Characterizing Replication Intermediates in the Amplified CHO Dihydrofolate Reductase Domain by Two Novel Gel Electrophoretic Techniques

REFERENCES

• Anachkova, B., and J. L. Hamlin. 1989. Replication in the amplified di-hydrofolate reductase domain in CHO cells may initiate at two distinct sites, one of which is a repetitive sequence element. Mol. Cell. Biol. 9:532–540.
   PubMedGoogle Scholar
• Benard, M., C. Lagnel, and G. Pierron. 1995. Site-specific initiation of DNA replication within the non-transcribed spacer of Physarum rDNA. Nucleic Acids Res. 23:1447–1453.
   PubMedGoogle Scholar
• Benard, M., and G. Pierron. 1992. Mapping of a Physarum chromosomal origin of replication tightly linked to a developmentally-regulated profilin gene. Nucleic Acids Res. 20:3309–3315.
   PubMedGoogle Scholar
• Braunstein, J. D., D. Schulze, T. DelGiudice, A. Furst, and C. L. Schildkraut. 1982. The temporal order of replication of murine immunoglobulin heavy chain constant region sequences corresponds to their linear order in the genome. Nucleic Acids Res. 10:6887–6902.
   PubMed Web of Science ®Google Scholar
• Brewer, B. J., and W. L. Fangman. 1987. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell 51:463–471.
   PubMed Web of Science ®Google Scholar
• Brewer, B. J., and W. L. Fangman. 1988. A replication fork barrier at the 3′ end of yeast ribosomal RNA genes. Cell 55:637–643.
   PubMed Web of Science ®Google Scholar
• Brun, C., P. A. Dijkwel, R. D. Little, J. L. Hamlin, C. S. Schildkraut, and J. A. Huberman. 1995. The patterns of replication intermediates from a complex mammalian origin are identical to those of a simple origin from S. cerevisiae. Chromosoma 104:92–102.
   PubMedGoogle Scholar
• Burhans, W. C., and J. A. Huberman. 1994. DNA replication origins in animal cells: a question of context? Science 263:639–640.
   PubMedGoogle Scholar
• Burhans, W. C., J. E. Selegue, and N. H. Heintz. 1986. Isolation of the origin of replication associated with the amplified Chinese hamster dihydrofolate reductase domain. Proc. Natl. Acad. Sci. USA 83:7790–7794.
   PubMedGoogle Scholar
• Burhans, W. C., L. T. Vassilev, M. S. Caddle, N. H. Heintz, and M. L. DePamphilis. 1990. Identification of an origin of bidirectional DNA replication in mammalian chromosomes. Cell 62:955–965.
   PubMedGoogle Scholar
• Carroll, S. M., M. L. DeRose, J. L. Kolman, G. H. Nonet, R. E. Kelly, and G. M. Wahl. 1993. Localization of a bidirectional DNA replication origin in the native locus and in episomally amplified murine adenosine deaminase loci. Mol. Cell. Biol. 13:2971–2981.
   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
• DePamphilis, M. L. 1993. Origins of DNA replication that function in eu-karyotic cells. Curr. Opin. Cell Biol. 5:434–441.
   PubMedGoogle Scholar
• Dijkwel, P. A., and J. D’Anna. Unpublished data.
   Google Scholar
• Dijkwel, P. A., and J. L. Hamlin. 1988. Matrix attachment regions are positioned near replication initiation sites, genes, and an interamplicon junction in the amplified dihydrofolate reductase domain of Chinese hamster ovary cells. Mol. Cell. Biol. 8:5398–5409.
   PubMedGoogle Scholar
• Dijkwel, P. A., and J. L. Hamlin. 1992. Initiation of DNA replication in the dihydrofolate reductase locus is confined to the early S period in CHO cells synchronized with the plant amino acid mimosine. Mol. Cell. Biol. 12:3715–3722.
