What influences DNA replication rate in budding yeast?

PLoS ONE

Volumn 5, Issue 4, 2010, Pages

  Spiesser, Thomas W ^a   Diener, Christian ^a   Barberis, Matteo ^a,b   Klipp, Edda ^a  

^a HUMBOLDT UNIVERSITY   (Germany)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DNA REPLICATION; DNA SEQUENCE; DNA STRUCTURE; DNA SYNTHESIS; DNA TEMPLATE; FUNGAL GENOME; FUNGUS GROWTH; NONHUMAN; PREDICTION; STOCHASTIC MODEL; DNA REPLICATION ORIGIN; GENETICS; KINETICS; METABOLISM; MOVEMENT (PHYSIOLOGY); SACCHAROMYCETALES; THEORETICAL MODEL;

SACCHAROMYCETALES;

DNA DIRECTED DNA POLYMERASE; FUNGAL DNA;

DNA REPLICATION; DNA, FUNGAL; DNA-DIRECTED DNA POLYMERASE; KINETICS; MODELS, THEORETICAL; MOVEMENT; REPLICATION ORIGIN; SACCHAROMYCETALES;

EID: 77956564182     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0010203     Document Type: Article

References (45)

1. Stinchcomb DT, Struhl K, Davis RW (1979) Isolation and characterisation of a yeast chromosomal replicator. Nature 282: 39-43.
2. Zannis-Hadjopoulos M, Price GB (1998) Regulatory parameters of dna replication. Crit Rev Eukaryot Gene Expr 8: 81-106.
3. Françon P, Maiorano D, Méchali M (1999) Initiation of dna replication in eukaryotes: questioning the origin. FEBS Lett 452: 87-91.
4. Dutta A, Bell SP (1997) Initiation of dna replication in eukaryotic cells. Annu Rev Cell Dev Biol 13: 293-332.
5. Bell SP, Dutta A (2002) Dna replication in eukaryotic cells. Annu Rev Biochem 71: 333-374.
6. Weigel C, Schmidt A, Ruckert B, Lurz R, Messer W (1997) Dnaa protein binding to individual dnaa boxes in the escherichia coli replication origin, oric. EMBO J 16: 6574-6583.
7. Stillman B (2005) Origin recognition and the chromosome cycle. FEBS Lett 579: 877-884.
8. Aparicio OM, Stout AM, Bell SP (1999) Differential assembly of cdc45p and dna polymerases at early and late origins of dna replication. Proc Natl Acad Sci U S A 96: 9130-9135.
9. Zou L, Stillman B (2000) Assembly of a complex containing cdc45p, replication protein a, and mcm2p at replication origins controlled by s-phase cyclindependent kinases and cdc7p-dbf4p kinase. Mol Cell Biol 20: 3086-3096.
10. Nguyen VQ, Co C, Irie K, Li JJ (2000) Clb/cdc28 kinases promote nuclear export of the replication initiator proteins mcm2-7. Curr Biol 10: 195-205.
11. Francis LI, Randell JCW, Takara TJ, Uchima L, Bell SP (2009) Incorporation into the prereplicative complex activates the mcm2-7 helicase for cdc7-dbf4 phosphorylation. Genes Dev 23: 643-654.
12. Takeda DY, Dutta A (2005) Dna replication and progression through s phase. Oncogene 24: 2827-2843.
13. Nick-McElhinny SA, Gordenin DA, Stith CM, Burgers PMJ, Kunkel TA (2008) Division of labor at the eukaryotic replication fork. Mol Cell 30: 137-144.
14. Okazaki R, Okazaki T, Sakabe K, Sugimoto K (1967) Mechanism of dna replication possible discontinuity of dna chain growth. Jpn J Med Sci Biol 20: 255-260.
15. Ogawa T, Okazaki T (1980) Discontinuous dna replication. Annu Rev Biochem 49: 421-457.
16. Kunkel TA, Burgers PM (2008) Dividing the workload at a eukaryotic replication fork. Trends Cell Biol 18: 521-527.
17. Burgers PMJ (2009) Polymerase dynamics at the eukaryotic dna replication fork. J Biol Chem 284: 4041-4045.
18. Raghuraman MK, Winzeler EA, Collingwood D, Hunt S, Wodicka L, et al. (2001) Replication dynamics of the yeast genome. Science 294: 115-121.
19. Wintersberger E (2000) Why is there late replication? Chromosoma 109: 300-307.
20. Zhang Z, Shibahara K, Stillman B (2000) Pcna connects dna replication to epigenetic inheritance in yeast. Nature 408: 221-225.
21. Ji N, Allshire RC, Klar AJ, Grewal SI (2001) A role for dna polymerase alpha in epigenetic control of transcriptional silencing in fission yeast. EMBO J 20: 2857-2866.
