In search of the holy replicator (original) (raw)

References

  1. Jacob, F., Brenner, S. & Cuzin, F. On the regulation of DNA replication in bacteria. Cold Spring Harb. Symp. Quant. Biol. 28, 329–348 (1964).
    Google Scholar
  2. Chakraborty, T., Yoshinaga, K., Lother, H. & Messer, W. Purification of the E. coli dnaA gene product. EMBO J. 1, 1545–1549 (1982).
    CAS PubMed PubMed Central Google Scholar
  3. Bell, S. P. & Stillman, B. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature 357, 128–134 (1992).
    CAS Google Scholar
  4. Timmis, K., Cabello, F. & Cohen, S. N. Cloning, isolation, and characterization of replication regions of complex plasmid genomes. Proc. Natl Acad. Sci. USA 72, 2242–2246 (1975).
    CAS Google Scholar
  5. Yasuda, S. & Hirota, Y. Cloning and mapping of the replication origin of Escherichia coli. Proc. Natl Acad. Sci. USA 74, 5458–5462 (1977).
    CAS Google Scholar
  6. Fujita, M. Q., Yoshikawa, H. & Ogasawara, N. Structure of the dnaA region of Pseudomonas putida: conservation among three bacteria, Bacillus subtilis, Escherichia coli and P. putida. Mol. Gen. Genet. 215, 381–387 (1989).
    CAS Google Scholar
  7. Taylor, J. H. Rates of chain growth and units of replication in DNA of mammalian chromosomes. J. Mol. Biol. 31, 579–594 (1968).
    CAS Google Scholar
  8. Huberman, J. A. & Riggs, A. D. On the mechanism of DNA replication in mammalian chromosomes. J. Mol. Biol. 32, 327–341 (1968).
    CAS Google Scholar
  9. Stambrook, P. J. & Flickinger, R. A. Changes in chromosomal DNA replication patterns in developing frog embryos. J. Exp. Zool. 174, 101–113 (1970).
    CAS Google Scholar
  10. Callan, H. G. Replication of DNA in the chromosomes of eukaryotes. Proc. R. Soc. Lond. B 181, 19–41 (1972).
    CAS Google Scholar
  11. Blumenthal, A. B., Kriegstein, H. J. & Hogness, D. S. The units of DNA replication in Drosophila melanogaster chromosomes. Cold Spring Harb. Symp. Quant. Biol. 38, 205–223 (1974).
    CAS Google Scholar
  12. Taylor, J. H. Increase in DNA replication sites in cells held at the beginning of S phase. Chromosoma 62, 291–300 (1977).
    CAS Google Scholar
  13. Hand, R. Eucaryotic DNA: organization of the genome for replication. Cell 15, 317–325 (1978).
    CAS Google Scholar
  14. Mueller, G. C. & Kajiwara, K. Early- and late-replicating deoxyribonucleic acid complexes in HeLa nuclei. Biochim. Biophys. Acta 114, 108–115 (1966).
    CAS Google Scholar
  15. Balazs, I., Brown, E. H. & Schildkraut, C. L. The temporal order of replication of some DNA cistrons. Cold Spring Harb. Symp. Quant. Biol. 38, 239–245 (1973).
    Google Scholar
  16. Struhl, K., Stinchcomb, D. T., Scherer, S. & Davis, R. W. High-frequency transformation of yeast: autonomous replication of hybrid DNA molecules. Proc. Natl Acad. Sci. USA 76, 1035–1039 (1979).
    CAS Google Scholar
  17. Huberman, J. A., Spotila, L. D., Nawotka, K. A., El-Assouli, S. M. & Davis, L. R. The in vivo replication origin of the yeast 2 microns plasmid. Cell 51, 473–481 (1987).
    CAS Google Scholar
  18. Brewer, B. J. & Fangman, W. L. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell 51, 463–471 (1987).
    CAS Google Scholar
  19. Huberman, J. A., Zhu, J., Davis, L. R. & Newlon, C. S. Close association of a DNA replication origin and an ARS element on chromosome III of the yeast Saccharomyces cerevisiae. Nucleic Acids Res. 16, 6373–6384 (1988).
    CAS PubMed PubMed Central Google Scholar
  20. Celniker, S. E., Sweder, K., Srienc, F., Bailey, J. E. & Campbell, J. L. Deletion mutations affecting autonomously replicating sequence ARS1 of Saccharomyces cerevisiae. Mol. Cell. Biol. 4, 2455–2466 (1984).
