Hierarchical length and sequence preferences establish a single major piRNA 3'-end

Abstract

PIWI-interacting RNAs (piRNAs) guard germline genomes against the deleterious action of retroviruses and other mobile genetic elements. How piRNAs faithfully discriminate between self and non-self to restrict all mobile elements while sparing essential genes remains a key outstanding question in genome biology. PiRNAs use extensive base-pairing to recognize their targets and variable 3ends could change the specificity and efficacy of piRNA silencing. Here, we identify conserved rules that ensure the generation of a single major piRNA 3end in flies and mice. Our data suggest that the PIWI proteins initially define a short interval on pre-piRNAs that grants access to the ZUC-processor complex. Within this Goldilocks zone, the preference of the ZUC-processor to cut in front of a Uridine determines the ultimate processing site. We observe a mouse-specific roadblock that relocates the Goldilocks zone and generates an opportunity for consecutive trimming by PNLDC1. Our data reveal a conserved hierarchy between length and sequence preferences that controls the piRNA sequence space. The unanticipated precision of 3end formation bolsters the emerging understanding that the functional piRNA sequence space is tightly controlled to ensure effective defense. Key findingsO_LIEvery piRNA has a single major 3end C_LIO_LILength preference trumps sequence preference during 3end formation. C_LIO_LIRelocation of the Goldilocks zone generates opportunity for trimming of mouse piRNAs. C_LI