Two tiers of piRNA clusters balance diversification of piRNAs with limitation of off-target effects

PIWI-interacting RNAs (piRNAs) are important factors in the protection of the genome against nucleic acid invaders such as transposons. piRNAs are encoded in the genome in regions known as piRNA clusters, but major questions remain surrounding their regulation. Two such questions are how the piRNA clusters are recognized as piRNA sources, and how the piRNA response can expand from these regions to facilitate the recognition of novel invading sequences without risking the targeting of essential cellular mRNAs. Here, we investigated the piRNA clusters of the planarian S, mediterranea, and found that the clusters differ regarding the PIWI proteins their piRNAs bind to, as well as their chromatin features. We uncovered a subset of piRNA clusters that had unique chromatin features and atypical transcription. piRNAs from these clusters were depleted of genic content, stabilized by 3 methylation and were not dependent on the ping-pong mechanism. We therefore named these clusters Seed clusters. We identified a second set of piRNA clusters that we called Spread clusters, which had features reminiscent of pseudogenes or aberrant genic transcripts. piRNA generation from these clusters relied on ping-pong, and piRNAs largely remained unmethylated. Further, we found that many more regions in the genome generated single ping-pong events, suggesting that ping-pong is used as a means to diversify the collection of piRNA-generating transcripts beyond the Seed clusters. We propose that this two-tiered organization of the piRNA clusters allows the stable targeting of known genomic threats by the piRNAs generated from the Seed clusters, while the flexible generation of additional diverse piRNAs from Spread clusters as well as other aberrant transcripts increases the sequence space probed by the piRNA system. The absence of methylation on these additional piRNAs decreases their lifespan and limits the chances of a run-away response. This two-tiered organization thus solves a core challenge of the piRNA system and may be a widespread feature of piRNA systems across animals.