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. 2020 Apr 27;9:e56731. doi: 10.7554/eLife.56731

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© 2020, Manage et al

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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Figure 5. — (A) Table indicating the number of genes for which the total small RNA levels are either increased or reduced by at least two-fold for each indicated mutant. All genes also met the requirements of having at least 10 RPM in either mutant or control and a DESeq2 adjusted p-value of ≤0.05. (B) Box plots displaying total small RNAs levels mapping to genes from the indicated small RNA pathways in simr-1 mutants compared to wild-type animals raised at 20°C. Details regarding definition of small RNA target gene classes is provided in the Materials and Methods section. At least 10 RPM in wild-type or simr-1 mutant libraries was required to be included in the analysis. (C) Heat maps displaying total small RNAs levels targeting mutator-target genes or CSR-1-target genes in simr-1 mutants raised at 20°C, a single generation at 25°C, or two, seven, or 10 generations at 25°C relative to wild-type at the same temperature and generation. (D) Venn diagrams indicating overlap of genes depleted of total small RNAs by two-fold or more in mutants compared to wild-type. (E) Reads per total million reads mapping to piRNA and piRNA-target gene loci in wild-type and simr-1 mutants raised at either 20°C, or for a single generation at 25°C, indicate that piRNAs are not reduced in simr-1 mutants. Error bars indicate standard deviation of two replicate libraries. (F) Scatter plots display piRNA reads per million total reads in wild-type and simr-1 mutants (top) and wild-type and prg-1 mutants (bottom). Genes with two-fold increase in piRNA abundance and DESeq2 adjusted p-value≤0.05 are colored dark red and genes with two-fold reduction in piRNA abundance and DESeq2 adjusted p-value≤0.05 are colored light blue. The percentage of total piRNAs with an increase or reduction of greater than two-fold is indicated in the corners of the graph. n.s. denotes not significant and indicates a p-value>0.05 and **** indicates a p-value≤0.0001. See Supplementary file 8 for more details regarding statistical analysis.

Figure 5—figure supplement 1. — (A) Table indicating the number of genes for which the total small RNA levels are either increased or reduced by at least two-fold for each indicated mutant. All genes also met the requirements of having at least 10 RPM in either mutant or control and a DESeq2 adjusted p-value of ≤0.05. (B) Box plots displaying total small RNAs levels mapping to genes from the indicated small RNA pathways in simr-1 mutants compared to wild-type animals raised at 20°C. Details regarding definition of small RNA target gene classes is provided in the Materials and Methods section. At least 10 RPM in wild-type or simr-1 mutant libraries was required to be included in the analysis. (C) Heat maps displaying total small RNAs levels targeting mutator-target genes or CSR-1-target genes in simr-1 mutants raised at 20°C, a single generation at 25°C, or two, seven, or 10 generations at 25°C relative to wild-type at the same temperature and generation. (D) Venn diagrams indicating overlap of genes depleted of total small RNAs by two-fold or more in mutants compared to wild-type. (E) Reads per total million reads mapping to piRNA and piRNA-target gene loci in wild-type and simr-1 mutants raised at either 20°C, or for a single generation at 25°C, indicate that piRNAs are not reduced in simr-1 mutants. Error bars indicate standard deviation of two replicate libraries. (F) Scatter plots display piRNA reads per million total reads in wild-type and simr-1 mutants (top) and wild-type and prg-1 mutants (bottom). Genes with two-fold increase in piRNA abundance and DESeq2 adjusted p-value≤0.05 are colored dark red and genes with two-fold reduction in piRNA abundance and DESeq2 adjusted p-value≤0.05 are colored light blue. The percentage of total piRNAs with an increase or reduction of greater than two-fold is indicated in the corners of the graph. n.s. denotes not significant and indicates a p-value>0.05 and **** indicates a p-value≤0.0001. See Supplementary file 8 for more details regarding statistical analysis.