miRNAs are now accepted as crucial and frequent components of regulatory pathways. We are currently pursuing projects to predict target sites in animal genomes.
miRNAs and alternative isoforms.
We have carried out a detailed analysis of microRNA target sites and their location in alternative 3'UTRs. The supplementary data contains the detailed list of predictions from that analysis (Majoros and Ohler, Spatial preferences of microRNA targets in 3' untranslated regions, BMC Genomics 2007.)
miRNA target prediction without conservation.
It is an open question how conserved miRNA target sites are. Many target prediction algorithms rely heavily on conservation, but in some settings, e.g. for predicting viral miRNA targets, it does not make much sense to assume conservation. We are thus developing approaches to predict target sites without relying on the conservation in several genomes. For instance, we have used sequence with expression data to predict targets for the miRNAs of the human Kaposi-sarcoma associated herpes virus (KSHV) (Gottwein et al., Nature 2007).