High throughput PRIME editing screens identify functional DNA variants in the human genome

Despite tremendous progress in detecting DNA variants associated with human disease, interpreting their functional impact in a high-throughput and base-pair resolution manner remains challenging. Here, we develop a novel pooled prime editing screen method, PRIME, which can be applied to characterize...

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Published inbioRxiv : the preprint server for biology
Main Authors Ren, Xingjie, Yang, Han, Nierenberg, Jovia L, Sun, Yifan, Chen, Jiawen, Beaman, Cooper, Pham, Thu, Nobuhara, Mai, Takagi, Maya Asami, Narayan, Vivek, Li, Yun, Ziv, Elad, Shen, Yin
Format Journal Article
LanguageEnglish
Published United States 12.07.2023
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Summary:Despite tremendous progress in detecting DNA variants associated with human disease, interpreting their functional impact in a high-throughput and base-pair resolution manner remains challenging. Here, we develop a novel pooled prime editing screen method, PRIME, which 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 bp enhancer via PRIME-mediated saturation mutagenesis. Next, we applied PRIME to functionally characterize 1,304 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 PRIME capable of characterizing genetic variants at base-pair resolution and scale, advancing accurate genome annotation for disease risk prediction, diagnosis, and therapeutic target identification.