   PubMedGoogle Scholar
• Dijkwel, P. A., and J. L. Hamlin. 1995. The Chinese hamster dihydrofolate reductase origin consists of multiple potential nascent-strand start sites. Mol. Cell. Biol. 15:3023–3031.
   PubMedGoogle Scholar
• Dijkwel, P. A., J. P. Vaughn, and J. L. Hamlin. 1991. Mapping of replication initiation sites in mammalian genomes by two-dimensional gel analysis: stabilization and enrichment of replication intermediates by isolation on the nuclear matrix. Mol. Cell. Biol. 11:3850–3859.
   PubMedGoogle Scholar
• Dijkwel, P. A., J. P. Vaughn, and J. L. Hamlin. 1994. Replication initiation sites are distributed widely in the amplified CHO dihydrofolate reductase domain. Nucleic Acids Res. 22:4989–4996.
   PubMedGoogle Scholar
• Dubey, D. D., J. Zhu, D. L. Carlson, K. Sharma, and J. A. Huberman. 1994. Three ARS elements contribute to the ura4 replication origin region in the fission yeast, Schizosaccharomyces pombe. EMBO J. 13:3638–3647.
   PubMedGoogle Scholar
• Feinberg, A. P., and B. Vogelstein. 1983. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132:6–13.
   PubMed Web of Science ®Google Scholar
• Ferguson, B. M., B. J. Brewer, A. E. Reynolds, and W. L. Fangman. 1991. A yeast origin of replication is activated late in S phase. Cell 65:507–515.
   PubMed Web of Science ®Google Scholar
• Giacca, M., L. Zentilin, P. Norio, S. Diviacco, D. Dimitrova, G. Contreas, G. Biamonti, G. Perini, F. Weighardt, S. Riva, and A. Falaschi. 1994. Fine mapping of a replication origin of human DNA. Proc. Natl. Acad. Sci. USA 91:7119–7123.
   PubMed Web of Science ®Google Scholar
• Gilbert, D. M., H. Miyazawa, and M. L. DePamphilis. 1995. Site-specific initiation of DNA replication in Xenopus egg extract requires nuclear structure. Mol. Cell. Biol. 15:2942–2954.
   PubMed Web of Science ®Google Scholar
• Gilbert, D. M., H. Miyazawa, F. S. Nallaseth, J. M. Ortega, J. J. Blow, and M. L. DePamphilis. 1993. Site-specific initiation of DNA replication in metazoan chromosomes and the role of nuclear organization. Cold Spring Harbor Symp. Quant. Biol. 58:475–485.
   PubMedGoogle Scholar
• Hamlin, J. L., P. J. Mosca, and V. V. Levenson. 1994. Defining origins of replication in mammalian cells. Biochim. Biophys. Acta 1198:85–111.
   PubMedGoogle Scholar
• Handeli, S., A. Klar, M. Meuth, and H. Cedar. 1989. Mapping replication units in animal cells. Cell 57:909–920.
   PubMedGoogle Scholar
• Heck, M. M., and A. C. Spradling. 1990. Multiple replication origins are used during Drosophila chorion gene amplification. J. Cell Biol. 110:903–914.
   PubMed Web of Science ®Google Scholar
• Heintz, N. H., and J. L. Hamlin. 1982. An amplified chromosomal sequence that includes the gene for dihydrofolate reductase initiates replication within specific restriction fragments. Proc. Natl. Acad. Sci. USA 79:4083–4087.
   PubMedGoogle Scholar
• Hyrien, O., and M. Mechali. 1993. Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of Xenopus early embryos. EMBO J. 12:4511–4520.
   PubMed Web of Science ®Google Scholar
• James, C. D., and M. Leffak. 1986. Polarity of DNA replication through the avian alpha-globin locus. Mol. Cell. Biol. 6:976–984.
   PubMedGoogle Scholar
• Kalejta, R. F., and J. L. Hamlin. 1996. Composite patterns in neutral/neutral two-dimensional gels demonstrate inefficient replication origin usage. Mol. Cell. Biol. 16:4915–4922.
