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In human, nearly half of the known microRNAs (miRNAs) are encoded within the introns of protein-coding genes. The embedment of these miRNA genes within the sequences of protein-coding genes alludes to a possible functional relationship between intronic miRNAs and their hosting genes. Several studies, using predicted targets, suggested that intronic miRNAs influence their hosts’ function either antagonistically or synergistically. New experimental data of miRNA expression patterns and targets enable exploring this putative association by relying on actual data rather than on predictions. Here, our analysis based on currently available experimental data implies that the potential functional association between intronic miRNAs and their hosting genes is limited. For host-miRNA examples where functional associations were detected, it was manifested by either autoregulation, common targets of the miRNA and hosting gene, or through the targeting of transcripts participating in pathways in which the host gene is involved. This low prevalence of functional association is consistent with our observation that many intronic miRNAs have independent transcription start sites and are not coexpressed with the hosting gene. Yet, the intronic miRNAs that do show functional association with their hosts were found to be more evolutionarily conserved compared to other intronic miRNAs. This might suggest a selective pressure to maintain this architecture when it has a functional consequence.

Assessing the functional association of intronic miRNAs with their host genes