3' Nucleotide Asymmetry Directs miRNA Strand Selection

During miRNA biogenesis, double-stranded precursors are processed into duplexes comprising functionally distinct strands. The guide strand directs the miRNA-induced silencing complex (miRISC) to complementary mRNA targets, while the passenger strand is degraded. As each strand has different molecular targets, strand selection effectively determines the target repertoire of the miRISC. Previous studies suggest that 5' nucleotide identity and thermodynamic asymmetries determine miRNA strand choice in vitro. However, these guidelines cannot fully explain the observed strand preference of all miRNAs in vivo. Here, we demonstrate a conserved role for 3' nucleotide asymmetry in facilitating miRNA strand selection in Caenorhabditis elegans and human HEK293T cells. Our data show that a favorable 3' nucleotide on miRNA passenger strands can promote selection of the opposing guide strand. We propose that terminal nucleotide asymmetries on both strands of miRNA duplexes promote accurate strand selection in vivo.