Currently, most microRNA predictors perform so poorly that it was easy to assume that secondary structure formation has a more important role in target recognition, instead of relying in sequence complementarity alone. To further evaluate this hypothesis, this group previously reported the development of a quantitative (luminiscent) assay for measuring repression by microRNAs, and here they employed this methodology over a selection of targets that were engineered for specific sequence mutations. These in vitro (cell culture) observations were used to train an in silico model, which they implemented into a new predictor, available from their website.
[...] Our results show that site accessibility is as important as sequence match in the seed for determining the efficacy of microRNA- mediated translational repression, and they suggest that effective microRNA binding also requires unpairing of the local region flanking the target. We introduce a parameter-free thermodynamic model that explains these effects and shows that preferential positioning of microRNA target sites in regions of high accessibility is a conserved feature in genomes. Our findings thus indicate that the thermodynamics of intra- and intermolecular base pairing account for a significant portion of the microRNA- target interaction, consistent with observations for siRNA- target interactions. However, our model does not explain the entire variance in our experiments. This may be in part due to limitations of RNA structure prediction algorithms and their inability to account for the effects that RNA binding proteins have on secondary structures. Moreover, microRNAs bind as part of the RISC complex, [... and] RISC proteins are likely to constrain base-pairing interactions between microRNA and target site and otherwise influence the mechanics of the duplex formation.Kertesz M. et al. 2007. Nat Genet 39:1278-84
epigenetics
More comments can be found in the same issue of Nature Genetics.
