Multiple Functional Elements Comprise a Mammalian Chromosomal Replicator

REFERENCES

• Abdurashidova, G., M. Deganuto, R. Klima, S. Riva, G. Biamonti, M. Giacca, and A. Falaschi. 2000. Start sites of bidirectional DNA synthesis at the human lamin B2 origin. Science 287: 2023–2026.
   PubMed Web of Science ®Google Scholar
• Aerts, J., W. Wynendaele, R. Paridaens, M. R. Christiaens, W. van den Bogaert, A. T. van Oosterom, and F. Vandekerckhove. 2001. A real-time quantitative reverse transcriptase polymerase chain reaction (RT-PCR) to detect breast carcinoma cells in peripheral blood. Ann. Oncol. 12: 39–46.
   PubMedGoogle Scholar
• Aladjem, M. I., L. W. Rodewald, C. M. Lin, S. Bowman, D. M. Cimbora, L. L. Brody, E. M. Epner, M. Groudine, and G. M. Wahl. 2002. Replication initiation patterns in the beta-globin loci of totipotent and differentiated murine cells: evidence for multiple initiation regions. Mol. Cell. Biol. 22: 442–452.
   PubMedGoogle Scholar
• Altman, A. L., and E. Fanning. 2001. The Chinese hamster dihydrofolate reductase replication origin beta is active at multiple ectopic chromosomal locations and requires specific DNA sequence elements for activity. Mol. Cell. Biol. 21: 1098–1110.
   PubMedGoogle Scholar
• Austin, R. J., T. L. Orr-Weaver, and S. P. Bell. 1999. Drosophila ORC specifically binds to ACE3, an origin of DNA replication control element. Genes Dev. 13: 2639–2649.
   PubMedGoogle 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 34: 779–787.
   PubMed Web of Science ®Google Scholar
• Berberich, S., A. Trivedi, D. C. Daniel, E. M. Johnson, and M. Leffak. 1995. In vitro replication of plasmids containing human c-myc DNA. J. Mol. Biol. 245: 92–109.
   PubMed Web of Science ®Google Scholar
• Bielinsky, A. K., and S. A. Gerbi. 1999. Chromosomal ARS1 has a single leading strand start site. Mol. Cell 3: 477–486.
   PubMed Web of Science ®Google Scholar
• Bielinsky, A. K., and S. A. Gerbi. 2001. Where it all starts: eukaryotic origins of DNA replication. J. Cell Sci. 114: 643–651.
   PubMedGoogle Scholar
• Chuang, R. Y., and T. J. Kelly. 1999. The fission yeast homologue of Orc4p binds to replication origin DNA via multiple AT-hooks. Proc. Natl. Acad. Sci. USA 96: 2656–2661.
   PubMed Web of Science ®Google Scholar
• Clyne, R. K., and T. J. Kelly. 1995. Genetic analysis of an ARS element from the fission yeast Schizosaccharomyces pombe. EMBO J. 14: 6348–6357.
   PubMed Web of Science ®Google Scholar
• Connolly, A. R., L. G. Cleland, and B. W. Kirkham. 1995. Mathematical considerations of competitive polymerase chain reaction. J. Immunol. Methods 187: 201–211.
   PubMedGoogle Scholar
• Delidakis, C., and F. C. Kafatos. 1989. Amplification enhancers and replication origins in the autosomal chorion gene cluster of Drosophila. EMBO J. 8: 891–901.
   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
• Dhar, S. K., K. Yoshida, Y. Machida, P. Khaira, B. Chaudhuri, J. A. Wohlschlegel, M. Leffak, J. Yates, and A. Dutta. 2001. Replication from oriP of Epstein-Barr virus requires human ORC and is inhibited by geminin. Cell 106: 287–296.
   PubMed Web of Science ®Google Scholar
• Dijkwel, P. A., S. Wang, and J. L. Hamlin. 2002. Initiation sites are distributed at frequent intervals in the Chinese hamster dihydrofolate reductase origin of replication but are used with very different efficiencies. Mol. Cell. Biol. 22: 3053–3065.
