6584 Nucleic Acids Research, 2011, Vol. 39, No. 15 29. Hyppa,R.W. and Smith,G.R. (2009) Using Schizosaccharomyces pombe meiosis to analyze DNA recombination intermediates. Methods Mol. Biol., 557, 235–252. 30. Brewer,B.J. and Fangman,W.L. (1987) The localization of replication origins on ARS plasmids in S. cerevisiae. Cell, 51, 463–471. 31. Possoz,C., Filipe,S.R., Grainge,I. and Sherratt,D.J. (2006) Tracking of controlled Escherichia coli replication fork stalling and restart at repressor-bound DNA in vivo. EMBO J., 25, 2596–2604. 32. Maundrell,K. (1990) nmt1 of ﬁssion yeast. A highly transcribed gene completely repressed by thiamine. J. Biol. Chem., 265, 10857–10864. 33. Ivanov,E.L., Sugawara,N., Fishman-Lobell,J. and Haber,J.E. (1996) Genetic requirements for the single-strand annealing pathway of double-strand break repair in Saccharomyces cerevisiae. Genetics, 142, 693–704. 34. Mimitou,E.P. and Symington,L.S. (2011) DNA end resection-unraveling the tail. DNA Repair, 10, 344–348. 35. Cobb,J.A., Schleker,T., Rojas,V., Bjergbaek,L., Tercero,J.A. and Gasser,S.M. (2005) Replisome instability, fork collapse, and gross chromosomal rearrangements arise synergistically from Mec1 kinase and RecQ helicase mutations. Genes Dev., 19, 3055–3069. 36. Cotta-Ramusino,C., Fachinetti,D., Lucca,C., Doksani,Y., Lopes,M., Sogo,J. and Foiani,M. (2005) Exo1 processes stalled replication forks and counteracts fork reversal in checkpoint-defective cells. Mol. Cell, 17, 153–159. 37. Cobb,J.A., Bjergbaek,L., Shimada,K., Frei,C. and Gasser,S.M. (2003) DNA polymerase stabilization at stalled replication forks requires Mec1 and the RecQ helicase Sgs1. EMBO J., 22, 4325–4336. 38. Kaye,J.A., Melo,J.A., Cheung,S.K., Vaze,M.B., Haber,J.E. and Toczyski,D.P. (2004) DNA breaks promote genomic instability by impeding proper chromosome segregation. Curr. Biol., 14, 2096–2106. 39. Azvolinsky,A., Dunaway,S., Torres,J.Z., Bessler,J.B. and Zakian,V.A. (2006) The S. cerevisiae Rrm3p DNA helicase moves with the replication fork and affects replication of all yeast chromosomes. Genes Dev., 20, 3104–3116. 40. Ivessa,A.S., Lenzmeier,B.A., Bessler,J.B., Goudsouzian,L.K., Schnakenberg,S.L. and Zakian,V.A. (2003) The Saccharomyces cerevisiae helicase Rrm3p facilitates replication past nonhistone protein-DNA complexes. Mol. Cell, 12, 1525–1536. 41. Pinter,S.F., Aubert,S.D. and Zakian,V.A. (2008) The Schizosaccharomyces pombe Pfh1p DNA helicase is essential for the maintenance of nuclear and mitochondrial DNA. Mol. Cell Biol., 28, 6594–6608. 42. Young,L.S. and Rickinson,A.B. (2004) Epstein-Barr virus: 40 years on. Nat. Rev. Cancer, 4, 757–768. 43. Lindner,S.E. and Sugden,B. (2007) The plasmid replicon of Epstein-Barr virus: mechanistic insights into efﬁcient, licensed, extrachromosomal replication in human cells. Plasmid, 58, 1–12. 44. Sun,W., Nandi,S., Osman,F., Ahn,J.S., Jakovleska,J., Lorenz,A. and Whitby,M.C. (2008) The ﬁssion yeast FANCM ortholog Fml1 promotes recombination at stalled replication forks and limits crossing over during double-strand break repair. Mol. Cell, 32, 118–128. 45. Labib,K. and Hodgson,B. (2007) Replication fork barriers: pausing for a break or stalling for time? EMBO Rep., 8, 346–353. 46. 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. 