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. 2022 Dec 21;9:49. doi: 10.1038/s41439-022-00226-5

Fig. 1. Human MHC genomic map, HLA gene duplications and haplotypic crossovers during meiosis.

Fig. 1

A Gene map of the HLA genomic region that corresponds to the genomic coordinates of 29602228 (GABBR1) to 33410226 (KIFC1) on chromosome 6 in the human genome GRCh38.p13 primary assembly of the NCBI map viewer. The regions separated by arrows show the HLA sub-regions such as extended class I, class I, class III, classical class II and extended class II regions from telomere (left and top side) to centromere (right and bottom side). The red and blue double, horizontal arrows show the spans of alpha, kappa and beta blocks, and framework (FW), non-HLA gene blocks, FW1 and FW2, respectively. The Class III region is composed of non-HLA genes or FW genes, but is known traditionally as Class III. White or coloured (orange, red and blue) boxes, grey, and black boxes show protein-coding genes, non-coding RNAs (ncRNAs), and pseudogenes, respectively. Red, green and blue letters indicate HLA class I, MIC, and class II genes, respectively. Adapted from Shiina et al.1,2. B Cis and trans structural orientation of duplicated and inverted HLA class I and class II genes within their duplication blocks (alpha, kappa, beta, delta and epsilon) relative to the telomeric and centromeric ends (left to right, respectively) of the HLA super-locus. The duplicated MIC pseudogenes, MICE, MICG, MICF, MICD, MICC, and their locations in the alpha block (A) are not shown in B. All MIC pseudogenes and genes in the MHC genomic region are coded in the opposite direction to all the HLA class I genes and pseudogenes6. Solid arrows indicate the 5′ to 3′ direction of coding genes and dotted arrows indicate the 5′ to 3′ direction of pseudogenes (italicised). The structural variants for the HLA-DRB3, DRB4 and DRB5 genes in the class II region and the C4 genes in the class III region are indicated by the enclosed vertical boxes. The location and distribution of the duplicated genes are not shown to exact genomic scale. C Chromosomal or SNP density crossover (XO) junction in comparisons between two homozygous haplotype pairs (AB/AB and ab/ab) and two heterozygous recombinant (haplotype) pairs (AB/Ab and aB/ab). Chromosomal recombination is shown with a XO located between loci A and B within haplotype region ‘AB’ and between loci a and b within haplotype region ‘ab’ in a diploid cell during meiosis.