PT - JOURNAL ARTICLE AU - McGeary, Sean E. AU - Lin, Kathy S. AU - Shi, Charlie Y. AU - Bisaria, Namita AU - Bartel, David P. TI - The biochemical basis of microRNA targeting efficacy AID - 10.1101/414763 DP - 2018 Jan 01 TA - bioRxiv PG - 414763 4099 - http://biorxiv.org/content/early/2018/09/11/414763.short 4100 - http://biorxiv.org/content/early/2018/09/11/414763.full AB - MicroRNAs (miRNAs) act within Argonaute proteins to guide repression of mRNA targets. Although various approaches have provided insight into target recognition, the sparsity of miRNA–target affinity measurements has limited understanding and prediction of targeting efficacy. Here, we adapted RNA bind-n-seq to enable measurement of relative binding affinities between Argonaute–miRNA complexes and all ≤12-nucleotide sequences. This approach revealed noncanonical target sites unique to each miRNA, miRNA-specific differences in canonical target-site affinities, and a 100-fold impact of dinucleotides flanking each site. These data enabled construction of a biochemical model of miRNA-mediated repression, which was extended to all miRNA sequences using a convolutional neural network. This model substantially improved prediction of cellular repression, thereby providing a biochemical basis for quantitatively integrating miRNAs into gene-regulatory networks.