   PubMedGoogle Scholar
• Diviacco, S., P. Norio, L. Zentilin, S. Menzo, M. Clementi, G. Biamonti, S. Riva, A. Falaschi, and M. Giacca. 1992. A novel procedure for quantitative polymerase chain reaction by coamplification of competitive templates. Gene 122: 313–320.
   PubMed Web of Science ®Google Scholar
• Dutta, A., and S. P. Bell. 1997. Initiation of DNA replication in eukaryotic cells. Annu. Rev. Cell Dev. Biol. 13: 293–332.
   PubMed Web of Science ®Google Scholar
• Edwards, M. C., A. V. Tutter, C. Cvetic, C. H. Gilbert, T. A. Prokhorova, and J. C. Walter. 2002. MCM2-7 complexes bind chromatin in a distributed pattern surrounding the origin recognition complex in Xenopus egg extracts. J. Biol. Chem. 277: 33049–33057.
   PubMed Web of Science ®Google Scholar
• Giacca, M., C. Pelizon, and A. Falaschi. 1997. Mapping replication origins by quantifying relative abundance of nascent DNA strands using competitive polymerase chain reaction. Methods 13: 301–312.
   PubMedGoogle Scholar
• Gilbert, D. M. 2001. Making sense of eukaryotic DNA replication origins. Science 294: 96–100.
   PubMedGoogle Scholar
• Gomez, M., and F. Antequera. 1999. Organization of DNA replication origins in the fission yeast genome. EMBO J. 18: 5683–5690.
   PubMedGoogle Scholar
• Harland, R. M., and R. A. Laskey. 1980. Regulated replication of DNA microinjected into eggs of Xenopus laevis. Cell 21: 761–771.
   PubMedGoogle Scholar
• Hiebert, S. W., M. Lipp, and J. R. Nevins. 1989. E1A-dependent trans-activation of the human MYC promoter is mediated by the E2F factor. Proc. Natl. Acad. Sci. USA 86: 3594–3598.
   PubMed Web of Science ®Google Scholar
• Hyrien, O., C. Maric, and M. Mechali. 1995. Transition in specification of embryonic metazoan DNA replication origins. Science 270: 994–997.
   PubMed Web of Science ®Google Scholar
• Imagawa, M., R. Chiu, and M. Karin. 1987. Transcription factor AP-2 mediates induction by two different signal-transduction pathways: protein kinase C and cAMP. Cell 51: 251–260.
   PubMed Web of Science ®Google Scholar
• Kamath, S., and M. Leffak. 2001. Multiple sites of replication initiation in the human beta-globin gene locus. Nucleic Acids Res. 29: 809–817.
   PubMedGoogle Scholar
• Kim, S. M., and J. A. Huberman. 1998. Multiple orientation-dependent, synergistically interacting, similar domains in the ribosomal DNA replication origin of the fission yeast, Schizosaccharomyces pombe. Mol. Cell. Biol. 18: 7294–7303.
   PubMedGoogle Scholar
• Kobayashi, T., T. Rein, and M. L. DePamphilis. 1998. Identification of primary initiation sites for DNA replication in the hamster dihydrofolate reductase gene initiation zone. Mol. Cell. Biol. 18: 3266–3277.
   PubMedGoogle Scholar
• Kong, D., and M. L. DePamphilis. 2001. Site-specific DNA binding of the Schizosaccharomyces pombe origin recognition complex is determined by the Orc4 subunit. Mol. Cell. Biol. 21: 8095–8103.
   PubMed Web of Science ®Google Scholar
• Kong, D., and M. L. DePamphilis. 2002. Site-specific ORC binding, pre-replication complex assembly and DNA synthesis at Schizosaccharomyces pombe replication origins. EMBO J. 21: 5567–5576.
   PubMedGoogle Scholar
• Krysan, P. J., J. G. Smith, and M. P. Calos. 1993. Autonomous replication in human cells of multimers of specific human and bacterial DNA sequences. Mol. Cell. Biol. 13: 2688–2696.
