Fig. 6: The E granule promotes the production of a subset of siRNAs in the germline.

a, b Scatter plots showing gene-by-gene comparisons of normalized siRNA abundances. siRNAs from wild-type, egc-1(-) and elli-1(-) animals were sequenced in a 5’ phosphate-independent method. 22G RNAs were mapped to the C. elegans genome and the number of reads complementary to each C. elegans gene was quantified. A cutoff criterion of a 2-fold change was applied to identify differentially expressed siRNAs. Genes with upregulated and downregulated siRNAs are shown in red and blue, respectively. c Proportional Venn diagram showing comparisons between sets of genes that are the targets of 22G RNAs in the indicated animals. Genes yielding ≥ 10 siRNA reads per million total small RNA reads (RPM) in wild-type animals, were selected for analysis. Soma-enriched siRNA targets were excluded from the above analysis⁴⁰. Overlaps between egc-1(ust134) and egc-1(ust206) are annotated as EGC-1 targets; overlaps between elli-1(ust203) and elli-1(ust204) are annotated as ELLI-1 targets. Genes targeted by twofold fewer siRNAs in egc-1(-) or elli-1(-) animals than in wild-type animals were identified as the E-class genes. d Proportional Venn diagram showing the overlap among EGO-1 siRNA targets and E-class genes. e Proportional Venn diagram showing the overlap among E-class genes and M-class genes. A list of E- and M-class genes is shown in Supplementary data 2. f Metaprofile analysis showing the distribution of normalized 22G RNA (sRNA-seq) reads (RPM) along M-class genes and E-class genes in control animals and mut-16 mutants. The metaprofiles were generated according to the method described previously in ref. ⁷⁷. g Metaprofile analysis showing the distribution of normalized 22G RNA (sRNA-seq) reads (RPM) along M-class genes in the indicated animals. The loss of EGC-1 or ELLI-1 does not overall affect the production of 22G RNAs mapping to the M-class genes. h Ratio of normalized 22G RNA reads from a representative subset of E-class genes and M-class genes in the indicated mutants to wild-type animals (WT = 1.0). bath-45, c38d9.2 and f15d4.5 are M-class genes; cls-2, F01G4.4 and tebp-2 are E-class genes.