Abstract
Despite several studies that defined the polymorphism of the nonclassical human leukocyte antigen-E (HLA-E), HLA-F, and HLA-G genes, most polymorphisms thus far examined in correlative studies were derived from the coding sequences of these genes. In addition, some discrepancies and ambiguities in the available data have persisted in current databases. To expand the data available and to resolve some of the discrepant data, we have defined protocols that allow for the amplification of 6 to 7 kb of contiguous genomic sequence for each gene, including all of the coding and intron sequences, approximately 2 kb of 5' flanking promoter sequence, and 1 kb of 3' flanking sequence. Using long-range polymerase chain reaction (PCR) protocols, generating either one or two PCR products depending on the locus, amplified genomic DNA was directly sequenced to completion using a set of about 30 primers over each locus to yield contiguous sequence data from both strands. Using this approach, we sequenced 33 genomic DNAs, from Asian, African American, and Caucasian samples. The results of this analysis confirmed several previously reported coding sequence variants, identified several new allelic variants, and also defined extensive variation in intron and flanking sequences. It was possible to construct haplotype maps and to identify tagging single nucleotide polymorphisms that can be used to detect the composite variation spanning all three genes.
Similar content being viewed by others
References
Agrawal S, Pandey MK (2003) The potential role of HLA-G polymorphism in maternal tolerance to the developing fetus. J Hematother Stem Cell Res 12:749–756
Chapman JM, Cooper JD, Todd JA, Clayton DG (2003) Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power. Hum Hered 56:18–31
Daza-Vamenta R, Glusman G, Rowen L, Guthrie B, Geraghty DE (2004) Genetic divergence of the rhesus macaque major histocompatibility complex. Genome Res 14:1501–1515
Ewing B, Green P (1998) Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res 8:186–194
Fujii T, Ishitani A, Geraghty DE (1994) A soluble form of the HLA-G antigen is encoded by a messenger ribonucleic acid containing intron 4. J Immunol 153:5516–5524
Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D (2002) The structure of haplotype blocks in the human genome. Science 296:2225–2229
Gazit E, Slomov Y, Goldberg I, Brenner S, Loewenthal R (2004) HLA-G is associated with pemphigus vulgaris in Jewish patients. Hum Immunol 65:39–46
Geraghty DE (1993) Structure of the HLA class I region and expression of its resident genes. Curr Opin Immunol 5:3–7
Geraghty DE, Koller BH, Orr HT (1987) A human major histocompatibility complex class I gene that encodes a protein with a shortened cytoplasmic segment. Proc Natl Acad Sci U S A 84:9145–9149
Geraghty DE, Wei XH, Orr HT, Koller BH (1990) Human leukocyte antigen F (HLA-F). An expressed HLA gene composed of a class I coding sequence linked to a novel transcribed repetitive element. J Exp Med 171:1–18
Geraghty DE, Koller BH, Hansen JA, Orr HT (1992a) The HLA class I gene family includes at least six genes and twelve pseudogenes and gene fragments. J Immunol 149:1934–1946
Geraghty DE, Stockschleader M, Ishitani A, Hansen JA (1992b) Polymorphism at the HLA-E locus predates most HLA-A and -B polymorphism. Hum Immunol 33:174–184
Geraghty DE, Fortelny S, Guthrie B, Irving M, Pham H, Wang R, Daza R, Nelson B, Stonehocker J, Williams L, Vu Q (2000) Data acquisition, data storage, and data presentation in a modern genetics laboratory. Rev Immunogenet 2:532–540
Geraghty DE, Daza R, Williams LM, Vu Q, Ishitani A (2002) Genetics of the immune response: identifying immune variation within the MHC and throughout the genome. Immunol Rev 190:69–85
Gobin SJ, van den Elsen PJ (2000) Transcriptional regulation of the MHC class Ib genes HLA-E, HLA-F, and HLA-G. Hum Immunol 61:1102–1107