   PubMedGoogle Scholar
• Kumar, S., and M. Leffak. 1991. Conserved chromatin structure in c-myc 5′ flanking DNA after viral transduction. J. Mol. Biol. 222: 45–57.
   PubMedGoogle Scholar
• Kumar, S., and M. Leffak. 1989. DNA topology of the ordered chromatin domain 5′ to the human c-myc gene. Nucleic Acids Res. 17: 2819–2833.
   PubMedGoogle Scholar
• Lawlis, S. J., S. M. Keezer, J. R. Wu, and D. M. Gilbert. 1996. Chromosome architecture can dictate site-specific initiation of DNA replication in Xenopus egg extracts. J. Cell Biol. 135: 1207–1218.
   PubMedGoogle Scholar
• Lee, J. K., K. Y. Moon, Y. Jiang, and J. Hurwitz. 2001. The Schizosaccharomyces pombe origin recognition complex interacts with multiple AT-rich regions of the replication origin DNA by means of the AT-hook domains of the spOrc4 protein. Proc. Natl. Acad. Sci. USA 98: 13589–13594.
   PubMedGoogle Scholar
• Lipford, J. R., and S. P. Bell. 2001. Nucleosomes positioned by ORC facilitate the initiation of DNA replication. Mol. Cell 7: 21–30.
   PubMed Web of Science ®Google Scholar
• Locatelli, G., F. Santoro, F. Veglia, A. Gobbi, P. Lusso, and M. S. Malnati. 2000. Real-time quantitative PCR for human herpesvirus 6 DNA. J. Clin. Microbiol. 38: 4042–4048.
   PubMed Web of Science ®Google Scholar
• Mahbubani, H. M., T. Paull, J. K. Elder, and J. J. Blow. 1992. DNA replication initiates at multiple sites on plasmid DNA in Xenopus egg extracts. Nucleic Acids Res. 20: 1457–1462.
   PubMedGoogle Scholar
• Malott, M., and M. Leffak. 1999. Activity of the c-myc replicator at an ectopic chromosomal location. Mol. Cell. Biol. 19: 5685–5695.
   PubMedGoogle Scholar
• McWhinney, C., and M. Leffak. 1990. Autonomous replication of a DNA fragment containing the chromosomal replication origin of the human c-myc gene. Nucleic Acids Res. 18: 1233–1242.
   PubMedGoogle Scholar
• McWhinney, C., and M. Leffak. 1988. Episomal persistence of a plasmid containing human c-myc DNA, vol. 6. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
   Google Scholar
• McWhinney, C., S. E. Waltz, and M. Leffak. 1995. Cis-acting effects of sequences within 2.4-kb upstream of the human c-myc gene on autonomous plasmid replication in HeLa cells. DNA Cell Biol. 14: 565–579.
   PubMedGoogle Scholar
• Michelotti, G. A., E. F. Michelotti, A. Pullner, R. C. Duncan, D. Eick, and D. Levens. 1996. Multiple single-stranded cis elements are associated with activated chromatin of the human c-myc gene in vivo. Mol. Cell. Biol. 16: 2656–2669.
   PubMed Web of Science ®Google Scholar
• Natale, D. A., R. M. Umek, and D. Kowalski. 1993. Ease of DNA unwinding is a conserved property of yeast replication origins. Nucleic Acids Res. 21: 555–560.
   PubMedGoogle Scholar
• O'Gorman, S., D. T. Fox, and G. M. Wahl. 1991. Recombinase-mediated gene activation and site-specific integration in mammalian cells. Science 251: 1351–1355.
   PubMed Web of Science ®Google Scholar
• Ohba, R., K. Matsumoto, and Y. Ishimi. 1996. Induction of DNA replication by transcription in the region upstream of the human c-myc gene in a model replication system. Mol. Cell. Biol. 16: 5754–5763.
