Selective Suppression of the Splicing-Mediated MicroRNA Pathway by the Terminal Uridyltransferase Tailor

• Published in: Molecular cell Vol. 59; no. 2; pp. 217 - 228
• Main Authors: Bortolamiol-Becet, Diane, Hu, Fuqu, Jee, David, Wen, Jiayu, Okamura, Katsutomo, Lin, Ching-Jung, Ameres, Stefan L., Lai, Eric C.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 16-07-2015
• Subjects: Animals; Base Sequence; Drosophila melanogaster - genetics; Drosophila melanogaster - metabolism; Drosophila Proteins - antagonists & inhibitors; Drosophila Proteins - genetics; Drosophila Proteins - metabolism; Evolution, Molecular; Female; Gene Knockdown Techniques; Genes, Insect; MicroRNAs - chemistry; MicroRNAs - genetics; MicroRNAs - metabolism; Nucleic Acid Conformation; Ovary - metabolism; RNA Nucleotidyltransferases - antagonists & inhibitors; RNA Nucleotidyltransferases - genetics; RNA Nucleotidyltransferases - metabolism; RNA Processing, Post-Transcriptional; RNA Splicing; Substrate Specificity
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2015.05.034

Several terminal uridyltransferases (TUTases) are known to modulate small RNA biogenesis and/or function via diverse mechanisms. Here, we demonstrate that Drosophila splicing-derived pre-miRNAs (mirtrons) are efficiently modified by the previously uncharacterized TUTase, Tailor. Tailor is necessary and sufficient for mirtron hairpin uridylation, and this modification inhibits mirtron biogenesis. Genome-wide analyses demonstrate that mirtrons are dominant Tailor substrates, and three features contribute to substrate specificity. First, reprogramming experiments show Tailor preferentially identifies splicing-derived miRNAs. Second, in vitro tests indicate Tailor prefers substrate hairpins over mature miRNAs. Third, Tailor exhibits sequence preference for 3′-terminal AG, a defining mirtron characteristic. Our work supports the notion that Tailor preferentially suppresses biogenesis of mirtrons, an evolutionarily adventitious pre-miRNA substrate class. Moreover, we detect preferential activity of Tailor on 3′-G canonical pre-miRNAs, and specific depletion of such loci from the pool of conserved miRNAs. Thus, Tailor activity may have had collateral impact on shaping populations of canonical miRNAs.
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•Splicing-derived pre-miRNAs (mirtrons) are preferentially uridylated among sRNAs•Mirtron uridylation is mediated by the TUTase Tailor, which inhibits their biogenesis•Tailor recognizes spliced hairpins and 3′-AG hairpins characteristic of mirtrons•Tailor opposes adventitious mirtron emergence, and shapes the canonical miRNA pool
Bortolamiol-Becet et al. demonstrate that biogenesis of Drosophila splicing-derived pre-miRNAs (mirtrons) is opposed by the substrate-selective action of the TUTase Tailor. We postulate this process counteracts the spurious generation of miRNAs from spliced introns, and that it has had collateral impact on shaping the population of canonical miRNAs.