In a small Baltic nation better known for its medieval old towns and digital governance than for immunogenetics, a team of researchers has now mapped one of the immune system’s most quietly important genes in unprecedented detail. By sequencing the complete HLA-E gene in 143 Estonian individuals, scientists from Maastricht University Medical Center and Tartu University Hospitals have uncovered four alleles never before recorded in the international HLA database, confirmed that this remarkably conserved gene behaves identically across Estonia’s genetically distinctive regions, and revealed striking associations between HLA-E variants and the classical HLA genes that sit alongside it on chromosome 6. The study, published open access in the journal Immunogenetics, offers one of the fullest portraits yet of a molecule that serves as a master regulator of natural killer cell activity.
HLA-E belongs to the family of non-classical MHC class I molecules, sometimes called class Ib, which play an essential role in immunomodulation. Unlike its celebrated cousins HLA-A, HLA-B and HLA-C, which bristle with hundreds of variants and dominate transplant matching, HLA-E has long been considered a genetic backwater. Structurally, however, it resembles the classical molecules closely: three extracellular domains pair with beta-2 microglobulin, forming a complex that presents peptides at the cell surface. What makes HLA-E unusual is what it displays. Instead of offering a wide menu of foreign peptides, it primarily binds self-peptides derived from the leader sequences of classical class I molecules, effectively monitoring whether other HLA molecules are being produced normally. When viruses or tumours suppress classical HLA expression, HLA-E levels at the surface drop, and natural killer cells, which survey the body through activating and inhibitory CD94/NKG2 receptors, interpret the silence as a warning. HLA-E also engages cytotoxic and regulatory CD8 T cells through their alpha-beta T cell receptors, giving it a dual role bridging innate and adaptive immunity.
For decades, only two HLA-E protein variants were known, differing by a single amino acid at position 107 of the alpha-2 domain: an arginine in HLA-E01:01 and a glycine in HLA-E01:03. That simplicity was partly an artefact of method. Most studies sequenced only exons 2 and 3, the segments encoding the peptide-binding groove, leaving the rest of the gene unexplored. As full-length sequencing technologies spread, researchers began finding more variability than expected. The IPD-IMGT/HLA database now lists 378 HLA-E alleles, though synonymous substitutions and one null allele mean these encode only 142 protein variants. Two large-scale efforts have since confirmed the richer picture: one analysed next-generation genotyping data from 2.5 million potential stem cell donors across 104 populations, and another used single-molecule real-time sequencing on 6,227 DNA samples, uncovering 86 novel alleles. Despite this hidden diversity, the two classic protein variants still account for roughly 99 percent of HLA-E worldwide, in nearly equal proportions, a pattern that has prompted suggestions of balancing selection maintaining functional differences between them. Laboratory work has shown that HLA-E01:03 achieves slightly higher cell surface expression than 01:01, owing to its marginally stronger peptide-binding affinity.
The Estonian population offered an intriguing test case. With around 1.3 million inhabitants, Estonia has been shaped by successive migration waves, geographic isolation and cultural influences, producing marked genetic structuring within the country, particularly between the south-east and the rest of the nation. Previous genomic studies have documented this regional differentiation in fine detail. Whether such structuring extends to HLA-E, however, was unknown, since the gene had been examined in Estonians only once before, through the large registry-based study that did not perform full-gene sequencing. The new research drew on the Estonian Biobank, selecting 143 DNA samples from a collection of more than 10,000 individuals born in Estonia and sampled in 2005. To ensure fair representation, the team chose equal numbers of participants from each of Estonia’s 15 counties, matched for age and gender, spanning ages 18 to 83, with 72 men and 71 women. The study was approved by the Ethics Review Committee on Human Research of the University of Tartu, and all participants gave written informed consent.
The methodological approach was deliberately thorough. Rather than targeting the familiar exons, the researchers amplified the complete HLA-E gene from the 5-prime untranslated region to the 3-prime untranslated region, capturing both coding sequences and the regulatory flanks in a single amplicon. Purified fragments were sequenced in both directions using the Sanger method, the gold standard for resolving single nucleotide variants in targeted regions. Allele frequencies were calculated directly as the number of observed alleles divided by twice the number of individuals, and regional comparisons employed chi-squared tests. To explore associations with the classical HLA genes, the team performed low-resolution typing of HLA-A, HLA-B and HLA-C using Luminex sequence-specific oligonucleotide probes, analysing the results with the PYPOP software package, which also confirmed that the HLA-E allelic distribution fitted Hardy-Weinberg equilibrium, with a P-value of 0.78 indicating no deviation from random mating expectations.
The sequencing effort yielded 16 distinct HLA-E alleles, four of which were entirely new to science: HLA-E01:01:01:51, 01:01:43, 01:01:01:53 and 01:01:01:54. For a population of this size, discovering four novel alleles is consistent with the yield of comparable full-length studies in other populations worldwide. Most of these variants differ only in non-coding or synonymous positions, so the 16 alleles boil down to just four protein variants: HLA-E01:01, 01:03, 01:06 and 01:09. Phenotype frequency calculations showed that 45 percent of Estonians carry both major variants in heterozygous form. The most common allele was HLA-E01:01:01:01/02 at a frequency of 0.441, followed by 01:03:02:01 at 0.357. Intriguingly, the peptide-binding grooves of the rarer variants mirror the common ones: HLA-E01:09 has a groove identical to 01:01 with its difference located in the alpha-3 domain, while 01:06 matches 01:03 in the groove but diverges in the alpha-3 domain.
