To determine which miRNAs would form the most complementary and stable duplex with the BK mRNA 3’UTR, we base-paired 109 rodent neuronal miRNAs with the known rat BK mRNA 3’UTR (AF135265), using RNAHybrid (Kruger and Rehmsmeier, 2006), and visually inspected each hybridization. Among promising miRNA species (Figure 3A) miR-9 was the best candidate, with high complementarity (Figure 3B), one of the lowest predicted free energy of hybridization (−22.3 kcal/mol), and a single miR-9 MRE (Figure S6). We confirmed our analysis using TargetScan (Lewis et al., 2005;Lewis et al., 2003, Grimson et al., 2007). These characteristics strongly suggested that miR-9 could bind to BK mRNA and cause its cleavage and downregulation.
