Fig. 3

Refinement of 3′ UTR annotations in S2 cells and development of a regression model that predicts miRNA targeting efficacy in Drosophila. a Poly(A) sites detected in S2 cells by 3P-seq, classified with respect to their previous annotation status. b Extension and contraction of longest 3′ UTR isoforms relative to the FlyBase annotations. For each gene with a poly(A) site detected using 3P-seq, the difference between the longest 3′ UTR isoform annotated using 3P-seq was compared to longest 3′ UTR isoform annotated at FlyBase. These differences were then binned as indicated, and the number of sites assigned to each bin is plotted. c Optimization of scoring of predicted 3′ supplementary pairing in flies. Predicted thermodynamic energy scores were computed for the pairing between a 9-nt region upstream of canonical 7–8-nt 3′UTR sites and a variable-length region of the miRNA with the indicated size (window size) that began at the indicated position of the miRNA. The heatmap displays the partial correlations between these scores and the repression associated with the corresponding sites, determined while controlling for site type. d Optimization of the scoring of predicted structural accessibility in flies. Predicted RNA structural accessibility scores were computed as the average pairing probabilities for variable-length (window size) regions that centered at the indicated mRNA position, shown with respect to the seed match of each canonical 7–8-nt 3′ UTR site. The heatmap displays the partial correlations between these values and the repression associated with the corresponding sites, determined while controlling for site type. e The contributions of site type and each of the six features of the context model. For each site type, the coefficients for the multiple linear regression are plotted for each feature. Because features were each scored on a similar scale, the relative contribution of each feature in discriminating between more or less effective sites was roughly proportional to the absolute value of its coefficient. Also plotted are the intercepts, which roughly indicate the discriminatory power of site type. Bars indicate the 95% confidence intervals of each coefficient. See also Additional file 2: Table S4, Table S5, and Figure S3A