Fig. 4

Analysis of vsiRNA-targeted RNAs. A Table of the genes targeted by vsiRNAs showing their gene ID, cleavage position, vsiRNA targeting, the level of their presence in different AGO IPs (showed as a heat map for their RPM accumulation), the accumulation of PARE reads in the predicted cleavage position (showed as a heat map for the percentage of reads from the specific mRNA that map to the cleavage position), and the fold change of mRNA expression under CMV infection (showed as a heat map of the fold change of mRNA expression in CMV vs mock). B PARE read profile relative to the predicted cleavage position identified by PAREsnip. C Analysis of GO term enrichment. Left panel shows the analysis according to molecular function and right panel shows the analysis for biological process. Blue-colored dots show categories enriched equal or more than 2-fold with a p value inferior to 0.05. D Proportion of 21-, 22-, and 24-nt sRNAs derived from vsiRNA-targeted genes in mock and CMV-infected sRNA libraries. E Box-plot representing the accumulation (log2 RPM) of 21- and 22-nt sRNAs derived from individual mRNAs in mock and CMV-infected sRNA libraries. Whiskers extend to data points that are less than 1.5 x IQR away from 1st/3rd quartile. p values are indicated in the comparisons and indicate the result of a paired t test with 2 tails. Two bioreplicates from PARE RNA libraries were generated and analyzed