Evolution of microRNAs and their targets: are all microRNAs biologically relevant?

Abstract

MicroRNAs (miRNAs) are defined by their precise processing from a longer stem-loop precursor and by their subsequent ability to direct the regulation of target RNAs distinct from the miRNA precursor. Several lines of evidence suggest that miRNAs arose at least twice during eukaryotic evolution from an ancestral, pan-eukaryotic small RNA producing molecular machinery, though alternative scenarios cannot be ruled out. A handful of plant miRNAs are strongly expressed, widely conserved among plants, and have identical targets in long-diverged species; most of these very well conserved miRNA-target relationships involve DNA-binding transcription factors with suspected roles in developmental control. In contrast, a much greater number of plant miRNAs are weakly expressed, poorly conserved, and have few if any readily identifiable targets. These miRNAs appear to be evolutionarily "transient", and many of them may be of little to no selective value. However, this ever-changing cast of transient miRNAs could provide a reservoir of potentially useful miRNAs from which new regulatory interactions sometimes are selected.