Research advances in CRISPR-based high-throughput genome editing

TENG Jiayao; REN Chuanhong; ZHU Ruiying; BAO Zehua

doi:10.12211/2096-8280.2025-073

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Research advances in CRISPR-based high-throughput genome editing

Invited Review | 更新时间：2026-05-22

- Research advances in CRISPR-based high-throughput genome editing
- Synthetic Biology Journal Vol. 7, Issue 2, Pages: 318-334(2026)
- 作者机构：
  
  1.浙江大学化学工程与生物工程学院，生物质化工教育部重点实验室，浙江杭州 310058
  2.浙江大学杭州国际科创中心，全省功能化学品智造重点实验室，浙江杭州 311215
  3.浙江大学化学工程与生物工程学院，生物工程研究所，浙江杭州 310058
  4.浙江大学化学工程与生物工程学院，浙江省智能生物材料重点实验室，浙江杭州 310058
- 作者简介：
- 基金信息：
- DOI：10.12211/2096-8280.2025-073
  CLC： Q812
- Received：15 July 2025，
  
  Revised：2025-10-30，
  
  Published：30 April 2026
- 稿件说明：
移动端阅览
滕佳尧，任传宏，朱芮莹，鲍泽华. 基于CRISPR系统的高通量基因组编辑研究进展［J］. 合成生物学， 2026， 7（2）： 318-334

TENG Jiayao， REN Chuanhong， ZHU Ruiying， BAO Zehua. Research advances in CRISPR-based high-throughput genome editing［J］. Synthetic Biology Journal， 2026， 7（2）： 318-334
滕佳尧，任传宏，朱芮莹，鲍泽华. 基于CRISPR系统的高通量基因组编辑研究进展［J］. 合成生物学， 2026， 7（2）： 318-334 DOI： 10.12211/2096-8280.2025-073.

TENG Jiayao， REN Chuanhong， ZHU Ruiying， BAO Zehua. Research advances in CRISPR-based high-throughput genome editing［J］. Synthetic Biology Journal， 2026， 7（2）： 318-334 DOI： 10.12211/2096-8280.2025-073.

摘要

高通量基因组编辑是快速分析大量基因突变功能和进行遗传育种的有效方法。相比于传统随机诱变，基于规律间隔成簇短回文重复序列（CRISPR）系统的基因组编辑具有效率高、可靶向的优点。通过设计靶向目标基因的向导RNA文库可以实现高通量基因组编辑和筛选。近年来，多种CRISPR系统以及CRISPR衍生基因编辑技术的开发进一步丰富了高通量基因组编辑工具箱。本文主要介绍基于CRISPR系统的高通量基因组编辑方法，包括CRISPR辅助的同源定向修复、碱基编辑系统、引导编辑系统等，并阐述了这些方法在不同领域的应用，如工业微生物育种、人类功能基因组学和作物改良。最后，对相关方法存在的物种适用性有限、突变多样性低、编辑范围窄、多基因编辑困难等问题以及潜在的解决方法进行讨论和展望。

Abstract

High-throughput genome editing is an effective approach for rapidly analyzing the function of massive genetic mutations and to perform genetic breeding. Compared with random mutagenesis

the Clustered

Regularly Interspaced Short Palindromic Repeats (CRISPR)-based genome editing is more efficient and programmable. High-throughput genome editing and screening is enabled by the design of guide RNA libraries targeting specific genes. In recent years

the high-throughput genome editing toolbox is enriched by various CRISPR systems and CRISPR-derived technologies. Here we review major CRISPR-based high-throughput genome editing methods

including CRISPR-assisted homology directed repair

base editing systems

and prime editing systems

and discuss their applications in different fields

including industrial microbial strain breeding

functional human genomics rese

arch

and crop improvement. These methods have been applied in improving the production capacity of microorganisms in industrial breeding

analyzing the functions of disease-associated single nucleotide variants (SNVs) in functional human genomics research

and enhancing the herbicide resistance of plants in crop improvement. Meanwhile

we also discuss limitations of these methods

including the limited species applicability

the low mutation diversity

the narrow editing window

and the difficulty in multiplex genome editing. We further provide prospects to address these limitations

including: firstly

expanding the applicable species from model organisms such as

Escherichia coli

and

Saccharomyces cerevisiae

to other important industrial microorganisms including

Actinomycetes

and

Pseudomonas aeruginosa

by using related CRISPR systems; secondly

increasing mutation diversity by developing more advanced editors

particularly base editors; thirdly

broadening the targeting region of genome editors by using PAM-relaxed or computationally designed Cas variants

as well as novel base editor and prime editor architectures; fourthly

scaling up multiplex genome editing for more targeted sites. With the development of artificial intelligence and automation platforms

as well as the continued rapid advancement of CRISPR and its derivative technologies

we expect that more advanced high-throughput genome editing technologies will emerge.

关键词

Keywords

references

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