Abstract
The HLA genetic region consists of a large multigene complex which includes a number of highly homologous α and β genes encoding class II polypeptides, clustered in three major loci, DP, DQ, and DR. Analysis of genomic polymorphisms at each of these loci is of considerable interest due to the role of particular structural polymorphisms in immune function, but this analysis has been hampered by difficulty in distinguishing between such highly homologous loci. We have identified locus-specific and exon-specific class II gene sequences in order to produce synthetic oligonucleotide probes which hybridize specifically to DQ β genes. Two such oligonucleotide probes are described which are specific for the β 1 and β 2exons of DQ (DC) β which identify DQ β genes in digests of cellular DNA and which can be used to characterize restriction sites flanking the two oligonucleotide-specific regions. By sequentially hybridizing these probes in modified Southern analyses, we have been able to generate a tentative “restriction map” of a newly identified DQ β allele from digests of total genomic DNA. This oligonucleotide mapping technique discriminates between two HLA-DQw3 + alleles, DQ3.1 and DQ3.2, permitting the recognition of structural polymorphisms with DQ β which are highly associated with type I diabetes mellitus.
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Andersson, M., Bohme, J., Andersson, G., Moller, E., Thorsby, E., Rask, L., and Peterson, P. A.: Genomic hybridization with class II transplantation antigen c DNA probes as a complementary technique in tissue typing. Hum. Immunol. 11: 57–67, 1984
Auffray, C., Korman, A. J., Roux-Dosseto, M., Bono, R., and Strominger, J. L.: cDNA clone for the heavy chain of the human B cell alloantigen DC1: Strong sequence homology to the HLA-DR heavy chain. Proc. Natl. Acad. Sci. U.S.A. 79: 6337–6341, 1982
Auffray, C., Koo, J., DeMars, R., and Strominger, J. L.: A minimum of four human class II α-chain genes are encoded in the HLA region of chromosome 6. Nature 304: 174–177, 1983
Auffray, C., Lillie, J. W., Arnot, D., Grossberger, D., Kappes, K., and Strominger, J. L.: Isotypic and allotypic variation of human class II histocompatibility antigen α-chain genes. Nature 308: 327–333, 1984
Bell, J. I., Estess, P., St. John, T., Saiki, R., Watling, D. L., Erlich, H. A., and McDevitt, H. O.: DNA sequence and characterization of human class II major histocompatibility complex β chains from the DRl haplotype. Proc. Natl. Acad. Sci. U.S.A. 82: 3405–3409, 1985
Bodmer, J. and Bodmer, W.: Histocompatibility 1984. Immunol. Today 5: 251–254, 1984
Bosch, M. L., Schreuder, G. M. T., Spits, H., Termijtelen, A., Tilanus, M. G. J., and Giphart, M. J.: Polymorphisms within the HLA-DRw6 haplotype. I. Restriction fragment length variation and its correlation with serology. J Immunol. 134: 3212–3217, 1985
Boss, J. M. and Strominger, J. L.: Cloning and sequence analysis of the human major histocompatibility complex gene DC-3β. Proc. Natl. Acad. Sci. U.S.A. 81: 5199–5203, 1984
Cairns, J. S., Curtsinger, J. M., Dahl, C. A., Freeman, S., Alter, B. J., and Bach, F. H.: Sequence polymorphisms of HLA DRβ1 alleles relating to T -cell recognized determinants. Nature 317: 166–168, 1985
Caruthers, M. H.: New methods for chemically synthesizing deoxyoligonucleotides. In S. M. Weisman (ed.): Methods of DNA and RNA Sequencing, pp. 1–22, Praeger Publishers, New York, New York, 1983
Chang, H., Moriuchi, T., and Silver, J.: The heavy chain of the human B cell alloantigen, HLA-DS, has a variable N-terminal region and a constant immunoglobulin-like region. Nature 305: 813–815, 1983
Cohen, D., LeGall, I., Marcadet, A., Font, M., Lalouel, J., and Dausset, J.: Clusters of HLA class II β restriction fragments describe allelic series. Proc. Natl. Acad. Sci. U.S.A. 81: 7870–7874, 1984
Cohen-Haguenauer, O., Robbins, E., Massart, C., Busson, M., Deschamps, L., Hors, J., Lalouel, J., Dausset, J., and Cohen, D.: A systematic study of HLA class II-β DNA restriction fragments in insulin-dependent diabetes mellitus. Proc. Natl. Acad. Sci. U.S.A. 82: 3335–3339, 1985
