Modelling RNA Structures that Mediate Specific Nucleic Acid Recognition applied to the Inference of MicroRNA-Target Interactions

MicroRNA genes produce functional RNA molecules, rather than proteins, and have been found to play essential roles in the post-transcriptional regulation of gene expression. These short, non-coding RNAs are able to specifically recognize nucleic acid sequences encoded in their targets. Although hundreds of microRNA genes have been identified, target genes have been found for only a few examples. Using probabilistic models to describe the RNA secondary structures which mediate interactions between a microRNA and its target, we are able to computationally predict microRNA regulatory events from genomic sequence data. Our models are applied to large-scale comparisons of genomic sequences from multiple species and are optimized using scores that incorporate experimentally-derived energetic parameters of RNA secondary structure formation.