Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs

Abstract

Transfection of small RNAs (si/miRNAs) into cells typically lowers expression of many genes. Unexpectedly, increased expression of genes also occurs. We investigated whether this upregulation results from a saturation effect, i.e. competition for intracellular small RNA processing machinery between the transfected si/miRNAs and the endogenous pool of microRNAs (miRNAs). To test this hypothesis, we analyzed genome-wide transcript responses from more than 150 published transfection experiments in 7 different cell types. We show that endogenous miRNA targets have significantly higher expression levels following transfection, consistent with an impaired effectiveness of endogenous miRNA repression. Further confirmation comes from concentration and temporal dependence. Strikingly, the profile of endogenous miRNAs can largely be inferred by correlating miRNA sites with gene expression changes after transfections. The saturation and competition effects present practical implications for miRNA target prediction, the design of si/shRNA genomic screens and siRNA therapeutics.