Haplotype Shuffling and Dimorphic Transposable Elements in the Human Extended Major Histocompatibility Complex Class II Region

Abstract

The major histocompatibility complex (MHC) on chromosome 6p21 is one of the most single-nucleotide polymorphism (SNP)-dense regions of the human genome and a prime model for the study and understanding of conserved sequence polymorphisms and structural diversity of ancestral haplotypes/conserved extended haplotypes. This study aimed to follow up on a previous analysis of the MHC class I region by using the same set of 95 MHC haplotype sequences downloaded from a publicly available BioProject database at the National Center for Biotechnology Information to identify and characterize the polymorphic human leukocyte antigen (HLA)-class II genes, the MTCO3P1 pseudogene alleles, the indels of transposable elements as haplotypic lineage markers, and SNP-density crossover (XO) loci at haplotype junctions in DNA sequence alignments of different haplotypes across the extended class II region (∼1 Mb) from the telomeric PRRT1 gene in class III to the COL11A2 gene at the centromeric end of class II. We identified 42 haplotypic indels (20 Alu, 7 SVA, 13 LTR or MERs, and 2 indels composed of a mosaic of different transposable elements) linked to particular HLA-class II alleles. Comparative sequence analyses of 136 haplotype pairs revealed 98 unique XO sites between SNP-poor and SNP-rich genomic segments with considerable haplotype shuffling located in the proximity of putative recombination hotspots. The majority of XO sites occurred across various regions including in the vicinity of MTCO3P1 between HLA-DQB1 and HLA-DQB3, between HLA-DQB2 and HLA-DOB, between DOB and TAP2, and between HLA-DOA and HLA-DPA1, where most XOs were within a HERVK22 sequence. We also determined the genomic positions of the PRDM9-recombination suppression sequence motif ATCCATG/CATGGAT and the PRDM9 recombination activation partial binding motif CCTCCCCT/AGGGGAG in the class II region of the human reference genome (NC_ 000006) relative to published meiotic recombination positions. Both the recombination and anti-recombination PRDM9 binding motifs were widely distributed throughout the class II genomic regions with 50% or more found within repeat elements; the anti-recombination motifs were found mostly in L1 fragmented repeats. This study shows substantial haplotype shuffling between different polymorphic blocks and confirms the presence of numerous putative ancestral recombination sites across the class II region between various HLA class II genes.

Haplotypic Associations and Differentiation of MHC Class II Polymorphic Alu Insertions at Five Loci With HLA-DRB1 Alleles in 12 Minority Ethnic Populations in China

“…For the other Alu insertions, HLA-DRB1 ∗ 09 was not found in the Wa, but it had a moderate to very strong association (51–100%) with AluDPB2 in thirteen populations and a low association (31.7%) in the Lisu. For a comparison of the haplotypic associations with actual genomic sequence linkages, Supplementary Table 2 shows the percentage linkage between these five POALIN with HLA-DRB1 alleles detected in the MHC class II haplotype sequences of 90 homozygous cell-lines ( Kulski et al, 2021 ). Because of ancestral recombination at sites between various Alu loci and the DRB1 allelic loci, the linkages detected in the cell lines were not present in all the different Chinese ethnic populations, although the general trends are maintained between and within populations.…”

“…To better assess the haplotypic associations between the POALINs and the HLA-DRB1 alleles, we examined their sequence linkages in 95 different MHC haplotype sequences ( Kulski et al, 2021 ) that were sequenced, partially annotated and assembled from HLA-homozygous cell lines by Norman et al (2017) .…”

“…The FASTA files of the 95 MHC class I, II and III genomic sequences were downloaded from the archives at NCBI BioProject with the accession number PRJEB6763 1 and submitted to the RepeatMasker webserver 2 for output files of annotated members of the interspersed repetitive DNA families, their locations in the sequence and their relative similarity or identity in comparison to reference sequences of SINEs, LINEs, LTRs, ERVs, DNA elements, small RNA, and simple repeats ( Kulski et al, 2021 ). The five MHC class II POALINs were easily identified within the RepeatMasker outputs on the basis of their location and flanking sequences and/or other repeats as previously described ( Kulski et al, 2010 ).…”

“…The HLA-DRB1 alleles for all of the 95 cell line sequences were determined and reported by Norman et al (2017) . Supplementary Table 2 is a summary of the sequence linkages between the 5 POALIN and the HLA-DRB1 alleles that were determined in 90 of the sequenced haplotypes ( Kulski et al, 2021 ). These were used as a comparative reference control to assist with a better interpretation of our results obtained for our haplotypic association analyses in 15 different populations.…”

“…By comparing the data of the MHC class II five-loci POALINs in Chinese Han with Japanese and Caucasian data, marked differences were observed between the three ethnic groups at the allelic or haplotypic levels. In addition, each POALIN was in significant linkage disequilibrium (LD) and/or haplotypically associated ( Kulski et al, 2020 , 2021 ) with a variety of HLA-DRB1 alleles in Chinese Han in Yunnan province ( Shi et al, 2014 ). These results showed that POALINs whether investigated alone or together with the HLA class II alleles are informative genetic markers for the identification of allele and haplotype lineages and variations within the same and/or different populations.…”