Figure 4. The prg-1(−) mutant alters levels of small RNAs corresponding to many loci.

(A) Scatterplots depict antisense small RNAs per gene in young adult prg-1(−) animals at various generations, relative to small RNAs per gene in wildtype animals. Counts are per 10⁶ reads mapped to the ce11 genome and represent the mean of two biological replicates. Colored dots indicate genes meeting three criteria: (i) an aggregate small RNA count for the two samples > 50, (ii) a raw fold change of > 4-fold relative to wildtype, and (iii) passed a Bayesian maximum likelihood filter using a cutoff FDR (False Discovery Ratio) of 0.05 per gene. Generations assayed are indicated as followed: number of generations (n) since start of the transgenerational fertility assay (G_n), the generation of sterility (G_sterility), and number of generations (n) prior to complete sterility (G_sterility-n). The two prg-1(−) replicates used here went sterile at G₁₇ and G₁₈. Number of genes with > 4-fold and < 4-fold small RNAs in the various generations: G₁= 114 and 705, G₇= 137 and 781, G_sterility-3= 131 and 2108, and G_sterility-1= 201 and 2341.

See also Figure S4A–D.

(B) Proportion of antisense ribosomal RNAs (risiRNAs) and the remaining subset of up-regulated small RNAs from the prg-1(−) G_sterility-3 generation (n=197) in wildtype and across generations in prg-1(−). Values are the mean of two biological replicates, represented as a proportion of mapped antisense RNAs. Error bars represent standard error of the mean. (C) Genomic distribution of loci with> 4-fold increase of small RNAs in G_sterility-1 prg-1(−) relative to wildtype. Red regions indicate locations of genes with upregulated small RNAs.

See also Figure S4E and Table S1.