Identification and consequences of miRNA–target interactions — beyond repression of gene expression

Key Points Experimental approaches such as genetic screening, mRNA expression profiling, and Argonaute crosslinking and immunoprecipitation aim to identify microRNA (miRNA) targets and/or individual binding sites within them. Computational analyses of the resultant high-throughput data reveal the miRNA targets with high accuracy and resolution. Factors that define functional miRNA interaction sites include miRNA 'seed' complementarity, structural accessibility, and sequence and positional biases. These factors support modulatory interactions with RNA-binding proteins. miRNA seed families and clusters of co-expressed miRNAs are prevalent and may contribute to regulation of individual pathways across tissues and developmental stages. 'Non-canonical' miRNA-binding sites seem to be prevalent, and their functionality should be further investigated. Outcomes of miRNA–target interactions include repression and increased precision of target gene expression, as well as induction of correlations in the expression levels of different targets. Computational modelling of miRNA–target interactions has provided insights into their consequences on target expression. This Review discusses the main experimental approaches for microRNA (miRNA) target identification, as well as the modulators and the consequences of miRNA–target interactions. It also highlights the role of computational modelling in furthering the conceptual understanding of miRNA functions in gene regulatory networks. Comparative genomics analyses and high-throughput experimental studies indicate that a microRNA (miRNA) binds to hundreds of sites across the transcriptome. Although the knockout of components of the miRNA biogenesis pathway has profound phenotypic consequences, most predicted miRNA targets undergo small changes at the mRNA and protein levels when the expression of the miRNA is perturbed. Alternatively, miRNAs can establish thresholds in and increase the coherence of the expression of their target genes, as well as reduce the cell-to-cell variability in target gene expression. Here, we review the recent progress in identifying miRNA targets and the emerging paradigms of how miRNAs shape the dynamics of target gene expression.