Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints.
Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints.
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DOI：
10.1038/s41467-023-42695-4
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发表时间：
2023-11-18
影响因子：
16.6
通讯作者：
Liu, Qi
中科院分区：
文献类型：
--
作者：
Chen, Qinchang;Chuai, Guohui;Zhang, Haihang;Tang, Jin;Duan, Liwen;Guan, Huan;Li, Wenhui;Li, Wannian;Wen, Jiaying;Zuo, Erwei;Zhang, Qing;Liu, Qi
强大的CRISPR基因组编辑系统受到其脱靶效应的阻碍，并且由于缺乏对CRISPR分子机制的深入理解，现有计算工具在全基因组脱靶预测方面的性能有限。在这项研究中，我们提出将分子动力学（MD）模拟纳入CRISPR系统的计算分析中，并提出CRISOT，一个包含四个相关模块的集成工具套件，即，CRISOT-FP、CRISOT-Score、CRISOT-Spec、CRISORT-Opti分别用于RNA-DNA分子相互作用指纹生成、全基因组CRISPR脱靶预测、sgRNA特异性评估和Cas9系统的sgRNA优化。我们全面的计算和实验测试表明，CRISOT通过广泛的计算机验证和概念验证实验验证优于现有工具。此外，CRISOT显示出准确预测碱基编辑器和主要编辑器的脱靶效应的潜力，表明衍生的RNA-DNA分子相互作用指纹捕获了不同CRISPR系统之间RNA-DNA相互作用的潜在机制。总的来说，CRISOT为全基因组CRISPR脱靶预测、评估和sgRNA优化提供了一个有效且可推广的框架，以改善CRISPR基因组编辑中的靶向特异性。CRISPR-Cas脱靶分析很重要。在这里，作者将分子动力学模拟纳入CRISPR编辑的计算分析中，并报告了CRISOT工具套件，并将其应用于全基因组CRISPR脱靶预测和sgRNA优化。
The powerful CRISPR genome editing system is hindered by its off-target effects, and existing computational tools achieved limited performance in genome-wide off-target prediction due to the lack of deep understanding of the CRISPR molecular mechanism. In this study, we propose to incorporate molecular dynamics (MD) simulations in the computational analysis of CRISPR system, and present CRISOT, an integrated tool suite containing four related modules, i.e., CRISOT-FP, CRISOT-Score, CRISOT-Spec, CRISORT-Opti for RNA-DNA molecular interaction fingerprint generation, genome-wide CRISPR off-target prediction, sgRNA specificity evaluation and sgRNA optimization of Cas9 system respectively. Our comprehensive computational and experimental tests reveal that CRISOT outperforms existing tools with extensive in silico validations and proof-of-concept experimental validations. In addition, CRISOT shows potential in accurately predicting off-target effects of the base editors and prime editors, indicating that the derived RNA-DNA molecular interaction fingerprint captures the underlying mechanisms of RNA-DNA interaction among distinct CRISPR systems. Collectively, CRISOT provides an efficient and generalizable framework for genome-wide CRISPR off-target prediction, evaluation and sgRNA optimization for improved targeting specificity in CRISPR genome editing. Analysis of CRISPR-Cas off-targets is important. Here the authors incorporate molecular dynamics simulations in the computational analysis of CRISPR editing and report the CRISOT tool suite and apply this to genome-wide CRISPR off-target prediction and sgRNA optimisation.
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