In Xenopus Egg Extracts, DNA Replication Initiates Preferentially at or near Asymmetric AT Sequences

REFERENCES

• Aggarwal, B. D., and B. R. Calvi. 2004. Chromatin regulates origin activity in Drosophila follicle cells. Nature 430:372–376.
   PubMed Web of Science ®Google Scholar
• Aladjem, M. I. 2007. Replication in context: dynamic regulation of DNA replication patterns in metazoans. Nat. Rev. Genet. 8:588–600.
   PubMed Web of Science ®Google Scholar
• Anglana, M., F. Apiou, A. Bensimon, and M. Debatisse. 2003. Dynamics of DNA replication in mammalian somatic cells: nucleotide pool modulates origin choice and interorigin spacing. Cell 114:385–394.
   PubMed Web of Science ®Google 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
• Bielinsky, A. K., and S. A. Gerbi. 1998. Discrete start sites for DNA synthesis in the yeast ARS1 origin. Science 279:95–98.
   PubMedGoogle Scholar
• Blow, J. J., and R. A. Laskey. 1986. Initiation of DNA replication in nuclei and purified DNA by a cell-free extract of Xenopus eggs. Cell 47:577–587.
   PubMed Web of Science ®Google Scholar
• Blow, J. J., P. J. Gillespie, D. Francis, and D. A. Jackson. 2001. Replication origins in Xenopus egg extract are 5-15 kilobases apart and are activated in clusters that fire at different times. J. Cell Biol. 152:15–25.
   PubMed Web of Science ®Google 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
• Cox, L. S., and R. A. Laskey. 1991. DNA replication occurs at discrete sites in pseudonuclei assembled from purified DNA in vitro. Cell 66:271–275.
   PubMedGoogle Scholar
• Danis, E., K. Brodolin, S. Menut, D. Maiorano, C. Girard-Reydet, and M. Mechali. 2004. Specification of a DNA replication origin by a transcription complex. Nat. Cell Biol. 6:721–730.
   PubMedGoogle Scholar
• DePamphilis, M. L. 1999. Replication origins in metazoan chromosomes: fact or fiction? Bioessays 21:5–16.
   PubMedGoogle Scholar
• Harvey, K. J., and J. Newport. 2003. CpG methylation of DNA restricts prereplication complex assembly in Xenopus egg extracts. Mol. Cell. Biol. 23:6769–6779.
   PubMedGoogle Scholar
• Hyrien, O., and M. Mechali. 1992. Plasmid replication in Xenopus eggs and egg extracts: a 2D gel electrophoretic analysis. Nucleic Acids Res. 20:1463–1469.
   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
• 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
• 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., T. R. Coleman, and M. L. DePamphilis. 2003. Xenopus origin recognition complex (ORC) initiates DNA replication preferentially at sequences targeted by Schizosaccharomyces pombe ORC. EMBO J. 22:3441–3450.
   PubMed Web of Science ®Google Scholar
• Laskey, R. A., and R. M. Harland. 1982. Replication origins in the Xenopus egg. Cell 31:503.
   PubMedGoogle Scholar
• Lemaitre, J. M., E. Danis, P. Pasero, Y. Vassetzky, and M. Mechali. 2005. Mitotic remodeling of the replicon and chromosome structure. Cell 123:787–801.
   PubMedGoogle Scholar
• Lee, J. K., K. Y. Moon, Y. Jiang, and J. Hurwitz. 2001. 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
• Li, C. J., J. A. Bogan, D. A. Natale, and M. L. DePamphilis. 2000. Selective activation of pre-replication complexes in vitro at specific sites in mammalian nuclei. J. Cell Sci. 113:887–898.
   PubMedGoogle Scholar
• Lin, C. M., H. Fu, M. Martinovsky, E. Bouhassira, and M. I. Aladjem. 2003. Dynamic alterations of replication timing in mammalian cells. Curr. Biol. 13:1019–1028.
   PubMed Web of Science ®Google Scholar
• Lucas, I., M. Chevrier-Miller, J. M. Sogo, and O. Hyrien. 2000. Mechanisms ensuring rapid and complete DNA replication despite random initiation in Xenopus early embryos. J. Mol. Biol. 296:769–786.