    CAS PubMed PubMed Central Google Scholar
  21. Marahrens, Y. & Stillman, B. A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science 255, 817–823 (1992).
    CAS Google Scholar
  22. Harland, R. M. & Laskey, R. A. Regulated replication of DNA microinjected into eggs of Xenopus laevis. Cell 21, 761–771 (1980).
    CAS Google Scholar
  23. Mechali, M. & Kearsey, S. Lack of specific sequence requirement for DNA replication in Xenopus eggs compared with high sequence specificity in yeast. Cell 38, 55–64 (1984).
    CAS Google Scholar
  24. Heintz, N. H. & Hamlin, J. L. 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 (1982).
    CAS Google Scholar
  25. Gilbert, D. & Cohen, S. N. Autonomous replication in mouse cells: a correction. Cell 56, 143–144 (1989).
    CAS Google Scholar
  26. Masukata, H., Satoh, H., Obuse, C. & Okazaki, T. Autonomous replication of human chromosomal DNA fragments in human cells. Mol. Biol. Cell 4, 1121–1132 (1993).
    CAS PubMed PubMed Central Google Scholar
  27. Krysan, P. J. & Calos, M. P. Replication initiates at multiple locations on an autonomously replicating plasmid in human cells. Mol. Cell. Biol. 11, 1464–1472 (1991).
    CAS PubMed PubMed Central Google Scholar
  28. Burhans, W. C., Vassilev, L. T., Caddle, M. S., Heintz, N. H. & DePamphilis, M. L. Identification of an origin of bidirectional DNA replication in mammalian chromosomes. Cell 62, 955–965 (1990).
    CAS Google Scholar
  29. Vaughn, J. P., Dijkwel, P. A. & Hamlin, J. L. Replication initiates in a broad zone in the amplified CHO dihydrofolate reductase domain. Cell 61, 1075–1087 (1990).
    CAS Google Scholar
  30. Gilbert, D. M. Making sense of eukaryotic DNA replication origins. Science 294, 96–100 (2001).
    CAS PubMed PubMed Central Google Scholar
  31. Kobayashi, T., Rein, T. & DePamphilis, M. Identification of primary initiation sites for DNA replication in the hamster DHFR gene initiation zone. Mol. Cell. Biol. 18, 3266–3277 (1998).
    CAS PubMed PubMed Central Google Scholar
  32. Dijkwel, P. A., Wang, S. & Hamlin, J. L. 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 (2002).
    CAS PubMed PubMed Central Google Scholar
  33. Hyrien, O. & Mechali, M. Plasmid replication in Xenopus eggs and egg extracts: a 2D gel electrophoretic analysis. Nucleic Acids Res. 20, 1463–1469 (1992).
    CAS PubMed PubMed Central Google Scholar
  34. Mahbubani, H. M., Paull, T., Elder, J. K. & Blow, J. J. DNA replication initiates at multiple sites on plasmid DNA in Xenopus egg extracts. Nucleic Acids Res. 20, 1457–1462 (1992).
    CAS PubMed PubMed Central Google Scholar
  35. Gilbert, D. M., Miyazawa, H. & DePamphilis, M. L. Site-specific initiation of DNA replication in Xenopus egg extract requires nuclear structure. Mol. Cell. Biol. 15, 2942–2954 (1995).
    CAS PubMed PubMed Central Google Scholar
  36. Hyrien, O., Maric, C. & Mechali, M. Transition in specification of embryonic metazoan DNA replication origins. Science 270, 994–997 (1995).
    CAS Google Scholar
  37. Sasaki, T., Sawado, T., Yamaguchi, M. & Shinomiya, T. Specification of regions of DNA replication initiation during embryogenesis in the 65-kilobase _DNApol_α-dE2F locus of Drosophila melanogaster. Mol. Cell. Biol. 19, 547–555 (1999).
    CAS PubMed PubMed Central Google Scholar
  38. Vashee, S. et al. Sequence-independent DNA binding and replication initiation by the human origin recognition complex. Genes Dev. 17, 1894–1908 (2003).
    CAS PubMed PubMed Central Google Scholar
  39. Wu, J. -R. & Gilbert, D. M. A distinct G1 step required to specify the Chinese hamster DHFR replication origin. Science 271, 1270–1272 (1996).
    CAS Google Scholar
  40. Danis, E. et al. Specification of a DNA replication origin by a transcription complex. Nature Cell Biol. 6, 721–730 (2004).
