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. 1992 Aug 15;89(16):7601–7605. doi: 10.1073/pnas.89.16.7601

In vivo footprint analysis of the HLA-DRA gene promoter: cell-specific interaction at the octamer site and up-regulation of X box binding by interferon gamma.

K L Wright 1, J P Ting 1
PMCID: PMC49758  PMID: 1502171

Abstract

Analysis of the major histocompatibility complex class II gene promoter DRA has previously identified at least five cis-acting regions required for maximal expression. We have examined the DRA promoter for protein-DNA interactions in the intact cell, which may mediate transcriptional activation. Using in vivo genomic footprinting we identified interactions in B-cell lines at the octamer site and the Y, X1, and X2 boxes. Class II antigen expressing T-cell lines maintained contacts identical to B-cell lines, while class II-negative T-cell lines exhibited no interactions. In lymphoid cell lines, the octamer site is occupied and required for maximal expression. This is most likely due to the presence of the lymphoid-specific OTF-2 factor. In contrast, the class II-positive nonlymphoid glioblastoma cell line does not exhibit interactions at the octamer site despite the presence of the ubiquitous OTF-1 factor and an open binding site. Thus, the DRA promoter discriminates against OTF-1 activation at the level of DNA binding in the glioblastoma line. Interferon gamma induces class II expression in this glioblastoma cell line and, in parallel, up-regulates X1 and X2 box protein-DNA interactions, while all other interactions remain unchanged. These results suggest that interferon gamma functions on a poised promoter by altering weak, nonproductive interactions at the X boxes to strong interactions. These findings provide direct in vivo evidence to strongly suggest that the modulation of X1 and X2 interactions is an important constituent of the interferon gamma induction pathway.