   PubMedGoogle Scholar
• Okuno, Y., H. Satoh, M. Sekiguchi, and H. Masukata. 1999. Clustered adenine/thymine stretches are essential for function of a fission yeast replication origin. Mol. Cell. Biol. 19: 6699–6709.
   PubMed Web of Science ®Google Scholar
• Postel, E. H., S. E. Mango, and S. J. Flint. 1989. A nuclease-hypersensitive element of the human c-myc promoter interacts with a transcription initiation factor. Mol. Cell. Biol. 9: 5123–5133.
   PubMedGoogle Scholar
• Roussel, M. F., J. N. Davis, J. L. Cleveland, J. Ghysdael, and S. W. Hiebert. 1994. Dual control of myc expression through a single DNA binding site targeted by ets family proteins and E2F-1. Oncogene 9: 405–415.
   PubMedGoogle Scholar
• Sambrook, J., E. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
   Google Scholar
• Schepers, A., M. Ritzi, K. Bousset, E. Kremmer, J. L. Yates, J. Harwood, J. F. Diffley, and W. Hammerschmidt. 2001. Human origin recognition complex binds to the region of the latent origin of DNA replication of Epstein-Barr virus. EMBO J. 20: 4588–4602.
   PubMedGoogle Scholar
• Shinomiya, T., and S. Ina. 1993. DNA replication of histone gene repeats in Drosophila melanogaster tissue culture cells: multiple initiation sites and replication pause sites. Mol. Cell. Biol. 13: 4098–4106.
   PubMedGoogle 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
• Simpson, R. T. 1990. Nucleosome positioning can affect the function of a cis-acting DNA element in vivo. Nature 343: 387–389.
   PubMed Web of Science ®Google Scholar
• Tao, L., Z. Dong, M. Leffak, M. Zannis-Hadjopoulos, and G. Price. 2000. Major DNA replication initiation sites in the c-myc locus in human cells. J. Cell. Biochem. 78: 442–457.
   PubMedGoogle Scholar
• Tao, L., T. Nielsen, P. Friedlander, M. Zannis-Hadjopoulos, and G. Price. 1997. Differential DNA replication origin activities in human normal skin fibroblast and HeLa cell lines. J. Mol. Biol. 273: 509–518.
   PubMedGoogle Scholar
• Trivedi, A., S. E. Waltz, S. Kamath, and M. Leffak. 1998. Multiple initiations in the c-myc replication origin independent of chromosomal location. DNA Cell Biol. 17: 885–896.
   PubMedGoogle Scholar
• Umek, R. M., and D. Kowalski. 1990. Thermal energy suppresses mutational defects in DNA unwinding at a yeast replication origin. Proc. Natl. Acad. Sci. USA 87: 2486–2490.
   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
• Walter, J., and J. Newport. 2000. Initiation of eukaryotic DNA replication: origin unwinding and sequential chromatin association of Cdc45, RPA, and DNA polymerase alpha. Mol. Cell 5: 617–627.
   PubMed Web of Science ®Google Scholar
• Waltz, S. E., A. A. Trivedi, and M. Leffak. 1996. DNA replication initiates non-randomly at multiple sites near the c-myc gene in HeLa cells. Nucleic Acids Res. 24: 1887–1894.
   PubMed Web of Science ®Google Scholar
• Wilmes, G. M., and S. P. Bell. 2002. The B2 element of the Saccharomyces cerevisiae ARS1 origin of replication requires specific sequences to facilitate pre-RC formation. Proc. Natl. Acad. Sci. USA 99: 101–106.
   PubMedGoogle Scholar
• Wu, J. R., G. Yu, and D. M. Gilbert. 1997. Origin-specific initiation of mammalian nuclear DNA replication in a Xenopus cell-free system. Methods 13: 313–324.
   PubMedGoogle Scholar
• Zobel, A., F. Kalkbrenner, S. Guehmann, M. Nawrath, G. Vorbrueggen, and K. Moelling. 1991. Interaction of the v- and c-Myb proteins with regulatory sequences of the human c-myc gene. Oncogene 6: 1397–1407.
   PubMedGoogle Scholar