Multiplex gene editing by CRISPR-Cpf1 through autonomous processing of a single crRNA array

Abstract

Microbial CRISPR-Cas defense systems have been adapted as a platform for genome editing applications built around the RNA-guided effector nucleases, such as Cas9. We recently reported the characterization of Cpf1, the effector nuclease of a novel type V-A CRISPR system, and demonstrated that it can be adapted for genome editing in mammalian cells (Zetsche et al., 2015). Unlike Cas9, which utilizes a trans-activating crRNA (tracrRNA) as well as the endogenous RNaseIII for maturation of its dual crRNA:tracrRNA guides (Deltcheva et al., 2011), guide processing of the Cpf1 system proceeds in the absence of tracrRNA or other Cas (CRISPR associated) genes (Zetsche et al., 2015) (Figure 1a), suggesting that Cpf1 is sufficient for pre-crRNA maturation. This has important implications for genome editing, as it would provide a simple route to multiplex targeting. Here, we show for two Cpf1 orthologs that no other factors are required for array processing and demonstrate multiplex gene editing in mammalian cells as well as in the mouse brain by using a designed single CRISPR array.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=164 SRC=\"FIGDIR/small/049122_fig1.gif\" ALT=\"Figure 1\">\nView larger version (35K):\norg.highwire.dtl.DTLVardef@1f0c15corg.highwire.dtl.DTLVardef@126a6fdorg.highwire.dtl.DTLVardef@9d6a2eorg.highwire.dtl.DTLVardef@a61f75_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1C_FLOATNO Cpf1 mediates processing of pre-crRNA. (a) Schematic of pre-crRNA processing for Cas9 and Cpf1. Cleavage sites indicated with red triangle. (b) In vitro processing of FnCpf1 pre-crRNA transcript (80 nM) with purified AsCpf1 or LbCpf1 protein ([~]320 nM). In the presence of Cpf1 nuclease the pre-crRNA was cleaved in a distinct pattern, indicating cleavage at similar sequence motifs. RNA molecules without Cpf1 DR features where not cleaved by Cpf1 (control RNA). (c) RNAseq analysis of FnCpf1 pre-crRNA cleavage products, as shown in (b). A high fraction of sequence reads smaller than 65nt are cleavage products of spacers flanked by DR sequences.\n\nC_FIG