 for NotI fragment J are filtered and presented as in Figure S2C.
(1.9 MB PDF)
Figure S6. Southern Blot Analyses of DSBs in the 1.8-Mb Region at the Left End of Chromosome I
(A) Physical map and Southern blot hybridizations of NotI fragments encompassing 0.2–2 Mb from the left end of Chromosome I probed from the right (R) or left (L), as indicated. Haploid strain GP5411 (rad50S) was induced, and at the times indicated DNA was extracted and analyzed for DSBs by Southern blot hybridization as described by Young et al. .
(B) Coarse mapping of DSB positions from Figure S6A NotI blots.
(C) Finer scale mapping of the DSB sites identified in Figures S6A and S2C was carried out using DNA from haploid strain GP5411 and diploid strain GP3087 (rad50S), prepared as in Figure S6A. Also shown are blots bridging NotI fragments where breaks were observed in the bridging blots. One DSB site was refractory to analysis. The restriction enzyme used, its length, and the fragment end probed (R or L) are indicated. The DSBs are numbered as in Figures 3 and 4.
(1.3 MB PDF)
Figure S7. Rec12-DNA Linkages across the Entire S. pombe Genome
Data, filtered as in Figure S2C, are the IP:WCE ratios before induction (0 h; blue line) and 5 h after induction (red line; mean of two haploid experiments). Bars indicate the extent of the centromeric repeats. Carets indicate prominent (red) and weak (black) Rec12 peaks. Note that ∼0.5 Mb of rDNA, not shown, is at each end of Chromosome III.
(9.6 MB PDF)
Figure S8. Among Prominent Rec12 Peaks, Stronger Peaks Occur More Frequently in Large IGRs
Each prominent Rec12 peak was allocated to one of four bins based on its peak integral (i.e., strength). The percentage of all peaks in each bin that lie in IGRs >3 kb is indicated. Bin boundaries were chosen to allocate approximately equal numbers of peaks to each bin.
(11 KB PDF)
Figure S9. Meiotic DSB Positions and Relative Intensities are Similar in rad50+ and rad50S Backgrounds and in pat1+ and pat1–114 Backgrounds
S. pombe pat1–114 strains were meiotically induced and analyzed for DSBs essentially as described . pat1+ strains were induced as described  without restoration of a nitrogen source at the beginning of the induction and with more vigorous agitation of cultures and use of baffled flasks. DNA from the times indicated was digested with NotI, separated on pulsed-field gels, and Southern hybridized using a 32P-labelled probe for the left end of the NotI-J fragment. The strains used were: (A) GP3718 (pat1–114 rad50S), (B) GP1979 (pat1–114 rad50+), (C) GP3124 (pat1+ rad50S), (D) GP3121 (pat1+ rad50+). W, well positions; 0, full-length NotI-J restriction fragment; 1, mbs1; and 2, mbs2. Quantitation of mbs1 and mbs2 at the time-point of maximal breakage is given on the right of each gel. Maximal DSB frequencies are greater in rad50S than rad50+ inductions because of DSB accumulation in rad50S. Maximal DSB frequencies are reduced in pat1+ compared to pat1–114 inductions due to greater asynchrony in the pat1+ inductions and a lower proportion of cells progressing through meiosis in that background.
(2.0 MB PDF)
Figure S10. Plots of Neighbor Dissimilarity (log2) against IP:WCE Hybridization Ratios for Each Probe of Chromosome I Using Data from the Haploid and Diploid Experiments (Strains GP6013 and GP6203)
Neighbor dissimilarity is expressed by calculating the absolute value of log2 (probe IP:WCE ratio/neighbor IP:WCE ratio), using both neighboring probes, and taking the lesser value.
(A) 0 h, haploid.
(B) Mean 5 h, haploid.
(C) 0 h, diploid.
(D) 5 h, diploid.
Note that high IP:WCE hybridization ratios in 0-h data are spikes; they have high dissimilarity relative to either neighboring probe. For these probes, dissimilarity rises with IP:WCE ratio, indicating that the neighboring probes have low (background) ratios, unrelated to that of the spikes. These spike probes are also seen in 5-h data, but another distribution of probes with high IP:WCE ratios and low neighbor dissimilarity is seen. These probes reflect genuine Rec12-enrichment with elevated IP:WCE ratios across