Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey. Pancer Z, Amemiya CT, Ehrhardt GR, Ceitlin J, Gartland GL, Cooper MD.Nature. 2004 Jul 8;430(6996):174-80. PMID: 15241406

We showed in this paper that a representative basal vertebrate, the sea lamprey, uses a completely different genetic tool kit for generating its adaptive immune system. Rather than employ immunoglobulin domains in its immune molecules, it uses leucine rich repeat cassettes which it mixes and matches to generate its variable lymphocyte receptors utilizing a process analogous to VDJ recombination. Amemiya was highly involved in this discovery and did all the genomics (BAC library construction, screening, clone sequencing). This work is significant in that it showed that two major evolutionary lineages invented separate solutions to the problem of adaptive immunity, both solutions relying on somatic genome recombination to generate diversity.

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We are continuing this work at UCM, both on the immunology-genomics aspects and on the use of the system for generating lampribodies (monoclonal antibodies against targeted immunogens). We also have good evidence that the variable lymphocyte receptors may be involved in early embryonic development.

Programmed loss of millions of base pairs from a vertebrate genome. Smith JJ, Antonacci F, Eichler EE, Amemiya CT. Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11212-7. doi: 10.1073/pnas.0902358106. Epub 2009 Jun 26. PMID: 19561299

Genetic consequences of programmed genome rearrangement. Smith JJ, Baker C, Eichler EE, Amemiya CT. Curr Biol. 2012 Aug 21;22(16):1524-9. doi: 10.1016/j.cub.2012.06.028. Epub 2012 Jul 19. PMID: 22818913

While working on the variable lymphocyte receptors of lampreys we made a serendipitous discovery: that the lamprey genome is undergoing massive programmed genome rearrangement during embryonic development so that 20% of its genome is lost. Importantly, the germline genome remains intact so the integrity of the species is kept. The rearrangements are programmed in that the same DNAs are lost from animal to animal. The genes that are deleted from the soma were posited to be involved in pluripotency functions, a hypothesis that we have largely confirmed via subsequent work, although we still are working out the details by which rearrangements take place. This work is significant in our understanding of the mechanisms by which stable rearrangements occur in light of the fact that chromosomal rearrangements are rampant and unchecked in many cancers.

Developmental Biology blog describing the findings and significance

We are continuing this work at UCM and seek to understand the mechanism by which the rearrangements occur and how the rearrangement machinery may be related to that involved in the immune system.

The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Smith JJ, Timoshevskaya N, Ye C, Holt C, Keinath MC, Parker HJ, Cook ME, Hess JE, Narum SR, Lamanna F, Kaessmann H, Timoshevskiy VA, Waterbury CKM, Saraceno C, Wiedemann LM, Robb SMC, Baker C, Eichler EE, Hockman D, Sauka-Spengler T, Yandell M, Krumlauf R, Elgar G, Amemiya CT. Nat Genet. 2018 Feb;50(2):270-277. doi: 10.1038/s41588-017-0036-1. Epub 2018 Jan 22.PMID: 29358652

This paper was largely driven by a former postdoc in the laboratory, Jeramiah Smith (now a faculty member at University of Kentucky). It was necessary to sequence the germline genome of the lamprey in order to make inferences with regard to the mechanisms by which it undergoes global programmed genome rearrangement (i.e., How does it shed 20% of its somatic DNA during embryonic development). This work is significant because we were able to generate chromonome length super-contigs utilizing linking tools (BioNano, HiC, meiotic map). By comparing our somatic genome (which we published in 2013 in Nature Genetics) with this assembly, we will learn about the nature of the global genome rearrangement that the lampreys (and all agnathans) undergo during development. We are also investigating the possibility that the propensity for global genome rearrangement may have contributed to the mode of rearrangements seen in the variable lymphocyte receptor genes of the immune system.

