Multiple Single-Stranded cis Elements Are Associated with Activated Chromatin of the Human c-myc Gene In Vivo

REFERENCES

• Alter, P., C. Rius, F. Mata, A. Zorilla, C. Cabanas, T. Billon, and C. Bernabeu. 1992. Camptothecin induces differentiation and stimulates the expression of differentiation-related genes in U937 human promonocytic leukemia cells. Cancer Res. 52:1245–1251.
   PubMedGoogle Scholar
• Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, and J. A. Smith (ed.). 1989. Current protocols in molecular biology. John Wiley & Sons, New York.
   Google Scholar
• Avigan, M. I., B. Strober, and D. Levens. 1990. A far upstream element stimulates c-myc expression in undifferentiated leukemia cells. J. Biol. Chem. 265:18538–18545.
   PubMed Web of Science ®Google Scholar
• Battey, J., C. Moulding, R. Taub, W. Murphy, T. Stewart, H. Potter, G. Lenoir, and P. Leder. 1983. The human c-myc oncogene: structural consequences of translocation into the IgH locus in Burkitt lymphoma. Cell 4:779–787.
   Google Scholar
• Bazar, L., D. Meighen, V. Harris, R. Duncan, D. Levens, and M. Avigan. 1995. Targeted melting and binding of a DNA regulatory clement by a transactivator of c-myc. J. Biol. Chem. 270:8241–8248.
   PubMedGoogle Scholar
• Bentley, D. L., and M. Groudine. 1986. A block to elongation is largely responsible for decreased transcription of c-myc in differentiated HL60 cells. Nature (London) 321:702–706.
   PubMed Web of Science ®Google Scholar
• Bentley, D. L., and M. Groudine. 1986. Novel promoter upstream of the human c-myc gene and regulation of c-myc expression in B-cell lymphomas. Mol. Cell. Biol. 6:3481–3489.
   PubMedGoogle Scholar
• Berg, J. M. 1992. Sp1 and the subfamily of zinc finger proteins with guaninerich binding sites. Proc. Natl. Acad. Sci. USA 89:11109–11110.
   PubMedGoogle Scholar
• Bergemann, A. D., and E. M. Johnson. 1992. The HeLa Pur factor binds single-stranded DNA at a specific element conserved in gene flanking regions and origins of DNA replication. Mol. Cell. Biol. 12:1257–1265.
   PubMed Web of Science ®Google Scholar
• Bergemann, A. D., Z.-W. Ma, and E. M. Johnson. 1992. Sequence of cDNA comprising the human pur gene and properties of the encoded protein. Mol. Cell. Biol. 12:5673–5682.
   PubMed Web of Science ®Google Scholar
• Borowiec, J. A., L. Zhang, S. Sasse-Dwight, and J. D. Gralla. 1987. DNA supercoil promoter formation of a bent repressor loop in lac DNA. J. Mol. Biol. 196:101–111.
   PubMed Web of Science ®Google Scholar
• Bossone, S., C. Asselin, A. Patel, and K. Marcu. 1992. MAZ. a zinc finger protein, binds to c-myc and C2 gene sequences regulating transcriptional initiation and termination. Proc. Natl. Acad. Sci. USA 89:7452–7456.
   PubMed Web of Science ®Google Scholar
• Cozzarelli, N. R., and J. C. Wang. 1990. DNA topology and its biological effects. Cold Spring Harbor Laboratory, Cold Spring Harbor Press, N.Y.
   Google Scholar
• Dayn, A., S. Malkhosyan, and S. M. Mirkin. 1992. Transcriptionally driven cruciform formation in vivo. Nucleic Acids Res. 20:5991–5997.
   PubMed Web of Science ®Google Scholar
• DesJardins, E., and N. Hay. 1993. Repeated CT-elements bound by zinc finger proteins control the absolute and relative activities of the two principal human c-myc promoters. Mol. Cell. Biol. 13:5710–5724.
   PubMedGoogle Scholar
• Dony, C., M. Kessel, and P. Gruss. 1985. Post-transcriptional control of myc and p53 expression during differentiation of the embryonal carcinoma cell line F9. Nature (London) 317:636–639.
   PubMedGoogle Scholar
• Dunaway, M., and E. Ostrander. 1993. Local domains of supercoiling activate a eukaryotic promoter in vivo. Nature (London) 361:746–748.
