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Zhang C, He X, Kwok YK, Wang F, Xue J, Zhao H, Suen KW, Wang CC, Ren J, Chen GG, Lai PBS, Li J, Xia Y, Chan AM, Chan WY, Feng B. Homology-independent multiallelic disruption via CRISPR/Cas9-based knock-in yields distinct functional outcomes in human cells. BMC Biol 2018; 16:151. [PMID: 30593266 PMCID: PMC6310992 DOI: 10.1186/s12915-018-0616-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 11/28/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Cultured human cells are pivotal models to study human gene functions, but introducing complete loss of function in diploid or aneuploid cells has been a challenge. The recently developed CRISPR/Cas9-mediated homology-independent knock-in approach permits targeted insertion of large DNA at high efficiency, providing a tool for insertional disruption of a selected gene. Pioneer studies have showed promising results, but the current methodology is still suboptimal and functional outcomes have not been well examined. Taking advantage of the promoterless fluorescence reporter systems established in our previous study, here, we further investigated potentials of this new insertional gene disruption approach and examined its functional outcomes. RESULTS Exemplified by using hyperploid LO2 cells, we demonstrated that simultaneous knock-in of dual fluorescence reporters through CRISPR/Cas9-induced homology-independent DNA repair permitted one-step generation of cells carrying complete disruption of target genes at multiple alleles. Through knocking-in at coding exons, we generated stable single-cell clones carrying complete disruption of ULK1 gene at all four alleles, lacking intact FAT10 in all three alleles, or devoid of intact CtIP at both alleles. We have confirmed the depletion of ULK1 and FAT10 transcripts as well as corresponding proteins in the obtained cell clones. Moreover, consistent with previous reports, we observed impaired mitophagy in ULK1-/- cells and attenuated cytokine-induced cell death in FAT10-/- clones. However, our analysis showed that single-cell clones carrying complete disruption of CtIP gene at both alleles preserved in-frame aberrant CtIP transcripts and produced proteins. Strikingly, the CtIP-disrupted clones raised through another two distinct targeting strategies also produced varied but in-frame aberrant CtIP transcripts. Sequencing analysis suggested that diverse DNA processing and alternative RNA splicing were involved in generating these in-frame aberrant CtIP transcripts, and some infrequent events were biasedly enriched among the CtIP-disrupted cell clones. CONCLUSION Multiallelic gene disruption could be readily introduced through CRISPR/Cas9-induced homology-independent knock-in of dual fluorescence reporters followed by direct tracing and cell isolation. Robust cellular mechanisms exist to spare essential genes from loss-of-function modifications, by generating partially functional transcripts through diverse DNA and RNA processing mechanisms.
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Affiliation(s)
- Chenzi Zhang
- School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China
| | - Xiangjun He
- School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China
| | - Yvonne K Kwok
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China
| | - Feng Wang
- School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China
| | - Junyi Xue
- School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,Institute for Tissue Engineering and Regenerative Medicine (iTERM), The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, 518057, China
| | - Hui Zhao
- School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,Institute for Tissue Engineering and Regenerative Medicine (iTERM), The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, 518057, China
| | - Kin Wah Suen
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China
| | - Chi Chiu Wang
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China
| | - Jianwei Ren
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China
| | - George G Chen
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,State Key Laboratory in Oncology in South China, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China
| | - Paul B S Lai
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,State Key Laboratory in Oncology in South China, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,Prince of Wales Hospital, Shatin, New Territories, Hong Kong, Special Administrative Region of China
| | - Jiangchao Li
- Vascular Biology Research Institute, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, People's Republic of China
| | - Yin Xia
- School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, 518057, China
| | - Andrew M Chan
- School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.,SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, 518057, China
| | - Wai-Yee Chan
- School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China. .,Institute for Tissue Engineering and Regenerative Medicine (iTERM), The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China. .,SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, 518057, China. .,Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Bo Feng
- School of Biomedical Sciences, CUHK-GIBH CAS Joint Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China. .,Institute for Tissue Engineering and Regenerative Medicine (iTERM), The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China. .,SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen, 518057, China. .,Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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