Differences in gene conversion rates among exons between HLA-A and HLA-B loci

To examine whether gene conversion occurs between two homologous loci of HLA-A and HLA-B, DNA sequences were compared and the differences or the numbers of substitutions per site at synonymous and nonsynonymous sites were calculated in the coding region and in the non-coding region. (1) Totally differences at synonymous sites in introns and coding regions are small as compared with the differences in the 5' flanking region. This indicates that gene conversion should occur between HLA-A and HLA-B loci. (2) In exon2 and exon3, the differences at synonymous sites are smaller than at nonsynonymous sites. This suggests that these exons are subject to positive natural selection, which is consistent with the reports of Hughes and Nei [1,2], because exon2 and exon3 encode alpha 1 and alpha 2 domains of the HLA molecule respectively which include mainly the antigen recognition sites (ARS). (3) in exon4, the difference at the synonymous site is the same as that in the 5' flanking region, which suggests that gene conversion does not frequently occur. The difference in this exon is extremely small at the nonsynonymous sites. This exon encodes the alpha 3 domain which does not have the antigen recognition sites but have an important function in maintaining the structure of the HLA molecule. From the above results, it can be concluded that gene conversion between HLA-A and HLA-B occurs more frequently in the two exons, exon2 and exon3 which have ARS regions. Furthermore, to examine a possibility that the variability of GC content along sequence influences the difference, the GC content was calculated along the sequence.