The Rpd3-Sin3 histone deacetylase regulates replication timing and enables intra-S origin control in Saccharomyces cerevisiae

Molecular and Cellular Biology

Volumn 24, Issue 11, 2004, Pages 4769-4780

  Aparicio, Jennifer G ^a   Viggiani, Christopher J ^a   Gibson, Daniel G ^a   Aparicio, Oscar M ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; HISTONE DEACETYLASE; RPD3 PROTEIN; SIN3 PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CELL CYCLE S PHASE; CHROMATIN STRUCTURE; CONTROLLED STUDY; ENZYME ACTIVATION; FUNGAL GENE; GENE CONTROL; GENE EXPRESSION REGULATION; GENE REPLICATION; GENE SILENCING; NONHUMAN; PRIORITY JOURNAL; RPD3 GENE; SACCHAROMYCES CEREVISIAE; SIN3 GENE; TRANSCRIPTION REGULATION;

CELL CYCLE PROTEINS; DNA REPLICATION; GENE EXPRESSION REGULATION, FUNGAL; HISTONE DEACETYLASES; PROTEIN-SERINE-THREONINE KINASES; REPRESSOR PROTEINS; S PHASE; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTORS; TRANSCRIPTION INITIATION SITE;

EUKARYOTA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 2442660397     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.24.11.4769-4780.2004     Document Type: Article

References (55)

