Occupancy of Upstream Regulatory Sites In Vivo Coincides with Major Histocompatibility Complex Class I Gene Expression in Mouse Tissues

REFERENCES

• Abravaya, K., B. Phillips, and R. I. Morimoto. 1991. Heat shock-induced interactions of heat shock transcription factor and the human hsp70 promoter examined by in vivo footprinting. Mol. Cell. Biol. 11:586–592.
   PubMedGoogle Scholar
• Angel, P., M. Imagawa, R. Chiu, B. Stein, R. J. Imbra, H. J. Rahmsdor, C. Jonat, P. Herrlich, and M. Karin. 1987. Phorbo- lester-inducible genes contain a common cis element recognized by a TPA-modulated trans-acting factor. Cell 49:729–739.
   PubMed Web of Science ®Google Scholar
• Arnold, B., H.-G. Burgert, A. L. Archibald, and S. Kvist. 1984. Complete nucleotide sequence of the murine H-2Kk gene. Comparison of three H-2K locus alleles. Nucleic Acids Res. 12:9473–9487.
   PubMed Web of Science ®Google Scholar
• Baldwin, A., and P. Sharp. 1987. Binding of a nuclear factor to a regulatory sequence in the promoter of the mouse H-2Kb class I major histocompatibility gene. Mol. Cell. Biol. 7:305–313.
   PubMed Web of Science ®Google Scholar
• Beato, M. 1989. Gene regulation by steroid hormones. Cell 56:335–344.
   PubMed Web of Science ®Google Scholar
• Becker, K. G., and K. Ozato. Unpublished data.
   Google Scholar
• Becker, P. B., S. Ruppert, and G. Schutz. 1987. Genomic footprinting reveals cell type-specific DNA binding of ubiquitous factors. Cell 51:435–443.
   PubMed Web of Science ®Google Scholar
• Burke, P. A., S. Hirschfeld, Y. Shirayoshi, J. W. Kasik, K. Hamada, E. Appella, and K. Ozato. 1989. Developmental and tissue-specific expression of nuclear proteins that bind the regulatory element of the major histocompatibility complex class I gene. J. Exp. Med. 169:1309–1321.
   PubMedGoogle Scholar
• Burke, P. A., and K. Ozato. 1988. Regulation of major histocompatibility complex class I gene. Year Immunol. 4:23–40.
   Google Scholar
• Chamberlain, J. W. Unpublished data.
   Google Scholar
• Chamberlain, J. W., J. A. Nolan, H. A. Conrad, H. A. Vasavada, H. H. Vasavada, H. Ploegh, S. Ganguly, C. A. Janeway, Jr., and S. M. Weissman. 1988. Tissue-specific and cell surface expression of major histocompatibility complex class I heavy (HLA- B7) and light (hβ-2m) chain genes in transgenic mice. Proc. Natl. Acad. Sci. USA 85:7690–7694.
   PubMedGoogle Scholar
• Chamberlain, J. W., H. A. Vasavada, S. Ganguly, and S. M. Weissman. 1991. Identification of cis sequences controlling efficient position-independent tissue-specific expression of human major histocompatibility complex class I genes in transgenic mice. Mol. Cell. Biol. 11:3564–3572.
   PubMedGoogle Scholar
• Chodosh, L. A., A. S. Baldwin, R. W. Carthew, and P. A. Sharp. 1988. Human CCAAT-binding proteins have heterologous subunits. Cell 53:11–24.
   PubMed Web of Science ®Google Scholar
• David-Watine, B., A. Israel, and P. Kourilsky. 1990. The regulation and expression of MHC class I genes. Immunol. Today 11:286–292.
   PubMedGoogle Scholar
• Dey, A., D. W. Nebert, and K. Ozato. 1991. The AP-1 site and the cAMP- and serum response elements of the c-fos gene are constitutively occupied in vivo. DNA Cell Biol. 10:537–544.
   PubMed Web of Science ®Google Scholar
• Diamond, M. I., J. N. Miner, S. K. J. Yoshinaga, and K. R. Yamamoto. 1990. Transcription factor interactions: selectors of positive or negative regulation from a single DNA element. Science 249:1266–1272.
   PubMed Web of Science ®Google Scholar
• Ehrlich, R., J. E. Maguire, and D. S. Singer. 1988. Identification of negative and positive regulatory elements associated with a class I major histocompatibility complex gene. Mol. Cell. Biol. 8:695–703.
   PubMedGoogle Scholar
• Ehrlich, R., S. Sharrow, J. Maguire, and D. S. Singer. 1989. Expression of a MHC class I transgene: effect of in vivo alpha/beta-interferon treatment. Immunogenetics 30:18–26.
