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整个王国的CRISPR指南设计使用ALLEGRO

Amirsadra Mohseni¹, Reyhane Ghorbani Nia², Aida Tafrishi²

¹Computer Science and Engineering, University of California, Riverside, CA 92521, United States.

Nucleic acids research

|August 19, 2025

概括

ALLEGRO是一种用于设计CRISPR单向导RNA库的新算法. 它使成千上万种物种的高效基因组编辑成为可能,推动了各种真菌的遗传研究.

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
分子生物学分子生物学

背景情况:

克里斯普尔基因组编辑依赖于单导向RNA (sgRNA) 设计.
现有的sgRNA设计工具是特定于物种的,并且不能扩展到大型,多样化的数据集.
这限制了对比基因组学,进化研究和跨不同种类的生物技术的应用.

研究的目的:

为各种物种开发一个可扩展和有效的sgRNA库设计工具.
为了使数千种物种的多个基因同时成为目标.
为整个分类群体促进普遍的sgRNA图书馆开发.

主要方法:

介绍ALLEGRO,一种使用整数线性编程的组合优化算法.
开发最小的,高效的sgRNA库,针对数千种物种.
在多种真菌物种中对ALLEGRO设计的sgRNA进行实验验证 (例如, *Kluyveromyces marxianus*, *Komagataella phaffii*, *Yarrowia lipolytica*, *Saccharomyces cerevisiae*).
应用 sgRNA 库,使用通用的 Cas9 核核蛋白递送系统.

主要成果:

艾利格罗成功设计了紧的sgRNA集,针对2000多种真菌物种的多个基因.
实验验证证了在测试物种中有效的CRISPR基因组编辑.
在以前未经测试的真菌基因组中成功应用ALLEGRO库 (例如*Rhodotorula araucariae*).

结论:

ALLEGRO为设计通用sgRNA库提供了一种高效的方法.
该算法可在多种不同的真菌种群中进行可扩展的CRISPR基因组编辑.
这一进步支持更广泛的基因研究和生物技术应用在未经探索的生物体.

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