Human endogenous retrovirus (HERVK9) structural polymorphism with haplotypic HLA-A allelic associations

Abstract

The frequency and HLA-A allelic associations of a HERVK9 DNA structural polymorphism located in close proximity to the highly polymorphic HLA-A gene within the major histocompatibility complex (MHC) genomic region were determined in Japanese, African Americans, and Australian Caucasians to better understand its human population evolutionary history. The HERVK9 insertion or deletion was detected as a 3' LTR or a solo LTR, respectively, by separate PCR assays. The average insertion frequency of the HERVK9.HG was significantly different (P < 1.083e(-6)) between the Japanese (0.59) and the African Americans (0.34) or Australian Caucasians (0.37). LD analysis predicted a highly significant (P < 1.0e(-5)) linkage between the HLA-A and HERVK9 alleles, probably as a result of hitchhiking (linkage). Evolutionary time estimates of the solo, 5' and 3' LTR nucleotide sequence divergences suggest that the HERVK9 was inserted 17.3 MYA with the first structural deletion occurring 15.1 MYA. The LTR/HLA-A haplotypes appear to have been formed mostly during the past 3.9 MY. The HERVK9 insertion and deletion, detected by a simple and economical PCR method, is an informative genetic and evolutionary marker for the study of HLA-A haplotype variations, human migration, the origins of contemporary populations, and the possibility of disease associations.

Figure 1.—

Genomic map of the HLA class I gene and pseudogene cluster from HLA-J to HLA-G within the α-block of the MHC shows the location of the HERVK9.HG deletion and insertion polymorphism in haplotypes HAPL A and HAPL B, respectively. HAPL B shows the HERVK9 insertion and not the orthologous HLA class I genes for convenience. The centromeric end of the sequences is on the left and the telomeric end is on the right of the sequences. The locations of the HLA-90, HLA-75, and HLA-F genes telomeric of HLA-G are not shown. The DNA regions amplified by the PCR reactions shown in Figure 2 are indicated by the double horizontal arrows labeled “PCR-A del” and “PCR-B ins.” The double horizontal arrow at the top indicates the approximate distance between the HERVK9.HG deletion and the HLA-A locus. The genes and genomic regions of the PAC clones 544A6 and 779F20 that were used as positive and negative DNA samples for the PCR reactions to detect the HERVK9.HG polymorphism are indicated by the horizontal lines at the bottom (Shiina et al. 1999). The genomic map is based on the MHC class I genomic sequence reported by Hampe et al. (1999) and submitted to GenBank as accession no. AF055066.

Figure 2.—

PCR detection of the HERVK9.HG insertion or deletion. (A) The PCR strategy used to detect the HERVK9i insertion (top) and the solo LTR (M9) sequence as the remnants of the HERVK9 deletion (bottom). The labeled vertical arrows indicate the relative locations of the PCR primers. The dotted lines indicate the homologous recombination between the 5′ LTR (M9) and the 3′ LTR (M9) involved in the HERVK9.HG deletion and the generation of the solo LTR (M9) sequence. “M9” is an abbreviation for MER9. (B) PCR products with the HERVK9 insertion (625 bp) primers and deletion (556 bp) primers. The homozygous insertion products are in lanes 1, 6, 7, and 9 and the PGF cell line. The homozygous deletion products are in lanes 2 and the COX cell line. The heterozygous products are in lanes 3, 4, 5, 8, and 10.