1. Aparicio, O. M. 1999. Characterization of proteins bound to chromatin by immunoprecipitation from whole-cell extracts, p. 21.3.1-21.3.12. In F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed.), Current protocols in molecular biology, vol. 4. John Wiley and Sons, Inc., New York, N.Y.
2. Aparicio, O. M., A. M. Stout, and S. P. Bell. 1999. Differential assembly of Cdc45p and DNA polymerases at early and late origins of DNA replication. Proc. Natl. Acad. Sci. USA 96:9130-9135.
3. Aparicio, O. M., D. M. Weinstein, and S. P. Bell. 1997. Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phase. Cell 91:59-69.
4. Bell, S. P. 2002. The origin recognition complex: from simple origins to complex functions. Genes Dev. 16:659-672.
5. Bernstein, B. E., J. K. Tong, and S. L. Schreiber. 2000. Genomewide studies of histone deacetylase function in yeast. Proc. Natl. Acad. Sci. USA 97:13708-13713.
6. Bickmore, W. A., and A. D. Carothers. 1995. Factors affecting the timing and imprinting of replication on a mammalian chromosome. J. Cell Sci. 108:2801-2809.
7. Burke, T. W., J. G. Cook, M. Asano, and J. R. Nevins. 2001. Replication factors MCM2 and ORC1 interact with the histone acetyltransferase HBO1. J. Biol. Chem. 276:15397-15408.
8. Cook, P. R. 1999. The organization of replication and transcription. Science 284:1790-1795.
9. Cosgrove, A. J., C. A. Nieduszynski, and A. D. Donaldson. 2002. Ku complex controls the replication time of DNA in telomere regions. Genes Dev. 16:2485-2490.
10. Davie, J. K., R. J. Trumbly, and S. Y. Dent. 2002. Histone-dependent association of Tup1-Ssn6 with repressed genes in vivo. Mol. Cell. Biol. 22:693-703.
11. Diffley, J. F., J. H. Cocker, S. J. Dowell, and A. Rowley. 1994. Two steps in the assembly of complexes at yeast replication origins in vivo. Cell 78:303-316.
12. 1 phase. Mol. Cell 4:983-993.
13. Donaldson, A. D., M. K. Raghuraman, K. L. Friedman, F. R. Cross, B. J. Brewer, and W. L. Fangman. 1998. CLB5-dependent activation of late replication origins in S. cerevisiae. Mol. Cell 2:173-182.
14. Dubey, D. D., L. R. Davis, S. A. Greenfeder, L. Y. Ong, J. G. Zhu, J. R. Broach, C. S. Newton, 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. Ehrenhofer-Murray, A. E., D. H. Rivier, and J. Rine. 1997. The role of Sas2, an acetyltransferase homologue of Saccharomyces cerevisiae, in silencing and ORC function. Genetics 145:923-934.
16. Epstein, C. B., and F. R. Cross. 1992. CLB5: a novel B cyclin from budding yeast with a role in S phase. Genes Dev. 6:1695-1706.
17. Fangman, W. L., and B. J. Brewer. 1992. A question of time: replication origins of eukaryotic chromosomes. Cell 71:363-366.
18. Friedman, K. L., J. D. Diller, B. M. Ferguson, S. V. Nyland, B. J. Brewer, and W. L. Fangman. 1996. Multiple determinants controlling activation of yeast replication origins late in S phase. Genes Dev. 10:1595-1607.
19. Gavin, A. C., M. Bosche, R. Krause, P. Grandi, M. Marzioch, A. Bauer, J. Schultz, J. M. Rick, A. M. Michon, C. M. Cruciat, M. Remor, C. Hofert, M. Schelder, M. Brajenovic, H. Ruffner, A. Merino, K. Klein, M. Hudak, D. Dickson, T. Rudi, V. Gnau, A. Bauch, S. Bastuck, B. Huhse, C. Leutwein, M. A. Heurtier, R. R. Copley, A. Edelmann, E. Querfurth, V. Rybin, G. Drewes, M. Raida, T. Bouwmeester, P. Bork, B. Seraphin, B. Kuster, G. Neubauer, and G. Superti-Furga. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141-147.
20. Gilbert, D. M. 2001. Making sense of eukaryotic DNA replication origins. Science 294:96-100.
21. Gilbert, D. M. 2002. Replication timing and transcriptional control: beyond cause and effect. Curr. Opin. Cell Biol. 14:377-383.
22. Heun, P., T. Laroche, M. K. Raghuraman, and S. M. Gasser. 2001. The positioning and dynamics of origins of replication in the budding yeast nucleus. J. Cell Biol. 152:385-400.
23. Iizuka, M., and B. Stillman. 1999. Histone acetyltransferase HBO1 interacts with the ORC1 subunit of the human initiator protein. J. Biol. Chem. 274:23027-23034.
24. Kadosh, D., and K. Struhl. 1997. Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell 89:365-371.
25. Kuhne, C., and P. Linder. 1993, A new pair of B-type cyclins from Saccharomyces cerevisiae that function early in the cell cycle. EMBO J. 12:3437-3447.
26. Kurdistani, S. K., D. Robyr, S. Tavazoie, and M. Grunstein. 2002. Genomewide binding map of the histone deacetylase Rpd3 in yeast. Nat. Genet. 31:248-254.
27. Mallory, M. J., and R. Strich. 2003. Umelp represses meiotic gene transcription in Saccharomyces cerevisiae through interaction with the histone deacetylase Rpd3p. J. Biol. Chem. 278:44727-44734.
28. McCarroll, R. M., and W. L. Fangman. 1988. Time of replication of yeast centromeres and telomeres. Cell 54:505-513.
