Our Research
Chris Amemiya, PhD
Title:
Member
Email Address:
Phone Number:
Office (206) 287-1011, Lab (206) 287-1010, Fax (206) 342-6578
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. 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.
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 to 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
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. The African coelacanth genome provides insights into tetrapod evolution. Nature. 2013 Apr 17;496(7445):311-316. PMID: 23598338.
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. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet. 2013 Feb 24;45(4):415-421. PMID: 23435085.
Sumiyama K, Miyake T, Grimwood J, Stuart A, Dickson M, Schmutz J, Ruddle FH, Myers RM, Amemiya CT. 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. 2012 Dec;318(8):639-50. PMID: 22951979.
Smith JJ, Baker C, Eichler EE, Amemiya CT. Genetic consequences of programmed genome rearrangement. Curr Biol. 2012 Aug 21;22(16):1524-9. PMID: 22818913; PMCID: PMC3427415.
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. The genomic basis of adaptive evolution in threespine sticklebacks. Nature. 2012 Apr 4;484(7392):55-61. PMID: 22481358; PMCID: PMC3322419.
Cheng Y, Stuart A, Morris K, Taylor R, Siddle H, Deakin J, Jones M, Amemiya CT, Belov K. Antigen-presenting genes and genomic copy number variations in the Tasmanian devil MHC. BMC Genomics. 2012 Mar 12;13:87. PMID: 22404855; PMCID: PMC3414760.
Smith JJ, Sumiyama K, Amemiya CT. A living fossil in the genome of a living fossil: Harbinger transposons in the coelacanth genome. Mol Biol Evol. 2012 Mar;29(3):985-93. PMID: 22045999; PMCID: PMC3278475.
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. 2012;4(9):937-53. PMID: 22851613; PMCID: PMC3509897.
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. Genomic restructuring in the Tasmanian devil facial tumour: chromosome painting and gene mapping provide clues to evolution of a transmissible tumour. PLoS Genet. 2012;8(2):e1002483. PMID: 22359511; PMCID: PMC3280961.
Chen L, Zhao P, Wells L, Amemiya CT, Condie BG, Manley NR. Mouse and zebrafish Hoxa3 orthologues have nonequivalent in vivo protein function. Proc Natl Acad Sci U S. 2010 Jun 8;107(23):10555-60. PMID: 20498049; PMCID: PMC2890846.
Amemiya CT, Powers TP, Prohaska SJ, Grimwood J, Schmutz J, Dickson M, Miyake T, Schoenborn MA, Myers RM, Ruddle FH, Stadler PF. Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome. Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3622-7. PMID: 20139301; PMCID: PMC2840454.
Saha NR, Smith J, Amemiya CT. Evolution of adaptive immune recognition in jawless vertebrates. Semin Immunol. 2010 Feb;22(1):25-33. PMID: 20056434; PMCID: PMC2823822.
Smith JJ, Antonacci F, Eichler EE, Amemiya CT. Programmed loss of millions of base pairs from a vertebrate genome. Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11212-7. PMID: 19561299; PMCID: PMC2708698.
Danilova N, Amemiya CT. Going adaptive: the saga of antibodies. Ann N Y Acad Sci. 2009 Jun;1168:130-55. Review. PMID: 19566706.
Amemiya CT, Prohaska SJ, Hill-Force A, Cook A, Wasserscheid J, Ferrier DE, Pascual-Anaya J, Garcia-Fernàndez J, Dewar K, Stadler PF. The amphioxus Hox luster: characterization, comparative genomics, and evolution. J Exp Zool B Mol Dev Evol. 2008 Jul 15;310(5):465-77. PMID: 18351584.
Amemiya CT, Saha NR, Zapata A. Evolution and development of immunological structures in the lamprey. Curr Opin Immunol. 2007 Oct;19(5):535-41. PMID: 17875388; PMCID: PMC2093943.
Amemiya CT, Wagner GP. Animal evolution: when did the 'Hox system' arise? Curr Biol. 2006 Jul 25;16(14):R546-8. PMID: 16860733.
Ferrier DE, Dewar K, Cook A, Chang JL, Hill-Force A, Amemiya C. The chordate ParaHox cluster. Curr Biol. 2005 Oct 25;15(20):R820-2. PMID: 16243016.
Pancer Z, Amemiya CT, Ehrhardt GR, Ceitlin J, Gartland GL, Cooper MD. Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey. Nature. 2004 Jul 8;430(6996):174-80. PMID: 15241406.
Powers TP, Amemiya CT. Evidence for a Hox14 paralog group in vertebrates. Curr Biol. 2004 Mar 9;14(5):R183-4. PMID: 15028231.
Danke J, Miyake T, Powers T, Schein J, Shin H, Bosdet I, Erdmann M, Caldwell R, Amemiya CT. Genome resource for the Indonesian coelacanth, Latimeria menadoensis. J Exp Zool A Comp Exp Biol. 2004 Mar 1;301(3):228-34. PMID:14981781.
Wagner GP, Amemiya C, Ruddle F. Hox cluster duplications and the opportunity for evolutionary novelties. Proc Natl Acad Sci U S A. 2003 Dec 9;100 5):14603-6. PMID: 14638945; PMCID: PMC299744.
Ota T, Rast JP, Litman GW, Amemiya CT. Lineage-restricted retention of a primitive immunoglobulin heavy chain isotype within the Dipnoi reveals an evolutionary paradox. Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2501-6. PMID: 12606718; PMCID: PMC151370.
Martinez P, Amemiya CT. Genomics of the HOX gene cluster. Comp Biochem Physiol B Biochem Mol Biol. 2002 Dec;133(4):571-80. Review. PMID: 12470820.
Zapata A, Amemiya CT. Phylogeny of lower vertebrates and their immunological structures. Curr Top Microbiol Immunol. 2000;248:67-107. Review. PMID: 10793475.
Dr. Amemiya’s Department of Biology Web site, University of Washington
Dr. Amemiya’s Institute for Stem Cell and Regenerative Medicine Web site, University of Washington
Dr. Amemiya’s Molecular and Cellular Biology Web site, University of Washington
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