Chris Amemiya, PhD
Title:
Member
Email Address:
Phone Number:
(206) 583-6573
Background
Dr. Amemiya was born and raised in Hawaii. He completed his undergraduate studies at Purdue University and received his PhD in genetics from Texas A&M University. He was a recipient of an Alfred P. Sloan Fellowship in Molecular Studies of Evolution and completed postdoctoral studies with Dr. Gary Litman in comparative immunology (Tampa Bay Research Institute, Florida.). He took a second postdoctoral fellowship where he worked on the Human Genome Project with Dr. Pieter de Jong (Lawrence Livermore National Laboratory, California). After his postdoctoral training, Dr. Amemiya became a faculty member (Assistant-Associate Professor) in the Center for Human Genetics at the Boston University School of Medicine for seven years, where he taught medical genetics and studied the genetics of Duncan’s disease, an X-linked immunodeficiency disorder. While in Boston he participated in a mutation screen for immunodeficiency loci in zebrafish and began working on the comparative genomics and evolution of vertebrate HOX clusters. Dr. Amemiya moved to Benaroya Research Institute in 2001.
Areas of Research
We are interested in the origins of novelty and innovation in vertebrates, with special emphasis on the adaptive immune system and vertebrate bauplan. We use whatever tools are necessary to address fundamental biological questions, particularly large-insert cloning, comparative genomics, computational biology and developmental biology. Although our research is fundamental in scope, we are always looking for ways in which our findings may be relevant and applicable to biomedical research. Projects ongoing in the lab include efforts to characterize the antibody-based immune system of the so-called jawless vertebrates (lampreys and hagfishes). These animals do not utilize immunoglobulin domains for immune recognition molecules but instead use a completely different toolkit that centers on leucine rich repeat modules. We wish to understand the mode by which diversity is generated at the genomic and developmental levels and how the mechanism emerged in the first place. This work is tied into our recent work on the lamprey genome indicating that 20% of the chromatin (including coding sequences) is lost during embryonic development. The mechanism by which this loss is occurring is a central focus of the laboratory. Lastly, we have been studying the organization of HOX clusters across phylogeny. Hox genes are intimately involved in developmental patterning of the embryo and are often thought of as facilitators of evolutionary change. By studying the patterns of HOX clusters between major phylogenetic groups we hope to deduce how the Hox genes and their regulatory elements have contributed to vertebrate evolution and structural novelty.
Selected Publications
Zapata, A. and Amemiya, C. T. 2000. Phylogeny of lower vertebrates and their immunological structures. Curr. Topics Microbiol. Immunol. 248: 67-110.
Martinez, P. and Amemiya, C. T. 2002. Genomics of the HOX gene cluster. Comp. Bioch. Physiol. Part B 133: 569-578.
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. PNAS 100: 2501-1506.
Wagner, G. P., Amemiya, C. T., and Ruddle, F. H. 2003. Hox cluster duplications and the genetics of evolutionary novelties, PNAS 100: 14603-14606.
Powers, T. P. and Amemiya, C. T. 2004. Evidence for vertebrate Hox14 paralog group. Current Biology 14: R183-184.
Pancer, Z., Amemiya, C. T., Ehrhardt, G. R. A., Ceitlin, J., Gartland, G. L., and Cooper, M. D. 2004. Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey. Nature 430: 174-180.
Danke, J., Miyake, T., Powers, T., Schein, J., Shin, H., Bosdet, I., Erdmann, M., Caldwell, R. and Amemiya, C. T. 2004. Genome resource for the Indonesian coelacanth. J. Exptl. Zool., 301A: 228-234.
Ferrier, D. E. K., Dewar, K., Cook, A., Chang, J. L., Hill-Force, A. and Amemiya, C. 2005. The chordate ParaHox cluster. Current Biology 15: R820-822.
Amemiya, C. T. and Wagner, G. P. 2006. Animal Evolution: When did the "Hox system" arise? (Dispatch). Current Biology 16: R546-548.
Amemiya, C. T., Saha, N. R., and Zapata, A. G. 2007. Evolution and development of immunological structures in the lamprey. Curr. Opin. Immunol. 19: 535-541.
Amemiya, C. T., Prohaska, S. J., Hill-Force, A., Ferrier, D. E. K., Anaya, J. P., Garcia-Fernandez, J., Dewar, K., and Stadler, P. F. 2008. The amphioxus Hox cluster: Characterization, comparative genomics, and evolution. J. Exptl Zool. (Molec. Dev. Evol.) 310: 465-477.
Smith, J. J., Antonacci, F., Eichler, E. E., and Amemiya, C. T. 2009. Programmed loss of millions of base pairs from a vertebrate genome. PNAS 106: 11212-11217.
Amemiya, C. T. and Danilova. 2009. Going adaptive: the saga of antibodies. Annals of the New York Academy of Sciences 1168: 130-155.
Amemiya, C. T., Powers, T. P., Prohaska, S. J., Grimwood, J., Schmutz, J., Dickson, M., Miyake, T., Schoenborn, M. A., Myers, R. M., Ruddle, F. H., and Stadler, P. F. 2010. HOX clusters of Latimeria: Complete characterization provides further evidence for slow evolution of the coelacanth genome. PNAS, Epub ahead of print.
Saha, N. R., Smith, J. J., and Amemiya, C. T. 2010. Evolution of adaptive immune recognition in jawless vertebrates. Seminars in Immunology, Epub ahead of print.
Dr. Amemiya’s Department of Biology Web site, University of Washington
Dr. Amemiya’s Molecular and Cellular Biology Web site, University of Washington