Fig. 3: Using NaP-TRAP to predict the translation of zebrafish 5’ UTRs.

a A schematic detailing global changes in translation during the maternal-to-zygotic transition in the developing zebrafish embryo (top left). The 5’ UTR library was generated by tiling the 5’ UTRs of 1725 zebrafish genes (bottom left). The NaP-TRAP workflow with the addition of spike-ins at the RNA extraction step (right). b Comparison of translation values between 2 and 6 hpf of the 5’ UTR library (two-sided Mann-Whitney U-test; p < 10⁻¹⁰⁰; N = 8529 reporters). Minima and maxima of the box represent the first and third quartiles, respectively, whereas the whiskers correspond to 1.5x the interquartile range (Q1-Q3). The center of the box is the median. c Schematic detailing random forest regression model feature selection (k-mer counts 1-6 nt and features characterizing upstream ORFs). d–e Scatterplot comparing each model’s prediction to the experimentally derived translation values of a test set of reporters (test set = 30% of reporters used; N = 2559 reporters; two-sided Pearson’s R) (d, e). f, g The correlation between the top 12 features and translation (measured using permuted feature importance Supplementary Fig. 4e-f; blue refers to a positive correlation and purple refers to a negative correlation; two-sided Spearman Rank Correlation Coefficient).