Gobin SJ, Keijsers V, van Zutphen M, van den Elsen PJ (1998) The role of enhancer A in the locus-specific transactivation of classical and nonclassical HLA class I genes by nuclear factor kappa B. J Immunol 161:2276–2283
Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8:195–202
Grimsley C, Kawasaki A, Gassner C, Sageshima N, Nose Y, Hatake K, Geraghty DE, Ishitani A (2002) Definitive high resolution typing of HLA-E allelic polymorphisms: identifying potential errors in existing allele data. Tissue Antigens 60:206–212
Hirankarn N, Kimkong I, Mutirangura A (2004) HLA-E polymorphism in patients with nasopharyngeal carcinoma. Tissue Antigens 64:588–592
Horton R, Wilming L, Rand V, Lovering RC, Bruford EA, Khodiyar VK, Lush MJ, Povey S, Talbot CC Jr, Wright MW, Wain HM, Trowsdale J, Ziegler A, Beck S (2004) Gene map of the extended human MHC. Nat Rev Genet 5:889–899
Hunt JS, Petroff MG, McIntire RH, Ober C (2005) HLA-G and immune tolerance in pregnancy. FASEB J 19:681–693
Hylenius S, Andersen AM, Melbye M, Hviid TV (2004) Association between HLA-G genotype and risk of pre-eclampsia: a case-control study using family triads. Mol Hum Reprod 10:237–246
Ishitani A, Geraghty DE (1992) Alternative splicing of HLA-G transcripts yields proteins with primary structures resembling both class I and class II antigens. Proc Natl Acad Sci U S A 89:3947–3951
Ishitani A, Kishida M, Sageshima N, Yashiki S, Sonoda S, Hayami M, Smith AG, Hatake K (1999) Re-examination of HLA-G polymorphism in African Americans. Immunogenetics 49:808–811
Ishitani A, Sageshima N, Lee N, Dorofeeva N, Hatake K, Marquardt H, Geraghty DE (2003) Protein expression and peptide binding suggest unique and interacting functional roles for HLA-E, F, and G in maternal–placental immune recognition. J Immunol 171:1376–1384
Kaiser BK, Barahmand-Pour F, Paulsene W, Medley S, Geraghty DE, Strong RK (2005) Interactions between NKG2x immunoreceptors and HLA-E ligands display overlapping affinities and thermodynamics. J Immunol 174:2878–2884
Kirszenbaum M, Djoulah S, Hors J, Prost S, Dausset J, Carosella ED (1999) Polymorphism of HLA-G gene and protein. J Reprod Immunol 43:105–109
Koller BH, Geraghty DE, Shimizu Y, DeMars R, Orr HT (1988) HLA-E. A novel HLA class I gene expressed in resting T lymphocytes. J Immunol 141:897–904
Kovats S, Main EK, Librach C, Stubblebine M, Fisher SJ, DeMars R (1990) A class I antigen, HLA-G, expressed in human trophoblasts. Science 248:220–223
Le Bouteiller P, Rodriguez AM, Mallet V, Girr M, Guillaudeux T, Lenfant F (1996) Placental expression of HLA class I genes. Am J Reprod Immunol 35:216–225
Lee N, Geraghty DE (2003) HLA-F surface expression on B cell and monocyte cell lines is partially independent from tapasin and completely independent from TAP. J Immunol 171:5264–5271
Lee N, Malacko AR, Ishitani A, Chen MC, Bajorath J, Marquardt H, Geraghty DE (1995) The membrane-bound and soluble forms of HLA-G bind identical sets of endogenous peptides but differ with respect to TAP association. Immunity 3:591–600
Lee N, Goodlett DR, Ishitani A, Marquardt H, Geraghty DE (1998a) HLA-E surface expression depends on binding of TAP-dependent peptides derived from certain HLA class I signal sequences. J Immunol 160:4951–4960
Lee N, Llano M, Carretero M, Ishitani A, Navarro F, Lopez-Botet M, Geraghty DE (1998b) HLA-E is a major ligand for the natural killer inhibitory receptor CD94/NKG2A. Proc Natl Acad Sci U S A 95:5199–5204
Llano M, Lee N, Navarro F, Garcia P, Albar JP, Geraghty DE, Lopez-Botet M (1998) HLA-E-bound peptides influence recognition by inhibitory and triggering CD94/NKG2 receptors: preferential response to an HLA-G-derived nonamer. Eur J Immunol 28:2854–2863
Margulies EH, Green ED (2003) Detecting highly conserved regions of the human genome by multispecies sequence comparisons. Cold Spring Harb Symp Quant Biol 68:255–263