   PubMedGoogle Scholar
• Evans, R. M. 1988. Steroid and thyroid hormone receptor superfamily. Science 240:889–895.
   PubMed Web of Science ®Google Scholar
• Fan, C.-M., and T. Maniatis. 1990. A DNA-binding protein containing two widely separated zinc finger motifs that recognize the same DNA sequence. Genes Dev. 4:29–42.
   PubMedGoogle Scholar
• Fisch, T. M., R. Prywes, and R. G. Roeder. 1989. An AP-1 binding site in the c-fos gene can mediate induction by epidermal growth factor and 12-O-tetradecanoyl-phorbol-13-acetate. Mol. Cell. Biol. 9:1327–1331.
   PubMed Web of Science ®Google Scholar
• Ganguly, S., H. Vasavada, and S. M. Weissman. 1989. Multiple enhancer-like sequences in HLA-B7 gene. Proc. Natl. Acad. Sci. USA 86:5247–5251.
   PubMedGoogle Scholar
• Garrity, P., and B. Wold. 1992. Effects of different DNA polymerases in ligation-mediated PCR: enhanced genomic sequencing and in vivo footprinting. Proc. Natl. Acad. Sci. USA 89:1021–1025.
   PubMedGoogle Scholar
• Ghosh, S., A. M. Gifford, L. Riviere, P. Tempst, G. P. Nolan, and D. Baltimore. 1990. Cloning of the p50 DNA binding subunit of NF-κB: homology to rel and dorsal. Cell 62:1019–1029.
   PubMed Web of Science ®Google Scholar
• Gorman, C. L., L. F. Moffat, and B. Howard. 1982. Recombinant genomes which express chloramphenicol acetyltransferase in mammalian cells. Mol. Cell. Biol. 2:1044–1051.
   PubMed Web of Science ®Google Scholar
• Gross, D. S., K. E. English, W. C. Kerry, and S. Lee. 1990. Genomic footprinting of the yeast HSP82 promoter reveals marked distortion of the DNA helix and constitutive occupancy of heat shock and TATA elements. J. Mol. Biol. 216:611–631.
   PubMedGoogle Scholar
• Guessow, D., R. S. Rein, I. Meyer, W. de Hoog, G. H. Seemann, F. M. Hochstenbach, and H. L. Ploegh. 1987. Isolation, expression, and the primary structure of HLA-Cwl and HLA-CW2 genes: evolutionary aspects. Immunogenetics 25:313–322.
   PubMedGoogle Scholar
• Hamada, K., S. L. Gleason, B.-Z. Levi, S. Hirschfeld, E. Appella, and K. Ozato. 1989. H-2RIIBP, a member of the nuclear hormone receptor superfamily that binds to both the regulatory element of major histocompatibility complex class I genes and the estrogen response element. Proc. Natl. Acad. Sci. USA 86:8289–8293.
   PubMed Web of Science ®Google Scholar
• Herrera, R. E., P. E. Shaw, and A. Nordheim. 1989. Occupation of the c-fos serum response element in vivo by a multi-protein complex is unaltered by growth factor induction. Nature (London) 340:68–70.
   PubMedGoogle Scholar
• Hood, L., M. Steinmetz, and B. Malissen. 1983. Genes of the major histocompatibility complex of the mouse. Annu. Rev. Immunol. 1:529–568.
   PubMed Web of Science ®Google Scholar
• Isamat, M., J. Girdlestone, and C. Milstein. 1990. Nucleotide sequence of an HLA-Bw57 gene. Nucleic Acids Res. 18:6702.
   PubMedGoogle Scholar
• Israel, A., A. Kimura, A. Fournier, M. Fellous, and P. Kourilsky. 1986. Interferon response sequence potentiates activity of an enhancer in the promoter region of a mouse H-2 gene. Nature (London) 322:743–746.
   PubMedGoogle Scholar
• Israel, A., O. Le Bail, D. Hatat, J. Piette, M. Kieran, F. Logeat, D. Wallach, M. Fellous, and P. Kourilsky. 1989. TNF stimulates expression of mouse MHC class I genes by inducing an NFκB- like enhancer binding activity which displaces constitutive factors. EMBO J. 8:3793–3800.
   PubMedGoogle Scholar
• Jackson, P. D., T. Evans, J. M. Nickol, and G. Felsenfeld. 1989. Developmental modulation of protein binding to β-globin gene regulatory sites within chicken erythrocyte nuclei. Genes Dev. 3:1860–1873.