   PubMed Web of Science ®Google Scholar
• Duncan, R. D., L. Bazar, G. Michelotti, T. Tomonaga, H. Krutzsch, M. Avigan, and D. Levens. 1994. A sequence-specific, single strand binding protein activates the far upstream of c-myc and defines a new DNA binding motif. Genes Dev. 8:465–480.
   PubMedGoogle Scholar
• Duncan, R., I. Collins, T. Tomonaga, T. Zheng, and D. Levens. 1996. A unique transactivation sequence motif is found in the carboxyl-terminal domain of the single-strand-binding protein FBP. Mol. Cell. Biol. 16:2274–2282.
   PubMedGoogle Scholar
• Duyao, M., A. Buckler, and G. Sonenshein. 1990. Interaction of an NF-kappa B-like factor with a site upstream of the c-myc promoter. Proc. Natl. Acad. Sci. USA 87:4727–4731.
   PubMed Web of Science ®Google Scholar
• Dyson, P., T. Littlewood, A. Forster, and T. H. Rahbitts. 1985. Chromatin structure of transcriptionally active and inactive human c-myc alleles. EMBO J. 4:2885–2891.
   PubMedGoogle Scholar
• Dyson, P., and T. H. Rahbitts. 1985. Chromatin structure of the c-myc gene in Burkitt lymphomas with upstream and downstream translocation points. Proc. Natl. Acad. Sci. USA 82:1984–1988.
   PubMed Web of Science ®Google Scholar
• Eick, D., and G. W. Bornkamm. 1986. Transcriptional arrest within the first exon is a fast control mechanism in c-myc gene expression. Nucleic Acids Res. 14:8331–8346.
   PubMed Web of Science ®Google Scholar
• Freeman, L. A., and W. T. Garrard. 1992. DNA supercoiling in chromatin structure and gene expression. Crit. Rev. Eukaryotic Gene Expression 2:165–209.
   PubMedGoogle Scholar
• Fukuchi, K., S. Tomoyasu, K. Watanabe, H. Suzuki, T. Kaetsu, Y. Takagi, N. Tsuruoka, and K. Gomi. 1991. Increased expression of the proto-oncogene, c-myc, in human neuroblastoma cells by reversible inhibition of cell growth. Anticancer Res. 11:1967–1973.
   PubMedGoogle Scholar
• Garrity, P. A., and B. J. 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
• Gazin, C., S. Dupont de Dinechin, A. Hampe, J. M. Masson, P. Martin, D. Stehelin, and F. Galibert. 1984. Nucleotide sequence of the human c-myc locus: provocative open reading frame within the first exon. EMBO J. 3:383–387.
   PubMed Web of Science ®Google Scholar
• Giardina, C., and J. T. Lis. 1995. Dynamic protein-DNA architecture of a yeast heat shock promoter. Mol. Cell. Biol. 15:2737–2744.
   PubMedGoogle Scholar
• Giardina, C., M. Perez-Riba, and J. T. Lis. 1992. Promoter melting and TFIID complexes on Drosophila genes in vivo. Genes Dev. 6:2190–2200.
   PubMed Web of Science ®Google Scholar
• Grosso, L. E., and H. C. Pitot. 1985. Transcriptional regulation of c-myc during chemically induced differentiation of HL-60 cultures. Cancer Res. 45:847–850.
   PubMed Web of Science ®Google Scholar
• Hiebert, S. W., M. Lipp, and J. R. Nevins. 1989. E1A-dependent transactivation of the human c-myc promoter is mediated by the E2F factor. Proc. Natl. Acad. Sci. USA 86:3594–3598.
   PubMed Web of Science ®Google Scholar
• Hochschild, A., and M. Ptashne. 1986. Cooperative binding of λ repressors to sites separated by integral turns of the DNA helix. Cell 44:681–687.
   PubMed Web of Science ®Google Scholar
• Kahn, J., E. Yun, and D. Crothers. 1994. Detection of localized DNA flexibility. Nature (London) 368:163–166.
   PubMed Web of Science ®Google Scholar
• Kelly, K., and U. Siebenlist. 1986. The regulation and expression of c-myc in normal and malignant cells. Annu. Rev. Immunol. 4:317–338.
   PubMed Web of Science ®Google Scholar
• Kohl, N. E., N. Kanda, R. R. Schreck, G. Bruns, S. A. Latt, F. Gilbert, and F. W. Alt. 1983. Transposition and amplification of oncogene-related sequences in human neuroblastomas. Cell 35:359–367.
