.H.* (2012) Opposing Nodal and BMP signals regulate left-right asymmetry in the sea urchin larva. PLoS Biology, 10(10), e1001402.
  35. Wu H.R., Chen Y.T., Su Y.H., Luo Y.J., Holland L.Z., Yu J.K.* (2011) Asymmetric localization of germline markers Vasa and Nanos during early development in the amphioxus Branchiostoma floridae. Developmental Biology, 353, 147-159.
  36. Chen J.H., Luo YJ, Su Y.H.* (2011) The dynamic gene expression patterns of transcription factors constituting the sea urchin aboral ectoderm gene regulatory network. Developmental Dynamics, 240, 410-421.
  37. Su Y.H.* (2009) Gene regulatory networks for ectoderm specification in sea urchin embryos. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, 1789, 261-267 (invited review).
  38. Su Y.H., Li E., Geiss G.K., Longabaugh W.J., Kramer A, Davidson E.H.* (2009) A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo. Developmental Biology, 329, 410-421. 
  39. Nam J, Su Y.H., Lee P.Y., Robertson A.J., Coffman J.A., Davidson E.H.* (2007) Cis-regulatory control of the nodal gene, initiator of the sea urchin oral ectoderm gene network. Developmental Biology, 306, 860-869.
  40. Churamani D, Boulware M.J., Geach T.J., Martin A.C., Moy G.W., Su Y.H., Vacquier V.D., Marchant J.S., Dale L, Patel S.* (2007) Molecular characterization of a novel intracellular ADP-ribosyl cyclase. PLoS One, 2(8): e797.
  41. Roux, M.M., Townley, I.K., Raisch, M., Reade, A., Bradham, C., Humphreys, G., Gunaratne, H.J., Killian, C.E., Moy, G., Su, Y.H., Ettensohn, C.A., Wilt, F., Vacquier, V.D., Burke, R.D., Wessel, G., and Foltz, K.R.* (2006) A functional genomic and proteomic perspective of sea urchin calcium signaling and egg activation. Dev Biol., 300, 416-433.
  42. Sea Urchin Genome Sequencing Consortium* (2006) The genome of the sea urchin Strongylocentrotus purpuratus. Science, 314, 941-952.
  43. Su, Y.H. and Vacquier, V.D.* (2006) Cyclic GMP-specific phosphodiesterase-5 regulates motility of sea urchin spermatozoa. Mol. Biol. Cell, 17, 114-121.
  44. Su, Y.H.*, Chen, S.H, Zhou, H., and Vacquier, V.D. (2005) Tandem mass spectrometry identifies proteins phosphorylated by cyclic AMP-dependent protein kinase when sea urchin sperm undergo the acrosome reaction. Developmental Biology, 285, 116-125.
  45. Su, Y.H. and Vacquier, V.D.* (2002) A flagellar K+-dependent Na+/Ca2+ exchanger keeps Ca2+ low in sea urchin spermatozoa. Proc. Natl. Acad. Sci. USA, 99, 6743-6748.
  46. Jang, C.W., Chen C.H., Chen, C.C., Chen, Jy.J., Su, Y.H., and Chen, R.H.* (2002) TGF-beta induces apoptosis through Smad-mediated expression of DAP-kinase. Nature Cell Biol., 4, 51-58.
  47. Tsai, Y.T.#, Su, Y.H.#, Fang, S.S., Huang, T.N., Qiu, Y., Jou, Y.S., Shih, H.M., Kung, H.J., and Chen, R.H.* (2000) Etk, a Btk family tyrosine kinase, mediates cellular transformation by linking Src to STAT3 activation. Mol. Cell Biol., 20, 2043-2054 (#contributed equally).
  48. Chen, R.H., Chang, M.C., Su, Y.H., Tsai, Y.T., and Kuo, M.L.* (1999) Interleukin-6 inhibits transforming growth factor-b-induced apoptosis through the phosphatidylinositol 3-kinase/Akt and signal transducers and activators of transcription 3 pathways. J. Biol. Chem., 274, 23013-23019.
  49. Hwang, S.P.L.*, Lin, Y.C., Su, Y.H., and Chen, C.P. (1999) Accelerated development of embryonic spicule and micromere-derived primary mesenchyme cell culture of the sea urchin Stomopneustes variolaris (Lamarck). Invertebr. Reprod. Dev., 35, 89-93.
  50. Chen, R.H.*, Su, Y.H., Chuang, R.L.C., and Chang, T.Y. (1998) Suppression of transforming growth factor-b-induced apoptosis through a phosphatidylinositol 3-kinase/Akt-dependent pathway. Oncogene, 17,1959-1968.