Marsh SG, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Geraghty DE, Hansen JA, Hurley CK, Mach B, Mayr WR, Parham P, Petersdorf EW, Sasazuki T, Schreuder GM, Strominger JL, Svejgaard A, Terasaki PI, Trowsdale J (2005) Nomenclature for factors of the HLA system, 2004. Tissue Antigens 65:301–369
Murphy WJ, Bourque G, Tesler G, Pevzner P, O’Brien SJ (2003) Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps. Hum Genomics 1:30–40
Nicolae D, Cox NJ, Lester LA, Schneider D, Tan Z, Billstrand C, Kuldanek S, Donfack J, Kogut P, Patel NM, Goodenbour J, Howard T, Wolf R, Koppelman GH, White SR, Parry R, Postma DS, Meyers D, Bleecker ER, Hunt JS, Solway J, Ober C (2005) Fine mapping and positional candidate studies identify HLA-G as an asthma susceptibility gene on chromosome 6p21. Am J Hum Genet 76:349–357
Ober C, Aldrich CL, Chervoneva I, Billstrand C, Rahimov F, Gray HL, Hyslop T (2003) Variation in the HLA-G promoter region influences miscarriage rates. Am J Hum Genet 72:1425–1435
Pfeiffer KA, Fimmers R, Engels G, van der Ven H, van der Ven K (2001) The HLA-G genotype is potentially associated with idiopathic recurrent spontaneous abortion. Mol Hum Reprod 7:373–378
Rousseau P, Masternak K, Krawczyk M, Reith W, Dausset J, Carosella ED, Moreau P (2004) In vivo, RFX5 binds differently to the human leucocyte antigen-E, -F, and -G gene promoters and participates in HLA class I protein expression in a cell type-dependent manner. Immunology 111:53–65
Shiroishi M, Tsumoto K, Amano K, Shirakihara Y, Colonna M, Braud VM, Allan DS, Makadzange A, Rowland-Jones S, Willcox B, Jones EY, van der Merwe PA, Kumagai I, Maenaka K (2003) Human inhibitory receptors Ig-like transcript 2 (ILT2) and ILT4 compete with CD8 for MHC class I binding and bind preferentially to HLA-G. Proc Natl Acad Sci U S A 100:8856–8861
Solier C, Mallet V, Lenfant F, Bertrand A, Huchenq A, Le Bouteiller P (2001) HLA-G unique promoter region: functional implications. Immunogenetics 53:617–625
Stewart CA, Horton R, Allcock RJ, Ashurst JL, Atrazhev AM, Coggill P, Dunham I, Forbes S, Halls K, Howson JM, Humphray SJ, Hunt S, Mungall AJ, Osoegawa K, Palmer S, Roberts AN, Rogers J, Sims S, Wang Y, Wilming LG, Elliott JF, de Jong PJ, Sawcer S, Todd JA, Trowsdale J, Beck S (2004) Complete MHC haplotype sequencing for common disease gene mapping. Genome Res 14:1176–1187
Strong RK, Holmes MA, Li P, Braun L, Lee N, Geraghty DE (2003) HLA-E allelic variants. Correlating differential expression, peptide affinities, crystal structures, and thermal stabilities. J Biol Chem 278:5082–5090
Takeuchi F, Yanai K, Morii T, Ishinaga Y, Taniguchi-Yanai K, Nagano S, Kato N (2005) Linkage disequilibrium grouping of SNPs reflecting haplotype phylogeny for efficient selection of tag SNPs. Genetics 170:291-304
Tripathi P, Abbas A, Naik S, Agrawal S (2004) Role of 14-bp deletion in the HLA-G gene in the maintenance of pregnancy. Tissue Antigens 64:706–710
Wiltshire S, Morris AP, McCarthy MI, Cardon LR (2005) How useful is the fine-scale mapping of complex trait linkage peaks? Evaluating the impact of additional microsatellite genotyping on the posterior probability of linkage. Genet Epidemiol 28:1–10
Acknowledgements
The expert technical assistance of Scott Medley is gratefully acknowledged. This work was supported by National Institute of Health grants AI33484 and AI49245 to DEG. A.I. was supported in part by Grant in Aid number 05671391 from the Ministry of Education, Science, and Culture in Japan and by National Institutes of Health grant AI49213. L.P.Z. was supported by CA106320.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Pyo, CW., Williams, L.M., Moore, Y. et al. HLA-E, HLA-F, and HLA-G polymorphism: genomic sequence defines haplotype structure and variation spanning the nonclassical class I genes. Immunogenetics 58, 241–251 (2006). https://doi.org/10.1007/s00251-005-0076-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00251-005-0076-z