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. 1985 Oct 25;13(20):7515–7528. doi: 10.1093/nar/13.20.7515

The genomic organisation and nucleotide sequence of the HLA-SB(DP) alpha gene.

S K Lawrance, H K Das, J Pan, S M Weissman
PMCID: PMC322059  PMID: 2997750

Abstract

We have isolated a unique fragment of the HLA-DR alpha gene and probed human genomic DNA at low stringency to search for homologous sequences. A minimum of six non-polymorphic cross-hybridizing high molecular weight fragments were found in all DNAs examined. In order to obtain molecular clones of these cross-hybridizing fragments, we constructed lambda and cosmid libraries of human DNA and screened them at low stringency with the HLA-DR alpha gene specific subclone. We have isolated clones corresponding to each of the six fragments and, in this paper, describe those which contain the gene encoding HLA-SB(DP) alpha.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Auffray C., Lillie J. W., Arnot D., Grossberger D., Kappes D., Strominger J. L. Isotypic and allotypic variation of human class II histocompatibility antigen alpha-chain genes. Nature. 1984 Mar 22;308(5957):327–333. doi: 10.1038/308327a0. [DOI] [PubMed] [Google Scholar]
  2. Bell J. I., Estess P., St John T., Saiki R., Watling D. L., Erlich H. A., McDevitt H. O. DNA sequence and characterization of human class II major histocompatibility complex beta chains from the DR1 haplotype. Proc Natl Acad Sci U S A. 1985 May;82(10):3405–3409. doi: 10.1073/pnas.82.10.3405. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Biggin M. D., Gibson T. J., Hong G. F. Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci U S A. 1983 Jul;80(13):3963–3965. doi: 10.1073/pnas.80.13.3963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Blin N., Stafford D. W. A general method for isolation of high molecular weight DNA from eukaryotes. Nucleic Acids Res. 1976 Sep;3(9):2303–2308. doi: 10.1093/nar/3.9.2303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Collins F. S., Weissman S. M. The molecular genetics of human hemoglobin. Prog Nucleic Acid Res Mol Biol. 1984;31:315–462. doi: 10.1016/s0079-6603(08)60382-7. [DOI] [PubMed] [Google Scholar]
  6. Das H. K., Biro P. A., Cohen S. N., Erlich H. A., von Gabain A., Lawrance S. K., Lemaux P. G., McDevitt H. O., Peterlin B. M., Schulz M. F. Use of synthetic oligonucleotide probes complementary to genes for human HLA-DR alpha and beta as extension primers for the isolation of 5'-specific genomic clones. Proc Natl Acad Sci U S A. 1983 Mar;80(6):1531–1535. doi: 10.1073/pnas.80.6.1531. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Das H. K., Lawrance S. K., Weissman S. M. Structure and nucleotide sequence of the heavy chain gene of HLA-DR. Proc Natl Acad Sci U S A. 1983 Jun;80(12):3543–3547. doi: 10.1073/pnas.80.12.3543. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Eckels D. D., Lake P., Lamb J. R., Johnson A. H., Shaw S., Woody J. N., Hartzman R. J. SB-restricted presentation of influenza and herpes simplex virus antigens to human T-lymphocyte clones. Nature. 1983 Feb 24;301(5902):716–718. doi: 10.1038/301716a0. [DOI] [PubMed] [Google Scholar]
  10. Gladstone P., Fueresz L., Pious D. Gene dosage and gene expression in the HLA region: evidence from deletion variants. Proc Natl Acad Sci U S A. 1982 Feb;79(4):1235–1239. doi: 10.1073/pnas.79.4.1235. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Gorski J., Rollini P., Long E., Mach B. Molecular organization of the HLA-SB region of the human major histocompatibility complex and evidence for two SB beta-chain genes. Proc Natl Acad Sci U S A. 1984 Jul;81(13):3934–3938. doi: 10.1073/pnas.81.13.3934. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hisajima H., Nishida Y., Nakai S., Takahashi N., Ueda S., Honjo T. Structure of the human immunoglobulin C epsilon 2 gene, a truncated pseudogene: implications for its evolutionary origin. Proc Natl Acad Sci U S A. 1983 May;80(10):2995–2999. doi: 10.1073/pnas.80.10.2995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Hohn B. In vitro packaging of lambda and cosmid DNA. Methods Enzymol. 1979;68:299–309. doi: 10.1016/0076-6879(79)68021-7. [DOI] [PubMed] [Google Scholar]