22. Mechali M (2001) Dna replication origins: from sequence specificity to epigenetics. Nat Rev Genet 2: 640-645.
23. Pasero P, Bensimon A, Schwob E (2002) Single-molecule analysis reveals clustering and epigenetic regulation of replication origins at the yeast rdna locus. Genes Dev 16: 2479-2484.
24. Antequera F (2004) Genomic specification and epigenetic regulation of eukaryotic dna replication origins. EMBO J 23: 4365-4370.
25. Zhou J, Chau C, Deng Z, Stedman W, Lieberman PM (2005) Epigenetic control of replication origins. Cell Cycle 4: 889-892.
26. Hamlin JL, Mesner LD, Lar O, Torres R, Chodaparambil SV, et al. (2008) A revisionist replicon model for higher eukaryotic genomes. J Cell Biochem 105: 321-329.
27. Tabancay AP, Forsburg SL (2006) Eukaryotic dna replication in a chromatin context. Curr Top Dev Biol 76: 129-184.
28. Kohzaki H, Ito Y, Murakami Y (1999) Context-dependent modulation of replication activity of saccharomyces cerevisiae autonomously replicating sequences by transcription factors. Mol Cell Biol 19: 7428-7435.
29. Nieduszynski CA, Blow JJ, Donaldson AD (2005) The requirement of yeast replication origins for pre-replication complex proteins is modulated by transcription. Nucleic Acids Res 33: 2410-2420.
30. Mori S, Shirahige K (2007) Perturbation of the activity of replication origin by meiosis-specific transcription. J Biol Chem 282: 4447-4452.
31. Lucchini R, Sogo JM (1994) Chromatin structure and transcriptional activity around the replication forks arrested at the 39 end of the yeast rrna genes. Mol Cell Biol 14: 318-326.
32. Deshpande AM, Newlon CS (1996) Dna replication fork pause sites dependent on transcription. Science 272: 1030-1033.
33. Wellinger RE, Prado F, Aguilera A (2006) Replication fork progression is impaired by transcription in hyperrecombinant yeast cells lacking a functional tho complex. Mol Cell Biol 26: 3327-3334.
34. Chabes A, Stillman B (2007) Constitutively high dntp concentration inhibits cell cycle progression and the dna damage checkpoint in yeast saccharomyces cerevisiae. Proc Natl Acad Sci U S A 104: 1183-1188.
35. Pruitt KD, Tatusova T, Maglott DR (2007) Ncbi reference sequences (refseq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35: D61-D65.
36. Kirkpatrick S, Gelatt CD, Vecchi MP (1983) Optimization by simulated annealing. Science 220: 671-680.
37. Zhu C, Byrd RH, Lu P, Nocedal J (1997) Algorithm 778: L-bfgs-b: Fortran subroutines for large-scale bound-constrained optimization. ACM Trans Math Softw 23: 550-560.
38. Spearman C (1987) The proof and measurement of association between two things. The American Journal of Psychology 100: 441-471.
39. Holm S (1979) A simple sequentially rejective multiple test procedure. Scand J Stat 6: 65-70.
40. Akaike H (1974) A new look at the statistical model identification. IEEE Trans Autom 19: 716-723.
41. R-Development-Core-Team (2008) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0.
42. Spiesser TW, Klipp E, Barberis M (2009) A model for the spatiotemporal organization of dna replication in saccharomyces cerevisiae. Mol Genet Genomics 282: 25-35.
43. Donaldson AD, Raghuraman MK, Friedman KL, Cross FR, Brewer BJ, et al. (1998) Clb5-dependent activation of late replication origins in s. cerevisiae. Mol Cell 2: 173-182.
44. McCune HJ, Danielson LS, Alvino GM, Collingwood D, Delrow JJ, et al. (2008) The temporal program of chromosome replication: genome-wide replication in clb5Delta saccharomyces cerevisiae. Genetics 180: 1833-1847.
45. Hiraga SI, Hagihara-Hayashi A, Ohya T, Sugino A (2005) Dna polymerases alpha, delta, and epsilon localize and function together at replication forks in saccharomyces cerevisiae. Genes Cells 10: 297-309.