Widespread roles for piRNAs and WAGO-class siRNAs in shaping the germline transcriptome of Caenorhabditis elegans

To explore the roles of piRNAs and WAGO-class 22G-RNAs in regulating gene expression and transposon silencing in Caenorhabditis elegans, we used RNA-seq to assess changes in small RNA and mRNA levels in prg-1 and mut-16 mutants, which disable the piRNA and WAGO-class 22G-RNA pathways respectively. We identified numerous roles for piRNAs and WAGO-class 22G-RNAs in regulating germline genes, including transposons, histones, and spermatogenic and oogenic transcripts. Small RNA and mRNA high-throughput sequencing was done using RNA isolated from whole animals and from the dissected distal gonads of wild type and prg-1 and mut-16 mutant animals. Differential expression analysis was done to identify mRNAs enriched in distal gonads relative to whole animals and in prg-1 and mut-16 mutants relative to wild type animals.