Genomic and Transcriptomic Analyses of Prime Editing Guide RNA-Independent Off-Target Effects by Prime Editors

Prime editors (PEs) were developed to induce versatile edits at a guide-specified genomic locus. With all RNA-guided genome editors, guide-dependent off-target (OT) mutations can occur at other sites bearing similarity to the intended target. However, whether PEs carry the additional risk of guide-independent mutations elicited by their unique enzymatic moiety (i.e., reverse transcriptase) has not been examined systematically in mammalian cells. Here, we developed a cost-effective sensitive platform to profile guide-independent OT effects in human cells. We did not observe guide-independent OT mutations in the DNA or RNA of prime editor 3 (PE3)-edited cells, or alterations to their telomeres, endogenous retroelements, alternative splicing events, or gene expression. Together, our results showed undetectable prime editing guide RNA-independent OT effects of PE3 in human cells, suggesting the high editing specificity of its reverse-transcriptase moiety.