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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高通量 PRIME 编辑屏幕可识别人类基因组中的功能性 DNA 变异。
DOI：
10.1101/2023.07.12.548736
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Shen,Yin
中科院分区：
文献类型：
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作者：
Ren,Xingjie;Yang,Han;Nierenberg,JoviaL;Sun,Yifan;Chen,Jiawen;Beaman,Cooper;Pham,Thu;Nobuhara,Mai;Takagi,MayaAsami;Narayan,Vivek;Li,Yun;Ziv,Elad;Shen,Yin
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，我们开发了一种合并的引物编辑筛选方法，PRIME，可以应用于在一个具有高重现性的单一实验中表征数千个编码和非编码变体。为了展示其应用，我们首先通过PRIME介导的单碱基解析分析鉴定了716 bp MYC增强子的必需核苷酸。接下来，我们应用PRIME对1，304个全基因组关联研究（GWAS）确定的与乳腺癌相关的非编码变异和来自ClinVar的3，699个变异进行了功能表征。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性而发挥功能。总的来说，我们证明了PRIME能够以单碱基分辨率和规模表征遗传变异，推进准确的基因组注释，用于疾病风险预测，诊断和治疗靶点识别。
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.