(A and B) Comparative analysis of reads from RNA-seq protocols (as indicated). The histograms represent the frequency of reads sharing the same 5′ end at the rps-4 locus (A), and at a non-annotated locus on chromosome X (B). The genome coordinates are indicated. A log2 scale is provided for each set of histograms. Mature 21U-RNA reads are enriched in the “oxidized” vs “control” (A) and “PRG-1 IP” vs “Input” (A and B) samples as indicated. Closed triangles indicate the positions of mature 21U-RNAs enriched in the PRG-1 IP. In (B), the red bars correspond to WAGO-dependent 22G-RNAs likely targeting non-annotated transcripts (dashed arrows) of unknown length.
(C) Enlarged regions indicating the precise positions of corresponding CIP-TAP (orange) and PRG-1 IP (green) reads relative to the YRNU motif indicated below the sequence. Note that one of the TS sites for rps-4 is “RR” rather than “YR”. The open triangles above the CIP-TAP bars point to the likely precursor of the mature 21U-RNAs, which are indicated by the closed triangles below the PRG-1 IP bars.