Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
Nature. 2024 Apr;628(8008):639-647. doi: 10.1038/s41586-024-07259-6. Epub 2024 Apr 3.
Prime editing enables the precise modification of genomes through reverse transcription of template sequences appended to the 3' ends of CRISPR-Cas guide RNAs. To identify cellular determinants of prime editing, we developed scalable prime editing reporters and performed genome-scale CRISPR-interference screens. From these screens, a single factor emerged as the strongest mediator of prime editing: the small RNA-binding exonuclease protection factor La. Further investigation revealed that La promotes prime editing across approaches (PE2, PE3, PE4 and PE5), edit types (substitutions, insertions and deletions), endogenous loci and cell types but has no consistent effect on genome-editing approaches that rely on standard, unextended guide RNAs. Previous work has shown that La binds polyuridine tracts at the 3' ends of RNA polymerase III transcripts. We found that La functionally interacts with the 3' ends of polyuridylated prime editing guide RNAs (pegRNAs). Guided by these results, we developed a prime editor protein (PE7) fused to the RNA-binding, N-terminal domain of La. This editor improved prime editing with expressed pegRNAs and engineered pegRNAs (epegRNAs), as well as with synthetic pegRNAs optimized for La binding. Together, our results provide key insights into how prime editing components interact with the cellular environment and suggest general strategies for stabilizing exogenous small RNAs therein.
先导编辑通过将模板序列反向转录到 CRISPR-Cas 引导 RNA 的 3' 末端,实现对基因组的精确修饰。为了鉴定先导编辑的细胞决定因素,我们开发了可扩展的先导编辑报告器,并进行了全基因组 CRISPR 干扰筛选。从这些筛选中,一个单一的因素成为了先导编辑的最强介导因素:小 RNA 结合外切核酸酶保护因子 La。进一步的研究表明,La 促进了各种方法(PE2、PE3、PE4 和 PE5)、编辑类型(取代、插入和缺失)、内源性基因座和细胞类型的先导编辑,但对依赖标准、未扩展的引导 RNA 的基因组编辑方法没有一致的影响。先前的工作表明,La 结合 RNA 聚合酶 III 转录物 3' 末端的多尿嘧啶序列。我们发现 La 与多聚尿嘧啶化的先导编辑引导 RNA(pegRNA)的 3' 末端在功能上相互作用。根据这些结果,我们开发了一种与 La 的 RNA 结合、N 端结构域融合的先导编辑蛋白 (PE7)。该编辑器提高了表达 pegRNA 和工程 pegRNA (epegRNA) 以及针对 La 结合优化的合成 pegRNA 的先导编辑效率。总之,我们的研究结果提供了关键的见解,说明先导编辑组件如何与细胞环境相互作用,并提出了在其中稳定外源小 RNA 的一般策略。
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