Interference of the Simian Virus 40 Origin of Replication by the Cytomegalovirus Immediate Early Gene Enhancer: Evidence for Competition of Active Regulatory Chromatin Conformation in a Single Domain

REFERENCES

• Ariga, H., Imamura, Y., and Iguchi-Ariga, S. M. M.. 1989. DNA replication origin and transcriptional enhancer in c-myc gene share the c-myc protein binding sequences. EMBO J. 8:4273–4279
   PubMedGoogle Scholar
• Arizumi, K., Ghosh, M. R., and Tucker, P. W.. 1993. Elements in the immunoglobulin heavy-chain enhancer directly regulate simian virus 40 ori-dependent DNA replication. Mol. Cell. Biol. 13:5629–5636
   PubMedGoogle Scholar
• Bates, D. B., Boye, E., Asai, T., and Kogoma, T.. 1997. The absence of effect of gid or mioC transcription on the initiation of chromosomal replication in Escherichia coli. Proc. Natl. Acad. Sci. USA 94:12497–12502
   PubMedGoogle Scholar
• Benard, M., and Pirron, G.. 1999. Early activated replication origin within the cell cycle-regulated histone H4 genes in Physarum. Nucleic Acids Res. 27:2091–2098
   PubMedGoogle Scholar
• Biamonti, G., Perini, G., Weighardt, F., Riva, S., Giacca, M., Norio, P., Zentilin, I., Diviacco, S., Dimitrova, D., and Falschi, A.. 1992. A human DNA replication origin: localization and transcription characterization. Chromosoma 102:S24–S31
   PubMedGoogle Scholar
• Binninger, D., Ferdinand, F. J., and Rubsamen-Waigmann, H.. 1989. Inhibition of SV40 DNA replication by rous sarcoma virus LTR enhancer. Arch. Virol. 107:291–299
   PubMedGoogle Scholar
• Boulikas, T.. 1996. Common structural features of replication origins in all life forms. J. Cell. Biochem. 60:297–316
   PubMedGoogle Scholar
• Brewer, B. J., and Fangman, W. L.. 1993. Initiation at closely spaced replication origins on ARS plasmids. Science 262:1728–1731
   PubMedGoogle Scholar
• Brewer, B. J., and Fangman, W. L.. 1994. Initiation preference at a yeast origin of replication. Proc. Natl. Acad. Sci. USA 91:3418–3422
   PubMedGoogle Scholar
• Breindl, M., Harbers, K., and Jaenisch, R.. 1984. Retrovirus-induced lethal mutation in collagen I gene of mice is associated with an altered chromatin structure. Cell 38:9–16
   PubMed Web of Science ®Google Scholar
• Bruand, C., and Ehrlich, S. D.. 1998. Transcription-driven DNA replication of plasmid pAMbeta1 in Bacillus subtilis. Mol. Microbiol. 30:135–145
   PubMedGoogle Scholar
• Chen, S., Reger, R., Miller, C., and Hyman, L. E.. 1996. Transcriptional terminators of RNA polymerase II are associated with yeast replication origins. Nucleic Acids Res. 24:2885–2893
   PubMedGoogle Scholar
• Cheng, L., and Kelly, T. L.. 1989. Transcriptional activator nuclear factor 1 stimulates the replication of SV40 minichromosomes in vivo and in vitro. Cell 59:541–551
   PubMedGoogle Scholar
• Chittenden, T., Frey, A., and Levine, A. J.. 1991. Regulated replication of episomal simian virus 40 origin plasmid in COS7 cells. J. Virol. 65:5944–5951
   PubMedGoogle Scholar
• Chu, Y., Huang, T. S., and Hsu, M. T.. 1990. P1 nuclease defines a subpopulation of active SV40 chromatin-a new nuclease hypersensitivity assay. Nucleic Acids Res. 18:3705–3711
   PubMedGoogle Scholar
• DeBeer, M. A. P., and Fox, C. A.. 1999. A role for a replicator dominance mechanism in silencing. EMBO J. 18:3808–3819
   PubMedGoogle Scholar
• Delgado, S., Gomez, M., Bird, A., and Antequera, F.. 1998. Initiation of DNA replication at CpG islands in mammalian chromosomes. EMBO J. 17:2426–2435
   PubMed Web of Science ®Google Scholar
• DePamphilis, M. L.. 1993. How transcription factors regulate origins of DNA replication in eukaryotic cells. Trends Cell Biol. 3:161–167
   PubMedGoogle Scholar
• DePamphilis, M. L.. 1993. Eukaryotic DNA replication: anatomy of an origin. Annu. Rev. Biochem. 62:29–63
   PubMedGoogle Scholar
• DePamphilis, M. L.. 1999. Replication origins in metazoan chromosomes: fact or fiction? Bioessay 21:5–16
