Multiple determinants controlling activation of yeast replication origins late in S phase

Genes and Development

Volumn 10, Issue 13, 1996, Pages 1595-1607

  Friedman, Katherine L ^a   Diller, John D ^a,b   Ferguson, Betsy M ^a,c   Nyland, Sarah V M ^a   Brewer, Bonita J ^a   Fangman, Walton L ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

^c OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

Author keywords

2D agarose gels; Chromosomal domains; chromosome walk; Saccharomyces cerevisiae

Indexed keywords

DNA;

ARTICLE; CELL CYCLE S PHASE; CHROMOSOME 14; CHROMOSOME ARM; CHROMOSOME MAP; DNA FLANKING REGION; DNA REPLICATION ORIGIN; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; TELOMERE; YEAST;

SACCHAROMYCES CEREVISIAE;

EID: 0029781449     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.10.13.1595     Document Type: Article

References (60)

1. Bell, S.P. and B. Stillman. 1992. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature 357: 128-134.
2. Blow, J.J. and R.A. Laskey. 1988. A role for the nuclear envelope in controlling DNA replication within the cell cycle. Nature 332: 546-548.
3. Brewer, B.J. and W.L. Fangman. 1987. The localization of replication origins on ARS plasmids in Saccharomyces cerevisiae. Cell 51: 463-471.
4. _. 1993. Initiation at closely spaced replication origins in a yeast chromosome. Science 262: 1728-1731.
5. Brewer, B.J., D. Lockshon, and W.L. Fangman. 1992. The arrest of replication forks in the rDNA of yeast occurs independently of transcription. Cell 71: 267-276.
6. Brewer, B.J., J.D. Diller, K.L. Friedman, K.M. Kolor, M.K. Raghuraman, and W.L. Fangman. 1993. The topography of chromosome replication in yeast. Cold Spring Harbor Symp. Quant. Biol. 58: 425-434.
7. Broach, J.R., Y.Y. Li, J. Feldman, M. Jayaram, J. Abraham, K.A. Nasmyth, and J.B. Hicks. 1983. Localization and sequence analysis of yeast origins of DNA replication. Cold Spring Harbor Symp. Quant. Biol. 2: 1165-1173.
8. Carle, G.F. and M.V. Olson. 1985. An electrophoretic karyotype for yeast. Proc. Natl. Acad. Sci. 82: 3756-3760.
9. Deng, W.P. and J.A. Nickoloff. 1992. Site-directed mutagenesis of virtually any plasmid by eliminating a unique site. Anal. Biochem. 200: 81-88.
10. Deshpande, A.M. and C.S. Newlon. 1992. The ARS consensus sequence is required for chromosomal origin function in Saccharomyces cerevisiae. Mol. Cell. Biol. 12: 4305-4313.
11. Dhar, V., D. Mager, A. Iqbal, and C.L. Schildkraut. 1988. The coordinate replication of the human β-globin gene domain reflects its transcriptional activity and nuclease hypersensitivity. Mol Cell. Biol. 8: 4958-4965.
12. Diffley, J.F. and J.H. Cocker. 1992. Protein-DNA interactions at a yeast replication origin. Nature 357: 169-172.
13. Drouin, R., N. Lemieux, and C.L. Richer. 1990. Analysis of DNA replication during S phase by means of dynamic chromosome banding at high resolution. Chromosoma 99: 273-280.
14. Dubey, D.D., L.R. Davis, S.A. Greenfeder, L.Y. Ong, J.G. Zhu, J.R. Broach, C.S. Newlon, and J.A. Huberman. 1991. Evidence suggesting that the ARS elements associated with silencers of the yeast mating-type locus HML do not function as chromosomal DNA replication origins. Mol. Cell. Biol. 11:5346-5355.
15. Epner, E., W.C. Forrester, and M. Groudine. 1988. Asynchronous DNA replication within the human β-globin gene locus. Proc. Natl. Acad. Sci. 85: 8081-8085.
