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

Cell. 2016 Feb 25;164(5):962-73. doi: 10.1016/j.cell.2016.01.008.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bombyx / enzymology*
  • Bombyx / genetics*
  • Bombyx / metabolism
  • Insect Proteins / metabolism*
  • Mitochondria / metabolism
  • RNA Processing, Post-Transcriptional*
  • RNA, Small Interfering / metabolism*
  • RNA-Binding Proteins / metabolism*


  • Insect Proteins
  • RNA, Small Interfering
  • RNA-Binding Proteins