Characterisation of a novel HLA-A pseudogene, HLA-BEL, with significant sequence identity with a gorilla MHC class I gene

During the development of an HLA-A polymerase chain reaction using sequence -specific oligonucleotide probes (PCR-SSOP) method far the identification o f HLA-A*24 and -A*30 alleles, group amplification resulted in the formation of an unusual PCR product in certain individuals This fragment was approxi mately 900 bp smaller than the experted product and was also detected in so me non-HLA-A*24 and -A*3D-positive individuals acting as negative controls for the group specific amplification. Nucleotide sequence analysis of this product identified it as a unique class I gene sequence displaying homology to both primate and human class I A-locus genes. The entire gene was ampli fied using PCR and the complete DNA sequence information from exon 1 to exo n 8, including introns, was determined. A recombination event was identifie d which results in the fusion of intron 2 with intron 3, causing a deletion of the intervening exon 3 sequence. In addition, there are two cytosine in sertions in the poly-cytosine stretch at the start of exon 4 which cause a frameshift and premature termination. The exon 1 and 2 sequences most close ly align with the gorilla allele A*0501, displaying only five mismatches. P CR analysis has established that the gene is associated with the following HLA-A types: HLA-A*3001, -A*3301, -A*3303, -A*6802, A*2901, -A*0203, -A*020 5 and -A*31012. Reverse transcription (RT)-PCR analysis of individuals cont aining this gene failed to detect any mRNA transcription, suggesting that t his is a previously undescribed non-expressed class I pseudogene which we h ave provisionally named HLA-BEL. Its unique gene structure gives a possible insight into the evolutionary pathway that created HLA class I genes.