在Cas9变种中,指南特定的效率损失和非目标减量
Liang Zhang1, Wei He1, Rongjie Fu1
1Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Nucleic acids research
|August 24, 2023
概括
高保真性Cas9变体 (HiFi,LZ3) 减少了CRISPR的目标外效应,但可以降低目标上的效率. GuideVar软件预测了这些变体的效率和非目标活动,帮助sgRNA选择.
科学领域:
- 分子生物学分子生物学
- 基因编辑技术的技术
- 生物信息学是一种生物信息学.
背景情况:
- 高忠实度聚类定期间隔的平行体重复 (CRISPR) 相关蛋白9 (Cas9) 变体旨在最大限度地减少目标外突变.
- 这些变体通常与野生型SpCas9.9相比,在目标上的效率降低.
- 在多种单向导RNA (sgRNAs) 中对变异性能的系统评估至关重要.
研究的目的:
- 综合评估HiFi和LZ3 Cas9变体的效率和目标外的配置文件.
- 为了确定影响高保真 Cas9 变异的 sgRNA 效率的依赖序列的因素.
- 开发一种用于优化这些变异的sgRNA选择的预测计算工具.
主要方法:
- 利用高通量可行性选来评估数千个sgRNAs.
- 采用合成配对的sgRNA-目标系统进行精确的评估.
- 开发了GuideVar,这是一个基于转移学习的计算框架.
主要成果:
- 大约20%的sgRNAs在HiFi或LZ3变体下显示出显著的效率损失.
- 与特定种子和非种子区域序列上下文相关的效率损失.
- 在不同的sgRNA中观察到异于目标效应的序列依赖性减少.
- GuideVar准确地预测了目标效率和目标外影响.
结论:
- 高保真Cas9变体表现出可变的效率和取决于sgRNA序列的脱特征.
- 在REC3领域的变异突变可能有助于效率的变化.
- GuideVar有效地优先考虑sgRNAs的高保真变体,从而提高实验结果.
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