   PubMedGoogle Scholar
• Dubey, D. D., Davis, L. R., Greenfeder, S. A., Ong, L. Y., Zhu, J. G. et al. 1991. Evidence suggesting that the ARS elements associated with silencers of the yeast mating type locus HML do not function as chromosomal DNA replication origin. Mol. Cell. Biol. 11:5346–5355
   PubMedGoogle Scholar
• Dubey, D. D., Zhu, J., Carlson, D. L., Sharma, K., and Huberman, J. A.. 1994. Three ARS elements contribute to the ura4 replication origin in the fission yeast, Schizosaccharomyces pombe. EMBO J. 13:3638–3647
   PubMedGoogle Scholar
• Fromm, M., and Berg, P.. 1983. Simian virus 40 early- and late-region promoter functions are enhanced by the 72-base-pair repeat inserted at distant locations and inverted orientations. Mol. Cell. Biol. 3:991–999
   PubMed Web of Science ®Google Scholar
• Gallagher, R. C., and Blackburn, E. H.. 1998. A promoter region mutation affecting replication of the tetrahymena ribosomal DNA minichromosome. Mol. Cell. Biol. 18:3021–3033
   PubMedGoogle Scholar
• Gencheva, M., Anachkova, B., and Russev, G.. 1996. Mapping the sites of initiation of DNA replication in rat and human rRNA genes. J. Biol. Chem. 271:2608–2614
   PubMedGoogle Scholar
• Goldman, M. A., Holmquist, G. P., Gray, M. C., Caston, L. A., and Nag, A.. 1984. Replication timing of genes and middle repetitive sequences. Science 224:686–692
   PubMedGoogle Scholar
• Gorman, C. H., Moffat, L. F., and Howard, B. H.. 1982. Recombinant genomes which express chloramphenicol acetyltransferase in mammalian cells. Mol. Cell. Biol. 2:1044–1051
   PubMed Web of Science ®Google Scholar
• Grass, D. S., Read, D., Lewis, E. D., and Manley, J. L.. 1987. Cell- and promoter-specific activation of transcription by DNA replication. Genes Dev. 1:1065–1074
   PubMedGoogle Scholar
• Gross, G. R., and Garrard, W. T.. 1988. Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57:159–197
   PubMed Web of Science ®Google Scholar
• Guo, W., Tang, W. J., Bu, X., Bermudez, V., Martin, M., and Folk, W. R.. 1996. AP1 enhancers polyomavirus DNA replication by promoting T-antigen-mediated unwinding of DNA. J. Virol. 70:4914–4918
   PubMedGoogle Scholar
• Guo, Z.-S., and DePamphilis, M. L.. 1992. Specific transcription factors stimulate simian virus 40 and polyomavirus origins of DNA replication. Mol. Cell. Biol. 12:2514–2524
   PubMedGoogle Scholar
• Guptasarma, P.. 1995. Does replication-induced transcription regulate synthesis of the myriad low copy number proteins of Escherichia coli? Bioessay 17:987–997
   PubMedGoogle Scholar
• Haase, S. B., Heinzel, S. S., and Calos, M. P.. 1994. Transcription inhibits the replication of autonomously replicating plasmids in human cells. Mol. Cell. Biol. 14:2516–2524
   PubMedGoogle Scholar
• Hartung, S., Jaenisch, R., and Breindl, M.. 1986. Retrovirus insertion inactivates mouse alpha1(I) collagen gene by blocking initiation of transcription. Nature 320:365–367
   PubMedGoogle Scholar
• Hase, T., Nakai, M., and Masamune, Y.. 1989. Transcription of a region downstream from lambda ori is required for replication of plasmids derived from coliphage lambda. Mol. Gen. Genet. 216:120–125
   PubMedGoogle Scholar
• Hassan, A. B., and Cook, P. R.. 1994. Does transcription by RNA polymerase play a direct role in the initiation of replication? J. Cell Sci. 107:1381–1387
   PubMedGoogle Scholar
• Hatton, K. S., Dhar, V., Brown, E. H., Iqbal, M. A., Stuart, S., Didamn, V. T., and Schildkraut, C. L.. 1988. Replication program of active and inactive multigene families in mammalian cells. Mol. Cell. Biol. 8:2149–2158
   PubMed Web of Science ®Google Scholar
• Heintz, N. H.. 1992. Transcription factors and the control of DNA replication. Curr. Opin. Cell Biol. 4:459–467
   PubMedGoogle Scholar
• Hirt, B.. 1967. Selective extraction of polyoma DNA from infected mouse cell cultures. J. Mol. Biol. 20:365–369
