Fig. 4

Analysis of RNA editing by long-read sequencing. A Distribution of mismatch types at different steps of our regular separate samples analysis workflow with REDItools. B Distribution of mismatch types at different steps of a modified separate samples analysis workflow where variant calling was performed with the IsoPhase tool. C Venn diagram comparing the number of editing sites detected by each computational pipeline. D Venn diagram comparing the number of editing sites identified through Illumina short-read sequencing analysis and PacBio long-read sequencing analysis. E Box plot showing the difference in editing rate of a site between two isoforms and the distance of that site to the closest splice junction in the gene. F An example in the 3’UTR of cdc27 illustrating how editing may regulate splicing. The ADAR target is at chr9_10S:5,524,147 (xenLae2) and is highlighted in red, while the 3’ splice site is at chr9_10S: 5,524,143–5,524,144. We found that the editing rate of the unspliced isoform was 25.0%, while that of the spliced isoform was 0.0%. The polypyrimidine tract is boxed in green, while the putative QKI binding site, whose consensus motif is ACUAAY-N_1–20-UAAY, is boxed in orange. Based on studies in mammals, the consensus sequence of the 3’ splice site consists of a stretch of at least 12 pyrimidines followed by an AG dinucleotide. Here, the requisite polypyrimidine tract is followed by a non-canonical CC dinucleotide. G Boxplots showing the editing patterns of genes with two target sites. H Secondary structure predictions of the 5’UTR of xarp when it is unedited and when the downstream target site in the gene is edited. In all boxplots, the box depicts the first to last quartiles, whiskers indicate 1.5 times the interquartile range, the center line represents the median, and points represent the outliers