   PubMed Web of Science ®Google Scholar
• Krumm, A., L. Hickey, and M. Groudine. 1995. Promoter-proximal pausing of RNA polymerase II defines a general rate-limiting step after transcription initiation. Genes Dev. 9:559–572.
   PubMed Web of Science ®Google Scholar
• Krumm, A., T. Meulia, M. Brunvand, and M. Groudine. 1992. The block to transcriptional elongation within the human c-myc gene is determined in the promoter-proximal region. Genes Dev. 6:2201–2213.
   PubMed Web of Science ®Google Scholar
• Larsen, A., and H. Weintraub. 1982. An altered DNA conformation detected by S1 nuclease occurs at specific regions in active chick globin chromatin. Cell 29:609–622.
   PubMed Web of Science ®Google Scholar
• Liu, L. F., and J. C. Wang. 1987. Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. USA 84:7024–7027.
   PubMed Web of Science ®Google Scholar
• Marcu, K. B., S. A. Bossone, and A. J. Patel. 1992. myc function and regulation. Annu. Rev. Biochem. 61:809–860.
   PubMed Web of Science ®Google Scholar
• Michelotti, E., T. Tomonaga, I.I. Krutzsch, and D. Levens. 1995. Cellular nucleic acid binding protein regulates the CT-clement of the human c-myc protooncogene. J. Biol. Chem. 270:9494–9499.
   PubMed Web of Science ®Google Scholar
• Negishi, Y., Y. Nishita, Y. Saegusa, I. Kakizaki, I. Galli, F. Kihara, K. Tamai, N. Miyajima, S. Iguchi-Ariga, and H. Ariga. 1994. Identification and cDNA cloning of single stranded DNA binding proteins that interact with the region upstream of the human c-myc gene. Oncogene 9:1133–1143.
   PubMedGoogle Scholar
• Nielsen, P. E. 1990. Chemical and photochemical probing of DNA complexes. J. Mol. Recognit. 3:1–25.
   PubMedGoogle Scholar
• Ramsperger, U., and H. Stahl. 1995. Unwinding of chromatin by the SV40 large T antigen DNA helicase. EMBO J. 14:3215–3225.
   PubMedGoogle Scholar
• Riggs, K., S. Saleque, K.-K. Wong, K. Merrell, J. S. Lee, Y. Shi, and K. Calame. 1993. Yin-vang 1 activates the c-myc promoter. Mol. Cell. Biol. 13:7487–7495.
   PubMed Web of Science ®Google Scholar
• Riou, J.-F., D. Lefevre, and G. Riou. 1989. Stimulation of the topoisomerase II induced cleavage sites in the c-myc protooncogene by antitumor drugs is associated with gene expression. Biochemistry 28:9104–9110.
   PubMed Web of Science ®Google Scholar
• Rubin, C. M., and C. W. Schmid. 1980. Pyrimidine-specific reactions useful for DNA sequencing. Nucleic Acids Res. 8:4613–4619.
   PubMed Web of Science ®Google Scholar
• Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
   Google Scholar
• Sasse-Dwight, S., and J. D. Gralla. 1988. Probing cooperative binding in vivo—the lac O1:O3 interaction. J. Mol. Biol. 202:107–119.
   PubMedGoogle Scholar
• Sasse-Dwight, S., and J. D. Gralla. 1991. Footprinting protein:DNA complexes in vivo. Methods EnzymoL 208:146–168.
   PubMedGoogle Scholar
• Schubach, W., and M. Groudine. 1984. Alteration of c-myc chromatin structure by avian leukosis virus integration. Nature (London) 307:702–708.
   PubMedGoogle Scholar
• Shi, Y., J. Glynn, L. Guilbert, T. Cotter, R. Bissonnette, and D. Green. 1992. Role for c-myc in activation-induced apoptotic cell death in T cell hybridomas. Science 257:212–214.
   PubMed Web of Science ®Google Scholar
• Siebenlist, U., P. Bressler, and K. Kelly. 1988. Two distinct mechanisms of transcriptional control operate on c-myc during differentiation of HL60 cells. Mol. Cell. Biol. 8:867–874.
   PubMed Web of Science ®Google Scholar
• Siebenlist, U., L. Hennighausen, J. Battey, and P. Leder. 1984. Chromatin structure and protein binding in the putative regulatory region of the c-myc gene in Burkitt lymphoma. Cell 37:381–391.
