Endogenous miRNA-200b/c activity and regulation explored by a functional dual fluorescence reporter

Since their discovery, microRNAs (miRNA)s have been widely studied in almost every field of biology and medicine, leading to the identification of important gene regulation circuits and cellular mechanisms. However, investigations are generally focused on the analysis of their downstream targets and biological functions in overexpression and knockdown approaches, while miRNAs endogenous levels and activity remain poorly investigated. Here, we used the cellular plasticity-regulating process of epithelial-to-mesenchymal transition (EMT) as a model to show the efficacy of a plasmid-based fluorescent sensor to separate cells with distinct EMT signatures, based on miR-200b/c activity. The system was further combined with a CRISPR-Cas9 screening platform to unbiasedly identify miR-200b/c upstream regulating genes. The sensor allows to infer miRNAs fundamental biological properties, as profiling of sorted cells indicated miR-200b/c as a molecular switch between EMT differentiation and proliferation, and suggested a role for metabolic enzymes in miR-200/EMT regulation. Analysis of miRNAs’ endogenous levels and activity could lead to a better comprehension of their biological role in physiology and disease. Gene expression analysis by RNAseq in colorectal carcinoma cell line HCT116 sorted for high and low activity of miR-200b/c