Identification and Functional Analysis of the Pre-piRNA 3′ Trimmer in Silkworms

PIWI-interacting RNAs (piRNAs) play a crucial role in transposon silencing in animal germ cells. In piRNA biogenesis, single-stranded piRNA intermediates are loaded into PIWI-clade proteins and cleaved by Zucchini/MitoPLD, yielding precursor piRNAs (pre-piRNAs). Pre-piRNAs that are longer than the mature piRNA length are then trimmed at their 3′ ends. Although recent studies implicated the Tudor domain protein Papi/Tdrkh in pre-piRNA trimming, the identity of Trimmer and its relationship with Papi/Tdrkh remain unknown. Here, we identified PNLDC1, an uncharacterized 3′-5′ exonuclease, as Trimmer in silkworms. Trimmer is enriched in the mitochondrial fraction and binds to Papi/Tdrkh. Depletion of Trimmer and Papi/Tdrkh additively inhibits trimming, causing accumulation of ∼35–40-nt pre-piRNAs that are impaired for target cleavage and prone to degradation. Our results highlight the cooperative action of Trimmer and Papi/Tdrkh in piRNA maturation. [Display omitted] •The exonuclease PNLDC1 is the pre-piRNA 3′ Trimmer in silkworms•PNLDC1 binds the Tudor protein Papi/Tdrkh on the mitochondrial surface•Papi/Tdrkh binds PIWI proteins, recruiting PIWI-bound pre-piRNAs to PNLDC1•Untrimmed pre-piRNAs are impaired for target cleavage and prone to degradation The exonuclease PNLDC1 is responsible for trimming the 3′ end of pre-piRNAs in silkworms, a process important for the target cleavage activity of piRNAs.