Conner, B. J., Reyes, A. A., Morin, C., Itakura, K., Teplitz, R. L., and Wallace, R. B.: Detection of sickle cell β s-globin allele by hybridization with synthetic oligonucleotides. Proc. Natl. Acad. Sci. U.S.A. 80: 278–282, 1983
Duquesnoy, R. J., Marrari, M., Hackbarth, S., and Zeevi, A.: Serological and cellular definition of a new HLA-DR associated determinant, MCI, and its association with rheumatoid arthritis. Hum. Immunol. 10: 165–176, 1984
Gorski, J., Rollini, P., Long, E., and Mach, B.: Molecular organization of the HLA-SB region of the human major histocompatibility complex and evidence for two SB β-chain genes. Proc. Natl. Acad. Sci. U.S.A. 81: 3934–3938, 1984
Gregerson, P. K., Shen, M., Song, Q., Merryman, P., Degar, S., Seki, T., Macari, J., Goldberg, D., Murphy, H., Schwenzer, J., Wang, C. Y., Winchester, R. J., Nepom, G. T., and Silver, J.: Molecular diversity of HLA-DR4 haplotypes. Proc. Natl. Acad. Sci. U.S.A. 83: 2642–2646, 1986
Gustafsson, K., Emmoth, E., Widmark, E., Bohme, J., Peterson, P. A., and Rask, L.: Isolation of a cDNA clone coding for an SB β-chain. Nature 309: 76–78, 1984a
Gustafsson, K., Wiman, E., Emmoth, E., Larhammar, D., Bohme, J., Hyldig-Nielsen, J. J., Ronne, H., Peterson, P. A., and Rask, L.: Mutations and selection in the generation of class 11 histocompatibility antigen polymorphisms. EMBO J. 3: 1655–1661, 1984b
Holbeck, S. L., Kim, S. J., Silver, J., Hansen, J. A., and Nepom, G. T.: HLA-DR4-associated haplotypes are genotypically diverse within HLA. J. Immunol. 135: 637–641, 1985
Hood, L., Steinmetz, M., and Malissen, B.: Genes of the major histocompatibility complex of the mouse. Anna. Rev. Immunol. 1: 529–568, 1983
Kim, S. J., Holbeck, S. L., Nisperos, B., Hansen, J. A., Maeda, H., and Nepom, G. T.: Identification of a polymorphic variant associated with HLA—DQw3 characterized by specific restriction sites within DQβ. Proc. Natl. Acad. Sci. U.S.A. 82: 8139–8143, 1985
Kormann, A. J., Knudsen, P. J., Kaufman, J. E., and Strominger, J. L.: cDNA clones for the heavy chain of HLA-DR antigens obtained after immunopurification of polysomes by monoclonal antibody. Proc. Natl. Acad. Sci. U.S.A. 79: 1844–1848, 1982
Larhammar, D., Schenning, L., Gustafsson, K., Wiman, K., Claesson, L., Rask, L., and Peterson, P. A.: Complete amino acid sequence of an HLA-DR antigen-like 0 chain as predicted from the nucleotide sequence: Similarities with immunoglobulins and HLA-A, -B, and -C antigens. Proc. Natl. Acad. Sci. U.S.A. 79: 3687–3691, 1982
Larhammar, D., Hyldig-Nielsen, J. J., Servenius, B., Andersson, G., Rask, L., and Peterson, P. A.: Exon-intron organization and complete nucleotide sequence of a human major histocompatibility antigen DCβ gene. Proc. Natl. Acad. Sci. U.S.A. 80: 7313–7317, 1983
Larhammar, D., Servenius, B., Rask, L., and Peterson, P. A.: Characterization of an HLA DR β pseudogene. Proc. Natl. Acad. Sci. U.S.A. 82: 1475–1479, 1985
Lawrance, S. K., Das, H. K., Pan, J., and Weissman, S. M.: The genomic organization and nucleotide sequence of the HLA-SB(DP) alpha gene. Nucleic Acids Res. 13: 7515–7528, 1985
Long, E. O., Wake, C. T., Gorski, J., and Mach, B.: Complete sequence of an HLA-DR β chain deduced from a cDNA clone and identification of multiple nonallelic DR 0 chain genes. EMBO J. 2: 389–394, 1983
Maniatis, T., Fritsch, E. F., and Sambrook, J. (eds.): Molecular Cloning, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 1982
Moriuchi, J., Moriuchi, T., and Silver, J.: Nucleotide sequence of an HLA-DQ a chain derived from a DRw9 cell line: Genetic and evolutionary implications. Proc. Natl. Acad. Sci. U.S.A. 82: 3420–3424, 1985
Nepom, B. S., Kim, S. J., and Nepom, G. T.: A deletion mutant defines DQ β variants within DR4-positive DQw3-positive haplotypes. Hum. Immunol., in press, 1986a
Nepom, B. S., Palmer, J., Kim, S. J., Hansen, J. A., Holbeck, S. L., and Nepom, G. T.: Specific genomic markers for the HLA-DQ subregion discriminate between DR4 positive IDDM and DR4 positive JRA. J. Exp. Med. 164: 345–350, 1986b