    CAS Google Scholar
  41. Kitsberg, D., Selig, S., Keshet, J. & Cedar, H. Replication structure of the human β-globin gene domain. Nature 368, 588–590 (1993).
    Google Scholar
  42. Aladjem, M. et al. Participation of the human β-globin locus control region in initiation of DNA replication. Science 270, 815–819 (1995).
    CAS Google Scholar
  43. Kalejta, R. F. et al. Distal sequences, but not ori-β/OBR-1, are essential for initiation of DNA replication in the Chinese hamster DHFR origin. Mol. Cell 2, 797–806 (1998).
    CAS Google Scholar
  44. Mesner, L. D., Li, X., Dijkwel, P. A. & Hamlin, J. L. The dihydrofolate reductase origin of replication does not contain any nonredundant genetic elements required for origin activity. Mol. Cell. Biol. 23, 804–814 (2003).
    CAS PubMed PubMed Central Google Scholar
  45. Handeli, S., Klar, A., Meuth, M. & Cedar, H. Mapping replication units in animal cells. Cell 57, 909–920 (1989).
    CAS Google Scholar
  46. Aladjem, M. I., Rodewald, L. W., Kolman, J. L. & Wahl, G. M. Genetic dissection of a mammalian replicator in the human β-globin locus. Science 281, 1005–1009 (1998).
    CAS Google Scholar
  47. Paixao, S. et al. Modular structure of the human lamin B2 replicator. Mol. Cell. Biol. 24, 2958–2967 (2004).
    CAS PubMed PubMed Central Google Scholar
  48. Wang, L. et al. The human β-globin replication initiation region consists of two modular independent replicators. Mol. Cell. Biol. 24, 3373–3386 (2004).
    CAS PubMed PubMed Central Google Scholar
  49. Liu, G., Malott, M. & Leffak, M. Multiple functional elements comprise a mammalian chromosomal replicator. Mol. Cell. Biol. 23, 1832–1842 (2003).
    CAS PubMed PubMed Central Google Scholar
  50. Altman, A. L. & Fanning, E. Defined sequence modules and an architectural element cooperate to promote initiation at an ectopic mammalian chromosomal replication origin. Mol. Cell. Biol. 24, 4138–4150 (2004).
    CAS PubMed PubMed Central Google Scholar
  51. Gavin, K., Hidaka, M. & Stillman, B. Conserved initiator proteins in eukaryotes. Science 270, 1667–1671 (1995).
    CAS Google Scholar
  52. Lee, D. G. & Bell, S. P. Architecture of the yeast origin recognition complex bound to origins of DNA replication. Mol. Cell. Biol. 17, 7159–7168 (1997).
    CAS PubMed PubMed Central Google Scholar
  53. Chuang, R. Y. & Kelly, T. J. The fission yeast homologue of Orc4p binds to replication origin DNA via multiple AT-hooks. Proc. Natl Acad. Sci. USA 96, 2656–2661 (1999).
    CAS Google Scholar
  54. Remus, D., Beall, E. L. & Botchan, M. R. DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC–DNA binding. EMBO J. 23, 897–907 (2004).
    CAS PubMed PubMed Central Google Scholar
  55. Aparicio, O. M., Weinstein, D. M. & Bell, S. P. Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phase. Cell 91, 59–69 (1997).
    CAS Google Scholar
  56. Ogawa, Y., Takahashi, T. & Masukata, H. Association of fission yeast Orp1 and Mcm6 proteins with chromosomal replication origins. Mol. Cell. Biol. 19, 7228–7236 (1999).
    CAS PubMed PubMed Central Google Scholar
  57. Bielinsky, A. K. et al. Origin recognition complex binding to a metazoan replication origin. Curr. Biol. 11, 1427–1431 (2001).
    CAS Google Scholar
  58. Austin, R. J., Orr-Weaver, T. L. & Bell, S. P. Drosophila ORC specifically binds to ACE3, an origin of DNA replication control element. Genes Dev. 13, 2639–2649 (1999).
    CAS PubMed PubMed Central Google Scholar
  59. Abdurashidova, G. et al. Localization of proteins bound to a replication origin of human DNA along the cell cycle. EMBO J. 22, 4294–4303 (2003).
    CAS PubMed PubMed Central Google Scholar
  60. Wyrick, J. J. et al. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 402, 418–421 (1999).
    CAS PubMed Google Scholar
  61. Breier, A. M., Chatterji, S. & Cozzarelli, N. R. Prediction of Saccharomyces cerevisiae replication origins. Genome Biol. 5, R22 (2004).