   PubMedGoogle Scholar
• Joly, E., L. Mucke, and M. B. A. Oldstone. 1991. Viral persistence in neurons explained by lack of major histocompatibility class I expression. Science 253:1283–1285.
   PubMedGoogle Scholar
• Jones-Youngblood, S. L., K. Wieties, J. Forman, and R. E. Hammer. 1990. Effect of the expression of a hepatocyte-specific MHC molecule in transgenic mice on T cell tolerance. J. Immunol. 144:1187–1195.
   PubMedGoogle Scholar
• Kara, C. J., and L. H. Glimcher. 1991. In vivo footprinting of MHC class II genes: bare promoters in the bare lymphocyte syndrome. Science 252:709–712.
   PubMedGoogle Scholar
• Katoh, S., K. Ozawa, S. Kondoh, E. Soeda, A. Israel, K. Shiroki, K. Fujinaga, K. Itakura, G. Gachelin, and K. Yokoyama. 1990. Identification of sequences responsible for positive and negative regulation by E1A in the promoter of H-2Kbm1 class I MHC gene. EMBO J. 9:127–135.
   PubMedGoogle Scholar
• Kieran, M., V. Blank, F. Logeat, J. Vandekerckhove, F. Lottspeich, O. Le Bail, M. B. Urban, P. Kourlisky, P. A. Baeuerie, and A. Israel. 1990. The DNA binding subunit of NF-κB is identical to factor KBF1 and homologous to the rel oncogene product. Cell 62:1007–1018.
   PubMed Web of Science ®Google Scholar
• Kimura, A., A. Israel, O. Le Bail, and P. Kourilsky. 1986. Detailed analysis of the mouse H-2Kb promoter: enhancer-like sequences and their role in the regulation of class I gene expression. Cell 44:261–272.
   PubMed Web of Science ®Google Scholar
• Klein, J. 1975. Biology of the mouse histocompatibility-2 complex. Springer-Verlag, New York.
   Google Scholar
• Korber, B., L. Hood, and I. Stroynowski. 1987. Regulation of murine class I genes by interferons is controlled by regions located both 5′ and 3′ to the transcription initiation site. Proc. Natl. Acad. Sci. USA 84:3380–3384.
   PubMedGoogle Scholar
• Korber, B., N. Mermod, L. Hood, and I. Stroynowski. 1988. Regulation of gene expression by interferon: control of H-2 promoter responses. Science 239:1302–1306.
   PubMed Web of Science ®Google Scholar
• Kvist, S., L. Roberts, and B. Dobberstein. 1983. Mouse histocompatibility genes: structure and organisation of a Kd gene. EMBO J. 2:245–254.
   PubMed Web of Science ®Google Scholar
• Lee, W., A. Haslinger, M. Karin, and R. Tijan. 1987. Activation of transcription by two factors that bind promoter and enhancer sequences of the human metallothionein gene and SV40. Nature (London) 325:368–372.
   PubMed Web of Science ®Google Scholar
• Lee, W., P. Mitchell, and R. Tijan. 1987. Purified transcription factor AP-1 interacts with TPA-inducible enhancer elements. Cell 49:741–752.
   PubMed Web of Science ®Google Scholar
• Leid, M., P. Kastner, R. Lyons, H. Nakshatri, M. Saunders, T. Zacharewski, J.-Y. Chen, A. Staub, J.-M. Garnier, S. Mader, and P. Chambon. 1992. Purification, cloning, and RXR identity of the HeLa cell factor with which RAR or TR heterodimerizes to bind target sequence efficiently. Cell 68:377–395.
   PubMed Web of Science ®Google Scholar
• Lenardo, M., A. K. Rustgi, A. R. Schievella, and R. Bernards. 1989. Suppression of MHC class I gene expression by N-myc through enhancer inactivation. EMBO J. 8:3351–3355.
   PubMed Web of Science ®Google Scholar
• Lonergan, M., A. Dey, and K. Ozato. Unpublished data.
   Google Scholar
• MacGregor, G. R., and T. Caskey. 1989. Construction of plasmids that express E. coliβ-galactosidase in mammalian cells. Nucleic Acids Res. 17:2365.
   PubMedGoogle Scholar
• Mangelsdorf, D. J., U. Borgmeyer, R. A. Heyman, J. Yang Zhou, E. S. Ong, A. E. Oro, A. Kakizuka, and R. M. Evans. 1992. Characterization of three RXR genes that mediate the action of 9-cis retinoic acid. Genes Dev. 6:329–344.
