PT  - JOURNAL ARTICLE
AU  - Mengzhu Liu
AU  - Weiwei Zhang
AU  - Changchang Xin
AU  - Jianhang Yin
AU  - Yafang Shang
AU  - Chen Ai
AU  - Jiaxin Li
AU  - Fei-long Meng
AU  - Jiazhi Hu
TI  - Global detection of DNA repair outcomes induced by CRISPR-Cas9
AID  - 10.1101/2021.02.15.431335
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.02.15.431335
4099  - http://biorxiv.org/content/early/2021/02/16/2021.02.15.431335.short
4100  - http://biorxiv.org/content/early/2021/02/16/2021.02.15.431335.full
AB  - 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, plasmid 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.Competing Interest StatementThe authors have declared no competing interest.