4.8 Article

Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag

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NATURE METHODS
卷 20, 期 6, 页码 898-+

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NATURE PORTFOLIO
DOI: 10.1038/s41592-023-01859-2

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PE-tag is a genome-wide approach for identifying potential off-target sites of prime editors, enabling high-throughput profiling and safety evaluation.
Prime editors have a broad range of potential research and clinical applications. However, methods to delineate their genome-wide editing activities have generally relied on indirect genome-wide editing assessments or the computational prediction of near-cognate sequences. Here we describe a genome-wide approach for the identification of potential prime editor off-target sites, which we call PE-tag. This method relies on the attachment or insertion of an amplification tag at sites of prime editor activity to allow their identification. PE-tag enables genome-wide profiling of off-target sites in vitro using extracted genomic DNA, in mammalian cell lines and in the adult mouse liver. PE-tag components can be delivered in a variety of formats for off-target site detection. Our studies are consistent with the high specificity previously described for prime editor systems, but we find that off-target editing rates are influenced by prime editing guide RNA design. PE-tag represents an accessible, rapid and sensitive approach for the genome-wide identification of prime editor activity and the evaluation of prime editor safety. PE-tag is a genome-wide approach to map the off-target effects of in vitro and in vivo prime editing.

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