Single-molecule analysis reveals clustering and epigenetic regulation of replication origins at the yeast rDNA locus

Genes and Development

Volumn 16, Issue 19, 2002, Pages 2479-2484

  Pasero, Philippe ^a   Bensimon, Aaron ^b   Schwob, Etienne ^a  

^a INSTITUT DE GÉNÉTIQUE MOLÉCULAIRE DE MONTPELLIER   (France)

^b INSTITUT PASTEUR   (France)

Author keywords

Aging; DNA combing; DNA replication; Recombination; Sir2

Indexed keywords

HISTONE DEACETYLASE; RIBOSOME DNA;

ARTICLE; DNA RECOMBINATION; DNA REPLICATION ORIGIN; EUKARYOTE; GENE CLUSTER; GENE LOCUS; GENE REPRESSION; GENETIC REGULATION; GENOME; MUTANT; NONHUMAN; PRIORITY JOURNAL; YEAST;

DNA REPLICATION; DNA, FUNGAL; DNA, RIBOSOMAL; HISTONE DEACETYLASES; REPETITIVE SEQUENCES, NUCLEIC ACID; REPLICATION ORIGIN; SACCHAROMYCES CEREVISIAE; SILENT INFORMATION REGULATOR PROTEINS, SACCHAROMYCES CEREVISIAE; SIRTUINS;

EUKARYOTA;

EID: 0036791653     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.232902     Document Type: Article

References (37)

