ZFIN ID: ZDB-LAB-970513-1
Chris T. Amemiya Lab
PI/Director: Amemiya, Chris
Co-PI / Senior
Miyake, Tsutomu
Contact Person: Amemiya, Chris
Email: camemiya@benaroyaresearch.org
URL: http://www.benaroyaresearch.org/our-research/laboratories/principal-scientists/amemiya-laboratory
Address: Department of Molecular Genetics Benaroya Research Institute at Virginia Mason 1201 Ninth Avenue Seattle, WA 98101 USA
Country: United States
Phone: (206) 583-6573
Fax: (206) 583-2297
Line Designation: None assigned


We investigate the molecular evolution, early development and regulation of the immune system, particularly "rearranging" genes (immunoglobulins, T-cell receptors and variable lymphocyte receptors) and those involved in lymphopoeisis. We also study the evolution of developmental regulation (hox and dlx genes) in chordates. Our laboratory is actively involved in incorporating large-fragment molecular cloning methods for novel developmental genetic studies and for "comparative genomics." We are developing improved transgenic methods for BACs in order to generate zebrafish models of human disease.

Saha, Nil Ratan Post-Doc Smith, Jeramiah Post-Doc Rego, Michael Research Staff
Stuart, Andrew Research Staff Perdana, Ilham Fish Facility Staff

Kapp, F.G., Perlin, J.R., Hagedorn, E.J., Gansner, J.M., Schwarz, D.E., O'Connell, L.A., Johnson, N.S., Amemiya, C., Fisher, D.E., Wölfle, U., Trompouki, E., Niemeyer, C.M., Driever, W., Zon, L.I. (2018) Protection from UV light is an evolutionarily conserved feature of the haematopoietic niche. Nature. 558(7710):445-448
Gawriluk, T.R., Simkin, J., Thompson, K.L., Biswas, S.K., Clare-Salzler, Z., Kimani, J.M., Kiama, S.G., Smith, J.J., Ezenwa, V.O., Seifert, A.W. (2016) Comparative analysis of ear-hole closure identifies epimorphic regeneration as a discrete trait in mammals. Nature communications. 7:11164
Braasch, I., Gehrke, A.R., Smith, J.J., Kawasaki, K., Manousaki, T., Pasquier, J., Amores, A., Desvignes, T., Batzel, P., Catchen, J., Berlin, A.M., Campbell, M.S., Barrell, D., Martin, K.J., Mulley, J.F., Ravi, V., Lee, A.P., Nakamura, T., Chalopin, D., Fan, S., Wcisel, D., Cañestro, C., Sydes, J., Beaudry, F.E., Sun, Y., Hertel, J., Beam, M.J., Fasold, M., Ishiyama, M., Johnson, J., Kehr, S., Lara, M., Letaw, J.H., Litman, G.W., Litman, R.T., Mikami, M., Ota, T., Saha, N.R., Williams, L., Stadler, P.F., Wang, H., Taylor, J.S., Fontenot, Q., Ferrara, A., Searle, S.M., Aken, B., Yandell, M., Schneider, I., Yoder, J.A., Volff, J.N., Meyer, A., Amemiya, C.T., Venkatesh, B., Holland, P.W., Guiguen, Y., Bobe, J., Shubin, N.H., Di Palma, F., Alföldi, J., Lindblad-Toh, K., Postlethwait, J.H. (2016) The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics. 48(4):427-37
Tang, W.J., Fernandez, J.G., Sohn, J.J., Amemiya, C.T. (2015) Chitin Is Endogenously Produced in Vertebrates. Current biology : CB. 25(7):897-900
Amemiya, C.T., Alfoldi, 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., Karaku, 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.J., 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., Palma, F.D., Lander, E.S., Meyer, A., and Lindblad-Toh, K. (2013) The African coelacanth genome provides insights into tetrapod evolution. Nature. 496:311-316
Crow, K.D., Smith, C.D., Cheng, J.F., Wagner, G.P., and Amemiya, C.T. (2012) An Independent Genome Duplication Inferred from Hox Paralogs in the American Paddlefish—A Representative Basal Ray-Finned Fish and Important Comparative Reference. Genome biology and evolution. 4(9):937-953
Raincrow, J.D., Dewar, K., Stocsits, C., Prohaska, S.J., Amemiya, C.T., Stadler, P.F., and Chiu, C.H. (2011) Hox clusters of the bichir (Actinopterygii, Polypterus senegalus) highlight unique patterns of sequence evolution in gnathostome phylogeny. Journal of experimental zoology. Part B, Molecular and developmental evolution. 316(6):451-64
Shono, T., Kurokawa, D., Miyake, T., and Okabe, M. (2011) Acquisition of glial cells missing 2 Enhancers Contributes to a Diversity of Ionocytes in Zebrafish. PLoS One. 6(8):e23746