Nature Genetics Blog describing the work

Evidence for Hox14 paralog group in vertebrates. Powers TP, Amemiya CT. Current Biology 2004; 14(5):PR183-R184. PMID: 15028231 DOI:10.1016/j.cub.2004.02.015

Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome. Amemiya CT, Powers TP, Prohaska SJ, Grimwood J, Schmutz J, Dickson M, Miyake T, Schoenborn MA, Myers RM, Ruddle FH, Stadler PF.Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3622-7. doi: 10.1073/pnas.0914312107. Epub 2010 Feb 5. PMID: 20139301

In these papers, we isolated and characterized the HOX clusters using Bacterial Artificial Chromosomes (BACs) of the coelacanth, Latimeria menadoensis. The first report is significant because we showed for the first time that the “primitive” vertebrate HOX cluster contained Hox14 genes, which has now been verified by other groups. The second paper is significant because we were able to isolate the entire regions of the four HOX clusters and subject them to DNA sequencing. BACs were long the method of choice for genome analysis of complex genomes and our laboratory had helped to develop the technology and produce many valuable BAC libraries, including the one from the coelacanth, a relict fish species that was thought to be extinct for 65 million years. Coelacanths are endangered so making a BAC library for studying its genome is doubly important since biological materials are not available due to its CITES protection. Sequencing of the HOX clusters was carried out and the analyses clearly showed that its molecular evolution rate was considerably slow than that of almost all vertebrates, somewhat in line with its given moniker of “living fossil.” We were also able to show that the Hoxa14 gene of the coelacanth is biologically functional, something that was confirmed subsequently by other groups. These studies were also critical as pilot studies for sequencing the entire coelacanth genome and for providing/depositing extended genome sequences that were used by the community in order to examine cis-regulatory aspects of the HOX clusters.

Current Biology Dispatch on the Hox14 discovery.

The African coelacanth genome provides insights into tetrapod evolution. 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. Nature. 2013 Apr 18;496(7445):311-6. doi: 10.1038/nature12027. PMID: 23598338

The discovery of the living coelacanth in 1938 is considered to be the most significant zoological find of the 20th century. There are lots of reasons for the interest in the coelacanth since it really does serve as an outgroup to the land vertebrates, tetrapods, and it can answer a lot of questions regarding evolution of structures thought to be unique to terrestrial vertebrates (e.g., limbs, lungs). The significance of the work was covered by the New York Times. Together with colleagues at Michigan State (Ingo Braasch) and the Federal University of Para, Brazil (Igor Schneider), we are continuing work on using targeted species at “sweet spots” (coelacanth, gar, lungfish) in order to address problems in vertebrate evolution.

VH gene organization in a relict species, the coelacanth Latimeria chalumnae: evolutionary implications. Amemiya CT, Ohta Y, Litman RT, Rast JR, Haire RN, Litman GW. PNAS July 15, 1993 90 (14) 6661-6665

This was Chris Amemiya’s first paper on the coelacanth. In this study we used old school technology (genomic libraries in lambda phage) in order to isolate its immunoglobulin genes via library screening with a mouse Ig variable region probe (S107). We then subcloned and sequenced ad nauseum in order to characterize its VH organization. Close examination of the downstream sequences revealed typical recombination signal sequences of D elements but we did not observe the overt “multi-cluster” organization seen in the horn shark. The V-D… V-D… organization was somewhat intermediate between that of the mouse/human and the shark. Two decades later, we were able to sequence the entire coelacanth genome (see above) and were able to corroborate this gene organization and the fact that the coelacanth contained two IgW-type heavy chain genes but no IgM.

Chitin is endogenously produced in vertebrates. Tang WJ, Fernandez J, Sohn JJ, Amemiya CT. Curr Biol. 2015 Mar 30;25(7):897-900. doi: 10.1016/j.cub.2015.01.058. Epub 2015 Mar 12. PMID: 25772447

In this paper we showed for the first time that chitin is actually made in vertebrates (fishes and amphibians). It was long considered dogma that chitin (the stuff that comprises arthropod exoskeletons – like crab and shrimp shells and insect carapaces) was not found in the vertebrates, i.e., was restricted to invertebrates and fungi. However, we found genes for vertebrate chitin synthase using comparative genomics and showed that these genes are synthesizing chitin. Chitin is considered the second most abundant polymer in nature next to cellulose. In addition, we showed that unlike the hard, mineralized horny structures found in exoskeletons, the chitin in vertebrates exists as water soluble composites, hydrogels, and that they are involved in many presumed functions in the vertebrates. This paper showed that the comparative genomics approach is useful for identifying biological novelty. More importantly, it is creating a new field of inquiry on emergent properties of a biopolymer.

Science Daily press release.

This line of research is being actively pursued here at UCM in conjunction with material scientists and biophysicists.