Nuclease Processing of BIR Intermediates 7/3-HMR and 7/3-HML intermediates, and to the uncut and cut chromosome VII (Chr. VII) are indicated. GAL, galactose; h, hours. (D) Quantification of BIR product accumulation. Quantification results of chromosome VII cleavage (DSB), 7/3-HMR, 7/3-HML and 7/3-MAT BIR intermediates are shown as percentage. Mean values and standard deviations for 2–3 independent experiments are shown. doi:10.1371/journal.pgen.1002979.g004 observation correlated with the increase of T7/3-MAT transloca- tions previously observed in these mutants (Figure 5B). The defects observed in rad1D and mus81D slx4D yen1D mutants could be explained by the known functions of Rad1 and Slx4 in SSA [50], which would be required for T7/3-HMR translocation formation by BIR/SSA. Indeed, in the control HMR-inc WT strain, the T7/3-MAT translocations represented about 55% of the translocations observed in 5-FOA-resistant survivors (Figure S7B). Figure 5. PFGE analysis of T7/3 translocations in SSE mutants. (A) PFGE followed by Southern analysis using the 3R1 probe (See Figure 1G) of Ura2 5-FOAr survivors in WT, pol32D, rad1D and mus81D slx4D yen1D strains. Black arrows indicate the positions of the T7/3-MAT and T7/3-HMR translocations and of the linear chromosome III (Chr. III). PFGE, pulse-field gel electrophoresis. (B) Graphical plotting of percent of translocants containing T7/3-MAT translocations of each strain tested. ** and *, differences with the WT statistically significant (p,0.01 and p,0.05, respectively, x2 with Yates’ correction). See Table S1 for complete statistical analysis. doi:10.1371/journal.pgen.1002979.g005 PLOS Genetics | www.plosgenetics.org 9 September 2012 | Volume 8 | Issue 9 | e1002979