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Selected References

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

  1. Basta P. V., Sherman P. A., Ting J. P. Detailed delineation of an interferon-gamma-responsive element important in human HLA-DRA gene expression in a glioblastoma multiform line. Proc Natl Acad Sci U S A. 1988 Nov;85(22):8618–8622. doi: 10.1073/pnas.85.22.8618. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Charron D. J., Engelman E. G., Benike C. J., McDevitt H. O. Ia antigens on alloreactive T cells in man detected by monoclonal antibodies. Evidence for synthesis of HLA-D/DR molecules of the responder type. J Exp Med. 1980 Aug 1;152(2 Pt 2):127s–136s. [PubMed] [Google Scholar]
  3. Church G. M., Gilbert W. Genomic sequencing. Proc Natl Acad Sci U S A. 1984 Apr;81(7):1991–1995. doi: 10.1073/pnas.81.7.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cogswell J. P., Basta P. V., Ting J. P. X-box-binding proteins positively and negatively regulate transcription of the HLA-DRA gene through interaction with discrete upstream W and V elements. Proc Natl Acad Sci U S A. 1990 Oct;87(19):7703–7707. doi: 10.1073/pnas.87.19.7703. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cogswell J. P., Zeleznik-Le N., Ting J. P. Transcriptional regulation of the HLA-DRA gene. Crit Rev Immunol. 1991;11(2):87–112. [PubMed] [Google Scholar]
  6. Collins T., Korman A. J., Wake C. T., Boss J. M., Kappes D. J., Fiers W., Ault K. A., Gimbrone M. A., Jr, Strominger J. L., Pober J. S. Immune interferon activates multiple class II major histocompatibility complex genes and the associated invariant chain gene in human endothelial cells and dermal fibroblasts. Proc Natl Acad Sci U S A. 1984 Aug;81(15):4917–4921. doi: 10.1073/pnas.81.15.4917. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cotner T., Williams J. M., Christenson L., Shapiro H. M., Strom T. B., Strominger J. Simultaneous flow cytometric analysis of human T cell activation antigen expression and DNA content. J Exp Med. 1983 Feb 1;157(2):461–472. doi: 10.1084/jem.157.2.461. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Cresswell P. Immunology: questions of presentation. Nature. 1990 Feb 15;343(6259):593–594. doi: 10.1038/343593a0. [DOI] [PubMed] [Google Scholar]
  9. Didier D. K., Schiffenbauer J., Woulfe S. L., Zacheis M., Schwartz B. D. Characterization of the cDNA encoding a protein binding to the major histocompatibility complex class II Y box. Proc Natl Acad Sci U S A. 1988 Oct;85(19):7322–7326. doi: 10.1073/pnas.85.19.7322. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dignam J. D., Lebovitz R. M., Roeder R. G. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 1983 Mar 11;11(5):1475–1489. doi: 10.1093/nar/11.5.1475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Dorn A., Bollekens J., Staub A., Benoist C., Mathis D. A multiplicity of CCAAT box-binding proteins. Cell. 1987 Sep 11;50(6):863–872. doi: 10.1016/0092-8674(87)90513-7. [DOI] [PubMed] [Google Scholar]
  12. Gerster T., Matthias P., Thali M., Jiricny J., Schaffner W. Cell type-specificity elements of the immunoglobulin heavy chain gene enhancer. EMBO J. 1987 May;6(5):1323–1330. doi: 10.1002/j.1460-2075.1987.tb02371.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Hooft van Huijsduijnen R. A., Bollekens J., Dorn A., Benoist C., Mathis D. Properties of a CCAAT box-binding protein. Nucleic Acids Res. 1987 Sep 25;15(18):7265–7282. doi: 10.1093/nar/15.18.7265. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hooft van Huijsduijnen R., Li X. Y., Black D., Matthes H., Benoist C., Mathis D. Co-evolution from yeast to mouse: cDNA cloning of the two NF-Y (CP-1/CBF) subunits. EMBO J. 1990 Oct;9(10):3119–3127. doi: 10.1002/j.1460-2075.1990.tb07509.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Houghton A. N., Thomson T. M., Gross D., Oettgen H. F., Old L. J. Surface antigens of melanoma and melanocytes. Specificity of induction of Ia antigens by human gamma-interferon. J Exp Med. 1984 Jul 1;160(1):255–269. doi: 10.1084/jem.160.1.255. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hume C. R., Lee J. S. Functional analysis of cis-linked regulatory sequences in the HLA DRA promoter by transcription in vitro. Tissue Antigens. 1990 Sep;36(3):108–115. doi: 10.1111/j.1399-0039.1990.tb01810.x. [DOI] [PubMed] [Google Scholar]
