Uridylation of RNA-hairpins by Tailor confines the emergence of novel miRNAs in Drosophila

Uridylation of diverse RNA species represents an emerging theme in post-transcriptional gene regulation. In the microRNA pathway, such modifications regulate small RNA biogenesis and stability in plants, worms and mammals. Here, we report the first uridylyltransferase that acts on small RNAs in Drosophila, which we refer to as Tailor. Tailor is the source for the majority of 3´ terminal uridine-modifications in small RNAs and predominantly targets precursor-miRNAs. Uridylation modulates the characteristic two-nucleotide 3´ overhangs of miRNA hairpins, which regulates pre-miRNA processing by Dicer-1. Furthermore, Tailor preferentially uridylates mirtron hairpins, thereby impeding the production of non-canonical microRNAs. Mirtron-selectivity is explained by unique primary sequence specificity of Tailor, selecting RNA substrates ending with a 3´ guanosine, a feature not previously observed for terminal uridylyltransferases. In contrast to mirtrons, conserved Drosophila pre-miRNAs are significantly depleted in 3´ guanosine, thereby escaping regulatory uridylation.Our data support the hypothesis that evolutionary adaptation to pre-miRNA uridylation shapes the nucleotide composition of pre-miRNA 3´ ends and may serve as a barrier for the de novo creation of miRNAs in Drosophila. Overall design: 10 small RNA libraries (3 replicates untreated, 4 replicates control RNAi [GFP, GFP/Luc], and 3 replicates CG1091 RNAi [CG1091]) from Drosophila S2 cells; 3 RNA libraries from 40-100 nt RNA (untreated, control RNAi, and CG1091 RNAi) from Drosophila S2 cells; 5 small RNA libraries (w1118; CG1091[c4-1] heterozygous and homozygous; CG1091[c4-6] heterozygous and homozygous) from whole 2-5 day old male Drosophila melanogaster flies; 3 libraries (In vitro tailing randomized substrate, Input, 2 min CG1091 treamtent, 5 min CG1091 treatment) on in vitro tailing reaction using a 37mer RNA substrate with four randomized nucleotides at the 3´ end