Since miRNA targets 3’UTRs, one possible explanation for the selective destruction of transcripts is the presence of multiple 3’UTRs (3’UTR heterogeneity) with only some of them containing miR-9 MRE. 3’UTR heterogeneity is a common feature of many genes (Hughes, 2006), and can result from: 1) alternative polyadenylation within the same 3’UTR, and/or 2) the presence of multiple 3’UTRs. Alternative polyadenylation signal (PAS) sites can produce mRNAs with 3’UTRs of different lengths (Legendre et al., 2006). We observed that the rat BK 3’UTR (AF135265) has two potential PAS sites bracketing miR-9 MRE, which potentially could produce a long 3’UTR with a miR-9 MRE, and a shorter 3’UTR lacking the miR-9 MRE (Figure S6).