  17. Hämmerling G. J. Tissue distribution of Ia antigens and their expression on lymphocyte subpopulations. Transplant Rev. 1976;30:64–82. [PubMed] [Google Scholar]
  18. Indiveri F., Wilson B. S., Russo C., Quaranta V., Pellegrino M. A., Ferrone S. Ia-like antigens on human T lymphocytes: relationship to other surface markers, role in mixed lymphocyte reactions, and structural profile. J Immunol. 1980 Dec;125(6):2673–2678. [PubMed] [Google Scholar]
  19. Kara C. J., Glimcher L. H. In vivo footprinting of MHC class II genes: bare promoters in the bare lymphocyte syndrome. Science. 1991 May 3;252(5006):709–712. doi: 10.1126/science.1902592. [DOI] [PubMed] [Google Scholar]
  20. 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]
  21. Kemler I., Schaffner W. Octamer transcription factors and the cell type-specificity of immunoglobulin gene expression. FASEB J. 1990 Mar;4(5):1444–1449. doi: 10.1096/fasebj.4.5.2407588. [DOI] [PubMed] [Google Scholar]
  22. Kunkel T. A., Roberts J. D., Zakour R. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 1987;154:367–382. doi: 10.1016/0076-6879(87)54085-x. [DOI] [PubMed] [Google Scholar]
  23. Lechler R. I., Norcross M. A., Germain R. N. Qualitative and quantitative studies of antigen-presenting cell function by using I-A-expressing L cells. J Immunol. 1985 Nov;135(5):2914–2922. [PubMed] [Google Scholar]
  24. Liou H. C., Boothby M. R., Finn P. W., Davidon R., Nabavi N., Zeleznik-Le N. J., Ting J. P., Glimcher L. H. A new member of the leucine zipper class of proteins that binds to the HLA DR alpha promoter. Science. 1990 Mar 30;247(4950):1581–1584. doi: 10.1126/science.2321018. [DOI] [PubMed] [Google Scholar]
  25. Matis L. A., Jones P. P., Murphy D. B., Hedrick S. M., Lerner E. A., Janeway C. A., Jr, McNicholas J. M., Schwartz R. H. Immune response gene function correlates with the expression of an Ia antigen. II. A quantitative deficiency in Ae:E alpha complex expression causes a corresponding defect in antigen-presenting cell function. J Exp Med. 1982 Feb 1;155(2):508–523. doi: 10.1084/jem.155.2.508. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Mirkovitch J., Decker T., Darnell J. E., Jr Interferon induction of gene transcription analyzed by in vivo footprinting. Mol Cell Biol. 1992 Jan;12(1):1–9. doi: 10.1128/mcb.12.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Moses H., Panek R. B., Benveniste E. N., Ting J. P. Usage of primary cells to delineate IFN-gamma-responsive DNA elements in the HLA-DRA promoter and to identify a novel IFN-gamma-enhanced nuclear factor. J Immunol. 1992 Jun 1;148(11):3643–3651. [PubMed] [Google Scholar]
  28. Mueller P. R., Wold B. In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. Science. 1989 Nov 10;246(4931):780–786. doi: 10.1126/science.2814500. [DOI] [PubMed] [Google Scholar]
  29. Nepom G. T., Erlich H. MHC class-II molecules and autoimmunity. Annu Rev Immunol. 1991;9:493–525. doi: 10.1146/annurev.iy.09.040191.002425. [DOI] [PubMed] [Google Scholar]
  30. Pfeifer G. P., Tanguay R. L., Steigerwald S. D., Riggs A. D. In vivo footprint and methylation analysis by PCR-aided genomic sequencing: comparison of active and inactive X chromosomal DNA at the CpG island and promoter of human PGK-1. Genes Dev. 1990 Aug;4(8):1277–1287. doi: 10.1101/gad.4.8.1277. [DOI] [PubMed] [Google Scholar]
  31. Pober J. S., Collins T., Gimbrone M. A., Jr, Cotran R. S., Gitlin J. D., Fiers W., Clayberger C., Krensky A. M., Burakoff S. J., Reiss C. S. Lymphocytes recognize human vascular endothelial and dermal fibroblast Ia antigens induced by recombinant immune interferon. Nature. 1983 Oct 20;305(5936):726–729. doi: 10.1038/305726a0. [DOI] [PubMed] [Google Scholar]
  32. Reith W., Barras E., Satola S., Kobr M., Reinhart D., Sanchez C. H., Mach B. Cloning of the major histocompatibility complex class II promoter binding protein affected in a hereditary defect in class II gene regulation. Proc Natl Acad Sci U S A. 1989 Jun;86(11):4200–4204. doi: 10.1073/pnas.86.11.4200. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Reith W., Herrero-Sanchez C., Kobr M., Silacci P., Berte C., Barras E., Fey S., Mach B. MHC class II regulatory factor RFX has a novel DNA-binding domain and a functionally independent dimerization domain. Genes Dev. 1990 Sep;4(9):1528–1540. doi: 10.1101/gad.4.9.1528. [DOI] [PubMed] [Google Scholar]