47. Burkhalter,M.D. and Sogo,J.M. (2004) rDNA enhancer affects replication initiation and mitotic recombination: Fob1 mediates nucleolytic processing independently of replication. Mol. Cell, 15, 409–421. 48. Fricke,W.M. and Brill,S.J. (2003) Slx1-Slx4 is a second structure-speciﬁc endonuclease functionally redundant with Sgs1-Top3. Genes Dev., 17, 1768–1778. 49. Coulon,S., Noguchi,E., Noguchi,C., Du,L.L., Nakamura,T.M. and Russell,P. (2006) Rad22/Rad52-dependent repair of ribosomal DNA repeats cleaved by Slx1-Slx4 endonuclease. Mol. Biol. Cell, 17, 2081–2090. 50. Jannink,G., Duplantier,B. and Sikorav,J.L. (1996) Forces on chromosomal DNA during anaphase. Biophys. J., 71, 451–465. 51. Ding,R., McDonald,K.L. and McIntosh,J.R. (1993) Three-dimensional reconstruction and analysis of mitotic spindles from the yeast, Schizosaccharomyces pombe. J. Cell. Biol., 120, 141–151. 52. Baxter,J. and Difﬂey,J.F. (2008) Topoisomerase II inactivation prevents the completion of DNA replication in budding yeast. Mol. Cell, 30, 790–802. 53. Noguchi,E., Noguchi,C., McDonald,W.H., Yates,J.R. 3rd and Russell,P. (2004) Swi1 and Swi3 are components of a replication fork protection complex in ﬁssion yeast. Mol. Cell Biol., 24, 8342–8355. 54. Calzada,A., Hodgson,B., Kanemaki,M., Bueno,A. and Labib,K. (2005) Molecular anatomy and regulation of a stable replisome at a paused eukaryotic DNA replication fork. Genes Dev., 19, 1905–1919. 55. Prado,F. and Aguilera,A. (2005) Impairment of replication fork progression mediates RNA polII transcription-associated recombination. EMBO J., 24, 1267–1276. 56. de la Loza,M.C., Wellinger,R.E. and Aguilera,A. (2009) Stimulation of direct-repeat recombination by RNA polymerase III transcription. DNA Repair, 8, 620–626. 57. Torres-Rosell,J., De Piccoli,G., Cordon-Preciado,V., Farmer,S., Jarmuz,A., Machin,F., Pasero,P., Lisby,M., Haber,J.E. and Aragon,L. (2007) Anaphase onset before complete DNA replication with intact checkpoint responses. Science, 315, 1411–1415. 58. Dulev,S., de Renty,C., Mehta,R., Minkov,I., Schwob,E. and Strunnikov,A. (2009) Essential global role of CDC14 in DNA synthesis revealed by chromosome underreplication unrecognized by checkpoints in cdc14 mutants. Proc. Natl Acad. Sci. USA, 106, 14466–14471. 59. Kamranvar,S.A., Gruhne,B., Szeles,A. and Masucci,M.G. (2007) Epstein-Barr virus promotes genomic instability in Burkitt’s lymphoma. Oncogene, 26, 5115–5123. 60. Gruhne,B., Sompallae,R., Marescotti,D., Kamranvar,S.A., Gastaldello,S. and Masucci,M.G. (2009) The Epstein-Barr virus nuclear antigen-1 promotes genomic instability via induction of reactive oxygen species. Proc. Natl Acad. Sci. USA, 106, 2313–2318. 61. d’Herouel,A.F., Birgersdotter,A. and Werner,M. (2010) FR-like EBNA1 binding repeats in the human genome. Virology, 405, 524–529. 62. Canaan,A., Haviv,I., Urban,A.E., Schulz,V.P., Hartman,S., Zhang,Z., Palejev,D., Deisseroth,A.B., Lacy,J., Snyder,M. et al. (2009) EBNA1 regulates cellular gene expression by binding cellular promoters. Proc. Natl Acad. Sci. USA, 106, 22421–22426. 63. Meister,P., Poidevin,M., Francesconi,S., Tratner,I., Zarzov,P. and Baldacci,G. (2003) Nuclear factories for signalling and repairing DNA double strand breaks in living ﬁssion yeast. Nucleic Acids Res., 31, 5064–5073.