Lang, M., Hadzhiev, Y., Siegel, N., Amemiya, C.T., Parada, C., Strähle, U., Becker, M.B., Muller, F., and Meyer, A. (2010) Conservation of shh cis-regulatory architecture of the coelacanth is consistent with its ancestral phylogenetic position. EvoDevo. 1(1):11
Chen, L., Zhao, P., Wells, L., Amemiya, C.T., Condie, B.G., and Manley, N.R. (2010) Mouse and zebrafish Hoxa3 orthologues have nonequivalent in vivo protein function. Proc. Natl. Acad. Sci. USA. 107(23):10555-10560
Crow, K., Amemiya, C.T., Roth, J., and Wagner, G.P. (2009) Hypermutability of HoxA13A and functional divergence from its paralog are associated with the origin of a novel developmental feature in zebrafish and related taxa (Cypriniformes). Evolution; international journal of organic evolution. 63(6):1574-1592
Trede, N.S., Ota, T., Kawasaki, H., Paw, B.H., Katz, T., Demarest, B., Hutchinson, S., Zhou, Y., Hersey, C., Zapata, A., Amemiya, C.T., and Zon, L.I. (2008) Zebrafish mutants with disrupted early T-cell and thymus development identified in early pressure screen. Developmental dynamics : an official publication of the American Association of Anatomists. 237(9):2575-2584
Trede, N.S., Medenbach, J., Damianov, A., Hung, L.H., Weber, G.J., Paw, B.H., Zhou, Y., Hersey, C., Zapata, A., Keefe, M., Barut, B.A., Stuart, A.B., Katz, T., Amemiya, C.T., Zon, L.I., and Bindereif, A. (2007) Network of coregulated spliceosome components revealed by zebrafish mutant in recycling factor p110. Proc. Natl. Acad. Sci. USA. 104(16):6608-6613
Kurokawa, D., Sakurai, Y., Inoue, A., Nakayama, R., Takasaki, N., Suda, Y., Miyake, T., Amemiya, C.T., and Aizawa, S. (2006) Evolutionary constraint on Otx2 neuroectoderm enhancers-deep conservation from skate to mouse and unique divergence in teleost. Proc. Natl. Acad. Sci. USA. 103(51):19350-19355
Smith, J.J., and Voss, S.R. (2006) Gene order data from a model amphibian (Ambystoma): New perspectives on vertebrate genome structure and evolution. BMC Genomics. 7:219
Crow, K.D., Stadler, P.F., Lynch, V.J., Amemiya, C., and Wagner, G.P. (2006) The "Fish Specific" Hox Cluster Duplication is Coincident with the Origin of Teleosts. Mol. Biol. Evol.. 23(1):121-136
Metscher, B.D., Takahashi, K., Crow, K., Amemiya, C., Nonaka, D.F., and Wagner, G.P. (2005) Expression of Hoxa-11 and Hoxa-13 in the pectoral fin of a basal ray-finned fish, Polyodon spathula: implications for the origin of tetrapod limbs. Evolution & development. 7(3):186-195
Wagner, G.P., Takahashi, K., Lynch, V., Prohaska, S.J., Fried, C., Stadler, P.F., and Amemiya, C. (2005) Molecular Evolution of Duplicated Ray Finned Fish HoxA Clusters: Increased Synonymous Substitution Rate and Asymmetrical Co-divergence of Coding and Non-coding Sequences. Journal of molecular evolution. 60(5):665-676
Noonan, J.P., Grimwood, J., Danke, J., Schmutz, J., Dickson, M., Amemiya, C.T., and Myers, R.M. (2004) Coelacanth genome sequence reveals the evolutionary history of vertebrate genes. Genome research. 14(12):2397-2405
Yoder, J.A., Litman, R.T., Mueller, M.G., Desai, S., Dobrinski, K.P., Montgomery, J.S., Buzzeo, M.P., Ota, T., Amemiya, C.T., Trede, N.S., Wei, S., Djeu, J.Y., Humphray, S., Jekosch, K., Hernandez Prada, J.A., Ostrov, D.A., and Litman, G.W. (2004) Resolution of the novel immune-type receptor gene cluster in zebrafish. Proc. Natl. Acad. Sci. USA. 101(44):15706-15711
Wang, W.C., Anand, S., Powell, D.R., Pawashe, A.B., Amemiya, C.T., and Shashikant, C.S. (2004) Comparative cis-regulatory analyses identify new elements of the mouse Hoxc8 early enhancer. Journal of experimental zoology. Part B, Molecular and developmental evolution. 302(5):436-445
Amores, A., Suzuki, T., Yan, Y.-L., Pomeroy, J., Singer, A., Amemiya, C., and Postlethwait, J.H. (2004) Developmental roles of pufferfish hox clusters and genome evolution in ray-fin fish. Genome research. 14(1):1-10
Chiu, C.H., Dewar, K., Wagner, G.P., Takahashi, K., Ruddle, F., Ledje, C., Bartsch, P., Scemama, J.L., Stellwag, E., Fried, C., Prohaska, S.J., Stadler, P.F., and Amemiya, C.T. (2004) Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution. Genome research. 14(1):11-17
