Fig. 8

Correlation between genome dominance, Pol IV-mediated gene silencing and siRNA loci occupancy. Subdivision of differentially expressed gene models (log2FC > |1|, FDR < 0.05) into singletons, duplicates in the two subgenomes, or non-syntenic genes show an enrichment for subgenome 2 homeologs and non-syntenic genes within the rpd1/rmr6 up-regulated targets (a). Percentages of singletons and duplicates were calculated on the total of genes assigned to subgenomes, while percentages of non-syntenic genes were referred to the total of FGS genes and are reported on an independent scale. The distribution plots of siRNA loci in flanking regions of genes belonging to different subgenome (b) reveal that subgenome 2 genes are more likely to have flanking 24 nt-siRNAs than subgenome 1, while non-syntenic genes are less covered by 24 nt-siRNA in their upstream region than syntenic ones. Similarly, the distribution of the 24sRNA loci along the flanking regions of rpd1/rmr6 up- or down-regulated genes (c) shows that mutant up-regulated genes tend to have fewer siRNA in their flanks than-downregulated ones