    PubMed PubMed Central Google Scholar
  62. Keller, C., Ladenburger, E. M., Kremer, M. & Knippers, R. The origin recognition complex marks a replication origin in the human TOP1 gene promoter. J. Biol. Chem. 277, 31430–31440 (2002).
    CAS Google Scholar
  63. Schepers, A. et al. Human origin recognition complex binds to the region of the latent origin of DNA replication of Epstein–Barr virus. EMBO J. 20, 4588–4602 (2001).
    CAS PubMed PubMed Central Google Scholar
  64. Royzman, I., Austin, R. J., Bosco, G., Bell, S. P. & Orr-Weaver, T. L. ORC localization in Drosophila follicle cells and the effects of mutations in dE2F and dDP. Genes Dev. 13, 827–840 (1999).
    CAS PubMed PubMed Central Google Scholar
  65. Bosco, G., Du, W. & Orr-Weaver, T. L. DNA replication control through interaction of E2F-RB and the origin recognition complex. Nature Cell Biol. 3, 289–295 (2001).
    CAS Google Scholar
  66. Beall, E. L., Bell, M., Georlette, D. & Botchan, M. R. Dm-myb mutant lethality in Drosophila is dependent upon mip130: positive and negative regulation of DNA replication. Genes Dev. 18, 1667–1680 (2004).
    CAS PubMed PubMed Central Google Scholar
  67. Aggarwal, B. D. & Calvi, B. R. Chromatin regulates origin activity in Drosophila follicle cells. Nature 430, 372–376 (2004).
    CAS Google Scholar
  68. Saha, S., Shan, Y., Mesner, L. D. & Hamlin, J. L. The promoter of the Chinese hamster ovary dihydrofolate reductase gene regulates the activity of the local origin and helps define its boundaries. Genes Dev. 18, 397–410 (2004).
    CAS PubMed PubMed Central Google Scholar
  69. Muller, M., Lucchini, R. & Sogo, J. M. Replication of yeast rDNA initiates downstream of transcriptionally active genes. Mol. Cell 5, 767–777 (2000).
    CAS Google Scholar
  70. Maric, C., Benard, M. & Pierron, G. Developmentally regulated usage of Physarum DNA replication origins. EMBO Rep. 4, 474–478 (2003).
    CAS PubMed PubMed Central Google Scholar
  71. Haase, S. B., Heinzel, S. S. & Calos, M. P. Transcription inhibits the replication of autonomously replicating plasmids in human cells. Mol. Cell. Biol. 14, 2516–2524 (1994).
    CAS PubMed PubMed Central Google Scholar
  72. Harvey, K. J. & Newport, J. CpG methylation of DNA restricts prereplication complex assembly in Xenopus egg extracts. Mol. Cell. Biol. 23, 6769–6779 (2003).
    CAS PubMed PubMed Central Google Scholar
  73. Rein, T., Kobayashi, T., Malott, M., Leffak, M. & DePamphilis, M. L. DNA methylation at mammalian replication origins. J. Biol. Chem. 274, 25792–25800 (1999).
    CAS Google Scholar
  74. Delgado, S., Gomez, M., Bird, A. & Antequera, F. Initiation of DNA replication at CpG islands in mammalian chromosomes. EMBO J. 17, 2426–2435 (1998).
    CAS PubMed PubMed Central Google Scholar
  75. Simpson, R. T. Nucleosome positioning can affect the function of a _cis_-acting DNA element in vivo. Nature 343, 387–389 (1990).
    CAS Google Scholar
  76. Lipford, J. R. & Bell, S. P. Nucleosomes positioned by ORC facilitate the initiation of DNA replication. Mol. Cell 7, 21–30 (2001).
    CAS Google Scholar
  77. Pasero, P., Bensimon, A. & Schwob, E. Single-molecule analysis reveals clustering and epigenetic regulation of replication origins at the yeast rDNA locus. Genes Dev. 16, 2479–2484 (2002).
    CAS PubMed PubMed Central Google Scholar
  78. Prioleau, M. N., Gendron, M. C. & Hyrien, O. Replication of the chicken β-globin locus: early-firing origins at the 5′ HS4 insulator and the ρ- and βA-globin genes show opposite epigenetic modifications. Mol. Cell. Biol. 23, 3536–3549 (2003).
