Fig. 4

Impact of DCL4 expression in S. cerevisiae on transcriptome and on putative sense/antisense RNA loci. A Expression of endogenous RNA transcripts in DCL4 expressing and non-expressing S. cerevisiae. Plasmid-transformed/non-induced cells were compared with plasmid-transformed copper-induced cells. MA-plots show the distribution of expression fold changes (in log2 scale) as a function of average expression (the baseMean value of DEseq2) of every locus in the compared samples. Positive log2FC values mean that the expression of the given locus was higher when HA-DCL4 was induced, whereas the negative log2 fold change value means that it was lower when HA-DCL4 was induced. Red dots represent expressions changed with an adjusted p-value < 0.05 (5% false discovery rate), absolute Fold Change > 1.5 fnd baseMean > 50. (see Additional file 2: Table S1). B Heat map representing the top 40 RNA loci with significant differential expression (adjusted p-value < 0.05 and abs(log2(FC)) > 0.585) upon induction of HA-DCL4 expression. C Representation of the genomic organization of the CUP1-1 and CUP1-2 clusters. As indicated with the black boxes, the CUP genes are organized in tandem, each with the RUF5-1 and 2 genes organized in antisense direction. Distribution of 21- and 22-nt long DCL4-derived sRNAs of positive (red) and negative (blue) strands. Boxes in gray are other genes associated with the loci of interest