For single- and double-stranded regions we obtained the observed (Oss and Ods, respectively) and expected (Ess and Eds, respectively) rates of editing from publicly available libraries (Table 1) as described in Materials and Methods.
After validation, the false positive rate of RNA editing site detection was approximately 40%.
This rate of gene editing (17.0% ± 0.35 for iPS cell and 13.6% ± 1.4 for HEK293 cells) was only observed when using a plasmid donor template (Mut plasmid) containing a mutated PAM, a sequence essential for cleavage by Cas9.
Although the rates of gene editing reported by Cai et al. are low and variable, they approach the levels required for effective gene therapy in whole animals including humans.
The extent to which this process occurs varies widely, with the highest rates of RNA editing seen in early diverging vascular plants such as ferns and lycophytes and the lowest seen in very early diverging lineages such as some liverworts [ 8].
Under this condition, on average 2 3% of the cells mutated at the target site were found to express yfp, thereby displaying a conversion of at least one gfp allele into yfp, which is a reasonable success rate of precise genome editing (Table S2).
The opposite condition is also found, e.g., in taxa with a high substitution rate and high levels of editing (e.g., ccmB in Lilaea).
After editing was complete, we calculated the error rate for each batch with the following formula: Error rate = Number of edits (Number of variables on form ) × (Number of forms in batch ) Similarly, we summed errors and forms over all batches to derive an error rate for each type of form.
The comparison of editing rates for wt and deacylation defective enzymes in the presence of tRNA shows that approximately 30% of overall editing originates from tRNA-dependent pretransfer editing.
No significant correlation was found either between substitution rate and the number of changes in edited sites in any of the sister group comparisons (Table 2), or between substitution rate and number of edited sites present in each taxa.