The regional analysis produced perhaps the most conceptually interesting null result. Despite Estonia’s well-documented genetic split between the south-eastern counties of Põlva, Tartu, Valga and Võru and the rest of the country, chi-squared comparisons of high-resolution HLA-E allele frequencies found no significant differences, whether comparing the south-east with the north-east or with all other counties. Nor did comparison with neighbouring populations reveal major differences. Drawing on the registry data covering Estonians, Finns, Russians, Latvians, Belarusians and Ukrainians, the study found Estonian frequencies sitting comfortably within the European pattern, while showing the expected clear divergence from Asian populations such as the Japanese, Indonesians and Chinese. A finer single-nucleotide comparison with Finnish samples from the 1000 Genomes Project, justified by the deep historical and genetic ties between the two peoples, showed broadly similar SNP frequencies, with modest differences at two positions: the T nucleotide at position 424, characteristic of HLA-E01:03:02G, was somewhat more prevalent in Estonians, while the T at position 1857, which defines HLA-E01:06, was less common than in Finns.
The association analysis added a layer of evolutionary depth. Although the arginine and glycine variants appear in almost equal numbers overall, they are not distributed evenly across the classical HLA haplotypes. HLA-A01 travelled preferentially with arginine 107, appearing with R in 12 percent of cases but with G in only 1 percent. HLA-A03 showed the opposite tendency, pairing with glycine at 15 percent versus arginine at 2 percent, and HLA-C04 was found exclusively with glycine. Several other allele groups displayed near-exclusive associations, though small sample sizes caution against over-interpretation. Examining complete HLA-A to HLA-B to HLA-C haplotypes sharpened the pattern further: eight of the ten most frequent haplotypes showed a clear preference for one variant or the other. Notably, HLA-A01 and HLA-A*03 share an identical leader peptide sequence that could bind HLA-E, so the driver of these associations cannot be the leader peptide itself. Nor did the dimorphism in the HLA-B leader peptide, methionine versus threonine at position minus 21, show any coherent relationship with the HLA-E variants, ruling out one obvious mechanistic explanation.
The findings collectively reinforce the view that HLA-E performs a conserved function preserved across diverse genetic backgrounds. Whatever historical migrations and admixture events shaped the broader Estonian genome, they left their fingerprints everywhere except on this gene, whose variation remained stable across regions and indistinguishable from that of neighbouring populations. This conservation, set against the extreme polymorphism of the classical class I genes, continues to fuel speculation about HLA-E’s evolutionary pathway and the functional significance of the single amino acid difference that defines its two main variants. The preferential haplotype associations documented here suggest that the R107G dimorphism does not drift independently but is woven into the broader architecture of the HLA region, echoing earlier observations in Chinese and French populations. For transplant immunology, stem cell donor registries and cancer immunotherapy research, each full-length dataset of this kind sharpens the picture of a molecule that, though long overshadowed by its classical relatives, may hold keys to immune regulation that medicine is only beginning to turn.
Subject of Research: Full-length genetic polymorphism of the non-classical HLA-E gene in the Estonian population, including novel allele discovery, regional variation, and associations with classical HLA class I genes.
Subject of Research: Biology
Article Title: Full-length gene polymorphism of the non-classical HLA-E in Estonian individuals
Article References: Olieslagers, T. I., Tagen, I., Groeneweg, M., Tilanus, M. G. J., Wieten, L., & Voorter, C. E. M. (2025). Full-length gene polymorphism of the non-classical HLA-E in Estonian individuals. Immunogenetics, 77(1), Article 24. https://doi.org/10.1007/s00251-025-01381-z
Image Credits: AI Generated
DOI: 10.1007/s00251-025-01381-z
Keywords: HLA-E, Estonia, allele frequency, population diversity, sequencing, polymorphism, natural killer cells, HLA class I, haplotypes, immunogenetics
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Juliet Wilcox. (September 4, 2026). Genetic diversity of full-length HLA-E gene characterized in Estonians. Scienmag. https://scienmag.com/genetic-diversity-of-full-length-hla-e-gene-characterized-in-estonians/
Juliet Wilcox. “Genetic diversity of full-length HLA-E gene characterized in Estonians.” Scienmag, 4 September 2026, https://scienmag.com/genetic-diversity-of-full-length-hla-e-gene-characterized-in-estonians/. Accessed 4 September 2026.
Juliet Wilcox. “Genetic diversity of full-length HLA-E gene characterized in Estonians.” Scienmag. September 4, 2026. https://scienmag.com/genetic-diversity-of-full-length-hla-e-gene-characterized-in-estonians/
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Tags: conservation of HLA-E across populationsfull-length HLA-E sequencing in Baltic populationsgenetic variation in Baltic populationsgenetic variation in immune system genesgenomic mapping of HLA-E in EstoniaHLA-E alleles and immune regulationHLA-E and classical HLA gene associationsHLA-E conservation across Estonian regionsHLA-E gene diversity in Estoniansimmunogenetics of HLA-Eimmunogenetics research in small populationsimmunomodulatory functions of HLA-Eimpact of HLA-E diversity on transplant compatibilityimpact of HLA-E variants on immune responsenatural killer cell activationnon-classical MHC class I moleculesnovel HLA-E alleles discoveryrole of HLA-E in natural killer cell regulation
