Argonaute Loading Improves the 5′ Precision of Both MicroRNAs and Their miRNA∗ Strands in Flies

MicroRNAs (miRNAs) are short regulatory RNAs that direct repression of their mRNA targets. The miRNA "seed"-nucleotides 2-7-establishes target specificity by mediating target binding. Accurate processing of the miRNA 5' end is thought to be under strong selective pressure because a shift by just one nucleotide in the 5' end of a miRNA alters its seed sequence, redefining its repertoire of targets (Figure 1). Animal miRNAs are produced by the sequential cleavage of partially double-stranded precursors by the RNase III endonucleases Drosha and Dicer, thereby generating a transitory double-stranded intermediate comprising the miRNA paired to its partially complementary miRNA* strand. Here, we report that in flies, the 5' ends of miRNAs and miRNA* strands are typically more precisely defined than their 3' ends. Surprisingly, the precision of the 5' ends of both miRNA and miRNA* sequences increases after Argonaute2 (Ago2) loading. Our data imply that either many miRNA* sequences are under evolutionary pressure to maintain their seed sequences-that is, they have targets-or that secondary constraints, such as the sequence requirements for loading small RNAs into functional Argonaute complexes, narrow the range of miRNA and miRNA 5' ends that accumulate in flies.