Nepom, G. T. and Holbeck, S. L.: A locus-specific oligodeoxynucleotide probe specific for HLA class 11 DQ beta genes. In J. W. Streilein, F. Ahmad, S. Black, B. Blomberg, and R. Voellmy (eds.): Advances in Gene Technology: Molecular Biology of the Immune System. Volume II, pp. 259–260, Cambridge University Press, Cambridge 1985
Nepom, G. T., Seyfried, C., and Nepom, B. S.: Immunogenetics of disease susceptibility. Pathol. Immunopath. Res. , in press, 1986
Okada, K., Boss, J. M., Prentice, H., Spies, T., Mengler, R., Auffray, C., Lillie, J., Grossberger, D., and Strominger, J. L.: Gene organization of DC and DX subregions of the human major histocompatibility complex. Proc. Natl. Acad. Sci. USA. 82: 3410–3414, 1985
Orkin, S. H., Markham, A. F., and Kazazian, H. H.: Direct detection of the common Mediterranean β-thalassemia gene with synthetic DNA probes. J. Clin. Invest. 71: 775–779, 1983
Owerbach, D., Lernmark, A., Platz, P., Ryder, L. P., Rask, L., Peterson, P. A., and Ludvigsson, J.: HLA-D region β chain DNA endonuclease fragments differ between HLA-DR identical healthy and insulin-dependent diabetic individuals. Nature 303: 815–817, 1983a
Owerbach, D., Lernmark, A., Rask, L., Peterson, P. A., Platz, P., and Svejgaard, A.: Detection of HLA-D/DR-related DNA polymorphisms in HLA-D homozygous typing cells. Proc. Natl. Acad. Sci. U.S.A.: 3758–3761, 1983b
Robinson, M. A., Long, E.O., Johnson, A. H., Hartzman, R. J., Mach, B., and Kindt, T. J.: Recombination within the HLA-D region: Correlation of molecular genotyping with functional data. J Exp. Med. 160: 222–238, 1984
Roux-Dosseto, M., Auffray, C., Lillie, J. W., Boss, J. M., Cohen, D., DeMars, R., Mawas, C., Seidman, J. G., and Strominger, J. L.: Genetic mapping of a human class II antigen β-chain cDNA clone to the SB region of the HLA complex. Proc. Natl. Acad. Sci. U.S.A. 80: 6036–6040, 1983
Schamboeck, A., Korman, A. J., Kamb, A., and Strominger, J. L.: Organization of the transcriptional unit of a human class II histocompatibility antigen: HLA-DR heavy chain. Nucleic Acids Res. 11: 8663–8675, 1983
Schenning, L., Larhammar, D., Bill, P., Wiman, K., Jonsson, A., Rask, L., and Peterson, P. A.: Both a and 0 chains of HLA-DC class 11 histocompatibility antigens display extensive polymorphisms in their amino-terminal domains. EMBO J. 3: 447–452, 1984
Servenius, B., Gustafsson, K., Widmark, E., Emmoth, E., Andersson, G., Larhammar, D., Rask, L., and Peterson, P. A.: Molecular map of the human HLA-SB (HLA-DP) region and sequence of an SB a (DP a) pseudogene. EMBO J. 3: 3209–3214, 1984
Spies, T., Sorrentino, R., Boss, J. M., Okada, K., and Strominger, J. L.: Structural organization of the DR subregion of the human major histocompatibility complex. Proc. Natl. Acad. Sci. U.S.A. 82: 5165–5169, 1985
Tiwari, J. L. and Terasaki, P. L.: HLA and Disease Associations, Springer-Verlag, New York, 1985
Tonelle, C., DeMars, R., and Long, E. O.: DO β: A new 0 chain gene in HLA D with a distinct regulation of expression. EMBO J. 4: 2839–2847, 1985
Trowsdale, J. and Kelly, A.: The human HLA class 11 a chain gene DZα is distinct from genes in the DP, DQ and DR subregions. EMBO J. 4: 2231–2237, 1985
Trowsdale, J., Lee, J., Carey, J., Grosveld, F., Bodmer, J., and Bodmer, W.: Sequences related to HLA-DR a chain on human chromosome 6: Restriction enzyme polymorphisms detected with DC chain probes. Proc. Natl. Acad. Sci. U.S.A. 80: 1972–1976, 1983
Trowsdale, J., Kelly, A., Lee, J., Carson, S., Austin, P., and Travers, P.: Linkage map of two HLA-SB β and two HLA-SBα related genes: An intron in one of the SB β genes contains a processed pseudogene. Cell 38: 241–249, 1984
Wake, C. T., Long, E. O., and Mach, B.: Allelic polymorphisms and complexity of the genes for HLA-DR β-chains — direct analysis by DNA-DNA hybridization. Nature 300: 372–374, 1982
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Holbeck, S.L., Nepom, G.T. Exon-specific oligonucleotide probes localize HLA-DQ β allelic polymorphisms. Immunogenetics 24, 251–258 (1986). https://doi.org/10.1007/BF00364529
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DOI: https://doi.org/10.1007/BF00364529