Extended Data Fig. 5: Additional data and analysis showing that increased BE3 expression induces higher numbers and frequencies of transcriptome-wide RNA cytosine edits in HEK293T cells.

a, Percentages of different predicted effects and locations of edited cytosines identified in each RNA-seq replicate from Extended Data Fig. 4c. b, Percentages (x-axis) and numbers (shown inside bars) of expressed genes in each RNA-seq replicate that have at least one edited cytosine. c, Sequence logos derived from edited cytosines identified in each RNA-seq duplicate experiment from Extended Data Fig. 4c for the RNF2, EMX1 and non-targeted gRNAs. Analysis done using RNA-seq data generated from cDNA; every T depicted should be considered a U in RNA. d, Venn diagram showing numbers of edited cytosines identified with the RNF2, EMX1 and non-targeted gRNAs. For each gRNA, the circle encompasses the union of cytosines identified in the two replicates (data derived from the experiments shown in Extended Data Fig. 4c). e, Venn diagrams showing all possible pairwise comparisons of edited cytosines identified in duplicate experiments performed with the RNF2, EMX1 and non-targeted gRNAs (data derived from the experiments shown in Extended Data Fig. 4c). f, Scatter plot correlating RNA editing frequencies (x-axis) of 154,264 cytosines previously shown to be edited by RNA-seq with DNA editing frequencies (y-axis) determined by WES performed with DNA derived from the same experiments (n = 3 biologically independent samples, pooled data). Superimposed histograms (top and right) depict the percentages of cytosines that show various editing rates on RNA (upper x-axis) or DNA (right y-axis).