Stochastic hybrid modeling of DNA replication across a complete genome (Proceedings of the National Academy of Sciences of the United States of America (2008) 105, 34, (12295-12300) DOI 10.1073/pnas.0805549105);Stochastic hybrid modeling of DNA replication across a complete genome

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 34, 2008, Pages 12295-12300

  Lygeros, J ^a   Koutroumpas, K ^a   Dimopoulos, S ^a,b   Legouras, I ^b   Kouretas, P ^a   Heichinger, C ^c,d   Nurse, P ^c,d   Lygerou, Z ^b  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF PATRAS   (Greece)

^c ROCKEFELLER UNIVERSITY   (United States)

^d IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

Cell cycle; Fission yeast; Random gap problem; Schizosaccharomyces pombe; Systems biology

Indexed keywords

DNA;

ARTICLE; CELL CYCLE G2 PHASE; CELL CYCLE S PHASE; DNA REPLICATION; DNA SYNTHESIS; GENOMICS; MITOSIS; PRIORITY JOURNAL; SENSITIVITY ANALYSIS; SIMULATION; STOCHASTIC MODEL; YEAST;

EUKARYOTA; SCHIZOSACCHAROMYCES POMBE; SCHIZOSACCHAROMYCETACEAE;

EID: 50449107544     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0905246106     Document Type: Erratum

References (38)

1. Kornberg A, Baker T (1992) DNA replication (WH Freeman, New York) 2nd Ed.
2. DePamphilis ME (2006) DNA Replication and human disease (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York).
3. Gilbert DM (2001) Making sense of eukaryotic DNA replication origins. Science 294:96-100.
4. Costa S, Blow JJ (2007) The elusive determinants of replication origins. EMBO Rep 8:332-334.
5. DePamphilis ML (1999) Replication origins in metazoan chromosomes: Fact or fiction? Bioessays 21:5-16.
6. Gilbert DM (2004) In search of the holy replicator. Nat Rev Mol Cell Biol 5:848-855.
7. Marahrens Y, Stillman B (1992) A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science 255:817-823.
8. Theis JF, Newlon CS (1997) The ARS309 chromosomal replicator of Saccharomyces cerevisiae depends on an exceptional ARS consensus sequence. Proc Natl Acad Sci USA 94:10786-10791.
9. Harland RM, Laskey RA (1980) Regulated replication of DNA microinjected into eggs of Xenopus laevis. Cell 21:761-771.
10. Mechali M, Kearsey S (1984) Lack of specific sequence requirement for DNA replication in Xenopus eggs compared with high sequence specificity in yeast. Cell 38:55-64.
11. Krysan PJ, Calos MP (1991) Replication initiates at multiple locations on an autonomously replicating plasmid in human cells. Mol Cell Biol 11:1464-1472.
12. Heintz NH, Hamlin JL (1982) 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.
13. Kitsberg D, Selig S, Keshet I, Cedar H (1993) Replication structure of the human beta-globin gene domain. Nature 366:588-590.
14. Hyrien O, Marheineke K, Goldar A (2003) Paradoxes of eukaryotic DNA replication: MCM proteins and the random completion problem. Bioessays 25:116-125.
15. Blow JJ, Gillespie PJ, Francis D, Jackson DA (2001) Replication origins in Xenopus egg extract Are 5-15 kilobases apart and are activated in clusters that fire at different times. J Cell Biol 152:15-25.
16. Hyrien O, Mechali M (1993) Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of Xenopus early embryos. EMBO J 12:4511-4520.
17. Conti C, et al. (2007) Replication fork velocities at adjacent replication origins are coordinately modified during DNA replication in human cells. Mol Biol Cell 18:3059-3067.
18. Rhind N (2006) DNA replication timing: Random thoughts about origin firing. Nat Cell Biol 8:1313-1316.
19. Legouras I, Xouri G, Dimopoulos S, Lygeros J, Lygerou Z (2006) DNA replication in the fission yeast: Robustness in the face of uncertainty. Yeast 23:951-962.
20. Dubey DD, Kim SM, Todorov IT, Huberman JA (1996) Large, complex modular structure of a fission yeast DNA replication origin. Curr Biol 6:467-473.
21. Wood V, et al. (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415:871-880.
22. Segurado M, de Luis A, Antequera F (2003) Genome-wide distribution of DNA replication origins at A T-rich islands in Schizosaccharomyces pombe. EMBO Rep 4:1048-1053.
23. Feng W, et al. (2006) Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication. Nat Cell Biol 8:148-155.
24. Heichinger C, Penkett CJ, Bahler J, Nurse P (2006) Genome-wide characterization of fission yeast DNA replication origins. EMBO J 25:5171-5179.
25. Hayashi M, et al. (2007) Genome-wide localization of pre-RC sites and identification of replication origins in fission yeast. EMBO J 26:2821.
26. Dai J, Chuang RY, Kelly TJ (2005) DNA replication origins in the Schizosaccharomyces pombe genome. Proc Natl Acad Sci USA 102:337-342.
27. Patel PK, Arcangioli B, Baker SP, Bensimon A, Rhind N (2006) DNA replication origins fire stochastically in fission yeast. Mol Biol Cell 17:308-316.
28. Cassandras C, Lygeros JE (2006) Stochastic Hybrid Systems (CRC Press, Boca Raton).
29. Davis MHA (1993) Markov Models and Optimization (Chapman and Hall, London).
30. Nasmyth K, Nurse P, Fraser RS (1979) The effect of cell mass on the cell cycle timing and duration of S-phase in fission yeast. J Cell Sci 39:215-233.
31. Kim SM, Huberman JA (2001) Regulation of replication timing in fission yeast. EMBO J 20:6115-6126.
32. Edwards MC, et al. (2002) MCM2-7 complexes bind chromatin in a distributed pattern surrounding the origin recognition complex in Xenopus egg extracts. J Biol Chem 277:33049-33057.
33. Fantes PA, Nurse P (1978) Control of the timing of cell division in fission yeast. Exp Cell Res 115:317-329.
34. Fantes PA (1977) Control of cell size and cycle time in Schizosaccharomyces pombe. J Cell Sci 24:51-67.
35. Nurse P (1975) Genetic control of cell size at cell division in yeast. Nature 256:547-551.
36. al-Khodairy F, Carr AM (1992) DNA repair mutants defining G2 checkpoint pathways in Schizosaccharomyces pombe. EMBO J 11:1343-1350.
37. Mitchison JM, Nurse P (1985) Growth in cell length in the fission yeast Schizosaccharomyces pombe. J Cell Sci 75:357-376.
38. Sveiczer A, Novak B, Mitchison JM (1996) The size control of fission yeast revisited. J Cell Sci 109:2947-2957.