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. 2014 Nov 28;10(11):764. doi: 10.15252/msb.20145123

Figure 5. swc5 frameshift as molecular basis of the Chromosome III hotspot.

Figure 5

  1. Sequence of Swc5 in the 968 and Y0036 genetic backgrounds, the latter containing the frameshift polymorphism swc5-fs.
  2. Average ratios and standard deviations for all three peptides determined from three independent replicates of strains 968 and Y0036. MS signals with signal-to-noise ratios of < 3 are not considered (#). Error bars indicate standard deviation. The peptides located after the frameshift could not be detected.
  3. Pearson's product-moment correlation coefficient of expression patterns between Δswc5 and swc5-Y0036 (frameshift polymorphism; swc5-fs) and swc5-968 (wild-type; swc5+) strains. For genes linked to the swc5 locus (hotspot targets; 871 genes), expression in Δswc5 was significantly more correlated with swc5-fs segregants (red) than with swc5+ segregants (blue) (*P = 1.3 × 10−11, Wilcoxon's signed-rank test). For genes not linked to the swc5 locus (non-targets; 5,593 genes), there was no difference in correlation. Thus, the swc5 deletion mimics the expression signature of the Y0036 allele at this locus.
  4. Average Pht1 (H2A.Z) occupancy at the 5′-ends of all coding genes in the parental strains of the recombinant yeast library. Genes were aligned at the transcription start site. Pht1 peaks at the +1 nucleosome after the transcription start site. There is significantly less Pht1 at the +1 nucleosome in Y0036 than in the 968 background (P < 10−15, one-sided Wilcoxon's signed-rank test, n = 5,016).
  5. Comparative average Pht1 occupancy in 968 (scw5+) of the genes linked (orange, n = 602) and not linked (gray, n = 4,504) to the swc5 locus. There is significantly more Pht1 at the +1 nucleosome in genes associated with the swc5 QTL than in others (P < 10−15, one-sided Wilcoxon's rank-sum test).