More than half of annotated human miRNAs are never expressed at levels sufficient for biological function

MicroRNAs (miRNAs) are widely studied for their role in post-transcriptional gene regulation, often using exogenous overexpression systems to reveal their functions. However, such approaches may not accurately reflect endogenous miRNA activity due to the substantially higher expression levels achieved experimentally. To address this, we sought to determine the minimal endogenous expression threshold required for a miRNA to exert biologically significant effects. By comparing these experimentally determined expression thresholds with small RNA sequencing datasets comprising hundreds of cell lines and tens of thousands of tissue samples, we found that more than half of all annotated miRNAs are never expressed at levels sufficient to be biologically relevant. This calls into question the conclusions of thousands of studies reporting functions for these lowly expressed miRNAs, whose results are likely attributable to artificial overexpression rather than physiological activity. Our study highlights the need for more rigorous evaluation of miRNA functionality in their native context, and provides further support to arguments that the size of the functional human "microRNAome" is far smaller than some estimates of miRNA numbers based upon small RNA sequencing data.