ZFIN Person: Amemiya, Chris

ZFIN ID: ZDB-PERS-960805-28

ZFIN ID: ZDB-PERS-960805-28

Amemiya, Chris

Email:	camemiya@ucmerced.edu
URL:	https://Amemiyalab.org
Affiliation:	Chris T. Amemiya Lab
Address:	Department of Molecular and Cell Biology University of California, Merced 5200 N. Lake Road Merced, CA 95343
Country:	United States
Phone:	12092283377
Fax:
ORCID ID:

BIOGRAPHY AND RESEARCH INTERESTS

I have been interested in the origins of novelty and innovation in organisms (primarily vertebrates) and how changes in the genome can facilitate molecular and organismal adaptation in the long term, and the onset of disease in the short term. My laboratory uses whatever tools are necessary to address fundamental biological questions. This includes large-insert cloning, comparative genomics, computational biology, molecular genetics, imaging, biochemistry, and developmental biology. We often employ "deep branches" in vertebrate phylogeny as they allow us to study the origin of characters germane to higher vertebrates, and they provide very good vantage points for making comparisons with other organisms for deducing the genetic basis of biological innovations, such as limbs, lungs, and adaptive immune systems. A common thread in my laboratory's research is the use of comparative genomics methods for deducing genomic features that may be important for emergence of novelty. I have been involved in genomics from my early career as a postdoctoral fellow with the Human Genome Project, and I developed early PAC and BAC libraries of the zebrafish (which were critical for physical mapping and positional cloning of many developmental genes. We have used zebrafish experimentally for many years in order to verify our molecular analyses and to validate our inferences. My lab continues to work in areas germane to evolution and development of cellular structures and morphologies. I am a new faculty member at UC Merced (started in Fall 2017) and was brought on as a senior member. My new roles include research mentorship of junior faculty and contributing to the growth of a new research university. I am also the newest Chair of the Quantitative & Systems Biology program at UC Merced.

Complete List of Published Work in MyBibliography:
http://www.ncbi.nlm.nih.gov/sites/myncbi/chris%20t..amemiya.2/bibliograpahy/40448317/public/?sort=date&direction=descending

PUBLICATIONS

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

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

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. Proceedings of the National Academy of Sciences of the United States of America. 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. Proceedings of the National Academy of Sciences of the United States of America. 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. Proceedings of the National Academy of Sciences of the United States of America. 103(51):19350-19355

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. Proceedings of the National Academy of Sciences of the United States of America. 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

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

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

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 & 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. Proceedings of the National Academy of Sciences of the United States of America. 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.

NON-ZEBRAFISH PUBLICATIONS
Recent non-ZF Pubs:

Olsen, A.S., Combs, J., Garcia, E., Elliott, J., Amemiya, C., de Jong, P. and Threadgill, G. 1993. Automated production of high density cosmid and YAC colony filters with a robotic workstation. Biotechniques 14: 116-123.

Litman, G.W., Rast, J.P., Shamblott, M.J., Haire, R.N., Hulst, M., Roess, W., Litman, R.T., Hinds-Frey, K.R. and Amemiya, C.T. 1993. Phylogenetic diversification of immunoglobulin genes and the antibody repertoire. Molecular Biology and Evolution 10: 60-72.

Mahadevan, M.S., Amemiya, C., Jansen, G., Sabourin, L., Baird, S., Neville, C.E., Lamerdin, J., Batzer, M., de Jong, P. and Korneluk, R. 1993. Structure and genomic sequence of the myotonic dystrophy (DM kinase) gene. Human Molecular Genetics 2: 299-304.

Bellefroid, E., Marine, J-C., Ried, T., Riviere, M., Coulie, P.J., Lecocq, P.J., Amemiya, C.T., de Jong, P.J., Szpirer, J., Poncelet, D.A., Szpirer, C., Ward, D.C. and Martial, J.A. 1993. Lymphoid restricted expression of multiple differentially spliced krab-finger genes clustered on human chromosome 19p12-p13.1. EMBO Journal 12: 1363-1374.

