CSR-1 inhibits piRNA binding and WAGO 22G-RNA synthesis with distinct modes of action. (A) Metagene trace shows the distribution of CSR-1 22G-RNAs along CSR-1 (top) or WAGO (bottom) targets. The solid line indicates the average number of CSR-1 22G-RNA read counts in CSR-1 or WAGO targeted mRNAs. The dotted lines indicate the average number plus/minus one standard error. (B) Metagene trace shows the distribution of piRNA binding events in wild type (orange) or in CSR-1 depleted animals (green) mapped to CSR-1 (top) or WAGO (bottom) targets. The piRNA–tRNA hybrid reads, which are expected to be nonspecific ligation products and thus remain unchanged between samples, are used for normalization. The solid line indicates the average number of piRNA binding events (read counts) in CSR-1 or WAGO targets. The dotted lines indicate the average number plus/minus one standard error. (C) Metagene trace shows the distribution of CSR-1 22G-RNAs mapped to the indicated CSR-1 subgroup genes, including 3′ end 22G enriched (top) or not enriched (bottom) CSR-1 targets. The solid line indicates the average number of CSR-1 22G-RNAs read counts in the indicated CSR-1 subgroup genes. The dotted lines indicate the average number plus/minus one standard error. (D) Metagene trace shows the distribution of piRNA binding events in wild type (orange) or in CSR-1 depleted animals (green) mapped to the indicated CSR-1 subgroup genes, including 3′ end 22G enriched (top) or not enriched (bottom) CSR-1 targets. The solid line indicates the average number of piRNA binding events (read counts) in the indicated CSR-1 subgroup genes. The dotted lines indicate the average number plus/minus one standard error. (E) Metagene traces show the distribution of WAGO-9 (HRDE-1) 22G-RNAs in wild type (orange) or in CSR-1 depleted animals (green) mapped to CSR-1 (top) or WAGO (bottom) targets. The miRNA mapped reads, which are expected to be nonspecific RNA cloned from these experiments and thus remain unchanged between samples, are used for normalization. The solid line indicates the average number of WAGO-9 22G-RNA read counts in CSR-1 or WAGO targets. The dotted lines indicate the average number plus/minus one standard error. (F) Metagene traces show the distribution of WAGO-9 (HRDE-1) 22G-RNAs in wild type (orange) or in CSR-1 depleted animals (green) mapped to the indicated CSR-1 subgroup genes, including 3′ end 22G enriched (top) or not enriched (bottom) CSR-1 targets. The miRNA mapped reads are used for normalization. The solid line indicates the average number of WAGO-9 22G-RNAs read counts in the indicated CSR-1 subgroup genes, including 3′ end 22G enriched (top) or not enriched (bottom) CSR-1 targets. The dotted lines indicate the average number plus/minus one standard error. The miRNA mapped reads are used for normalization between samples. (G) The ratio of piRNA binding events or WAGO-9 22G-RNAs in csr-1 depletion over control in high-density CSR-1 targeted windows and low-density CSR-1 targeted windows for germline mRNAs, CSR-1 targets, and WAGO targets. The piRNA–tRNA hybrids and the miRNA reads are used for normalization of piRNA binding and WAGO-9 22G-RNAs, respectively. Blue lines represent median values. The statistical significance (P-value) of the difference in fold change (csr-1 depletion over control) between two windows was calculated by the Mann–Whitney U-test.
