Absolute quantification of mammalian microRNAs. Absolute quantification of mammalian microRNAs

MicroRNAs (miRNAs) are small regulatory RNAs found in animals and plants. miRNAs act by directing Argonaute proteins to destabilize partially complementary targets or cleave perfectly paired transcripts. The intracellular concentration of a miRNA dictates the potency of repression, yet the absolute abundance of just a few miRNAs was determined in mammalian tissues. Here, our experiments in cultured cells show that the miRNA intracellular concentration predicts the efficacy of silencing of fully complementary targets. We also report the absolute levels of miRNAs in 15 human, mouse, and fly cell lines and in 17 mouse tissues, including eight regions of the brain. We find that miRNAs accumulate to ~6-fold greater levels in animal tissues compared to immortalized cultured cells: e.g., miR-1a abundance in the skeletal muscle is ~700,000 copies / 10 pg total RNA or ~0.1% of total RNA. We also identified several previously unreported tissue-specific miRNAs in mice. Strikingly, miRNA profiles in the eight regions of the brain were virtually indistinguishable with just two miRNAs expressed in one or two brain compartments. Nearly perfectly complementary transcripts are known to destabilize miRNAs via the ZSWIM8 pathway. We however show that the artificial expression of a fully complementary target does not destabilize miR-122 in the mouse liver, suggesting that therapies relying on tissue-specific miRNA-mediated cleavage are unlikely to impact the endogenous levels of miRNAs.