   Web of Science ®Google Scholar
• Hoang, A., Wang, W., and Gralla, J. D.. 1992. The replication activation potential of selected RNA polymerase II promoter elements at the simian virus 40 origin. Mol. Cell. Biol. 12:3087–3093
   PubMedGoogle Scholar
• Iguchi-Ariga, S. M. M., Ogawa, N., and Ariga, H.. 1993. Identification of the initiation region of DNA replication in the murine immunoglobulin heavy chain gene and possible function of the octamer motif as a putative DNA replication origin in mammalian cells. Biochim. Biophys. Acta 1172:73–81
   PubMedGoogle Scholar
• Ireton, K., and Grossman, A. D.. 1992. Coupling between gene expression and DNA synthesis early during development in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 89:8808–8812
   PubMedGoogle Scholar
• Kelly, R. E., DeRose, M. L., Draper, B. W., and Wahl, G. M.. 1995. Identification of an origin of bidirectional DNA replication in the ubiquitously expressed mammalian CAD gene. Mol. Cell. Biol. 15:4136–4148
   PubMedGoogle Scholar
• Keohane, A. M., Barlow, A. L., Waters, J., Bourn, D., and Turner, B. M.. 1999. H4 acetylation, XIST RNA and replication timing are coincident and define x;autosome boundaries in two abnormal X chromosomes. Hum. Mol. Genet. 8:377–383
   PubMedGoogle Scholar
• Kim, S.-M., and Huberman, J. A.. 1999. Influence of a replication enhancer on the hierarchy of origin efficiencies within a cluster of DNA replication origin. J. Mol. Biol. 288:867–882
   PubMedGoogle Scholar
• Kumano, M., Nakagawa, T., Imamura, Y., Galli, I., Ariga, H., and Iguchi-Ariga, S. M. M.. 1992. Stimulation of SV40 DNA replication by the human c-myc enhancer. FEBS Lett. 309:146–152
   PubMedGoogle Scholar
• Kwon, Y. S., Kim, J., and Kang, C.. 1998. Viability of E. coli cells containing phage RNA polymerase and promoter: interference of plasmid replication by transcription. Genet. Anal. 14:133–139
   PubMedGoogle Scholar
• Lee, D. Y., and Clayton, D. A.. 1998. Initiation of mitochondrial DNA replication by transcription and R-loop processing. J. Biol. Chem. 273:30614–30621
   PubMed Web of Science ®Google Scholar
• Lee, S.-T., Tarn, C., and Chang, K.-P.. 1993. Characterization of the switch of kinetoplast DNA minicircle dominance during development and reversion of drug resistance in Leishmania. Mol. Biochem. Parasitol. 58:187–204
   PubMedGoogle Scholar
• Leffak, M., and James, C. D.. 1989. Opposite replication polarity of the germ line c-myc gene in HeLa cells compared with that of two Burkitt lymphoma cell lines. Mol. Cell. Biol. 9:586–593
   PubMedGoogle Scholar
• Leonard, M. W., and Patient, R. K.. 1991. Evidence for torsional stress in transcriptionally nationally activated chromatin. Mol. Cell. Biol. 11:6128–6138
   PubMedGoogle Scholar
• Li, R., and Botchan, M. R.. 1994. Acidic transcription factors alleviate nucleosome-mediated repression of DNA replication of bovine papillomavirus type 1. Proc. Natl. Acad. Sci. USA 91:7051–7055
   PubMedGoogle Scholar
• MacAllister, T. W., Kelley, W. L., Miron, A., Stenzel, T. T., and Bastia, D.. 1991. Replication of plasmid R6K origin gamma in vitro, dependence on dual initiator proteins and inhibition by transcription. J. Biol. Chem. 266:16056–1606235
   PubMedGoogle Scholar
• Marahrens, Y., and Stillman, B.. 1994. Replicator dominance in an eukaryotic chromosome. EMBO J. 13:3395–3400
   PubMedGoogle Scholar
• Marczynski, G. T., and Shapiro, L.. 1993. Bacterial chromosome origins of replication. Curr. Opin. Genet. Dev. 3:775–782
   PubMed Web of Science ®Google Scholar
• Marczynski, G. T., Lentine, K., and Shapiro, L.. 1995. A developmentally regulated chromosomal origin of replication uses essential transcription elements. Genes Dev. 9:1543–1557
   PubMedGoogle Scholar
• Miron, A., Mukherjee, S., and Bastia, D.. 1992. Activation of distant replication origins in vivo by DNA looping as revealed by a novel mutant form of an initiator protein defective in cooperativity at a distance. EMBO J. 11:1205–1216
