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.
Vandepas LE, Warren KJ, Amemiya CT, Browne WE.Establishing and maintaining primary cell cultures derived from the ctenophore Mnemiopsis leidyi. J Exp Biol. 2017 Jan 30. pii: jeb.152371. doi: 10.1242/jeb.152371. [Epub ahead of print]. PMID: 28137975
Lima SQ, Costa CM, Amemiya CT, Schneider I. Morphological And Molecular Analyses of an Anatomical Novelty: The Pelvic Fin Filaments of the South American Lungfish. J Exp Zool B Mol Dev Evol. 2016 Nov 9. doi: 10.1002/jez.b.22711. [Epub ahead of print] PMID: 27862964
Schneider I and Amemiya CT. 2016. Developmental genetic toolkit for evolutionary developmental biology in Richard Kliman ed. Encyclopedia of Evolutionary Biology VI. pp 404-408. Academic Press (Elsevier, Waltham MA)
Nogueira AF, Costa CM, Lorena J, Moreira RN, Frota-Lima GN, Furtado C, Robinson M, Amemiya CT, Darnet S, Schneider I. Tetrapod limb and sarcopterygian fin regeneration share a core genetic programme. Nat Commun. 2016; 7: 13364. PMC5097137
Nuttle X, Giannuzzi G, Duyzend MH, Schraiber JG, Narvaiza I, Sudmant PH, Penn O, Chiatante G, Malig M, Huddleston J, Benner C, Camponeschi F, Ciofi-Baffoni S, Stessman HA, Marchetto MC, Denman L, Harshman L, Baker C, Raja A, Penewit K, Janke N, Tang WJ, Ventura M, Banci L, Antonacci F, Akey JM, Amemiya CT, Gage FH, Reymond A, Eichler EE. 2016. Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility. Nature 536:205-9. PMID: 27487209
Koch J, Lüdemann J, Spies R, Last M, Amemiya CT, Burmester T. 2016. Unusual diversity of myoglobin genes in the lungfish. Mol. Biol. Evol. . pii: msw159. [Epub ahead of print]. PMID: 27512111
Presnell JS, Vandepas LE, Warren KJ, Swalla BJ, Amemiya CT, Browne WE. 2016. The Presence of a Functionally Tripartite Through-Gut in Ctenophora Has Implications for Metazoan Character Trait Evolution. Curr. Biol. 2016 Aug 24. pii: S0960-9822(16)30931-9. doi: 10.1016/j.cub.2016.08.019. [Epub ahead of print]. PMID: 27568594.
Bryant SA, Herdy JR, Amemiya CT, Smith JJ. Characterization of Somatically-Eliminated Genes During Development of the Sea Lamprey (Petromyzon marinus). Mol Biol Evol. 2016 Jun 10. pii: msw104. [Epub ahead of print]. PMID: 27288344
Josberger E., Hassanzadeh P, Deng Y, Sohn J, Rego M, Amemiya CT, Rolandi M. 2016. Proton conductivity in ampullae of Lorenzini jelly. Science Advances 13 May 2016 Vol. 2, no. 5, e1600112 DOI: 10.1126/sciadv.1600112
Tacchi L, Larragoite ET, Muñoz P, Amemiya CT, Salinas I. African Lungfish Reveal the Evolutionary Origins of Organized Mucosal Lymphoid Tissue in Vertebrates. Curr Biol 2015 Sep 21;25(18):2417-24. doi: 10.1016/j.cub.2015.07.066. Epub 2015 Sep 3. PubMed PMID: 26344090; PubMed Central PMCID: PMC4869758
Tang WJ, Fernandez JG, Sohn JJ, Amemiya CT. 2015. Chitin is endogenously produced in vertebrates. Current Biology 2015 Mar 30; 25(7): 897–900. PMCID: PMC4382437
Antonacci F, Dennis MY, Huddleston J, Sudmant PH, Steinberg KM, Rosenfeld JA, Miroballo M, Graves TA, Vives L, Malig M, Denman L, Raja A, Stuart A, Tang J, Munson B, Shaffer LG, Amemiya CT, Wilson RK, Eichler EE. Palindromic GOLGA8 core duplicons promote chromosome 15q133 microdeletion and evolutionary instability. 2014. Nat Genet. 46: 1293-302. PMC4244265
Nitsche A, Doose G, Tafer H, Robinson M, Saha NR, Gerdol M, Canapa A, Hoffmann S, Amemiya CT, Stadler PF. 2014. Atypical RNAs in the coelacanth transcriptome. Journal of Experimental Zoology (Molecular and Developmental Evolution) 322:342-351. PMID: 24174405
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.
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.
Amemiya CT, Wagner GP. 2006. Animal evolution: when did the 'Hox system' arise? Curr Biol. 16:R546-8.
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. .
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.
Zapata A, Amemiya CT. 2000. Phylogeny of lower vertebrates and their immunological structures. Curr Top Microbiol Immunol. 248:67-107.