Do replication forks control late origin firing in Saccharomyces cerevisiae?

Nucleic Acids Research

Volumn 40, Issue 5, 2012, Pages 2010-2019

  Ma, Emilie ^a   Hyrien, Olivier ^b   Goldar, Arach ^a  

^a SERVICE DE CHIMIE BIOORGANIQUE ET DE MARQUAGE   (France)

^b PSL RESEARCH UNIVERSITY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN B; CYCLIN DEPENDENT KINASE; DNA;

ANIMAL CELL; ARTICLE; CELL CYCLE S PHASE; CELL TYPE; CONTROLLED STUDY; CORRELATION ANALYSIS; DNA REPLICATION; DNA REPLICATION ORIGIN; ENZYME ACTIVITY; EUKARYOTE; GENETIC VARIABILITY; MATHEMATICAL MODEL; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; WILD TYPE;

CYCLIN B; DNA REPLICATION TIMING; GENE DELETION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPLICATION ORIGIN; S PHASE; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 84855289466     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr982     Document Type: Article

References (43)

1. Huberman, J. A. and Riggs, A. D. (1968) On the mechanism of DNA replication in mammalian chromosomes. J. Mol. Biol., 32, 327-341.
2. Rhind, N., Yang, S. C.-H. and Bechhoefer, J. (2010) Reconciling stochastic origin firing with defined replication timing. Chromosome Res., 18, 35-43.
3. Yang, S. C.-H., Rhind, N. and Bechhoefer, J. (2010) Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing. Mol. Syst. Biol., 6, 404.
4. Maya-Mendoza, A., Olivares-Chauvet, P., Shaw, A. and Jackson, D. A. (2010) S phase progression in human cells is dictated by the genetic continuity of DNA foci. PLoS Genet., 6, e1000900.
5. Chagin, V. O., Stear, J. H. and Cardoso, M. C. (2010) Organization of DNA replication. Cold Spring Harb. Perspect. Biol., 2, a000737.
6. Czajkowsky, D. M., Liu, J., Hamlin, J. L. and Shao, Z. (2008) DNA combing reveals intrinsic temporal disorder in the replication of yeast chromosome VI. J. Mol. Biol., 375, 12-19.
7. Raghuraman, M. K., Winzeler, E. A., Collingwood, D., Hunt, S., Wodicka, L., Conway, A., Lockhart, D. J., Davis, R. W., Brewer, B. J. and Fangman, W. L. (2001) Replication dynamics of the yeast genome. Science, 294, 115-121.
8. Yabuki, N., Terashima, H. and Kitada, K. (2002) Mapping of early firing origins on a replication profile of budding yeast. Genes Cells, 7, 781-789.
9. Alvino, G. M., Collingwood, D., Murphy, J. M., Delrow, J., Brewer, B. J. and Raghuraman, M. K. (2007) Replication in hydroxyurea: it's a matter of time. Mol. Cell. Bio., 27, 6396-6406.
10. McCune, H. J., Danielson, L. S., Alvino, G. M., Collingwood, D., Delrow, J. J., Fangman, W. L., Brewer, B. J. and Raghuraman, M. K. (2008) The temporal program of chromosome replication: genomewide replication in clb5D Saccharomyces cerevisiae. Genetics, 180, 1833-1847.
11. Yang, S. C.-H. and Bechhoefer, J. (2008) How Xenopus laevis embryos replicate reliably: investigating the random-completion problem. Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 78(4 Pt 1), 041917.
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. Hyrien, O., Marheineke, K. and Goldar, A. (2003) Paradoxes of eukaryotic DNA replication: MCM proteins and the random completion problem. Bioessays, 25, 116-125.
14. Lucas, I., Chevrier-Miller, M., Sogo, J. M. and Hyrien, O. (2000) Mechanisms ensuring rapid and complete DNA replication despite random initiation in Xenopus early embryos. J. Mol. Biol., 296, 769-786.
15. Marheineke, K. and Hyrien, O. (2001) Aphidicolin triggers a block to replication origin firing in Xenopus egg extracts. J. Biol. Chem., 276, 17092-17100.
16. Goldar, A., Marsolier-Kergoat, M.-C. and Hyrien, O. (2009) Universal temporal profile of replication origin activation in eukaryotes. PLoS One, 4, e5899.
17. de Moura, A. P. S., Retkute, R., Hawkins, M. and Nieduszynski, C. A. (2010) Mathematical modelling of whole chromosome replication. Nucleic Acids Res., 38, 5623-5633.
18. Retkute, R., Nieduszynski, C. A. and de Moura, A. (2011) Dynamics of DNA replication in yeast. Phys. Rev. Lett., 107, 068103.
