Toolgen, Seoul, Republic of Korea.
Nat Commun. 2022 Dec 29;13(1):7975. doi: 10.1038/s41467-022-35743-y.
Prime editors (PEs) are powerful tools that widen the possibilities for sequence modifications during genome editing. Although methods based on the analysis of Cas9 nuclease or nickase activity have been used to predict genome-wide off-target activities of PEs, no tool that directly uses PEs for this purpose has been reported yet. In this study, we present a cell-based assay, named TAgmentation of Prime Editor sequencing (TAPE-seq), that provides genome-wide off-target candidates for PEs. TAPE-seq analyses are successfully performed using many different versions of PEs. The TAPE-seq predictions are compared with results from two other off-site prediction methods, Cas9 nuclease-based GUIDE-seq and Cas9 nickase-based Digenome-seq (nDigenome-seq). TAPE-seq shows a lower miss rate, and a higher area under the receiver operating characteristic curve compared to the other methods. TAPE-seq also identified valid off-target sites that were missed by the other methods.
先导编辑（Prime editors，PEs）是在基因组编辑过程中拓宽序列修饰可能性的强大工具。虽然基于 Cas9 核酸酶或 Nickase 活性分析的方法已被用于预测 PEs 的全基因组脱靶活性，但尚未有工具可直接用于此目的。在这项研究中，我们提出了一种基于细胞的测定方法，命名为 Prime Editor 测序的 TAgmentation（TAPE-seq），它为 PEs 提供了全基因组脱靶候选物。TAPE-seq 分析可成功应用于许多不同版本的 PEs。将 TAPE-seq 的预测结果与另外两种脱靶预测方法 Cas9 核酸酶基 GUIDE-seq 和 Cas9 Nickase 基 Digenome-seq（nDigenome-seq）的结果进行比较。与其他方法相比，TAPE-seq 显示出更低的漏检率和更高的接收者操作特征曲线下面积。TAPE-seq 还鉴定了其他方法错过的有效脱靶位点。
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