Large-scale multiplexed mosaic CRISPR perturbation in the whole organism

• Published in: Cell 2022-08, Vol.185 (16), p.3008-3024.e16
• Main Authors: Liu, Bo, Jing, Zhengyu, Zhang, Xiaoming, Chen, Yuxin, Mao, Shaoshuai, Kaundal, Ravinder, Zou, Yan, Wei, Ge, Zang, Ying, Wang, Xinxin, Lin, Wenyang, Di, Minghui, Sun, Yiwen, Chen, Qin, Li, Yongqin, Xia, Jing, Sun, Jianlong, Lin, Chao-Po, Huang, Xingxu, Chi, Tian
• Format: Article
• Language: English
• Subjects: Animals; CAR T; cell atlas; CRISPR-Cas Systems - genetics; Gene Editing; Genome; immunotherapy; in vivo CRISPR screen; Mice; mouse cell Perturb-Atlas; Perturb-seq; RNA, Guide, CRISPR-Cas Systems - genetics; RNA, Guide, CRISPR-Cas Systems - metabolism; Transgenes
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2022.06.039

Here, we report inducible mosaic animal for perturbation (iMAP), a transgenic platform enabling in situ CRISPR targeting of at least 100 genes in parallel throughout the mouse body. iMAP combines Cre-loxP and CRISPR-Cas9 technologies and utilizes a germline-transmitted transgene carrying a large array of individually floxed, tandemly linked gRNA-coding units. Cre-mediated recombination triggers expression of all the gRNAs in the array but only one of them per cell, converting the mice to mosaic organisms suitable for phenotypic characterization and also for high-throughput derivation of conventional single-gene perturbation lines via breeding. Using gRNA representation as a readout, we mapped a miniature Perturb-Atlas cataloging the perturbations of 90 genes across 39 tissues, which yields rich insights into context-dependent gene functions and provides a glimpse of the potential of iMAP in genome decoding. [Display omitted] •Inducible mosaic animal for perturbation (iMAP) combines Cre-LoxP and CRISPR-Cas•iMAP enables large-scale in situ multiplexed mosaic gene targeting and Perturb-Atlas mapping•iMAP enables rapid derivation of single-gene perturbation mouse lines via breeding•iMAP lines are permanent resources just as conventional transgenic lines iMAP is a multiplexed mosaic in situ gene-perturbation platform, which enables large-scale mapping of the Perturb-Atlases profiling genome function across the whole body and high-throughput derivation of single-gene perturbation mouse lines.