   PubMed Web of Science ®Google Scholar
• MacAlpine, D. M., H. K. Rodriguez, and S. P. Bell. 2004. Coordination of replication and transcription along a Drosophila chromosome. Genes Dev. 18:3094–3105.
   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
• Marahrens, Y., and B. Stillman. 1992. A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science 255:817–823.
   PubMed Web of Science ®Google Scholar
• Mechali, M., F. Mechali, and R. A. Laskey. 1983. Tumor promoter TPA increases initiation of replication on DNA injected into Xenopus eggs. Cell 35:63–69.
   PubMedGoogle Scholar
• Mechali, M., and S. Kearsey. 1984. Lack of specific sequence requirement for DNA replication in Xenopus eggs compared with high sequence specificity in yeast. Cell 38:55–64.
   PubMed Web of Science ®Google Scholar
• Mechali, M. 2001. DNA replication origins: from sequence specificity to epigentics. Nat. Rev. Genet. 2:640–645.
   PubMedGoogle Scholar
• Menut, S., J. M. Lemaitre, A. Hair, and M. Méchali. 1999. DNA replication and chromatin assembly using Xenopus egg extracts, p. 196-226. In J. D. Richter (ed.), Advances in molecular biology. Oxford University Press, Oxford, United Kingdom.
   Google Scholar
• Michalet, X., R. Ekong, F. Fougerousse, S. Rousseaux, C. Schurra, N. Hornigold, M. van Slegtenhors, S. Wolfe, J. Povey, J. S. Beckmann, et al. 1997. Dynamic molecular combing: stretching the whole human genome for high-resolution studies. Science 277:1518–1523.
   PubMed Web of Science ®Google Scholar
• Newport, J. 1987. Nuclear reconstitution in vitro: stages of assembly around protein-free DNA. Cell 48:205–217.
   PubMed Web of Science ®Google 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
• Pasero, P., A. Bensimon, and E. Schwob. 2002. Single-molecule analysis reveals clustering and epigenetic regulation of replication origins at the yeast rDNA locus. Genes Dev. 16:2479–2484.
   PubMed Web of Science ®Google Scholar
• Rein, T., T. Kobayashi, M. Malott, M. Leffak, and M. DePamphilis. 1999. DNA methylation at mammalian replication origins. J. Biol. Chem. 274:25792–25800.
   PubMedGoogle Scholar
• Remus, D., E. L. Beall, and M. R. Botchan. 2004. DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC-DNA binding. EMBO J. 23:897–907.
   PubMed Web of Science ®Google Scholar
• Sasaki, T., T. Sawado, M. Yamaguchi, and T. Shinomiya. 1999. Specification of regions of DNA replication initiation during embryogenesis in the 65-kilobase DNApolalpha-dE2F locus of Drosophila melanogaster. Mol. Cell. Biol. 19:547–555.
   PubMed Web of Science ®Google Scholar
• Segurado, M., A. de Luis, and F. Antequera. 2003. Genome-wide distribution of DNA replication origins at A+T-rich islands in Schizosaccharomyces pombe. EMBO Rep. 4:1048–1053.
   PubMed Web of Science ®Google Scholar
• Stefanovic, D., S. Stanojcic, A. Vindigni, A. Ochem, and A. Falaschi. 2003. In vitro protein-DNA interactions at the human lamin B2 replication origin. J. Biol. Chem. 278:42737–42743.
   PubMedGoogle Scholar
• Takahashi, T., and H. Masukata. 2001. Interaction of fission yeast ORC with essential adenine/thymine stretches in replication origins. Genes Cells 6:837–849.
   PubMedGoogle Scholar
• Vashee, S., C. Cvetic, W. Lu, P. Simancek, T. J. Kelly, and J. C. Walter. 2003. Sequence-independent DNA binding and replication initiation by the human origin recognition complex. Genes Dev. 17:1894–1908.
   PubMed Web of Science ®Google Scholar
• Walter, J., and J. W. Newport. 1997. Regulation of replicon size in Xenopus egg extracts. Science 275:993–995.
   PubMed Web of Science ®Google Scholar
• Walter, J., and J. W. 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
• Wang, L., C. M. Lin, J. O. Lopreiato, and M. I. Aladjem. 2006. Cooperative sequence modules determine replication initiation sites at the human beta-globin locus. Hum. Mol. Genet. 15:2613–2622.
   PubMedGoogle Scholar