High-accuracy crRNA array assembly strategy for multiplex CRISPR

Abstract

Simultaneous targeting of multiple loci with CRISPR system, a tool known as multiplex CRISPR, offers us more feasibility to manipulate and elucidate the intricate and redundant endogenous networks underlying complex cellular functions. Owing to the versatility of the continuously emerging Cas nucleases and the utilization of CRISPR arrays, multiplex CRISPR has been implemented by numerous in vitro and in vivo studies. However, a streamlined practical strategy for CRISPR array assembly with both convenience and accuracy is still lacking. Here, we present a novel high-accuracy, cost- and time-saving strategy for CRISPR array assembly. Using this strategy, we efficiently accomplished the assembly of up to twelve crRNAs (for AsCas12a) or fifteen crRNAs (for RfxCas13d) in a single reaction. Moreover, we reveal that CRISPR arrays driven by Pol II promoters exhibit a distinct targeting pattern compared to Pol III promoters, which could be exploited for specific distributions of CRISPR intensity. For long CRISPR arrays, we designed a better approach than simply selecting one from U6 or EF1a. Collectively, our study provides a flexible and powerful tool for the convenient implementation of multiplex CRISPR across DNA to RNA, facilitating the dissection of sophisticated cellular networks and the future realization of multi-target gene therapy.