   PubMedGoogle Scholar
• Nahreini, P., and Mathews, M. B.. 1995. Effects of the simian virus 40 origin of replication on transcription from the human immunodeficiency virus 1 promoter. J. Virol. 69:1296–1301
   PubMedGoogle Scholar
• Ogawa, T., and Okazaki, T.. 1991. Concurrent transcription from the gid and mioC promoters activates replication of an E. coli minichromosomes. Mol. Gen. Genet. 230:193–200
   PubMedGoogle Scholar
• Ohba, R., Matsumoto, K., and Ishimi, Y.. 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
• Pan, W. J., Gallagher, R. C., and Blackburn, E. H.. 1995. Replication of an rRNA gene origin plasmid in the Tetrahymena thermophila macronucleus is prevented by transcription through the origin from an RNA polymerase I promoter. Mol. Cell. Biol. 15:3372–3381
   PubMedGoogle Scholar
• Phi-van, L., Selke, C., Von Bodenhausen, A., and Stratling, W. H.. 1998. An initiation zone of chromosomal DNA replication at the chicken lysozyme gene locus. J. Biol. Chem. 273:18300–18307
   PubMedGoogle Scholar
• Pierron, G., Pallotta, D., and Benard, M.. 1999. The one-kilobase DNA fragment upstream of the ardC actin gene of Physarum polycephalum is both a replicator and a promoter. Mol. Cell. Biol. 19:3506–3514
   PubMedGoogle Scholar
• Pierron, G., and Sauer, H. W.. 1980. More evidence for replication-transcription coupling in Physarum polycephalum. J. Cell Sci. 41:105–113
   PubMedGoogle Scholar
• Razin, S. V., Vassetzky, Y. S., Kvartskhava, A. I., Grinenko, N. F., and Georgiev, G. P.. 1991. Transcriptional enhancer in the vicinity of a replication origin within the 5′ region of the chicken alpha-globin gene domain. J. Mol. Biol. 217:596–598
   Google Scholar
• Rhode, P. R., Elsasser, S., and Campbell, J. I.. 1992. Role of multifunctional autonomously replicating sequence binding factor 1 in the initiation of DNA replication and transcriptional control in Saccharomyces cerevisiae. Mol. Cell. Biol. 12:1064–1077
   PubMedGoogle Scholar
• Rippe, K., von Hippel, P. H., and Langowski, J.. 1995. Action at a distance: DNA-looping and initiation of transcription. Trends Biochem. Sci. 20:500–506
   PubMedGoogle Scholar
• Rivier, D. H., and Rine, J.. 1992. An origin of DNA replication and a transcription silencer require a common element. Science 256:659–663
   PubMedGoogle Scholar
• Roberts, J. M., and Weintraub, H.. 1988. Negative control of DNA replication in composite SV40-bovine papilloma virus plasmids. Cell 46:741–752
   Google Scholar
• Sakakibara, Y.. 1996. Rifampin-induced initiation of chromosome replication in dnaR-deficient Escherichia coli cells. J. Bacteriol. 178:1242–1247
   PubMedGoogle Scholar
• Sasaki, T., Sawado, T., Yamaguchi, M., and Shinomiya, T.. 1999. Specification of regions of DNA replication initiation during embryogenesis in the 65-kilobase DNApolα-dE2F locus of Drosophila melanogaster. Mol. Cell. Biol. 19:547–555
   PubMed Web of Science ®Google Scholar
• Schleif, R.. 1992. DNA looping. Annu. Rev. Biochem. 61:199–223
   PubMed Web of Science ®Google Scholar
• Schubach, W., and Groudine, M.. 1984. Alteration of c-myc chromatin structure by avian leukosis virus integration. Nature 307:702–708
   PubMedGoogle Scholar
• Shenk, T.. 1978. Construction of a viable SV40 variant containing two functional origins of DNA replication. Cell 13:791–798
   PubMedGoogle Scholar
• Shinomiya, T., and Sawako, I.. 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
• Simpson, R. T.. 1990. Nucleosome positioning can affect function of a cis-acting DNA element in vivo. Nature 343:387–389
   PubMed Web of Science ®Google Scholar
• Snyder, M., Sapolsky, R. J., and Davis, R. W.. 1988. Transcription interferes with elements important for chromosome maintenance in Saccharomyces cerevisiae. Mol. Cell. Biol. 8:2184–2194
   PubMedGoogle Scholar