Amemiya, C.T., Ohta, Y., Litman, R.T. Haire, R.N., Rast, J.P. and Litman, G.W. 1993. Implications of the immunoglobulin VH gene organization in the coelacanth, Latimeria chalumnae. Proceedings of the National Academy of Sciences 90: 6661-6665.

Litman, G.W., Amemiya, C.T., Hinds, K.R., Litman, R.S., Kokubu, F., Suzuki, D., Shamblott, M.J., Harding, F.A. and Haire, R.N. 1993. Evolutionary origins of immunoglobulin genes. In: Cooper, E.L., ed. Developmental Immunology, pp 108-128, Oxford University Press, New York.

Ioannou, P., Amemiya, C.T., Garnes, J., Kroisel, P.M., Shizuya, H., Chen, C., Batzer, M.A., and de Jong, P.J. 1994. A new bacteriophage P1-derived vector for the propagation of large human DNA fragments. Nature Genetics 6:84-89. (Co-first author).

Anderson, M., Amemiya, C., Luer, C., Litman, R., Rast, J., Niimura, Y. and Litman, G. 1994. Complete genomic sequence and patterns of transcription of a member of an unusual family of closely related, chromosomally dispersed immunoglobulin gene loci in Raja. International Immunology 6:1661-1670.

Litman, G.W., Rast, J.P., Hulst, M.A., Litman, R.T., Shamblott, M. J., Haire, R.N., Hinds-Frey, K.R., Buell, R.D., Margittai, M. Ohta, Y., Zilch, A.C., Good, R.A. and Amemiya, C.T. 1995. Evolutionary origins of immunoglobulin gene diversity. Progress in Immunology 8: 107-114.

Ohta, Y., Haire, R.N., Amemiya, C.T., Litman, R.T., Träger, T., Riess, O. and Litman, G.W. 1996. Human Txk: Genomic organization, structure, and contiguous physical linkage with the Tec gene. Oncogene 12: 937-942.

Ota, T. and Amemiya, C.T. 1996. An efficient, non-radioactive method for detection of restriction fragments from large P1 artificial chromosome clones. Genetic Analysis, Biomolecular Engineering 12: 173-178.

Ota, T., Rast, J.P., Margittai, M., Litman, G.W. and Amemiya, C.T. 1996. Studies on the early evolution of immunoglobulin genes. Current Topics on Molecular Evolution 1: 151-158.

Amemiya, C.T., Ota, T., Rast, J., Zon, L., and Litman, G.W. 1996. Organization and evolution of immunoglobulin genes, and identification of genes involved in regulation and ontogeny of the immune system. Current Topics on Molecular Evolution 1: 159-168.

Hoffman, S.M.G., Hromas, R., Amemiya, C. and Mohrenweiser, H.W. 1996. The localization of MZF-1 at the telomere of human chromosome 19q makes it vulnerable to degeneration in aging cells. Leukemia Research 20:81-283.

Amemiya, C.T., Ota, T. and Litman, G.W. 1996. Construction of P1 artificial chromosome (PAC) libraries from lower vertebrates. In: Birren, B. and Lai, E., eds. Nonmammalian Genomic Analysis: A Practical Guide, pp 223-256, Academic Press, NY.

Litman, G.W., Anderson, M.K., Rast, J.P. and Amemiya, C.T. 1997. Organization and mechanism of rearrangement of immunoglobulin genes in lower vertebrates. In: Herzenberg, L.A., Weir, D.M., Herzenberg, L.A. and Blackwell, C., eds. Weir's Handbook of Experimental Immunology, Chapter 18, Blackwell Science Limited, NY.

Strong, S.J., Ohta, Y., Litman, G.L. and Amemiya, C.T. 1997. Marked improvement of PAC and BAC cloning is achieved using electroelution of pulsed-field gel-separated partial digests of genomic DNA. Nucleic Acids Research: 25: 3959-3961.

