High-throughput PRIME-editing screens identify functional DNA variants in the human genome.
High-throughput PRIME-editing screens identify functional DNA variants in the human genome.
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DOI：
10.1016/j.molcel.2023.11.021
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发表时间：
2023-12
期刊：
影响因子：
16
通讯作者：
Xingjie Ren;Han Yang;Jovia L. Nierenberg;Yifan Sun;Jiawen Chen;Cooper Beaman;Thu Pham;Mai Nobu
中科院分区：
文献类型：
--
作者：
Xingjie Ren;Han Yang;Jovia L. Nierenberg;Yifan Sun;Jiawen Chen;Cooper Beaman;Thu Pham;Mai Nobu
尽管在检测与人类疾病相关的DNA变异方面取得了巨大进展，但以高通量和单碱基分辨率的方式解释其功能影响仍然具有挑战性。在这里，我们开发了一种汇集的启动编辑筛选方法，PRIME，可以在一个实验中用于表征数千个编码和非编码变体，具有高重复性。为了展示其应用，我们首先通过引物介导的单碱基分辨率分析确定了716 bpMYCenhancer的必需核苷酸。接下来，我们应用PRIME对1,304个全基因组关联研究（GWAS）鉴定的与乳腺癌相关的非编码变异体和来自ClinVar的3,699个变异体进行功能表征。我们发现103个非编码变异和156个不确定意义的变异通过影响细胞适应度而发挥功能。总之，我们证明了PRIME能够在单碱基分辨率和规模上表征遗传变异，为疾病风险预测、诊断和治疗靶点鉴定提供准确的基因组注释。
Despite tremendous progress in detecting DNA variants associated with human disease, interpreting their functional impact in a high-throughput and single-base resolution manner remains challenging. Here, we develop a pooled prime-editing screen method, PRIME, that can be applied to characterize thousands of coding and non-coding variants in a single experiment with high reproducibility. To showcase its applications, we first identified essential nucleotides for a 716 bpMYCenhancer via PRIME-mediated single-base resolution analysis. Next, we applied PRIME to functionally characterize 1,304 genome-wide association study (GWAS)-identified non-coding variants associated with breast cancer and 3,699 variants from ClinVar. We discovered that 103 non-coding variants and 156 variants of uncertain significance are functional via affecting cell fitness. Collectively, we demonstrate that PRIME is capable of characterizing genetic variants at single-base resolution and scale, advancing accurate genome annotation for disease risk prediction, diagnosis, and therapeutic target identification.