Global Detection of DNA Repair Outcomes Induced by CRISPR-Cas9

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2021 Aug 8

PMID 34365511

Citations 47

Authors

Mengzhu Liu

Weiwei Zhang

Changchang Xin

Jianhang Yin

Yafang Shang

Chen Ai

Jiaxin Li

Fei-Long Meng

Jiazhi Hu

Affiliations

Soon will be listed here.

Abstract

CRISPR-Cas9 generates double-stranded DNA breaks (DSBs) to activate cellular DNA repair pathways for genome editing. The repair of DSBs leads to small insertions or deletions (indels) and other complex byproducts, including large deletions and chromosomal translocations. Indels are well understood to disrupt target genes, while the other deleterious byproducts remain elusive. We developed a new in silico analysis pipeline for the previously described primer-extension-mediated sequencing assay to comprehensively characterize CRISPR-Cas9-induced DSB repair outcomes in human or mouse cells. We identified tremendous deleterious DSB repair byproducts of CRISPR-Cas9 editing, including large deletions, vector integrations, and chromosomal translocations. We further elucidated the important roles of microhomology, chromosomal interaction, recurrent DSBs, and DSB repair pathways in the generation of these byproducts. Our findings provide an extra dimension for genome editing safety besides off-targets. And caution should be exercised to avoid not only off-target damages but also deleterious DSB repair byproducts during genome editing.

Citing Articles

Prevalent integration of genomic repetitive and regulatory elements and donor sequences at CRISPR-Cas9-induced breaks.

Bi C, Yuan B, Zhang Y, Wang M, Tian Y, Li M Commun Biol. 2025; 8(1):94.

PMID: 39833279 PMC: 11747631. DOI: 10.1038/s42003-025-07539-5.

Large DNA deletions occur during DNA repair at 20-fold lower frequency for base editors and prime editors than for Cas9 nucleases.

Hwang G, Lee S, Oh M, Kim S, Habib O, Jang H Nat Biomed Eng. 2024; 9(1):79-92.

PMID: 39496933 PMC: 11754094. DOI: 10.1038/s41551-024-01277-5.

Synergistic combination of RAD51-SCR7 improves CRISPR-Cas9 genome editing efficiency by preventing R-loop accumulation.

Park S, Park S, Kwon Y, Choi E Mol Ther Nucleic Acids. 2024; 35(3):102274.

PMID: 39161621 PMC: 11331969. DOI: 10.1016/j.omtn.2024.102274.

Enhancing homology-directed repair efficiency with HDR-boosting modular ssDNA donor.

Jin Y, Zhang P, Liu L, Zhao X, Hu X, Liu S Nat Commun. 2024; 15(1):6843.

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A scalable and cGMP-compatible autologous organotypic cell therapy for Dystrophic Epidermolysis Bullosa.

Neumayer G, Torkelson J, Li S, McCarthy K, Zhen H, Vangipuram M Nat Commun. 2024; 15(1):5834.

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