MiRNAs control gene expression via recognition of specific sequences in the 3' untranslated region of target genes, leading to mRNA degradation and consequently translational repression. The regulatory impact of miRNAs does not only depend on their expression levels, but also on their targets' mRNA configuration. Via alternative polyadenylation mRNA isoforms are created that may or may not contain the respective miRNA target sequence, turning the regulatory between these two on or off. In the following article, we describe our protocol on how to combine a bioinformatics evaluation of a potential miRNA-target gene interaction using the public web framework miRIAD with 5' rapid amplification of cDNA ends (5'-RACE) in order to explore differential gene regulation by miRNAs through alternative polyadenylation.
Keywords: 3′ RACE; Alternative polyadenylation; Differential miRNA targeting; Intronic miRNAs; Tissue-specific regulation.