Sequence and Phylogenetic Analysis of the Untranslated Promoter Regions for HLA Class I Genes

Abstract

Polymorphisms located within the MHC have been linked to many disease outcomes by mechanisms not yet fully understood in most cases. Variants located within untranslated regions of HLA genes are involved in allele specific expression and may therefore underlie some of these disease associations. We determined sequences extending nearly 2kb upstream of the transcription start site for 68 alleles from 57 major lineages of classical HLA class I genes. The nucleotide diversity within this promoter segment roughly follows that seen within the coding regions, with HLA-B showing the highest (~1.9%), followed by HLA–A (~1.8%), and HLA–C showing the lowest diversity (~0.9%). In spite of its greater diversity, HLA-B mRNA expression levels determined in 178 European Americans do not vary in an allele- or lineage-specific manner, unlike the differential expression levels of HLA-A or HLA-C reported previously. Close proximity of promoter sequences in phylogenetic trees is roughly reflected by similarity of expression pattern for most HLA-A and -C loci. While promoter sequence divergence might impact promoter activity, we observed no clear link between the phylogenetic structure as represented by pairwise nucleotide differences in the promoter regions with estimated differences in mRNA expression levels for the classical class I loci. Further, no pair of class I loci showed coordinated expression levels, suggesting that distinct mechanisms across loci determine their expression level under non-stimulated conditions. These data serve as a foundation for more in depth analysis of the functional consequences of promoter region variation within the classical HLA class I loci.

HLA‐A promoter, coding, and 3′UTR sequences in a Brazilian cohort, and their evolutionary aspects

“…The expression profile of each allele is apparently related to both nucleotide variation and different methylation profile . In fact, our data indicate that at least 22 promoter variable sites could modify a potential CpG site (such as rs9260072) and the highly expressing alleles HLA‐A *23 and HLA‐A*24 could present fewer CpG sites. However, in both studies, HLA‐A expression levels were measured in specific cell lines.…”

“…Previous studies have showed allele‐specific mRNA levels, but closely related sequences presented a divergent expression pattern . The expression profile of each allele is apparently related to both nucleotide variation and different methylation profile .…”

“…Despite the presence of many variants at the HLA‐A promoter, the core promoter was found to be conserved. Ramsuran et al showed a great allele‐specific expression level variation, but there was not a clear relationship between sequence similarities and expression levels . However, it is not clear whether this low variability at the core promoter could also be detected when evaluating larger population samples.…”

“…Studies addressing the complete variability of HLA genes are scarce and usually do not include regulatory and intronic segments. Ramsuran et al explored this variability expanding nearly 2 kb upstream of the HLA‐A , HLA‐B , and HLA‐C transcription starting site in a few cell lines typed for frequent alleles. They used Sanger sequencing to assess the promoter variability of 19 HLA‐A alleles detected on homozygous cell lines.…”

Molecular evolution of elements controlling HLA‐C expression: Adaptation to a role as a killer‐cell immunoglobulin‐like receptor ligand regulating natural killer cell function

“…This association was confirmed in a genome‐wide expression quantitative trait analysis of HLA‐C mRNA levels determined by qPCR of peripheral blood mononuclear cell RNA from 273 individuals . Interestingly, the group of HLA‐C alleles that have the highest level of expression ( HLA‐C*01 , *04 , *06 , *12 , and *14 ), all possess the A residue associated with higher promoter activity . Furthermore, a second SNP located 20 bp upstream of the Oct‐1 site was also significantly associated with HLA‐C transcript levels, and this SNP is located within a putative NFAT‐AP1 binding site, suggesting the presence of an enhancer element in this region.…”