Figure 2.

Example of cleavage site detection within arfA, a known RNase III target (24). (A). Results of the DESeq2 analysis comparing wt and rnc-14 read start counts along the arfA transcript. Shown are the DESeq2 log₂ values of the fold change (FC) in read start counts between wt and rnc-14 (Log₂FC, upper panel) and the DESeq2 adjusted pvalue for multiple hypotheses testing expressed as -log₁₀, (-Log₁₀padj, lower panel). (B) Secondary structure prediction of arfA transcript. Arrows designate the cleavage sites detected here and by Garza-Sanchez et al. (24): Gray—detected only in our study, blue—detected only by Garza-Sanchez et al. (24) and black—detected in both studies. The two cleavage sites detected in our study determine a structural distance of 2 positions, corresponding to dangling ends of 2 nt on both strands. Nucleotide color indicates the log₂FC value. Note that C1 and C2 designate the cleavage sites (Panel B) as well as the positions downstream to the cleavage sites (Panel A).