   PubMedGoogle Scholar
• Kelly, R. E., M. L. DeRose, B. W. Draper, and G. M. Wahl. 1995. Identification of an origin of bidirectional DNA replication in the ubiquitously expressed mammalian CAD gene. Mol. Cell. Biol. 15:4136–4148.
   PubMedGoogle Scholar
• Leu, T. H., and J. L. Hamlin. 1989. High-resolution mapping of replication fork movement through the amplified dihydrofolate reductase domain in CHO cells by in-gel renaturation analysis. Mol. Cell. Biol. 9:523–531.
   PubMedGoogle Scholar
• Liang, C., and S. A. Gerbi. 1994. Analysis of an origin of DNA amplification in Sciara coprophila by a novel three-dimensional gel method. Mol. Cell. Biol. 14:1520–1529.
   PubMedGoogle Scholar
• Liang, C., J. D. Spitzer, H. S. Smith, and S. A. Gerbi. 1993. Replication initiates at a confined region during DNA amplification in Sciara DNA puff II/9A. Genes Dev. 7:1072–1084.
   PubMedGoogle Scholar
• Linskens, M. H., and J. A. Huberman. 1990. The two faces of higher eu-karyotic DNA replication origins. Cell 62:845–847.
   PubMedGoogle Scholar
• Linskens, M. H., and J. A. Huberman. 1990. Ambiguities in results obtained with 2D gel replicon mapping techniques. Nucleic Acids Res. 18:647–652.
   PubMedGoogle Scholar
• Little, R. D., T. H. Platt, and C. L. Schildkraut. 1993. Initiation and termination of DNA replication in human rRNA genes. Mol. Cell. Biol. 13:6600–6613.
   PubMedGoogle Scholar
• Ma, C., T.-H. Leu, and J. L. Hamlin. 1990. Multiple origins of replication in the dihydrofolate reductase amplicons of a methotrexate-resistant Chinese hamster cell line. Mol. Cell. Biol. 10:1338–1346.
   PubMedGoogle Scholar
• Milbrandt, J. D., N. H. Heintz, W. C. White, S. M. Rothman, and J. L. Hamlin. 1981. Methotrexate-resistant Chinese hamster ovary cells have amplified a 135-kilobase-pair region that includes the dihydrofolate reductase gene. Proc. Natl. Acad. Sci. USA 78:6043–6047.
   PubMedGoogle Scholar
• Nawotka, K. A., and J. A. Huberman. 1988. Two-dimensional gel elec-trophoretic method for mapping DNA replicons. Mol. Cell. Biol. 8:1408–1413.
   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
• Shinomiya, T., and S. Ina. 1994. Mapping an initiation region of DNA replication at a single-copy chromosomal locus in Drosophila melanogaster cells by two-dimensional gel methods and PCR-mediated nascent-strand analysis: multiple replication origins in a broad zone. Mol. Cell. Biol. 14:7394–7403.
   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
• Vassilev, L. T., W. C. Burhans, and M. L. DePamphilis. 1990. Mapping an origin of DNA replication at a single-copy locus in exponentially proliferating mammalian cells. Mol. Cell. Biol. 10:4685–4689.
   PubMedGoogle Scholar
• Vaughn, J. P., P. A. Dijkwel, and J. L. Hamlin. 1990. Replication initiates in a broad zone in the amplified CHO dihydrofolate reductase domain. Cell 61:1075–1087.
   PubMedGoogle Scholar
• Wu, J. R., and D. M. Gilbert. 1996. A distinct G1 step required to specify the Chinese hamster DHFR replication origin. Science 271:1270–1272.
   PubMed Web of Science ®Google Scholar
• Zhu, J., C. S. Newlon, and J. A. Huberman. 1992. Localization of a DNA replication origin and termination zone on chromosome III of Saccharomyces cerevisiae. Mol. Cell. Biol. 12:4733–4741.
   PubMedGoogle Scholar