Ascaris 26G-RNAs and 22G-RNAs targets. (A) Examples of distribution of 26G- and 22G-RNAs to mRNAs throughout development. Note that all small RNAs are antisense. (Red) 22G-RNAs; (blue) 26G-RNAs. Vertical dashed lines indicate the start and stop of the ORF. Numbers on left indicate the normalized read frequency of the gray line. Note that for 26G-RNA targets, only the profiles from testis 26G-RNAs are shown; for their complete profiles, see Supplemental Table S7 and Supplemental Figures S9 and S10. (B) Dynamic expression profiles of 22G-RNAs to 159 exemplary targets (see text). Normalized As.22G RNA reads mapping to each target mRNA were used for the heatmap. For each target, colors represent log2 values of fold changes to the average read frequencies of the As.22G RNAs during development. (C) Distribution of 26G- and 22G-RNAs on mRNAs predominantly targeted by one of the two types of small RNAs. Only mRNAs identified as near full length are used and include 138 26G-targeted mRNAs and 97 22G-targeted mRNAs (see Supplemental Table S7; Supplemental Figs. S9, S10). Plotted is the sum of the counts (y-axis) against the relative position (x-axis) on the cDNA from 5′ to 3′, with the 5′ end of the mRNA designated as 1 and the site of polyadenylation at the 3′ end designated as 100. (D) Venn diagram illustrating the relationship between the mRNAs targeted by 26G- or 22G-RNAs. (E) Ratio of defined testis 26G-RNA/22G-RNAs mRNA targets. (Upper panel) 26G-RNA targets, the 26G/22G ratio; (lower panel) 22G-RNA targets. (F) Expression profile of 26G-RNAs and 22G-RNAs in spermatogenesis is different for Ascaris and C. elegans (see Discussion). Note that for C. elegans, the total level of 26G-RNAs decreases during spermatogenesis with a concomitant and dramatic increase in 22G-RNAs targeting the same mRNAs. In contrast, the ratio of Ascaris 26G/22G RNAs to mRNAs remains the same during spermatogenesis and the 26G-RNAs are always the dominant small RNA species. Note that the figure does not represent absolute levels of the RNAs.
