IDENTIFICATION OF A NEW HLA PSEUDOGENE WITH SEQUENCE SIMILARITY TO THE GORILLA A LOCUS GENE

IDENTIFICATION OF A NEW HLA PSEUDOGENE WITH SEQUENCE SIMILARITY TO THE GORILLA A LOCUS GENE.
D.MIDDLETON, F.WILLIAMS AND MD.CURRAN. (N.Ireland Histocompatibility and Immunogenetics Laboratory, City Hospital, Belfast).

During the development of a PCR-SSOP method for the identification of HLA-A*24 and -A*30 alleles, group amplification using a specific primer from exon 2 and a HLA-A generic reverse primer from exon 4 resulted in the formation of an unusual PCR product in certain DNA samples. This fragment was approximately 900bp smaller than the expected product using these primers and was also detected in some non HLA-A*24 and -A*30 DNA samples which were acting as negative controls for the group specific amplification. Screening in excess of 500 normal individuals using this primer combination has established that the product is present in all individuals positive for the following HLA-A types:- HLA-A*3001, -A*3301, -A*3303, -A*6802, -A*2901 and on some occasions with -A*0205 and -A31012. The gene is not unique to the Northern Ireland population - the product has been identified in DNA samples from various populations world-wide.
Complete DNA sequence information from exon 1 to exon 8, including introns, has been obtained. A recombination event has been identified which results in the fusion of intron 2 (nuc.pos. 257) with intron 3 (nuc.pos. 604), causing a deletion of the intervening sequence (i.e. exon 3 and most of intron 3). The size of the deletion correlates with the ~900bp difference observed in the amplification product. In addition there are two cytosine insertions in the poly-cytosine stretch at the start of exon 4. The exon 2 sequence most closely aligns with the gorilla allele A*0501, displaying only five mismatches. The exon 4 sequence is identical to the now non-existing HLA-A*3302 allele except for the insertions at the poly C stretch.
Due to the large deletion and the cytosine insertions it is unlikely that this "gene" would be expressed. RT-PCR analysis of individuals containing this gene failed to detect any mRNA transcription, suggesting that this is a previously undescribed class I pseudogene.