a Comparison of A3A-dominated tumors (APOBEC3A+) and tumors without APOBEC mutations or activity (APOBEC-) revealed sites undergoing frequent APOBEC-dependent C->U RNA editing. The top 50 most frequently edited sites were aggregated into a logogram showing relative frequencies of the bases at each position. b Classification of sites by hairpin characteristics revealed structural preferences of APOBEC-dependent editing. UpC sites exposed in a hairpin loop are mutated at higher frequencies. The position of the U in the loop affects mutability, with the highest RNA editing frequencies observed for C’s positioned at the 3′-most position in a loop of four nucleotides. c Schematic representation of stem-loop structures in the genes DDOST and CYFIP1, the two most highly APOBEC-edited RNA sites in patient tumor samples. d RNA stem-loop editing levels detected in each patient were superimposed in green on the patients from Fig. 1b for whom RNA-sequencing data was available. e RNA stem-loop editing levels correlate strongly with the amount of A3A expression in patient tumors (ρ = +0.72, p = 3 × 10−55).