29. Melo, J., and D. Toczyski. 2002. A unified view of the DNA-damage checkpoint. Curr. Opin. Cell Biol. 14:237-245.
30. Newlon, C. S., I. Collins, A. Dershowitz, A. M. S. Deshpande, S. A. Greenfeder, L. Y. Ong, and J. F. Theis. 1993. Analysis of replication origin function in chromosome III of Saccharomyces cerevisiae. Cold Spring Harbor Symp. Quant. Biol. 58:415-423.
31. 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.
32. Paulovich, A. G., and L. H. Hartwell. 1995. A checkpoint regulates the rate of progression through S phase in S. cerevisiae in response to DNA damage. Cell 82:841-847.
33. Pellicioli, A., C. Lucca, G. Liberi, F. Marini, M. Lopes, P. Plevani, A. Romano, P. P. Di Fiore, and M. Foiani. 1999. Activation of Rad53 kinase in response to DNA damage and its effect in modulating phosphorylation of the lagging strand DNA polymerase. EMBO J. 18:6561-6572.
34. Pemberton, L. F., and G. Blobel. 1997. Characterization of the Wtm proteins, a novel family of Saccharomyces cerevisiae transcriptional modulators with roles in meiotic regulation and silencing. Mol. Cell. Biol. 17:4830-4841.
35. Raghuraman, M. K., B. J. Brewer, and W. L. Fangman. 1997. Cell cycle-dependent establishment of a late replication program. Science 276:806-809.
36. Raghuraman, M. K., E. A. Winzeler, D. Collingwood, S. Hunt, L. Wodicka, A. Conway, D. J. Lockhart, R. W. Davis, B. J. Brewer, and W. L. Fangman. 2001. Replication dynamics of the yeast genome. Science 294:115-121.
37. Robyr, D., Y. Suka, I. Xenarios, S. K. Kurdistani, A. Wang, N. Suka, and M. Grunstein. 2002. Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell 109:437-446.
38. Rundlett, S. E., A. A. Carmen, N. Suka, B. M. Turner, and M. Grunstein. 1998. Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3. Nature 392:831-835.
39. Rusche, L. N., A. L. Kirchmaier, and J. Rine. 2003. The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu. Rev. Biochem. 72:481-516.
40. Sanchez, Y., B. A. Desany, W. J. Jones, Q. Liu, B. Wang, and S. J. Elledge. 1996. Regulation of RAD53 by the ATM-like kinases MECI and TEL1 in yeast cell cycle checkpoint pathways. Science 271:357-360.
41. Santocanale, C., and J. F. Diffley. 1998. A Mec1- and Rad53-dependent checkpoint controls late-firing origins of DNA replication. Nature 395:615-618.
42. Schwob, E., and K. Nasmyth. 1993. CLB5 and CLB6, a new pair of B cyclins involved in DNA replication in Saccharomyces cerevisiae. Genes Dev. 7:1160-1175.
43. Shirahige, K., Y. Hori, K. Shiraishi, M. Yamashita, K. Takahashi, C. Obuse, T. Tsurimoto, and H. Yoshikawa. 1998. Regulation of DNA-replication origins during cell-cycle progression. Nature 395:618-621.
44. Stevenson, J. B., and D. E. Gottschling. 1999. Telomeric chromatin modulates replication timing near chromosome ends. Genes Dev. 13:146-151.
45. Struhl, K. 1998. Histone acetylation and transcriptional regulatory mechanisms. Genes Dev. 12:599-606.
46. Suka, N., Y. Suka, A. A. Carmen, J. Wu, and M. Grunstein. 2001. Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin. Mol. Cell 8:473-479.
47. Sun, Z., D. S. Fay, F. Marini, M. Foiani, and D. F. Stern. 1996. Spk1/Rad53 is regulated by Mec1-dependent protein phosphorylation in DNA replication and damage checkpoint pathways. Genes Dev. 10:395-406.
48. Tercero, J. A., and J. F. Diffley. 2001. Regulation of DNA replication fork progression through damaged DNA by the Mec1/Rad53 checkpoint. Nature 412:553-557.
49. Tercero, J. A., M. P. Longhese, and J. F. Diffley. 2003. A central role for DNA replication forks in checkpoint activation and response. Mol. Cell 11:1323-1336.
50. Vogelauer, M., L. Rubbi, I. Lucas, B. J. Brewer, and M. Grunstein. 2002. Histone acetylation regulates the time of replication origin firing. Mol. Cell 10:1223-1233.
51. Wach, A., A. Brachat, R. Pohlmann, and P. Philippsen. 1994. New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast 10:1793-1808.
52. Watson, A. D., D. G. Edmondson, J. R. Bone, Y. Mukai, Y. Yu, W. Du, D. J. Stillman, and S. Y. Roth. 2000. Ssn6-Tup1 interacts with class I histone deacetylases required for repression. Genes Dev. 14:2737-2744.
53. Williams, R. M., M. Primig, B. K. Washburn, E. A. Winzeler, M. Bellis, C. Sarrauste de Menthiere, R. W. Davis, and R. E. Esposito. 2002. The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast. Proc. Natl. Acad. Sci. USA 99:13431-13436.
54. Wyrick, J. J., J. G. Aparicio, T. Chen, J. D. Barnett, E. G. Jennings, R. A. Young, S. P. Bell, and O. M. Aparicio. 2001. Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science 294:2357-2360.
55. Zappulla, D. C., R. Sternglanz, and J. Leatherwood. 2002. Control of replication timing by a transcriptional silencer. Curr. Biol. 12:869-875.