1. Brewer, B.J. and Fangman, W.L. 1987. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell 51: 463-471.
2. -. 1988. A replication fork barrier at the 3′ end of yeast ribosomal RNA genes. Cell 55: 637-643.
3. Cimbora, D.M. and Groudine, M. 2001. The control of mammalian DNA replication: A brief history of space and timing. Cell 104: 643-646.
4. Defossez, P.A., Prusty, R., Kaeberlein, M., Lin, S.J., Ferrigno, P., Silver, P.A., Keil, R.L., and Guarente, L. 1999. Elimination of replication block protein Fob1 extends the life span of yeast mother cells. Mol. Cell 3: 447-455.
5. Defossez, P.A., Lin, S.J., and McNabb, D.S. 2001. Sound silencing: The Sir2 protein and cellular senescence. Bioessays 23: 327-332.
6. Fangman, W.L. and Brewer, B.J. 1991. Activation of replication origins within yeast chromosomes. Annu. Rev. Cell Biol. 7: 375-402.
7. Fritze, C.E., Verschueren, K., Strich, R., and Easton Esposito, R. 1997. Direct evidence for SIR2 modulation of chromatin structure in yeast rDNA. EMBO J. 16: 6495-6509.
8. Gasser, S.M. and Cockell, M.M. 2001. The molecular biology of the SIR proteins. Gene 279: 1-16.
9. Gerbi, S.A. and Bielinsky, A.K. 2002. DNA replication and chromatin. Curr. Opin. Genet. Dev. 12: 243-248.
10. Gotta, M., Strahl-Bolsinger, S., Renauld, H., Laroche, T., Kennedy, B.K., Grunstein, M., and Gasser, S.M. 1997. Localization of Sir2p: The nucleolus as a compartment for silent information regulators. EMBO J. 16: 3243-3255.
11. Guarente, L. 2000. Sir2 links chromatin silencing, metabolism, and aging. Genes & Dev. 14: 1021-1026.
12. Herrick, J., Stanislawski, P., Hyrien, O., and Bensimon, A. 2000. Replication fork density increases during DNA synthesis in X. laevis egg extracts. J. Mol. Biol. 300: 1133-1142.
13. Heun, P., Laroche, T., Raghuraman, M.K., and Gasser, S.M. 2001. The positioning and dynamics of origins of replication in the budding yeast nucleus. J. Cell Biol. 152: 385-400.
14. Hoppe, G.J., Tanny, J.C., Rudner, A.D., Gerber, S.A., Danaie, S., Gygi, S.P., and Moazed, D. 2002. Steps in assembly of silent chromatin in yeast: Sir3-independent binding of a Sir2/Sir4 complex to silencers and role for Sir2-dependent deacetylation. Mol. Cell. Biol. 22: 4167-4180.
15. Hyrien, O. 2000. Mechanisms and consequences of replication fork arrest. Biochimie 82: 5-17.
16. Imai, S., Armstrong, C.M., Kaeberlein, M., and Guarente, L. 2000. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403: 795-800.
17. Ivessa, A.S., Zhou, J.Q., and Zakian, V.A. 2000. The Saccharomyces Pif1p DNA helicase and the highly related Rrm3p have opposite effects on replication fork progression in ribosomal DNA. Cell 100: 479-489.
18. Johzuka, K. and Horiuchi, T. 2002. Replication fork block protein, Fob1, acts as an rDNA region specific recombinator in S. cerevisiae. Genes Cells 7: 99-113.
19. Kaeberlein, M., McVey, M., and Guarente, L. 1999. The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. Genes & Dev. 13: 2570-2580.
20. Kim, S.-M. and Huberman, J.A. 2001. Regulation of replication timing in fission yeast. EMBO J. 20: 6115-6126.
21. Kobayashi, T. and Horiuchi, T. 1996. A yeast gene product, Fob1 protein, required for both replication fork blocking and recombinational hotspot activities. Genes Cells 1: 465-474.
22. Kobayashi, T., Heck, D.J., Nomura, M., and Horiuchi, T. 1998. Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: Requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I. Genes & Dev. 12: 3821-3830.
23. Lengronne, A., Pasero, P., Bensimon, A., and Schwob, E. 2001. Monitoring S phase progression globally and locally using BrdU incorporation in TK(+) yeast strains. Nucleic Acids Res. 29: 1433-1442.
24. Liang, C., Weinreich, M., and Stillman, B. 1995. ORC and Cdc6p interact and determine the frequency of initiation of DNA replication in the genome. Cell 81: 667-676.
25. Linskens, M.H. and Huberman, J.A. 1988. Organization of replication of ribosomal DNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 8: 4927-4935.
26. Méchali, M. 2001. DNA replication origins: From sequence specificity to epigenetics. Nat. Rev. Genet. 2: 640-645.
27. Michalet, X., Ekong, R., Fougerousse, F., Rousseaux, S., Schurra, C., Hornigold, N., van Slegtenhorst, M., Wolfe, J., Povey, S., Beckmann, J.S., et al. 1997. Dynamic molecular combing: Stretching the whole human genome for high-resolution studies. Science 277: 1518-1523.
28. Muller, M., Lucchini, R., and Sogo, J.M. 2000. Replication of yeast rDNA initiates downstream of transcriptionally active genes. Mol. Cell 5: 767-777.
29. Pasero, P. and Schwob, E. 2000. Think global, act local - How to regulate S phase from individual replication origins. Curr. Opin. Genet. Dev. 10: 178-186.
30. Perez-Martin, J., Uria, J.A., and Johnson, A.D. 1999. Phenotypic switching in Candida albicans is controlled by a SIR2 gene. EMBO J. 18: 2580-2592.
31. Rose, M.D., Winston, F., and Hieter, P. 1990. Methods in yeast genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
32. Rothstein, R., Michel, B., and Gangloff, S. 2000. Replication fork pausing and recombination or "gimme a break." Genes & Dev. 14: 1-10.
33. Saffer, L.D. and Miller, O.L., Jr. 1986. Electron microscopic study of Saccharomyces cerevisiae rDNA chromatin replication. Mol. Cell. Biol. 6: 1148-1157.
34. Stevenson, J.B. and Gottschling, D.E. 1999. Telomeric chromatin modulates replication timing near chromosome ends. Genes & Dev. 13: 146-151.
35. Walmsley, R.M., Johnston, L.H., Williamson, D.H., and Oliver, S.G. 1984. Replicon size of yeast ribosomal DNA. Mol. Gen. Genet. 195: 260-266.
36. Ward, T.R., Hoang, M.L., Prusty, R., Lau, C.K., Keil, R.L., Fangman, W.L., and Brewer, B.J. 2000. Ribosomal DNA replication fork barrier and HOT1 recombination hot spot: Shared sequences but independent activities. Mol. Cell. Biol. 20: 4948-4957.
37. Zou, H. and R. Rothstein. 1997. Holliday junctions accumulate in replication mutants via a RecA homolog-independent mechanism. Cell 90: 87-96.