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gRNA-SeqRET:一种通用工具,用于针对性和基因组规模的gRNA设计和对 prokaryotes 和 eukaryotes 的序列提取

Lisa Simirenko¹, Jan-Fang Cheng^1,2, Ian Blaby^1,2

¹US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.

Frontiers in bioengineering and biotechnology

|September 18, 2023

概括

我们开发了gRNA-SeqRET,这是一个in silico工具,用于设计聚合指导RNA (gRNA) 库,用于在任何生物体中进行CRISPR查. 这种可扩展的工作流程有助于基因查和同质化臂设计,促进基因功能研究.

科学领域:

遗传学和基因组学遗传学和基因组学
生物信息学和计算生物学

背景情况:

高通量基因查,包括CRISPR技术,可以快速建立基因表型关联和序列功能关系.
聚合导向RNA (gRNA) 库和测序试验允许对非模型生物进行功能质询,并对目标位置进行定量适应性评估.

研究的目的:

开发一个自动化的,可扩展的in silico设计工作流程,用于构建聚合的gRNA组件.
创建一个工具,以帮助设计gRNA库,以准特定的基因组区域或整个基因组的原核生物和真核生物.

主要方法:

基于CCTop的gRNA序列区域提取工具 (gRNA-SeqRET) 工作流程的开发.
针对用户指定的区域或整个基因组的gRNA的自动选择.
自动批量提取序列区域用于基因构造中的同质性臂设计.
在密切相关的基因组之间应用gRNA库的in silico评估 (平均核酸标识>95%).

主要成果:

gRNA-SeqRET可为各种生物体实现gRNA库的自动化和可扩展设计.
该工具自动提取序列区域,方便对基因修改进行同质臂的设计.
在基分析表明设计的gRNA图书馆对于密切相关的基因组 (ANI>95%) 的显著相关性.

结论:

gRNA-SeqRET为设计高通量遗传查的gRNA库提供了一个有价值的计算资源.
工作流支持模型和非模型生物的功能基因组学研究.
该工具能够在密切相关的物种中设计可转移的gRNA库,这提高了它在比较基因组学中的实用性.

关键词:

克里斯普尔是什么意思?克里斯普尔是什么意思?这是一个CRISPR屏幕.批量DNA提取批量DNA提取设计工具设计工具设计工具在 gRNARNA 中.

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