19. Gauthier, M. G. and Bechhoefer, J. (2009) Control of DNA replication by anomalous reaction-diffusion kinetics. Phys. Rev. Lett., 102, 158104.
20. Goldar, A., Labit, H., Marheineke, K. and Hyrien, O. (2008) A dynamic stochastic model for DNA replication initiation in early embryos. PLoS One, 3, e2919.
21. Hyrien, O. and Goldar, A. (2010) Mathematical modelling of eukaryotic DNA replication. Chromosome Res., 18, 147-161.
22. Labib, K. (2010) How do Cdc7 and cyclin-dependent kinases trigger the initiation of chromosome replication in eukaryotic cells? Genes Dev., 24, 1208-1219.
23. Epstein, C. B. and Cross, F. R. (1992) CLB5: a novel B cyclin from budding yeast with a role in S phase. Genes Dev., 6, 1695-1706.
24. Jackson, L. P., Reed, S. I. and Haase, S. B. (2006) Distinct mechanisms control the stability of the related S-phase cyclins Clb5 and Clb6. Mol. Cell. Biol., 26, 2456-2466.
25. Schwob, E. and Nasmyth, K. (1993) CLB5 and CLB6, a new pair of B cyclins involved in DNA replication in Saccharomyces cerevisiae. Genes Dev., 7, 1160-1175.
26. Gibson, D. G., Aparicio, J. G., Hu, F. and Aparicio, O. M. (2004) Diminished S-phase cyclin-dependent kinase function elicits vital Rad53-dependent checkpoint responses in Saccharomyces cerevisiae. Mol. Cell. Biol., 24, 10208-10222.
27. Donaldson, A. D., Raghuraman, M. K., Friedman, K. L., Cross, F. R., Brewer, B. J. and Fangman, W. L. (1998) CLB5-dependent activation of late replication origins in S. cerevisiae. Mol. Cell, 2, 173-182.
28. Vincent, J. A., Kwong, T. J. and Tsukiyama, T. (2008) ATPdependent chromatin remodeling shapes the DNA replication landscape. Nat. Struct. Mol. Biol., 15, 477-484.
29. Lengronne, A., Pasero, P. A., 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.
30. Vernis, L., Piskur, J. and Diffley, J. F. X. (2003) Reconstitution of an efficient thymidine salvage pathway in Saccharomyces cerevisiae. Nucleic Acids Res., 31, e120.
31. Sherman, F. (1991) Getting started with yeast. Methods Enzymol., 194, 3-21.
32. Sambrook, J. and Russell, D. W. (2001) Molecular Cloning. A Laboratory Manual, 3rd edn. Cold Spring Harbor Laboratory Press, New York, pp. 6-31.
33. Labit, H., Goldar, A., Guilbaud, G., Douarche, C., Hyrien, O. and Marheineke, K. (2008) A simple and optimized method of producing silanized surfaces for FISH and replication mapping on combed DNA fibers. Biotechniques, 45, 649-52, 654, 656-8.
34. Marheineke, K., Goldar, A., Krude, T. and Hyrien, O. (2009) Use of DNA combing to study DNA replication in Xenopus and human cell-free systems. Methods Mo. l Biol., 521, 575-603.
35. Sekedat, M. D., Fenyö, D., Rogers, R. S., Tackett, A. J., Aitchison, J. D. and Chait, B. T. (2010) GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome. Mol. Syst. Biol., 6, 353.
36. Bertuzzi, A., Gandolfi, A., Germani, A. and Vitelli, R. (1983) A general expression for sequential DNA-fluorescence histograms. J. Theor. Biol., 102, 55-67.
37. Zietz, S. and Nicolini, C. (1978) Biomathematics and Cell Kinetics. Elsevier/North-Holland Biomedical Press, Amsterdam, pp. 357-394.
38. Nieduszynski, C. A., ichiro Hiraga, S., Ak, P., Benham, C. J. and Donaldson, A. D. (2007) OriDB: a DNA replication origin database. Nucleic Acids Res, 35(Database issue), D40-D46.
39. Bruni, C., Koch, G. and Rossi, C. (1983) On the inverse problem in flow cytometry recovering DNA distribution from FMF data. Cell Biophys., 5, 5-19.
40. Yang, S. C. H., Gauthier, M. G. and Bechhoefer, J. (2009) Computational methods to study kinetics of DNA replication. Methods Mol. Biol., 521, 555-573.
41. Bertuzzi, A., Gandolfi, A., Germani, A. and Vitelli, R. (1983) A general expression for sequential DNA-fluorescence histograms. J. Theor. Biol., 102, 55-67.
42. Bell, G. I. and Anderson, E. C. (1967) Cell growth and division. I. A mathematical model with applications to cell volume distributions in mammalian suspension cultures. Biophys. J., 7, 329-351.
43. Bruni, C., Koch, G. and Rossi, C. (1983) On the inverse problem in flow cytometry recovering DNA distribution from FMF data. Cell Biophys., 5, 5-19.