• Su, W., Middleton, T., Sugden, B., and Echols, H.. 1991. DNA looping between origin of replication of Epstein-Barr virus and its enhancer site: stabilization of an origin complex with Epstein-Barr nuclear antigen 1. Proc. Natl. Acad. Sci. USA 88:10870–10874
   PubMedGoogle Scholar
• Sussman, D. J., and Milman, T. A.. 1984. Short-term, high-efficiency expression of transfected DNA. Mol. Cell. Biol. 4:1641–1643
   PubMedGoogle Scholar
• Szymanski, P., and Woodworth, M.. 1990. A 69-base-pair monkey DNA sequence enhances simian virus 40 replication and transcription through multiple motifs. J. Virol. 64:1360–1365
   PubMedGoogle Scholar
• Taira, T., Iguchi-Ariga, S. M., and Ariga, H.. 1994. A novel DNA replication origin identified in the human shock protein 70 gene promoter. Mol. Cell Biol. 14:6386–6397
   PubMedGoogle Scholar
• Tanaka, S., Halter, D., Livingstone-Zatchej, M., Reszel, B., and Thoma, F.. 1994. Transcription through the yeast origin of replication ARS1 ends at the ABF1 binding site and affects extrachromosomal maintenance of minichromosomes. Nucleic Acids Res. 22:3904–3910
   PubMedGoogle Scholar
• Tasheva, E. S., and Roufa, D. J.. 1994. A mammalian origin of bidirectional DNA replication within the Chinese hamster RP14 locus. Mol. Cell. Biol. 14:5628–5635
   PubMed Web of Science ®Google Scholar
• Toledo, F., Baron, B., Fernandez, M. A., Lachages, A. M., Mayau, V., Buttin, G., and Debatisse, M.. 1998. OriGNA13: a narrow zone of preferential replication initiation in mammalian cells identified by 2D gel and competitive PCR replicon mapping techniques. Nucleic Acids Res. 26:2313–2321
   PubMedGoogle Scholar
• Villeponteau, B., Lundell, M., and Martinson, H.. 1984. Torsional stress promotes the DNase I sensitivity of active genes. Cell 39:468–478
   Google Scholar
• Vujcic, M., Miller, C. A., and Kowalski, D.. 1999. Activation of silent replication origins at autonomously replicating sequence elements near the HML locus in budding yeast. Mol. Cell. Biol. 19:6098–6109
   PubMedGoogle Scholar
• Wiesendanger, B., Lucchini, R., Koller, T., and Sogo, J. M.. 1994. Replication fork barriers in the Xenopus rDNA. Nucleic Acids Res. 22:5039–5046
   Google Scholar
• Wigmore, D. J., Eaton, R. W., and Scott, W. A.. 1980. Endonuclease-sensitive regions in SV40 chromatin from cells infected with duplicated mutants. Virology 104:462–473
   PubMedGoogle Scholar
• Williams, R. D., Lee, B. A., Jackson, S. P., and Proudfoot, N. J.. 1996. Activation domains of transcription factors mediate replication dependent transcription from a minimal HIV-1 promoter. Nucleic Acids Res. 24:549–557
   PubMedGoogle Scholar
• Wilson, A. C., and Patient, R. K.. 1993. DNA replication facilitates the action of transcriptional enhancers in transient expression assays. Nucleic Acids Res. 21:4296–4304
   PubMedGoogle Scholar
• Wolffe, A. P.. 1991. Implications of DNA replication for eukaryotic gene expression. J. Cell Sci. 99:201–206
   PubMedGoogle Scholar
• Wolffe, A. P., and Kurumizaka, H.. 1998. The nucleosome: a powerful regulator of transcription. Prog. Nucleic Acid Res. Mol. Biol. 61:379–422
   PubMed Web of Science ®Google Scholar
• Wong, S. C., and Schaffer, P. A.. 1991. Elements in the transcriptional regulatory region flanking herpes simplex virus type 1 oriS stimulate origin function. J. Virol. 65:2601–2611
   PubMedGoogle Scholar
• Zhao, Y., Miyagi, S., Kikawada, T., and Tsutsumi, K.. 1997. Sequence requirement for replication initiation at the rat aldolase B locus implicated in its functional correlation with transcription regulation. Biochem. Biophys. Res. Commun. 237:707–713
   PubMedGoogle Scholar
• Zhao, Y., Tsutsumi, R., Yamaki, M., Nagatsuka, Y., Ejiri, S.-I., and Tsutsumi, K.-I.. 1994. Initiation zone of DNA replication at the aldolase B locus encompass transcription promoter region. Nucleic Acids Res. 22:5385–5390
   PubMedGoogle Scholar