Evolution of piRNAs in nematodes

We reconstructed the evolutionary history of piRNAs in nematodes showing that the Ruby motif is 350MYA and is likely derived from snRNA core promoter sequence elements. We show that in C. elegans and related nematodes, piRNAs associate with H3K27me3 repressive domains and are tightly clustered in the genome, whereas in other species exemplified by Pristionchus pacificus, piRNAs localise to introns of highly expressed protein-coding genes marked by H3K36me3. In addition, we identify a novel cis-regulatory element downstream element that is required for piRNA transcription termination by promoting pausing of RNA polymerase II, resulting in transcription of extremely short capped RNAs from piRNA promoters. Altogether, we uncover new aspects of piRNA biogenesis through comparative analysis across nematodes.