The 3′-to-5′ Exoribonuclease Nibbler Shapes the 3′ Ends of MicroRNAs Bound to Drosophila Argonaute1

MicroRNAs (miRNAs) are ∼22 nucleotide (nt) small RNAs that control development, physiology, and pathology in animals and plants. Production of miRNAs involves the sequential processing of primary hairpin-containing RNA polymerase II transcripts by the RNase III enzymes Drosha in the nucleus and Dicer in the cytoplasm. miRNA duplexes then assemble into Argonaute proteins to form the RNA-induced silencing complex (RISC). In mature RISC, a single-stranded miRNA directs the Argonaute protein to bind partially complementary sequences, typically in the 3′ untranslated regions of messenger RNAs, repressing their expression. Here, we show that after loading into Argonaute1 (Ago1), more than a quarter of all Drosophila miRNAs undergo 3′ end trimming by the 3′-to-5′ exoribonuclease Nibbler (CG9247). Depletion of Nibbler by RNA interference (RNAi) reveals that miRNAs are frequently produced by Dicer-1 as intermediates that are longer than ∼22 nt. Trimming of miRNA 3′ ends occurs after removal of the miRNA∗ strand from pre-RISC and may be the final step in RISC assembly, ultimately enhancing target messenger RNA repression. In vivo, depletion of Nibbler by RNAi causes developmental defects. We provide a molecular explanation for the previously reported heterogeneity of miRNA 3′ ends and propose a model in which Nibbler converts miRNAs into isoforms that are compatible with the preferred length of Ago1-bound small RNAs. ► More than a quarter of all miRNAs in flies are trimmed after their production by Dicer-1 ► miRNA trimming occurs after loading into Ago1 and is limited by miRNA∗ strand removal ► The 3′-to-5′ exoribonuclease Nibbler trims miRNAs, enhancing miRNA function ► Nibbler is required for normal fly development