PT  - JOURNAL ARTICLE
AU  - Zexu Li
AU  - Zihan Li
AU  - Xiaolong Cheng
AU  - Xiaofeng Wang
AU  - Shixin Ma
AU  - Shengnan Wang
AU  - Zhiyan Lu
AU  - Han Zhang
AU  - Wenchang Zhao
AU  - Zhisong Chen
AU  - Yingjia Yao
AU  - Lumen Chao
AU  - Wei Li
AU  - Teng Fei
TI  - Intrinsic RNA targeting constrains the utility of CRISPR-Cas13 systems
AID  - 10.1101/2022.05.14.491940
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.05.14.491940
4099  - http://biorxiv.org/content/early/2022/05/14/2022.05.14.491940.short
4100  - http://biorxiv.org/content/early/2022/05/14/2022.05.14.491940.full
AB  - CRISPR-Cas13 systems have been adapted as versatile toolkits for RNA-related applications. Here we systematically evaluate the performance of several popular Cas13 family effectors (Cas13a, Cas13b and Cas13d) under lentiviral vectors and reveal surprisingly differential defects and characteristics of these systems. Using RNA immunoprecipitation sequencing, transcriptome profiling, biochemistry analysis, high-throughput CRISPR-Cas13 screening and machine learning approaches, we determine that each Cas13 system has its intrinsic RNA targets in mammalian cells. Viral process-related host genes can be targeted by Cas13 and affect production of fertile lentiviral particles, thereby restricting the utility of lentiviral Cas13 systems. Multiple RNase activities of Cas13 are involved in endogenous RNA targeting. Unlike target-induced nonspecific collateral effect, intrinsic RNA cleavage can be specific, target-independent and dynamically tuned by varied states of Cas13 nucleases. Our work provides guidance on appropriate use of lentiviral Cas13 systems and further raises cautions about intrinsic RNA targeting during Cas13-based basic and therapeutic applications.Competing Interest StatementW.L. is a paid consultant to Tavros Therapeutics, Inc. Others declared no competing interests.