   PubMed Web of Science ®Google Scholar
• Marks, M. S., P. L. Hallenbeck, T. Nagata, J. H. Segars, E. Appella, V. M. Nikodem, and K. Ozato. 1992. H-2RIIBP (RXRβ) heterodimerization provides a mechanism for combinatorial diversity in the regulation of retinoic acid and thyroid hormone responsiveness. EMBO J. 11:1419–1436.
   PubMed Web of Science ®Google Scholar
• Marks, M. S., B.-Z. Levi, J. H. Segars, P. H. Driggers, S. Hirschfeld, T. Nagata, E. Appella, and K. Ozato. 1992. H-2RI IBP expressed from a baculovirus vector binds to multiple hormone response elements. Mol. Endocrinol. 6:219–230.
   PubMedGoogle Scholar
• Martinez, E., and W. Wahli. 1991. Characterization of hormone response elements, p. 125–153. In M. G. Parker (ed.), Nuclear hormone receptor. Academic Press Limited, London.
   Google Scholar
• Maschek, U., W. Pulm, and J. Hammerling. 1989. Altered regulation of MHC class I genes in different tumor cell lines is reflected by distinct sets of DNase I hypersensitive sites. EMBO J. 8:2297–2304.
   PubMedGoogle Scholar
• Massa, P. T., K. Ozato, and D. E. McFarlin. Submitted for publication.
   Google Scholar
• Mirkovitch, J., and J. E. Darnell. 1991. Rapid in vivo footprinting technique identifies proteins bound to the TTR gene in the mouse liver. Genes Dev. 5:83–93.
   PubMedGoogle Scholar
• Mirkovitch, J., T. Decker, and J. E. Darnell. 1992. Interferon induction of gene transcription analyzed by in vivo footprinting. Mol. Cell. Biol. 12:1–9.
   PubMed Web of Science ®Google Scholar
• Miyamoto, M., T. Fujita, Y. Kimura, H. Maruyama, Y. Harada, Y. Sudo, T. Miyata, and T. Taniguchi. 1988. Regulated expression of a gene encoding a nuclear factor, IRF-1, that specifically binds to IFN-β gene regulatory elements. Cell 54:903–913.
   PubMed Web of Science ®Google Scholar
• Miyazaki, J., E. Apella, and K. Ozato. 1986. Negative regulation of the major histocompatibility class I gene in undifferentiated embryonal carcinoma cells. Proc. Natl. Acad. Sci. USA 83:9537–9541.
   PubMedGoogle Scholar
• Mueller, P. R., S. J. Salser, and B. Wold. 1988. Constitutive and metal-inducible protein: DNA interactions at the mouse metal- lothionine I promoter examined by in vivo and in vitro footprinting. Genes Dev. 2:412–427.
   PubMedGoogle Scholar
• Mueller, P. R., and B. Wold. 1989. In vivo footprinting of a muscle specific enhancer by ligation-mediated PCR. Science 246:780–786.
   PubMed Web of Science ®Google Scholar
• Naar, A. M., J.-M. Boutin, S. M. Lipkin, V. C. Yu, J. M. Holloway, C. K. Glass, and M. G. Rosenfeld. 1991. The orientation and spacing of core DNA-binding motifs dictate selective transcriptional response to three nuclear receptors. Cell 65:1267–1279.
   PubMed Web of Science ®Google Scholar
• Nagata, T., J. H. Segars, B.-Z. Levi, and K. Ozato. 1992. Retinoic acid dependent trans-activation of major histocompatibility complex class I promoters by a nuclear hormone receptor, H-2RIIBP, in undifferentiated embryonal carcinoma cells. Proc. Natl. Acad. Sci. USA 89:937–941.
   PubMedGoogle Scholar
• Nakamura, T., D. M. Donovan, K. Hamada, C. M. Sax, B. Norman, J. R. Flanagan, K. Ozato, H. Westphal, and J. Piatigorsky. 1990. Regulation of the mouse A-crystallin gene: isolation of a cDNA encoding a protein that binds to a cis sequence motif shared with the major histocompatibility complex class I gene and other genes. Mol. Cell. Biol. 10:3700–3708.
   PubMed Web of Science ®Google Scholar
• Picard, D., and W. Schaffner. 1984. A lymphocyte-specific enhancer in the mouse immunoglobulin κ gene. Nature (London) 307:80–82.
   PubMed Web of Science ®Google Scholar
• Reddy, P. M. S., and C. J. Shen. 1991. Protein-DNA interactions in vivo of an erythroid-specific, human β-globin locus enhancer. Proc. Natl. Acad. Sci. USA 88:8676–8680.
