Chris Amemiya, PhD
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 an X-linked immunodeficiency diseaser. 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. In 2007-2008, he served as a Program Director for the National Science Foundation in Washington D.C. He is a full professor in the Biology Department at the University of Washington.
Area of Research
Dr. Amemiya is interested in the origins of novelty and innovation in vertebrates, with special emphasis on the adaptive immune system and vertebrate bauplan. His lab uses whatever tools are necessary to address fundamental biological questions, particularly large-insert cloning, comparative genomics, computational biology and developmental biology. Although the research is fundamental in scope, his laboratory is always looking for ways in which their 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. These animals do not utilize immunoglobulin domains for immune recognition molecules but instead use a completely different toolkit that employs leucine rich repeat modules. Dr. Amemiya's laboratory wishes 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 to their 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, the group has 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 the laboratory hopes to deduce how the Hox genes and their regulatory elements have contributed to vertebrate evolution and structural novelty, such as the mammalian placenta. Many functional experiments are carried out in the zebrafish model system.
Amemiya CT. 2014. An Ancient Mariner: Biological implications of the coelacanth genome. The Biochemist 36: 23-27.
Saha NR, Ota T, Litman GW, Hansen J, Parra Z, Hsu E, Buonocore F, Canapa A, Cheng J-F, Amemiya CT. 2014. Genome complexity in the coelacanth is reflected in its adaptive immune system. J Exp Zool B (Mol Dev Evol.) 322:438-463.
Kawasaki K, Amemiya CT. 2014. SCPP Genes in the Coelacanth: Tissue mineralization genes shared by sarcopterygians. J Exp Zool B (Mol Dev Evol.) 322:390-402.
Amemiya CT, Dorrington R, Meyer A. 2014. The coelacanth and its genome. J Exp Zool B (Mol Dev Evol.) 322:317-321.
Chen, X, Bracht JR, Goldman AD, Dolzhenko E, Clay DM, Stewart EC, Perlman DH, Doak TG, Stuart A, Amemiya CT, Sebra RP, Landweber LF. 2014. The architecture of a scrambed genome reveals massive levels of genomic rearrangement during development. Cell 158:1187-1198.
Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Gamieldien J, Gnerre S, Gnirke A, Goldstone JV, Haerty W, Hahn ME, Hesse U, Hoffmann S, Johnson J, Karchner SI, Kuraku S, Lara M, Levin JZ, Litman GW, Mauceli E, Miyake T, Mueller MG, Nelson DR, Nitsche A, Olmo E, Ota T, Pallavicini A, Panji S, Picone B, Ponting CP, Prohaska SJ, Przybylski D, Saha NR, Ravi V, Ribeiro FJ, Sauka Spengler T, Scapigliati G, Searle SM, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tabbaa D, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K. 2013. The African coelacanth genome provides insights into tetrapod evolution. Nature. 496:311-316.
Robinson M, Amemiya CT. 2013. Coelacanths (Quick Guide). Current Biology 24:R62-3.
Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, Cook M, Krumlauf R, Wiedemann LM, Sower SA, Decatur WA, Hall JA, Amemiya CT, Saha NR, Buckley KM, Rast JP, Das S, Hirano M, McCurley N, Guo P, Rohner N, Tabin CJ, Piccinelli P, Elgar G, Ruffier M, Aken BL, Searle SM, Muffato M, Pignatelli M, Herrero J, Jones M, Brown CT, Chung-Davidson YW, Nanlohy KG, Libants SV, Yeh CY, McCauley DW, Langeland JA, Pancer Z, Fritzsch B, de Jong PJ, Zhu B, Fulton LL, Theising B, Flicek P, Bronner ME, Warren WC, Clifton SW, Wilson RK, Li W. 2013. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet. 45:415-421.
Sumiyama K, Miyake T, Grimwood J, Stuart A, Dickson M, Schmutz J, Ruddle FH, Myers RM, Amemiya CT. 2012. Theria-specific homeodomain and cis-regulatory element evolution of the Dlx3-4 bigene cluster in 12 different mammalian species. J Exp Zool B (Mol Dev Evol.) 318:639-650.
Smith JJ, Baker C, Eichler EE, Amemiya CT. 2012. Genetic consequences of programmed genome rearrangement. Curr Biol. 22:1524-1529.
Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E, Johnson J, Swofford R, Pirun M, Zody MC, White S, Birney E, Searle S, Schmutz J, Grimwood J, Dickson MC, Myers RM, Miller CT, Summers BR, Knecht AK, Brady SD, Zhang H, Pollen AA, Howes T, Amemiya C; Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team, Baldwin J, Bloom T, Jaffe DB, Nicol R, Wilkinson J, Lander ES, Di Palma F, Lindblad-Toh K, Kingsley DM. 2012. The genomic basis of adaptive evolution in threespine sticklebacks. Nature. 484:55-61.