   PubMed Web of Science ®Google Scholar
• Skerka, C., P. Zipfel, and U. Siebenlist. 1993. Two regulatory domains are required for downregulation of c-myc transcription in differentiating U937 cells. Oncogene 8:2135–2143.
   PubMedGoogle Scholar
• Spencer, C. A., and M. Groudine. 1991. Control of c-myc regulation in normal and neoplastic cells. Adv. Cancer Res. 56:1–48.
   PubMed Web of Science ®Google Scholar
• Spencer, C. A., R. LeStrange, W. Hayward, U. Novak, and M. Groudine. 1990. The block transcription elongation is promoter dependent in normal and Burkitt's lymphoma c-myc alleles. Genes Dev. 4:75–88.
   PubMed Web of Science ®Google Scholar
• Strobl, L. J., and D. Eick. 1992. Hold back of RNA polymerase II at the transcription start site mediates downregulation of c-myc in vivo. EMBO J. 11:3307–3314.
   PubMed Web of Science ®Google Scholar
• Strobl, L. J., F. Kohlhuber, J. Mautner, A. Polack, and D. Kick. 1993. Absence of a paused transcription complex from the P2-promoter of a translocated c-myc gene in Burkitt's lymphoma cells: implication for the c-myc P1/P2 promoter shift. Oncogene 8:1437–1447.
   PubMedGoogle Scholar
• Takai, T., Y. Nishita, S. Iguchi-Ariga, and H. Ariga. 1994. Molecular cloning of MSSP-2, a c-myc gene single-strand binding protein: characterization of binding specificity and DNA replication activity. Nucleic Acids Res. 22:5576–5581.
   PubMedGoogle Scholar
• Takimoto, M., J. Quinn, R. Farina, L. Staudt, and D. Levens. 1989. Fos/jun and octamer-binding protein interact with a common site in a negative dement of the human c-myc gene. J. Biol. Chem, 264:8992–8999.
   PubMedGoogle Scholar
• Takimoto, M., T. Tomonaga, M. Matunis, M. Avigan, H. Krutsch, G. Dreyfuss, and D. Levens. 1993. Specific binding of heterogeneous ribonucleoprotein particle protein K to the human c-myc promoter, in vitro. J. Biol. Chem. 268:18249–18258.
   PubMed Web of Science ®Google Scholar
• Tomonaga, T., and D. Levens. 1995. Heterogeneous nuclear ribonucleoprotein K is a DNA binding transactivator. J. Biol. Chem. 270:4875–4881.
   PubMedGoogle Scholar
• Vassilev, L., and E. M. Johnson. 1990. An initiation zone of chromosomal DNA replication located upstream of the c-myc gene in proliferating HeLa cells. Mol. Cell, Biol, 10:4899–4904.
   PubMedGoogle Scholar
• Walters, M. C., S. Fiering, J. Eidemiller, W. Magis, M. Groudine, and D. I. K. Martin. 1995. Enhancers increase the probability but not the level of gene expression. Proc, Natl. Acad. Sci USA 92:7125–7129.
   PubMed Web of Science ®Google Scholar
• Watanabe, T., E. Suriban, T. Mitchell, and D. Kufe. 1985. Human c-myc and N-ras expression during induction of HL-6G cellular differentiation, Biochem. Biophys. Res. Commun. 126:999–1005.
   PubMed Web of Science ®Google Scholar
• Wittig, B., S. Wolfi, T. Dorbic, W. Vahrson, and A. Rich. 1992. Transcription of human c-myc in permeabilized nuclei is associated with formation of Z-DNA in three discrete regions of the gene. EMBO J. 11:4653–4663.
   PubMed Web of Science ®Google Scholar
• Wolf, D. A., L. J. Srobl, A. Pullner, and D. Eick. 1995. Variable pause positions of RNA polymerase II lie proximal to the c-myc promoter, irrespective of transcriptional activity. Nucleic Acids Res. 23:3373–3379.
   PubMedGoogle Scholar
• Wu, C. 1980. The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature (London) 286:854–860.
   PubMed Web of Science ®Google Scholar
• Zhang, X., N. Jabrane-Ferrat, C. Asiedu, S. Samac, B. Peterlin, and M. Ehrlich. 1993. The major histocompatibility complex class II promoter-binding protein RFX (NF-X) is a methylated DNA-binding protein. Mol. Cell. Biol. 13:6810–6818.
   PubMedGoogle Scholar