   PubMedGoogle Scholar
• Reik, A., G. Schutz, and A. F. Stewart. 1991. Glucocorticoids are required for establishment and maintenance of an alteration in chromatin structure: induction leads to a reversible disruption of nucleosomes over an enhancer. EMBO J. 10:2569–2576.
   PubMedGoogle Scholar
• Schnitzer, J., and M. Schachner. 1981. Expression of Thy-1, H-2 and NS-4 cell surface antigens and tetanus toxin receptors in early postnatal and adult mouse cerebellum. J. Neuroimmunol. 1:429–456.
   PubMed Web of Science ®Google Scholar
• Shirayoshi, Y., P. A. Burke, E. Appella, and K. Ozato. 1988. Interferon-induced transcription of a major histocompatibility class I gene accompanies binding of inducible nuclear factors to the interferon consensus sequence. Proc. Natl. Acad. Sci. USA 85:5884–5888.
   PubMedGoogle Scholar
• Shirayoshi, Y., J. Miyazaki, P. A. Burke, K. Hamada, E. Appella, and K. Ozato. 1987. Binding of multiple nuclear factors to the 5′ upstream regulatory element of the major histocompatibility class I gene. Mol. Cell. Biol. 7:4542–4548.
   PubMedGoogle Scholar
• Singh, H., J. H. LeBowitz, A. S. Baldwin, and P. A. Sharp. 1988. Molecular cloning of an enhancer binding protein: isolation by screening of an expression library with a recognition site probe. Cell 52:415–423.
   PubMedGoogle Scholar
• Sugita, K., J. Miyazaki, E. Appella, and K. Ozato. 1987. Interferons increase transcription of a major histocompatibility complex class I gene via a 5′ interferon consensus sequence. Mol. Cell. Biol. 7:2625–2630.
   PubMed Web of Science ®Google Scholar
• Tibensky, D., and T. L. Delovitch. 1990. Promoter region of HLA-C genes: regulatory elements common to and different from those of HLA-A and HLA-B genes. Immunogenetics 32:210–213.
   PubMedGoogle Scholar
• Umesono, K., V. Giguere, C. K. Glass, M. G. Rosenfeld, and R. M. Evans. 1988. Retinoic acid and thyroid hormone induce gene expression through a common responsive element. Nature (London) 336:262–265.
   PubMed Web of Science ®Google Scholar
• Watts, S., J. M. Vogel, W. D. Harriman, T. Itoh, H. J. Stauss, and R. S. Goodenow. 1987. DNA sequence analysis of the C3H H-2Kk and H-2Dk loci: evolutionary relationships to H2 genes from four other mouse strains. J. Immunol. 139:3878–3885.
   PubMedGoogle Scholar
• Weih, F., D. Nitsch, A. Reik, and P. B. Becker. 1991. Analysis of CpG methylation and genomic footprinting at the tyrosine aminotransferase gene: DNA methylation alone is not sufficient to prevent protein binding in vivo. EMBO J. 10:2559–2568.
   PubMedGoogle Scholar
• Weiss, E. H., L. Golden, K. Fahrner, A. L. Mellor, J. J. Devlin, H. Bullman, H. Tiddens, H. Bud, and R. A. Flavell. 1984. Organisation and evolution of the class I gene family in the major histocompatibility complex of the C57BL/10 mouse. Nature (London) 310:650–655.
   PubMedGoogle Scholar
• Weiss, E. H., W. Kuon, C. Doerner, M. Lang, and G. Riethmueller. 1985. Organization, sequence and expression of the HLA-B27 gene: a molecular approach to analyze HLA and disease associations. Immunobiology 170:367–380.
   PubMedGoogle Scholar
• Wijnholds, J., E. Muller, and G. Ab. 1991. Oestrogen facilitates the binding of ubiquitous and liver-enriched nuclear proteins to the apoVLDL II promoter in vivo. Nucleic Acids Res. 19:33–41.
   PubMedGoogle Scholar
• Wong, G. H., P. F. Bartlett, I. Clark-Lewis, J. L. McKimm-Breschkin, and J. W. Schrader. 1985. Interferon-gamma induces the expression of H-2 and Ia antigens on brain cells. J. Neuroimmunol. 7:255–278.
   PubMed Web of Science ®Google Scholar
• Yu, V. C., C. Delsert, B. Anderson, J. M. Holloway, O. V. Devary, A. M. Naar, S. Y. Kim, J.-M. Boutin, C. K. Glass, and M. G. Rosenfeld. 1992. RXR: a coregulator that enhances binding of retinoic acid, thyroid hormone, and vitamin D receptors to their cognate response elements. Cell 67:1251–1266.
   Web of Science ®Google Scholar