A bioinformatics approach for investigating the determinants of Drosha processing

We use a bioinformatics approach to search for the biological features that determine the cleavage site of the Microprocessor complex (or Drosha) within known miRNA hairpins. Towards this goal, we employ a previously developed methodology, termed DuplexSVM, which can accurately identify the four ends of a miRNA:miRNA* duplex. Here we use DuplexSVM to study how the Drosha determines its cleavage site. We perform in silico mutagenesis experiments on 142 hairpins by changing the distance of the Drosha site from the loop tip or the stem - single stranded tails junction by adding or removing matching nucleotides. Our results suggest that the Drosha cleavage site is mainly determined by its distance from the terminal loop tip.