16. Feinberg, A.P. and B. Vogelstein. 1983. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132: 6-13.
17. Ferguson, B.M. 1990. "The origins of late replication in yeast." Ph.D. thesis, University of Washington, Seattle, WA.
18. Ferguson, B.M. and W.L. Fangman. 1992. A position effect on the time of replication origin activation in yeast. Cell 68: 333-339.
19. Ferguson, B.M., B.J. Brewer, and W.L. Fangman. 1991a. Temporal control of DNA replication in yeast. Cold Spring Harbor Symp. Quant. Biol. 56: 293-302.
20. Ferguson, B.M., B.J. Brewer, A.E. Reynolds, and W.L. Fangman. 1991b. A yeast origin of replication is activated late in S phase. Cell 65: 507-515.
21. Friedman, K.L. and B.J. Brewer. 1995. Analysis of replication intermediates by two-dimensional agarose gel electrophoresis. Methods Enzymol. 262: 613-627.
22. Gottschling, D.E., O.M. Aparicio, B.L. Billington, and V.A. Zakian. 1990. Position effect at S. cerevisiae telomeres: Reversible repression of Pol II transcription. Cell 63: 751-762.
23. Graham, I.R. and A. Chambers. 1994. Use of a selection technique to identify the diversity of binding sites for the yeast RAP1 transcription factor. Nucleic Acids Res. 22: 124-130.
24. Haber, J.E., P.C. Thorburn, and D. Rogers. 1984. Meiotic and mitotic behavior of dicentric chromosomes in Saccharomyces cerevisiae. Genetics 106: 185-205.
25. Halfter, H., U. Muller, E.L. Winnacker, and D. Gallwitz. 1989. Isolation and DNA-binding characteristics of a protein involved in transcription activation of two divergently transcribed, essential yeast genes. EMBO J. 8: 3029-3037.
26. Hand, R. 1975. Regulation of DNA replication on subchromosomal units of mammalian cells. J. Cell Biol. 64: 89-97.
27. _. 1978. Eucaryotic DNA: Organization of the genome for replication. Cell 15: 317-325.
28. Hatton, K.S., V. Dhar, E.H. Brown, M.A. Iqbal, S. Stuart, V.T. Didamo, and C.L. Schildkraut. 1988. Replication program of active and inactive multigene families in mammalian cells. Mol Cell. Biol. 8: 2149-2158.
29. Helms, C., M.Y. Graham, J.E. Dutchik, and M.V. Olson. 1985. A new method for purifying lambda DNA from phage lysates. DNA 4: 39-49.
30. Huang, R.Y. and D. Kowalski. 1993. A DNA unwinding element and an ARS consensus comprise a replication origin within a yeast chromosome. EMBO J. 12: 4521-4531.
31. Huberman, J.A., L.D. Spotila, K.A. Nawotka, S.M. El-Assouli, and L.R. Davis. 1987. The in vivo replication origin of the yeast two micron plasmid. Cell 51: 473-481.
32. Huberman, J.A., J.G. Zhu, L.R. Davis, and C.S. Newlon. 1988. 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.
33. Iwasaki, T., K. Shirahige, H. Yoshikawa, and N. Ogasawara. 1991. The direct cloning of the yeast genome using the gapfilling method and the complete physical mapping of Saccharomyces ceievisiae chromosome VI. Gene 109: 81-87.
34. Klein, F., T. Laroche, M.E. Cardenas, J.F.-X. Hofmann, D. Schweizer, and S.M. Gasser. 1992. Localization of RAP1 and topoisomerase II in nuclei and meiotic chromosomes of yeast. J. Cell Biol. 117: 935-948.
35. Louis, E.J. and J.E. Haber. 1992. The structure and evolution of subtelomeric Y' repeats in Saccharomyces cerevisiae. Genetics 131: 559-574.
36. Lyon, M.F. 1972. X-chromosome inactivation and developmental patterns in mammals. Biol. Rev. Camb. Philos. Soc. 47: 1-35.
37. Marahrens, Y. and B. Stillman. 1992. A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science 255: 817-823.