Cheng Y, Stuart A, Morris K, Taylor R, Siddle H, Deakin J, Jones M, Amemiya CT, Belov K. 2012. Antigen-presenting genes and genomic copy number variations in the Tasmanian devil MHC. BMC Genomics. 13:87.
Smith JJ, Sumiyama K, Amemiya CT. 2012. A living fossil in the genome of a living fossil: Harbinger transposons in the coelacanth genome. Mol Biol Evol. 29:985-993.
Crow KD, Smith CD, Cheng JF, Wagner GP, Amemiya CT. An independent genome duplication inferred from Hox paralogs in the American paddlefish--a representative basal ray-finned fish and important comparative reference. Genome Biol Evol. 4:937-953.
Deakin JE, Bender HS, Pearse AM, Rens W, O'Brien PC, Ferguson-Smith MA, Cheng Y, Morris K, Taylor R, Stuart A, Belov K, Amemiya CT, Murchison EP, Papenfuss AT, Graves JA. 2012. Genomic restructuring in the Tasmanian devil facial tumour: chromosome painting and gene mapping provide clues to evolution of a transmissible tumour. PLoS Genet. 8:e1002483.
Chen L, Zhao P, Wells L, Amemiya CT, Condie BG, Manley NR. 2010. Mouse and zebrafish Hoxa3 orthologues have nonequivalent in vivo protein function. Proc Natl Acad Sci USA 107:10555-10560.
Amemiya CT, Powers TP, Prohaska SJ, Grimwood J, Schmutz J, Dickson M, Miyake T, Schoenborn MA, Myers RM, Ruddle FH, Stadler PF. 2010. Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome. Proc Natl Acad Sci USA 107:3622-3627.
Saha NR, Smith J, Amemiya CT. Evolution of adaptive immune recognition in jawless vertebrates. 2010. Semin Immunol. 22:25-33.
Smith JJ, Antonacci F, Eichler EE, Amemiya CT. 2009. Programmed loss of millions of base pairs from a vertebrate genome. Proc Natl Acad Sci USA 106:11212-11217.
Danilova N, Amemiya CT. 2009. Going adaptive: the saga of antibodies. Ann NY Acad Sci. 1168:130-155.
Amemiya CT, Prohaska SJ, Hill-Force A, Cook A, Wasserscheid J, Ferrier DE, Pascual-Anaya J, Garcia-Fernàndez J, Dewar K, Stadler PF. 2008. The amphioxus Hox cluster: characterization, comparative genomics, and evolution. J Exp Zool B (Mol Dev Evol.) 310:465-77.
Amemiya CT, Saha NR, Zapata A. 2007. Evolution and development of immunological structures in the lamprey. Curr Opin Immunol.19:535-541.
Amemiya CT, Wagner GP. 2006. Animal evolution: when did the 'Hox system' arise? Curr Biol. 16:R546-8.
Ferrier DE, Dewar K, Cook A, Chang JL, Hill-Force A, Amemiya C. 2005. The chordate ParaHox cluster. Curr Biol. 15:R820-822.
Pancer Z, Amemiya CT, Ehrhardt GR, Ceitlin J, Gartland GL, Cooper MD. 2004. Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey. Nature 430:174-180..
Powers TP, Amemiya CT. 2014. Evidence for a Hox14 paralog group in vertebrates. Curr Biol. 14:R183-184. .
Danke J, Miyake T, Powers T, Schein J, Shin H, Bosdet I, Erdmann M, Caldwell R, Amemiya CT. 2004. Genome resource for the Indonesian coelacanth, Latimeria menadoensis. J Exp Zool A Comp Exp Biol. 301:228-234.
Wagner GP, Amemiya C, Ruddle F. 2003. Hox cluster duplications and the opportunity for evolutionary novelties. Proc Natl Acad Sci USA 100:14603-14606.
Ota T, Rast JP, Litman GW, Amemiya CT. 2003. Lineage-restricted retention of a primitive immunoglobulin heavy chain isotype within the Dipnoi reveals an evolutionary paradox. Proc Natl Acad Sci USA 100:2501-2506.
Martinez P, Amemiya CT. 2002. Genomics of the HOX gene cluster. Comp Biochem Physiol B Biochem Mol Biol.133:571-580.
Zapata A, Amemiya CT. 2000. Phylogeny of lower vertebrates and their immunological structures. Curr Top Microbiol Immunol. 248:67-107.