Large-Scale Sequencing of Human, Mouse, and Sheep Prion Protein Genes

Abstract

The prion protein (PrP), first identified in scrapie-infected rodents, is encoded by a single-copy chromosomal gene. PrP genes are conserved and have been identified in 13 species of mammals. Cloning and analysis of the PrP gene has revealed that pathogenic (PrPSc) and cellular (PrPC) isoforms of the prion protein do not reflect alternative splicing events but instead share the same amino acid sequence: these data first suggested the hypothesis that prion isoforms are alternate conformers1. However, at this time the mechanism involved in the transition between PrPC and PrPSc is obscure, as is the normal function of PrPC. We have therefore sought to identify PrP-linked genes that might feature in conformational transitions, and conserved regulatory elements that might offer insights into the physiology of PrPC. Accordingly, 145 kb of DNA from human and sheep PrP genes, and two alleles of Prn-p has been analysed for conserved regions, ORFs, potential exons, repetitive sequences, putative CpG islands, and possible polymorphic motifs. These sequences reveal unexpected features within the wild-type PrP genes of each of these species. The predominant allele of the mouse gene, Prn-pa, found in 44 inbred laboratory strains contains a 6878 nucleotide retroviral genome inserted into the anticoding strand of intron 2. This intracisternal A particle (IAP) element is (i) flanked by duplications of a AAGCTT nucleotide motif found once in the Prn-pb gene, and (ii) highly related to a transpositionally-competent prototype IAP element, differing principally in small deletion of the pol gene: these data are indicative of a recent transpositional orgin. In the case of the sheep PrP gene, the unusually long 3′ untranslated region (UTR) reflects in most part the presence of a “fossil” 1.2 kb mariner-like transposable element, which is absent from the human and mouse PrP genes. Chromosomal instability associated with mariner-like elements on chromosome 17 in humans suggests that DNA rearrangements may take place adjacent to the PrP gene in sheep, and also in cattle (which also exhibit an extended 3′ UTR and presumably harbor a mariner-like element). Lastly, the large intron of the human PrP gene contains a sequence analogous to exon 2 of the mouse and sheep PrP genes, flanked by consensus splice acceptor and donor sites: while it remains to be established that “exon 2” sequences are included in a subset of human PrP mRNAs, these data indicate that an ancestral PrP gene most likely exhibited a three exon structure.