The spatiotemporal program of replication in the genome of Lachancea kluyveri

Genome Biology and Evolution

Volumn 5, Issue 2, 2013, Pages 370-388

  Agier, Nicolas ^a   Romano, Orso Maria ^b   Touzain, Fabrice ^a,c   Lagomarsino, Marco Cosentino ^a   Fischer, Gilles ^a  

^a UMR 7238   (France)

^b UNIVERSITY OF MILAN   (Italy)

^c FRENCH AGENCY FOR FOOD   (France)

Author keywords

ACS; GC content; GC skew; Lachancea kluyveri; Replication; Saccharomyces cerevisiae

Indexed keywords

LACHANCEA; SACCHAROMYCES CEREVISIAE;

EID: 84876570536     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evt014     Document Type: Article

References (63)

1. Agier N, Fischer G. 2012. The mutational profile of the yeast genome is shaped by replication. Mol Biol Evol. 29:905-913.
2. Alvino GM, Collingwood D, Murphy JM, Delrow J, Brewer BJ, Raghuraman MK. 2007. Replication in hydroxyurea: it's a matter of time. Mol Cell Biol. 27:6396-6406.
3. Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27:573-580.
4. Bernardi G. 2007. The neoselectionist theory of genome evolution. Proc Natl Acad Sci U S A. 104:8385-8390.
5. Bernardi G, et al. 1985. Themosaic genome of warm-blooded vertebrates. Science 228:953-958.
6. Bradnam KR, Seoighe C, Sharp PM, Wolfe KH. 1999. G+C content variation along and among Saccharomyces cerevisiae chromosomes. Mol Biol Evol. 16:666-675.
7. Butler G, et al. 2004. Evolution of the MAT locus and its Ho endonuclease in yeast species. Proc Natl Acad Sci U S A. 101:1632-1637.
8. Chen CL, et al. 2010. Impact of replication timing on non-CpG and CpG substitution rates inmammalian genomes. Genome Res. 20:447-457.
9. Chen CL, et al. 2011. Replication-associated mutational asymmetry in the human genome. Mol Biol Evol. 28:2327-2337.
10. Czajkowsky DM, Liu J, Hamlin JL, Shao Z. 2008. DNA combing reveals intrinsic temporal disorder in the replication of yeast chromosome VI. J Mol Biol. 375:12-19.
11. de Moura AP, Retkute R, Hawkins M, Nieduszynski CA. 2010. Mathematical modelling of whole chromosome replication. Nucleic Acids Res. 38:5623-5633.
12. Di Rienzi SC, Collingwood D, Raghuraman MK, Brewer BJ. 2009. Fragile genomic sites are associated with origins of replication. Genome Biol Evol. 1:350-363.
13. Di Rienzi SC, et al. 2012. Maintaining replication origins in the face of genomic change. Genome Res. 22:1940-1952.
14. Drillon G, Carbone A, Fischer G. 2011. Combinatorics of chromosomal rearrangements based on synteny blocks and synteny packs. J Logic Comput., doi:10.1093/logcom/exr047
15. Dujon B. 1996. The yeast genome project: what did we learn? Trends Genet. 12:263-270.
16. Duret L, Galtier N. 2009. Biased gene conversion and the evolution of mammalian genomic landscapes. Annu Rev Genomics Hum Genet. 10:285-311.
17. Fabre E, et al. 2005. Comparative genomics in hemiascomycete yeasts: evolution of sex, silencing, and subtelomeres. Mol Biol Evol. 22: 856-873.
18. Gé nolevures Consortium, et al. 2009. Comparative genomics of protoploid Saccharomycetaceae. Genome Res. 19:1696-1709.
19. Gordon JL, Byrne KP, Wolfe KH. 2009. Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome. PLoS Genet. 5:e1000485.
20. Green P, Ewing B, Miller W, Thomas PJ, Green ED. 2003. Transcriptionassociated mutational asymmetry inmammalian evolution. Nat Genet. 33:514-517.
21. Gu X, Li WH. 1994. A model for the correlation of mutation rate with GC content and the origin of GC-rich isochores. J Mol Evol. 38:468-475.
22. Karnani N, Taylor C,Malhotra A, Dutta A. 2007. Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas. Genome Res. 17:865-876.
23. Koren A, et al. 2010. Epigenetically-inherited centromere and neocentromere DNA replicates earliest in S-phase. PLoS Genet. 6:e1001068.
24. Kreutzer DA, Essigmann JM. 1998. Oxidized, deaminated cytosines are a source of C ! T transitions in vivo. Proc Natl Acad Sci U S A. 95: 3578-3582.
25. Kurtzman CP. 2003. Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora. FEMS Yeast Res. 4: 233-245.
26. Lang GI, Murray AW. 2008. Estimating the per-base-pair mutation rate in the yeast Saccharomyces cerevisiae. Genetics 178:67-82.
27. Lang GI, Murray AW. 2011. Mutation rates across budding yeast chromosome VI are correlated with replication timing. Genome Biol Evol. 3: 799-811.
28. Liachko I, et al. 2010. A comprehensive genome-wide map of autonomously replicating sequences in a naive genome. PLoS Genet. 6: e1000946.
29. Liachko I, et al. 2011. Novel features of ARS selection in budding yeast Lachancea kluyveri. BMC Genomics 12:633.
30. Luo H, Li J, Eshaghi M, Liu J, Karuturi RK. 2010. Genome-wide estimation of firing efficiencies of origins of DNA replication from time-course copy number variation data. BMC Bioinformatics 11:247.
