Orientation of loci within the human major histocompatibility complex by chromosomal in situ hybridization.

Abstract

We have determined the localization and orientation of two genetic probes within the human major histocompatibility complex by chromosomal in situ hybridization.Our data indicate that a cloned genomic probe cross-hybridizing to HLA-A, -B, and -C heavy chain loci is homologous to sequences located on chromosome 6 at band p21.3 while a subclone of the genomic HLA-DR a-chain gene corresponding to the nonpolymorphic p34 protein is homologous to sequences in band 6p21.1. Our data suggest that this technique may permit the estimation of map distances between linked gene loci, assuming a uniform frequency of map units in the human genome. The relative positions of these genes was confirmed in a mother and son carrying a chromosome rearrangement involving 6p and 14p in which the sequences hybridizing to a DR a-chain genomic clone were found at the distal end of the 6p-chromosome [der(6)] while the sequences hybridizing to the HLA-A, -B, -C a-chain probe were found in the 14p+ chromosome [der(14)].The major histocompatibility complex (MHC) in humans is a cluster of at least three gene families encoding cell surface glycoproteins-i.e., genes for class I (HLA-A, -B, and -C) and class II (HLA-DR) antigens in addition to class III genes (complement factors)-and spans 2-3 x 103 kilobase pairs (kb) of DNA (1, 2). Genetic mapping by somatic cell hybridization (3-7) and by the segregation of unique chromosomal rearrangements involving the MHC in families (8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19) has permitted localization of the serologically polymorphic 45,000-dalton glycoproteins of the class I genes (HLA-A, -B, and -C) to the short arm of human chromosome 6, with the shortest region of overlap being the 6p21 band (7,17). Associated with the polymorphic glycoproteins of the HLA-A, -B, and -C antigens is a nonglycosylated 12,000-dalton invariant chain, 82-microglobulin, that has been assigned to human chromosome 15 (20,21). The class II genes, or the immune response genes, consist of heterodimers composed of a 34,000-dalton (HLA-DR a) glycoprotein for which no electrophoretic polymorphisms have been demonstrated and a polymorphic 29,000-dalton (HLA-DR (3) glycopeptide (21)(22)(23)(24)(25). Polymorphism of the HLA-DR , gene has permitted a regional assignment of this locus to chromosome 6 proximal to 6p22.4 by a family study (15).Recently, the HLA-DR a-chain locus has been mapped by using somatic cell hybrids (26) and, furthermore, this assignment has been refined to the region 6p2105-6p23 (27) by study of genomic blotting patterns in cell lines containing individual chromosomal deletions of the short arm of chromosome 6. Data on recombination within the HLA complex and with closely linked markers such as glyoxylase 1 (GLO 1) have permitted inferences to be drawn about the order and map distances between marker loci on the proximal portion of the short arm of chromosome 6, as follows: GLO 1-4 centimorgans (cM)-HLA-DR-0.3 cM-BF, C4B, C4A, C2-0.7 cM-HLA-B-0.1 cM-HLA-C-0.7 cM-HLA-A (16-18).Improvements in chromosomal i...

Diversity in G+C content at the third position of codons in vertebrate genes and its cause

“…To examine as many data as possible, DNA segments even corresponding to the partially sequenced genes are analysed. Since all data thus far available are listed, the contribution from immunoglobulin (IG) and major histocompatibility complex (MHC) genes turns out to become evident; MHC class II genes were omitted from the analysis because their chromosomal band location is discrepant between the papers (24,28). Even without the data of IG and MHC, essentially the same conclusion could be obtained.…”

Genes for the tumor necrosis factors alpha and beta are linked to the human major histocompatibility complex.

“…2), Southern blot analysis demonstrated the absence of the TNFa gene from one haplotype only in 6.3.6, 3.1.0, and 721.180, in accordance with 9.28.6 (Fig. 3) (33). The previous localization of the TNFa and TNF/3 genes by Southern blot analysis of human-murine somatic cell hybrids was between q12 and p23 (8).…”

The chromosome region containing the highly polymorphic HLA class I genes displays limited large scale variability in the human population.

“…Later, cloning of the genes encoding these molecules showed restriction fragment site polymorphisms both within and in the immediate surroundings of these genes. Sequence determination of several HLA class I genes gave hints that much of this polymorphism may be generated by events analogous to gene conversion occurring between two members of this large gene family which includes, in addition to the expressed HLA-A, -B and -C genes, 20-30 other related sequences probably all located in the same chromosome region, band p21.3 of chromosome 6 (Morton et al, 1984). The genetic map of this region indicates that HLA-A, -B and -C genes are contained within a segment of 1 centimorgan, the position of the other related genes is not known with certainty although it appears that most of them are clustered close by and telomeric to the HLA-A gene (Orr et al, 1982;Duceman et al, 1985).…”