Force, A., Shashikant, C., Stadler, P., and Amemiya, C.T. (2004) Comparative genomics, cis-regulatory elements, and gene duplication. The Zebrafish: Genetics, Genomics and Informatics, 2nd ed., Methods Cell Biol.. 77:545-561
Traver, D., Herbomel, P., Patton, E.E., Murphey, R.D., Yoder, J.A., Litman, G.W., Catic, A., Amemiya, C.T., Zon, L.I., and Trede, N.S. (2003) The zebrafish as a model organism to study development of the immune system. Advances in immunology. 81:253-330
Martinez, P. and Amemiya, C.T. (2002) Genomics of the HOX gene cluster. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology. 133(4):571-580
Yoder, J.A., Nielsen, M.E., Amemiya, C.T., and Litman, G.W. (2002) Zebrafish as an immunological model system. Microbes and infection. 4(14):1469-1478
Chiu, C.-H., Amemiya, C., Dewar, K., Kim, C.-B., Ruddle, F.H., and Wagner, G.P. (2002) Molecular evolution of the HoxA cluster in the three major gnathostome lineages. Proc. Natl. Acad. Sci. USA. 99(8):5492-5497
Willett, C.E., Kawasaki, H., Amemiya, C.T., Lin, S., and Steiner, L.A. (2001) Ikaros expression as a marker for lymphoid progenitors during zebrafish development. Developmental dynamics : an official publication of the American Association of Anatomists. 222(4):694-698
Bahary, N., Ransom, D.G., Barut, B., Daniluk, D.A., Ferrando, A.A., Saganic, W.J., Fenton, L., Zhou, Y., Amemiya, C.T., and Zon, L.I. (2000) Characterization, genetic and physical mapping of the zebrafish mutant cloche. Blood. 96(11):297
Trede, N.S., Ota, T., Kawasaki, H., Barut, B., Paw, B.H., Zhou, Y., Hersey, C., Zapata, A., Amemiya, C.T., and Zon, L.I. (2000) A genetic screen in the zebrafish defines mutations required for the development of the immune system. Blood. 96(11):2633
Chiu, C.-H., Nonaka, D., Xue, L., Amemiya, C.T., and Wagner, G.P. (2000) Evolution of Hoxa-11 in lineages phylogenetically positioned along the fin-limb transition. Molecular phylogenetics and evolution. 17(2):305-316
Chiu, C.H., Amemiya, C.T., Carr, J.L., Bhargava, J., Hwang, J.K., Shashikant, C.S., Ruddle, F.H., and Wagner, G.P. (2000) A recombinogenic targeting method to modify large-inserts for cis-regulatory analysis in transgenic mice: construction and expression of a 100-kb, zebrafish Hoxa-11b-lacZ reporter gene. Development genes and evolution. 210(2):105-109
Amemiya, C.T. and Zon, L.I. (1999) Generation of a zebrafish P1 artificial chromosome library. Genomics. 58(2):211-213
Ruddle, F.H., Amemiya, C.T., Carr, J.L., Kim, C.B., Ledje, C., Shashikant, C.S., and Wagner, G.P. (1999) Evolution of chordate hox gene clusters. Annals of the New York Academy of Sciences. 870:238-248
Amemiya, C.T., Zhong, T.P., Silverman, G.A., Fishman, M.C., and Zon, L.I. (1999) Zebrafish YAC, BAC, and PAC genomic libraries. In The Zebrafish: Genetics and Genomics, H.W. Detrich, III, M. Westerfield, and L.I. Zon, eds., San Diego, CA: Academic Press, Methods Cell Biol.. 60:235-258
Amores, A., Force, A., Yan, Y.-L. Joly, L., Amemiya, C., Fritz, A., Ho, R., Langeland, J., Prince, V., Wang, Y.-L., Westerfield, M., Ekker, M., and Postlethwait, J.H. (1998) Zebrafish hox clusters and vertebrate genome evolution. Science (New York, N.Y.). 282:1711-1714
Amemiya, C.T. (1998) The zebrafish and haematopoietic justice. Nature Genetics. 20:222-223
Amemiya, C., Ota, T., and Litman, G. (1996) Construction of P1 artificial chromosome (PAC) libraries from lower vertebrates. In Nonmammalian Genomic Analysis: A Practical Guide. B. Birren and E. Lai, eds. San Diego: Academic Press.
Miyake, T. and Hall, B.K. (1994) Miyake, T. and B. K. Hall. 1994. Development of in vitro organ culture techniques for differentiation and growth of cartilages and bones from teleost fish with comparisons with in vivo skeletal development. Jour. Exp. Zool., 268 (1): 22-43. The Journal of experimental zoology. 268(1):22-43
Miyake, T., Huysseune, A., Hall, B.K., and Smith, M.M. (1991) Development of a CAM-grafting system for skeletal tissues of fishes. American zoologist. 31:47A