31. Lynch M, et al. 2008. A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc Natl Acad Sci U S A. 105:9272-9277.
32. MacAlpine DM, Rodriguez HK, Bell SP. 2004. Coordination of replication and transcription along a Drosophila chromosome. Genes Dev. 18: 3094-3105.
33. Mancera E, Bourgon R, Brozzi A, Huber W, Steinmetz LM. 2008. High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature 454:479-485.
34. Marsolier-Kergoat MC. 2012. Asymmetry indices for analysis and prediction of replication origins in eukaryotic genomes. PLoS One 7:e45050.
35. Marsolier-Kergoat MC, Goldar A. 2012. DNA replication induces compositional biases in yeast. Mol Biol Evol. 29:893-904.
36. Marsolier-Kergoat MC, Yeramian E. 2009. GC content and recombination: reassessing the causal effects for the Saccharomyces cerevisiae genome. Genetics 183:31-38.
37. McCune HJ, et al. 2008. The temporal program of chromosome replication: genome-wide replication in clb5{Delta} Saccharomyces cerevisiae. Genetics 180:1833-1847.
38. Mugal CF, von Grunberg HH, Peifer M. 2009. Transcription-induced mutational strand bias and its effect on substitution rates in human genes. Mol Biol Evol. 26:131-142.
39. Muller CA, Nieduszynski CA. 2012. Conservation of replication timing reveals global and local regulation of replication origin activity. Genome Res. 22:1953-1962.
40. Muller H, Hennequin C, Dujon B, Fairhead C. 2007. Comparing MAT in the genomes of hemiascomycetous yeasts. In: Heitman J, Kronstad J, Taylor J, Casselton L, editors. Sex in fungi: molecular determination and evolutionary implications. Washington, DC: ASM Press.
41. Ng P, Keich U. 2008. GIMSAN: a Gibbs motif finder with significance analysis. Bioinformatics 24:2256-2257.
42. Nishant KT, et al. 2010. The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis. PLoS Genet. 6:e1001109.
43. Payen C, et al. 2009. Unusual composition of a yeast chromosome arm is associated with its delayed replication. Genome Res. 19:1710-1721.
44. Polak P, Arndt PF. 2008. Transcription induces strand-specific mutations at the 5' end of human genes. Genome Res. 18:1216-1223.
45. Pretlow TG 2nd, Pretlow TP. 1979. Centrifugal elutriation (counterstreaming centrifugation) of cells. Cell Biophys. 1:195-210.
46. Raghuraman MK, et al. 2001. Replication dynamics of the yeast genome. Science 294:115-121.
47. Ruderfer DM, Pratt SC, Seidel HS, Kruglyak L. 2006. Population genomic analysis of outcrossing and recombination in yeast. Nat Genet. 38: 1077-1081.
48. Sekedat MD, et al. 2010. GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome. Mol Syst Biol. 6: 353.
49. Sharp PM, Lloyd AT. 1993. Regional base composition variation along yeast chromosome III: evolution of chromosome primary structure. Nucleic Acids Res. 21:179-183.
50. Siow CC, Nieduszynska SR,Muller CA, Nieduszynski CA. 2012. OriDB, the DNA replication origin database updated and extended. Nucleic Acids Res. 40:D682-D686.
51. Souciet JL, et al. 2009. Comparative genomics of protoploid Saccharomycetaceae. Genome Res. 19:1696-1709.
52. Stamatoyannopoulos JA, et al. 2009. Human mutation rate associated with DNA replication timing. Nat Genet. 41:393-395.
53. Tourriere H, Versini G, Cordon-Preciado V, Alabert C, Pasero P. 2005. Mrc1 and Tof1 promote replication fork progression and recovery independently of Rad53. Mol Cell. 19:699-706.
54. Tsai IJ, Bensasson D, Burt A, Koufopanou V. 2008. Population genomics of the wild yeast Saccharomyces paradoxus: quantifying the life cycle. Proc Natl Acad Sci U S A. 105:4957-4962.
55. Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ. 2010. The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol. 8:e1000414.
56. Tuduri S, Tourriere H, Pasero P. 2010. Defining replication origin efficiency using DNA fiber assays. Chromosome Res. 18:91-102.
57. Vacic V, Iakoucheva LM, Radivojac P. 2006. Two sample logo: a graphical representation of the differences between two sets of sequence alignments. Bioinformatics 22:1536-1537.
58. Watanabe Y, et al. 2002. Chromosome-wide assessment of replication timing for human chromosomes 11q and 21q: disease-related genes in timing-switch regions. Hum Mol Genet. 11:13-21.
59. Wolfe KH, Sharp PM, LiWH. 1989. Mutation rates differ among regions of the mammalian genome. Nature 337:283-285.
60. Wolfe KH, Shields DC. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708-713.
61. Woodfine K, et al. 2004. Replication timing of the human genome. Hum Mol Genet. 13:191-202.
62. Yabuki N, Terashima H, Kitada K. 2002. Mapping of early firing origins on a replication profile of budding yeast. Genes Cells 7:781-789.
63. Yang SC, Rhind N, Bechhoefer J. 2010. Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing. Mol Syst Biol. 6:404.