Prime editing systems hold tremendous promise for the precise correction of pathogenic mutations. We developed a method to tag sequences modified by a prime editor to evaluate its genome-wide precision for therapeutic applications.
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Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019). This paper is the original description of a Cas9-based prime editing system.
Giannoukos, G. et al. UDiTaS, a genome editing detection method for indels and genome rearrangements. BMC Genomics 19, 212 (2018). This paper reports the UMI-based Tn5 tagmentation methodology.
Tsai, S. Q. et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat. Biotechnol. 33, 187–197 (2015). This paper reports the GUIDE-seq method to capture Cas9 nuclease-based off-target sites genome-wide.
Kim, D. Y., Moon, S. B., Ko, J. H., Kim, Y. S. & Kim, D. Unbiased investigation of specificities of prime editing systems in human cells. Nucleic Acids Res 48, 10576–10589 (2020). This paper reports a nickase-based Digenome-seq (nDigenome-seq) approach to identify single-strand breaks induced by Cas9 H840A nickase.
Petri, K. et al. CRISPR prime editing with ribonucleoprotein complexes in zebrafish and primary human cells. Nat. Biotechnol. 40, 189–193 (2021). This paper reports prime editing with purified prime editor protein.
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This is a summary of: Liang, S.-Q. et al. Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag. Nat. Methods https://doi.org/10.1038/s41592-023-01859-2 (2023)
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Capturing prime editor off-target sites within the genome. Nat Methods 20, 801–802 (2023). https://doi.org/10.1038/s41592-023-01860-9