Ancient, highly polymorphic human major histocompatibility complex DQA1 intron sequences

Abstract

A 438 basepair intron 1 sequence adjacent to exon 2 in the human major histocompatibility complex DQA1 gene defined 16 allelic variants in 69 individuals from wide ethnic backgrounds. In contrast, the most variable coding region spanned by the 247 basepair exon 2 defined 11 allelic variants. Our phylogenetic human intron 1 tree derived by the Bootstrap algorithm reflects the same relative allelic relationships as the reported DQA1 exon 2 tree [Gyllensten and Erlich, Hum Immunol 36:1-10, 1989]. Thus 3' DQA1 intron 1 and exon 2 have cosegregated since divergence of the human races. Comparison of human alleles to a Rhesus monkey DQA1 first intron sequence found only 10 nucleotide substitutions unique to Rhesus, with the other 428 positions (98%) found in at least one human allele. This high degree of homology reflects the evolutionary stability of intron sequences since these two species diverged over 20 million years ago. Because more intron 1 alleles exist than exon 2 alleles, these polymorphic introns can be used to improve tissue typing for transplantation, paternity testing, and forensics and to derive more complete phylogenetic trees. These results suggest that introns represent a previously underutilized polymorphic resource.

Allelic polymorphism in introns 1 and 2 of the HLA‐DQA1 gene

“…Within the present analysis, using two different cell lines for each allele, we have identified three alleles that share identical exons but differ for the intron sequences. The polymorphism in DQA1*0103 at position 232 was already noticed by McGinnis et al (22). The DQA1*0103 alleles in their study were all from Caucasian origin.…”

“…In the present study, the intron 1 and 2 sequences of HLA‐DQA1 have been determined from 15 different alleles. There is only one previous study on DQA1 intron sequences from 1994, where a 438 bp fragment of intron 1 adjacent to exon 2 was determined (22). At that time, there were more intron 1 alleles identified than exon 2 variants.…”

“…However, we were able to assign several intron 1 sequences to different alleles, based on the sequence determination of the complete coding region. For example, the DQA1*0501 with DRB1*1602 haplotype showed a C at position 149 in intron 1 (22). This substitution corresponds in our sequences with DQA1*0505, an allele not identified in 1994.…”

The nature of polymorphism of the HLA‐DRB intron sequences is lineage specific

“…In this article we address the question of whether the structural features of HLA-DRB introns may provide a similar basis for sequencing-based typing strategies. Little is known about the noncoding sequences of the different HLA class 11 alleles (14)(15)(16)(17)(18). The database of HLA-DRB genes is derived mainly from mRNA analysis or from DNA analysis of the polymorphic 2nd exon; here we have focused on the structural features of the intron 1 sequences of the fluorescence-labeled dideoxynucleotide termination reagents (dye terminators).…”

HLA-DQA1 Introns 2 and 3 Sequencing: DQA1 Sequencing-Based Typing and Characterization of a Highly Polymorphic Microsatellite at Intron 3 of DQA1*0505

“…The alignment of previously reported DQA1 intron 1 sequences [15] allowed us to design DQA1 consensus oligonucleotides to specifically amplify a DQA1-specific template from the 3= end of intron 1 to the 5= end of exon 4. The expected amplification product from all homozygous samples was consistently obtained by using primers DQA1I1 and DQA1E4R (Table 2).…”