  34. Reith W., Satola S., Sanchez C. H., Amaldi I., Lisowska-Grospierre B., Griscelli C., Hadam M. R., Mach B. Congenital immunodeficiency with a regulatory defect in MHC class II gene expression lacks a specific HLA-DR promoter binding protein, RF-X. Cell. 1988 Jun 17;53(6):897–906. doi: 10.1016/s0092-8674(88)90389-3. [DOI] [PubMed] [Google Scholar]
  35. Rosa F., Hatat D., Abadie A., Wallach D., Revel M., Fellous M. Differential regulation of HLA-DR mRNAs and cell surface antigens by interferon. EMBO J. 1983;2(9):1585–1589. doi: 10.1002/j.1460-2075.1983.tb01628.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Sasaki A., Levison S. W., Ting J. P. Comparison and quantitation of Ia antigen expression on cultured macroglia and ameboid microglia from Lewis rat cerebral cortex: analyses and implications. J Neuroimmunol. 1989 Nov;25(1):63–74. doi: 10.1016/0165-5728(89)90087-8. [DOI] [PubMed] [Google Scholar]
  37. Sasaki A., Levison S. W., Ting J. P. Differential suppression of interferon-gamma-induced Ia antigen expression on cultured rat astroglia and microglia by second messengers. J Neuroimmunol. 1990 Sep-Oct;29(1-3):213–222. doi: 10.1016/0165-5728(90)90164-I. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Servenius B., Rask L., Peterson P. A. Class II genes of the human major histocompatibility complex. The DO beta gene is a divergent member of the class II beta gene family. J Biol Chem. 1987 Jun 25;262(18):8759–8766. [PubMed] [Google Scholar]
  39. Sherman P. A., Basta P. V., Heguy A., Wloch M. K., Roeder R. G., Ting J. P. The octamer motif is a B-lymphocyte-specific regulatory element of the HLA-DR alpha gene promoter. Proc Natl Acad Sci U S A. 1989 Sep;86(17):6739–6743. doi: 10.1073/pnas.86.17.6739. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Sherman P. A., Basta P. V., Moore T. L., Brown A. M., Ting J. P. Class II box consensus sequences in the HLA-DR alpha gene: transcriptional function and interaction with nuclear proteins. Mol Cell Biol. 1989 Jan;9(1):50–56. doi: 10.1128/mcb.9.1.50. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Sugamura K., Fujii M., Kannagi M., Sakitani M., Takeuchi M., Hinuma Y. Cell surface phenotypes and expression of viral antigens of various human cell lines carrying human T-cell leukemia virus. Int J Cancer. 1984 Aug 15;34(2):221–228. doi: 10.1002/ijc.2910340213. [DOI] [PubMed] [Google Scholar]
  42. Takiguchi M., Ting J. P., Buessow S. C., Boyer C., Gillespie Y., Frelinger J. A. Response of glioma cells to interferon-gamma: increase in class II RNA, protein and mixed lymphocyte reaction-stimulating ability. Eur J Immunol. 1985 Aug;15(8):809–814. doi: 10.1002/eji.1830150813. [DOI] [PubMed] [Google Scholar]
  43. Tsang S. Y., Nakanishi M., Peterlin B. M. Mutational analysis of the DRA promoter: cis-acting sequences and trans-acting factors. Mol Cell Biol. 1990 Feb;10(2):711–719. doi: 10.1128/mcb.10.2.711. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Unanue E. R. The regulatory role of macrophages in antigenic stimulation. Part Two: symbiotic relationship between lymphocytes and macrophages. Adv Immunol. 1981;31:1–136. doi: 10.1016/s0065-2776(08)60919-0. [DOI] [PubMed] [Google Scholar]
  45. Vilen B. J., Cogswell J. P., Ting J. P. Stereospecific alignment of the X and Y elements is required for major histocompatibility complex class II DRA promoter function. Mol Cell Biol. 1991 May;11(5):2406–2415. doi: 10.1128/mcb.11.5.2406. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Wikstrand C. J., Grahmann F. C., McComb R. D., Bigner D. D. Antigenic heterogeneity of human anaplastic gliomas and glioma-derived cell lines defined by monoclonal antibodies. J Neuropathol Exp Neurol. 1985 May;44(3):229–241. doi: 10.1097/00005072-198505000-00002. [DOI] [PubMed] [Google Scholar]
  47. Zeleznik-Le N. J., Azizkhan J. C., Ting J. P. Affinity-purified CCAAT-box-binding protein (YEBP) functionally regulates expression of a human class II major histocompatibility complex gene and the herpes simplex virus thymidine kinase gene. Proc Natl Acad Sci U S A. 1991 Mar 1;88(5):1873–1877. doi: 10.1073/pnas.88.5.1873. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Zeleznik-Le N. J., Itoh-Lindstrom Y., Clarke J. B., Moore T. L., Ting J. P. The B cell-specific nuclear factor OTF-2 positively regulates transcription of the human class II transplantation gene, DRA. J Biol Chem. 1992 Apr 15;267(11):7677–7682. [PubMed] [Google Scholar]

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