Characterization of the Z lineage Major histocompatability complex class I genes in zebrafish

Abstract

Zebrafish (Danio rerio) are a valuable model for studying immunity, infection, and hematopoietic disease and have recently been employed for transplantation assays. However, the lack of syngeneic zebrafish creates challenges with identifying immune-matched individuals. The MHC class I genes, which mediate allogeneic recognition in mammals, have been grouped into three broad lineages in zebrafish: the classical U genes on chromosome 19, the Z genes which have been reported to map to chromosome 1, and the L genes that map to multiple loci. Transplantations between individual zebrafish that are matched at the U locus fail to consistently engraft suggesting that additional loci contribute to allogeneic recognition. Although two full-length zebrafish Z transcripts have been described, the genomic organization and diversity of these genes have not been reported. Herein we define ten Z genes on chromosomes 1 and 3 and on an unplaced genomic scaffold. We report that neither of the Z transcripts previously described match the current genome assembly and classify these transcripts as additional gene loci. We characterize full-length transcripts for 9 of these 12 genes. We demonstrate a high level of expression variation of the Z genes between individual zebrafish suggestive of haplotypic variation. We report low level sequence variation for individual Z genes between individual zebrafish reflecting a possible nonclassical function, although these molecules may still contribute to allogeneic recognition. Finally, we present a gene nomenclature system for the Z genes consistent with MHC nomenclature in other species and with the zebrafish gene nomenclature guidelines.

The MHC class I genes of zebrafish

“…Of note, a large fraction of the nonclassical MHC genes are not found within the core MHC locus but are instead scattered on additional chromosomes in humans (Horton et al 2004) and many other vertebrate species. This scattering of class I genes outside of the core MHC locus also applies to zebrafish (Dirscherl and Yoder 2014;McConnell et al 2014;Sambrook et al 2005). …”

“…As immunologically compatible zebrafish donors and recipients are not readily available, genotyping strategies have been and are being developed for identifying MHC-matched zebrafish. However, the number of described MHC class I loci in the zebrafish genome is growing (Dirscherl and Yoder 2014;McConnell et al 2014). In this review we will summarize the current knowledge on the polygenic, polymorphic and haplotypic nature of the zebrafish MHC class I gene families.…”

A nonclassical MHC class I U lineage locus in zebrafish with a null haplotypic variant

“…Primer pairs were designed to amplify the entire coding sequences of mhc1ula and mhc1uma by RT-PCR. A primer pair that amplifies a portion of the β- actin transcript was used as a positive control for cDNA quality as previously described (Dirscherl and Yoder 2014). …”

“…The zebrafish Z lineage genes are encoded on chromosomes 1 and 3 (Kruiswijk et al 2002; Dirscherl and Yoder 2014) and the nonclassical L lineage genes are encoded on chromosomes 3, 8, and 25 (Dijkstra et al 2007; Dirscherl et al 2014). …”

Fish to Learn: Insights into Blood Development and Blood Disorders from Zebrafish Hematopoiesis

“…Characterization of zebrafish MHC loci will provide immunologically compatible donor and recipient organisms to enhance transplantation assays, and will be critical for more rigorous experimental designs in matched genomic backgrounds. 62,63 Another limitation in the field of zebrafish hematopoiesis studies has been the lack of in vitro culture system for growing and differentiating HSCs. Two successful stromal lines have been described that support HSPCs: zebrafish kidney stromal cells (ZKS) 64 and zebrafish embryonic stromal trunk (ZEST) cells.…”