38. _. 1994. Replicator dominance in a eukaryotic chromosome. EMBO I. 13: 3395-3400.
39. McCarroll, R.M. and W.L. Fangman. 1988. Time of replication of yeast centromeres and telomeres. Cell 54: 505-513.
40. Miller, C.A. and D. Kowalski. 1993. Cis-acting components in the replication origin from ribosomal DNA of Saccharomyces ceievisiae. Mol. Cell. Biol. 13: 5360-5369.
41. Natale, D.A., A.E. Schubert, and D. Kowalski. 1992. DNA helical stability accounts for mutational defects in a yeast replication origin. Proc. Natl. Acad. Sci. 89: 2654-2658.
42. 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.
43. Newlon, C.S. and J.F. Theis. 1993. The structure and function of yeast ARS elements. Curr. Opin. Genet. Dev. 3: 752-758.
44. Newlon, C.S., L.R. Lipchitz, I. Collins, A. Deshpande, R.J. Devenish, R.P. Green, H.L. Klein, T.G. Palzkill, R.B. Ren, and S. Synn. 1991. Analysis of a circular derivative of Saccharomyces cerevisiae chromosome III: A physical map and identification and location of ARS elements [published erratum appears in Genetics 130: 235 (1992)]. Genetics 129: 343-357.
45. Olson, M.V., I.E. Dutchik, M.Y. Graham, G.M. Brodeur, C. Helms, M. Frank, M. MacCollin, R. Scheinman, and T Frank. 1986. Random-clone strategy for genomic restriction mapping in yeast. Proc. Natl. Acad. Sci. 83: 7826-7830.
46. Raghuraman, M.K., B.J. Brewer, and W.L. Fangman. 1994. Activation of a yeast replication origin near a double-stranded DNA break. Genes & Dev. 8: 554-562.
47. Rao, H., Y. Marahrens, and B. Stillman. 1994. Functional conservation of multiple elements in yeast chromosomal replicators. Mol. Cell. Biol. 14: 7643-7651.
48. Reynolds, A.E., R.M. McCarroll, C.S. Newlon, and W.L. Fangman. 1989. Time of replication of ARS elements along yeast chromosome III. Mol. Cell. Biol. 9: 4488-4494.
49. Rivier, D.H. and J. Rine. 1992. An origin of DNA replication and a transcription silencer require a common element. Science 256: 659-663.
50. Siede, W., A.S. Friedberg, and E.G. Friedberg. 1993. RAD9-dependent G1 arrest defines a second checkpoint for damaged DNA in the cell cycle of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. 90: 7985-7989.
51. Sikorski, R.S. and P. Hieter. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces ceievisiae. Genetics 122: 19-27.
52. Southern, E.M. 1975. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol 98: 503-517.
53. Stinchcomb, D.T., K. Struhl, and R.W. Davis. 1979. Isolation and characterisation of a yeast chromosomal replicator. Nature 282: 39-43.
54. Stinchcomb, D.T., C. Mann, and R.W. Davis. 1982. Centromeric DNA from Saccharomyces cerevisiae. J. Mol. Biol. 158: 157-190.
55. Theis, J.F. and C.S. Newlon. 1994. Domain B of ARS307 contains two functional elements and contributes to chromosomal replication origin function. Mol. Cell. Biol. 14: 7652-7659.
56. Van Houten, J.V. and C.S. Newlon. 1990. Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III. Mol. Cell. Biol. 10: 3917-3925.
57. Walker, S.S., S.C. Francesconi, and S. Eisenberg. 1990. A DNA replication enhancer in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. 87: 4665-4669.
58. Weinert, T.A. and L.H. Hartwell. 1988. The KADPgene controls the cell cycle response to DNA damage in Saccharomyces cerevisiae. Science 241: 317-322.
59. _. 1989. Control of G2 delay by the RAD9 gene of Saccharomyces cerevisiae. J. Cell Sci. (Suppl.) 12: 145-148.
60. 1-3 tails late in S phase. Cell 72: 51-60.