    CAS PubMed PubMed Central Google Scholar
  79. Lunyak, V. V., Ezrokhi, M., Smith, H. S. & Gerbi, S. A. Developmental changes in the Sciara II/9A initiation zone for DNA replication. Mol. Cell. Biol. 22, 8426–8437 (2002).
    CAS PubMed PubMed Central Google Scholar
  80. Zhou, J. et al. The origin of a developmentally regulated Igh replicon is located near the border of regulatory domains for Igh replication and expression. Proc. Natl Acad. Sci. USA 99, 13693–13698 (2002).
    CAS Google Scholar
  81. Anglana, M., Apiou, F., Bensimon, A. & Debatisse, M. Dynamics of DNA replication in mammalian somatic cells: nucleotide pool modulates origin choice and interorigin spacing. Cell 114, 385–394 (2003).
    CAS Google Scholar
  82. Norio, P. & Schildkraut, C. L. Plasticity of DNA replication initiation in Epstein–Barr virus episomes. PLoS Biol. 2, E152 (2004).
    PubMed PubMed Central Google Scholar
  83. Tsurimoto, T., Melendy, T. & Stillman, B. Sequential initiation of lagging and leading strand synthesis by two different polymerase complexes at the SV40 DNA replication origin. Nature 346, 534–539 (1990).
    CAS PubMed Google Scholar
  84. Weinberg, D. H. et al. Reconstitution of simian virus 40 DNA replication with purified proteins. Proc. Natl Acad. Sci. USA 87, 8692–8696 (1990).
    CAS Google Scholar
  85. Bergsma, D. J., Olive, D. M., Hartzell, S. W. & Subramanian, K. N. Territorial limits and functional anatomy of the simian virus 40 replication origin. Proc. Natl Acad. Sci. USA 79, 381–385 (1982).
    CAS Google Scholar
  86. Dhar, S. K. et al. Replication from oriP of Epstein–Barr virus requires human ORC and is inhibited by geminin. Cell 106, 287–296 (2001).
    CAS Google Scholar
  87. Norio, P., Schildkraut, C. L. & Yates, J. L. Initiation of DNA replication within oriP is dispensable for stable replication of the latent Epstein–Barr virus chromosome after infection of established cell lines. J. Virol. 74, 8563–8574 (2000).
    CAS PubMed PubMed Central Google Scholar
  88. Santocanale, C. & Diffley, J. ORC- and Cdc6-dependent complexes at active and inactive chromosomal replication origins in Saccharomyces cerevisiae. EMBO J. 15, 6671–6679 (1996).
    CAS PubMed PubMed Central Google Scholar
  89. Palacios DeBeer, M. A., Müller, U. & Fox, C. A. Differential DNA affinity specifies roles for the origin recognition complex in budding yeast heterochromatin. Genes Dev. 17, 1817–1822 (2003).
    PubMed PubMed Central Google Scholar
  90. Santocanale, C., Sharma, K. & Diffley, J. F. Activation of dormant origins of DNA replication in budding yeast. Genes Dev. 13, 2360–2364 (1999).
    CAS PubMed PubMed Central Google Scholar
  91. Vujcic, M., Miller, C. A. & Kowalski, D. Activation of silent replication origins at autonomously replicating sequence elements near the HML locus in budding yeast. Mol. Cell. Biol. 19, 6098–6109 (1999).
    CAS PubMed PubMed Central Google Scholar
  92. Walter, J. & Newport, J. W. Regulation of replicon size in Xenopus egg extracts. Science 275, 993–995 (1997).
    CAS PubMed Google Scholar
  93. Beall, E. L. et al. Role for a Drosophila Myb-containing protein complex in site-specific DNA replication. Nature 420, 833–837 (2002).
    CAS Google Scholar
  94. Ehrenhofer-Murray, A., Gossen, M., Pak, D., Botchan, M. & Rine, J. Separation of origin recognition complex functions by cross-species complementation. Science 270, 1671–1674 (1995).
    CAS Google Scholar
  95. Abdurashidova, G. et al. Start sites of bidirectional DNA synthesis at the human lamin B2 origin. Science 287, 2023–2026 (2000).
    CAS Google Scholar
  96. Schaarschmidt, D., Baltin, J., Stehle, I. M., Lipps, H. J. & Knippers, R. An episomal mammalian replicon: sequence-independent binding of the origin recognition complex. EMBO J. 23, 191–201 (2004).
    CAS Google Scholar

Download references