  14. Hurley C. K., Shaw S., Nadler L., Schlossman S., Capra J. D. Alpha and beta chains of SB and DR antigens are structurally distinct. J Exp Med. 1982 Nov 1;156(5):1557–1562. doi: 10.1084/jem.156.5.1557. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Ish-Horowicz D., Burke J. F. Rapid and efficient cosmid cloning. Nucleic Acids Res. 1981 Jul 10;9(13):2989–2998. doi: 10.1093/nar/9.13.2989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kappes D. J., Arnot D., Okada K., Strominger J. L. Structure and polymorphism of the HLA class II SB light chain genes. EMBO J. 1984 Dec 1;3(12):2985–2993. doi: 10.1002/j.1460-2075.1984.tb02245.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Kaufman J. F., Auffray C., Korman A. J., Shackelford D. A., Strominger J. The class II molecules of the human and murine major histocompatibility complex. Cell. 1984 Jan;36(1):1–13. doi: 10.1016/0092-8674(84)90068-0. [DOI] [PubMed] [Google Scholar]
  18. Kelly A., Trowsdale J. Complete nucleotide sequence of a functional HLA-DP beta gene and the region between the DP beta 1 and DP alpha 1 genes: comparison of the 5' ends of HLA class II genes. Nucleic Acids Res. 1985 Mar 11;13(5):1607–1621. doi: 10.1093/nar/13.5.1607. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Leder P., Tiemeier D., Enquist L. EK2 derivatives of bacteriophage lambda useful in the cloning of DNA from higher organisms: the lambdagtWES system. Science. 1977 Apr 8;196(4286):175–177. doi: 10.1126/science.322278. [DOI] [PubMed] [Google Scholar]
  20. Maniatis T., Hardison R. C., Lacy E., Lauer J., O'Connell C., Quon D., Sim G. K., Efstratiadis A. The isolation of structural genes from libraries of eucaryotic DNA. Cell. 1978 Oct;15(2):687–701. doi: 10.1016/0092-8674(78)90036-3. [DOI] [PubMed] [Google Scholar]
  21. Okada K., Boss J. M., Prentice H., Spies T., Mengler R., Auffray C., Lillie J., Grossberger D., Strominger J. L. Gene organization of DC and DX subregions of the human major histocompatibility complex. Proc Natl Acad Sci U S A. 1985 May;82(10):3410–3414. doi: 10.1073/pnas.82.10.3410. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Okada K., Prentice H. L., Boss J. M., Levy D. J., Kappes D., Spies T., Raghupathy R., Mengler R. A., Auffray C., Strominger J. L. SB subregion of the human major histocompatibility complex: gene organization, allelic polymorphism and expression in transformed cells. EMBO J. 1985 Mar;4(3):739–748. doi: 10.1002/j.1460-2075.1985.tb03691.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Poustka A., Rackwitz H. R., Frischauf A. M., Hohn B., Lehrach H. Selective isolation of cosmid clones by homologous recombination in Escherichia coli. Proc Natl Acad Sci U S A. 1984 Jul;81(13):4129–4133. doi: 10.1073/pnas.81.13.4129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Rimm D. L., Horness D., Kucera J., Blattner F. R. Construction of coliphage lambda Charon vectors with BamHI cloning sites. Gene. 1980 Dec;12(3-4):301–309. doi: 10.1016/0378-1119(80)90113-4. [DOI] [PubMed] [Google Scholar]
  25. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Servenius B., Gustafsson K., Widmark E., Emmoth E., Andersson G., Larhammar D., Rask L., Peterson P. A. Molecular map of the human HLA-SB (HLA-DP) region and sequence of an SB alpha (DP alpha) pseudogene. EMBO J. 1984 Dec 20;3(13):3209–3214. doi: 10.1002/j.1460-2075.1984.tb02280.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Shaw S., Johnson A. H., Shearer G. M. Evidence for a new segregant series of B cell antigens that are encoded in the HLA-D region and that stimulate secondary allogenic proliferative and cytotoxic responses. J Exp Med. 1980 Sep 1;152(3):565–580. doi: 10.1084/jem.152.3.565. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Shaw S., Pollack M. S., Payne S. M., Johnson A. H. HLA-linked B cell alloantigens of a new segregant series: population and family studies of the SB antigens. Hum Immunol. 1980 Sep;1(2):177–185. doi: 10.1016/0198-8859(80)90104-4. [DOI] [PubMed] [Google Scholar]
  29. Staden R. Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing. Nucleic Acids Res. 1982 Aug 11;10(15):4731–4751. doi: 10.1093/nar/10.15.4731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Termijtelen A., Meera Khan P., Shaw S., van Rood J. J. Mapping SB in relation to HLA and GLO1 using cells from first-cousin marriage offspring. Immunogenetics. 1983;18(5):503–512. doi: 10.1007/BF00364391. [DOI] [PubMed] [Google Scholar]
  31. Trowsdale J., Kelly A., Lee J., Carson S., Austin P., Travers P. Linkage map of two HLA-SB beta and two HLA-SB alpha-related genes: an intron in one of the SB beta genes contains a processed pseudogene. Cell. 1984 Aug;38(1):241–249. doi: 10.1016/0092-8674(84)90546-4. [DOI] [PubMed] [Google Scholar]

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