Rast, J.P., Amemiya, C.T., Litman, R.T., Strong, S., and Litman, G.W. 1998. Distinct forms of immunoglobulin heavy chain organization in the ratfish, Hydrolagus colliei. Immunogenetics 47: 234-245.

Anderson, M.K., Strong, S.J., Litman, R.T., Luer, C.A., Amemiya, C.T., Rast, J.P. and Litman, G.W. 1999. A long form of the IgX in the skate exhibits a striking resemblance to the novel IgW and IgNARC genes in the shark. Immunogenetics 49: 56-67.

Bhargava, J., Shashikant, C.S., Carr, J.L., Bentley, K.L., Amemiya, C.T., and Ruddle, F.H. pPAC-ResQ: a yeast-bacterial shuttle vector for capturing inserts from P1 and PAC clones by recombinogenic targeted cloning. Genomics 56: 337-339.

Ruddle, F.H., Amemiya, C.T., Carr, J.L., Ledje, C., Shashikant, C.S., and Wagner, G. P. 1999. Evolution of chordate Hox gene clusters. New York Academy of Sciences 870: 238-248.

Strong, S. P., Mueller, M. G., Litman, R. T., Hawke, N. A., Haire, R. P., Miracle, A. L., Rast, J. P., Amemiya, C. T., and Litman, G. W. 1999. A novel multigene family encodes diversified variable regions. Proceedings of the National Academy of Sciences USA 96: 15080-15085.

Kim, C.-B., Amemiya, C., Bailey, W., Kawasaki, K., Mezey, J., Miller, W., Minoshima, S., Shimizu, N., Wagner, G., and Ruddle, F. 2000. Hox cluster genomics in the horn shark, Heterodontus francisci. Proceedings of the National Academy of Sciences USA 97: 1655-1660.

Zapata, A. and Amemiya, C. T. 2000. Phylogeny of lower vertebrates and their immunological structures. Current Topics in Microbiology and Immunology 248: 67-110.

Kim, C. B., Amemiya, C. T., Bailey, W., Kawasaki, K., Mezey, J., Miller, W., Minoshima, S., Shimizu, N., Wagner, G., and Ruddle, F. H. 2000. Hox cluster genomics in the horn shark, Heterodontus francisci. Proceedings of the National Academy of Sciences USA 97: 1655-1660.

Amemiya, C. T., Ota, T., Mueller, G. and Litman, G. W. 2001. Generation and characterization of a PAC genomic library of the Southern pufferfish, Spheroides nephelus. GENE 272: 283-289.

Amemiya, C. T. and Ikuta, T. 2001. Large-insert cloning and its applications for studying the developmental biology of hematopoiesis. In: Zon, L. I., ed. Hematopoiesis: A developmental approach, pp 663-671. Oxford University Press.

Irvine, S. Q., Carr, J. L., Shimizu, N., Bailey, Amemiya, C., and Ruddle, F. H. 2002. Genomic analysis of the Hox clusters in the sea lamprey Petromyzon marinus, Journal of Experimental Zoology (Molecular and Developmental Evolution) 294: 47-62.

Kim, C.-H., Shashikant, C. S., Sumiyama, K., Wang, W. C. H., Amemiya, C. T. and Ruddle, F. H. 2003. Phylogenetic analysis of the mammalian Hoxc8 non-coding region. Journal of Structural and Functional Genomics 3: 195-199.

Ota, T., Nguyen, T., Huang, E., Detrich, W., and Amemiya, C. T. 2003. Positive Darwinian selection operating on immunoglobulin heavy chain of antarctic fishes, Journal of Experimental Zoology (Molecular and Developmental Evolution) 295B: 45-58.

Ota, T., Rast, J. P., Litman, G. W. and Amemiya, C. T. 2003. lineage-restricted retention of a primitive immunoglobulin heavy chain isotype within the Dipnoi reveals an evolutionary paradox. Proceedings of the National Academy of Sciences USA 100: 2501-2506.