A sliding-bulge structure at the Dicer processing site of pre-miRNA regulates alternative Dicer processing to generate 5’-isomiRs (pre-miR-203). Homo sapiens

5’-isomiRs expand the repertoire of miRNA targets. However, how they are generated is not well understood. Here, we showed that, for some miRNAs in mammalian cells, 5’-isomiRs are generated by alternative Dicer processing by using miRNA offset RNAs (moRs) to determine Drosha cleavage sites in cells. In addition, we showed that in miR-203, alternative Dicer processing is regulated by a conserved sliding-bulge structure at the Dicer processing site, which allows the pre-miRNA molecule to fold into two different structures that are processed differently by Dicer. So far no RNA motif that slides to change conformation and alter a protein–RNA interaction has been reported. Thus, our study revealed a novel RNA motif that regulates 5’-isomiR generation in some miRNAs. It might also contribute to regulating protein–RNA interactions in other biological processes, since it takes only one point mutation to generate the sliding bulge, and there are a large number of different RNAs in the cell. Overall design: Mutants as well as the wild type of pri-miR-203 were designed. They were constructed into pLL3.7 and transfected into 293FT cells. The small RNAs were then profiled with deep sequencing. Three independent profiling exprements (replicates) were included in the dataset. RNA sample from each mutant of each replicate was barcoded, multicomplexed and sequenced in a single run of illumina Miseq sequencing.