Efficient In Vivo Genome Editing Using RNA-Guided Nucleases

Bacteria and archaea have evolved an elegant adaptive defense mechanism which uses clustered regularly interspaced short palindromic repeats (CRISPR), together with CRISPR-associated (Cas) proteins, to provide acquired resistance to invading viruses and plasmids^1–3. The type II CRISPR/Cas system relies on uptake of foreign DNA fragments into CRISPR loci⁴ and subsequent transcription and processing of these CRISPR repeat-spacer arrays into short CRISPR RNAs (crRNAs)⁵, which in turn anneal to a trans-activating crRNA (tracrRNA) and direct sequence-specific silencing of foreign nucleic acid by Cas proteins^5–7 (Figure 1A). Recent in vitro studies have shown that a single synthetic guide RNA (gRNA), consisting of a fusion of crRNA and tracrRNA, can direct Cas9-mediated cleavage of target DNA⁶ (Figure 1B). However, an important question that currently remains unanswered is whether CRISPR/Cas-based systems can have broad utility for performing genome editing in a wide variety of whole organisms as has been shown with other technologies such as zinc finger nucleases (ZFNs)⁸ or transcription activator-like effector nucleases (TALENs)⁹. This capability of ZFNs and TALENs to mediate targeted in vivo modification of genomes has enabled both genetic studies and the development of disease models in a broad range of organisms that were previously difficult to alter. Here we explore the abilities of customizable gRNAs and Cas9 nuclease to efficiently modify endogenous genes in vivo in zebrafish embryos and show that this system provides a rapid and robust alternative to ZFNs and TALENs for performing genome editing in whole organisms.

To establish whether gRNAs can direct Cas9 nuclease-mediated alteration of endogenous genes in vivo in zebrafish, we constructed expression vectors that enable T7 RNA polymerase-mediated production of a capped, poly-adenylated mRNA encoding the monomeric Cas9 nuclease and of a customizable gRNA bearing 20 nucleotides (nts) of sequence complementary to a target site (Figure 1C). The sequence of our gRNA differs from another used previously in vitro⁶ in that it contains additional tracrRNA-derived sequences at its 3’ end (compare Figure 1B and 1C; also see Supplementary Table 1). For initial experiments, we designed and constructed a gRNA that harbors a targeting region complementary to a sequence in the fh gene (site #1) (Supplementary Table 2 and Methods).

To optimize the quantity of each RNA species to use for genome editing, we microinjected varying amounts of fh-targeted gRNA and Cas9-encoding mRNA into one-cell stage zebrafish embryos and then assessed the frequency of altered alleles in single embryos using a T7 Endonuclease I (T7EI) assay (Methods). We observed robust induction of targeted insertion/deletion mutations (indels) at all concentrations of RNAs tested (mean frequencies ranging from 10.0 to 52.7%) and in nearly all individual embryos tested (Supplementary Table 3). We note that the highest mean frequency of mutations was obtained when injecting a solution containing 12.5 ng/µl RNA and 300 ng/µl Cas9-encoding mRNA (Supplementary Table 3) and we therefore used these concentrations for all subsequent experiments. Sequencing of mutated fh alleles revealed indels that begin within or encompass the 5’ end of the DNA sequence complementary to the gRNA (Supplementary Figure 1). This pattern of mutations is consistent with the expected induction of a Cas9-induced double-stranded break (DSB) at this position⁶ within the genomic fh target site followed by error-prone NHEJ-mediated repair.

To test the robustness of the gRNA/Cas9 system in zebrafish, we constructed ten additional gRNAs targeting another sequence in the fh gene (site #2) and sites in nine additional endogenous genes (Supplementary Table 2). Strikingly, we found that for eight of the ten sites we targeted, co-injection of gRNA with Cas9-encoding mRNA induced high frequencies of targeted indels at these sites in all individual embryos tested (Table 1). Mean frequencies of mutagenesis for these eight successfully targeted sites ranged from 24.1% to 59.4% as judged by T7EI assay (Table 1) and did not appear to depend upon which DNA strand (sense or anti-sense) was targeted by the gRNA. Of note, we obtained high efficiencies of mutagenesis at two sites in the gsk3b and drd3 genes which we had been unable previously to alter using TALENs (Supplementary Table 4). For the remaining six successful targets, the mutation rates we observed were comparable to those we previously observed at targets in these same genes using ZFNs and/or TALENs (Table 1 and Supplementary Table 4). DNA sequencing of mutated alleles for all eight of these target sites confirmed the efficient introduction of targeted indels at the expected genomic locations (Figure 2 and Supplementary Figure 2). The lengths of indel mutations induced by RNA-guided Cas9 are similar to those of mutations induced by ZFNs and TALENs previously made by our groups (Supplementary Figure 3a). Furthermore, the nature of the mutations (i.e.—the relative abundance of insertions and deletions) also appears to be similar among all three platforms (Supplementary Figure 3b). Our results strongly suggest that the gRNA/Cas9 platform has a high success rate in zebrafish with a total of 9/11 (or >80%) of the sites we targeted showing robust alterations.

RNA-guided nucleases provide an important complementary technology to TALENs and ZFNs for genome editing in whole organisms. Only one customized gRNA is required to target a specific sequence in contrast to the need to design and assemble two TALENs or ZFNs for each site. gRNAs are encoded on short ~100 bp sequences and are therefore much simpler and easier to construct than TALENs or ZFNs. The short length of gRNA sequences also avoids undesirable complications associated with longer (typically 3 kb or more) and highly repetitive TALEN-encoding vectors (e.g. —delivery using viral vectors, challenges with DNA sequencing, potential for recombination). Furthermore, we successfully used our gRNA/Cas9 reagents to efficiently mutagenize sites in endogenous zebrafish genes that we were previously unable to alter previously using TALENs. It will be of interest to determine going forward why these TALENs fail to mutagenize their targets with high efficiency and also how gRNA-guided Cas9 nucleases are able to successfully alter such sites.

In its current implementation, our gRNA/Cas9 system described above can in principle target any sequence of the form 5’-GG-N₁₈-NGG-3’. Such sites occur once in every 128 bps of random DNA sequence. Constraints on the range of targetable sequences are due to sequence requirements imposed by the T7 promoter used to make gRNAs (GG at the 5’ end of the transcript) and by the requirement for a PAM sequence (NGG) in genomic DNA just 3’ to the target site⁶. Previous studies suggest that the T7 promoter requirement for a pair of guanines at the 5’ end of the transcript could be relaxed to allow for an adenine at either position¹⁰. Loosening this constraint would enable targeting of sequences of the form 5’-(G/A)(G/A)-N₁₈-NGG-3’, which occur once in every 32 bps of random DNA sequence. To simplify the identification of targetable sites, we have updated our web-based ZiFiT Targeter program^{11, 12} with this new functionality (http://zifit.partners.org/ZiFiT_Cas9). Future studies should be directed at performing larger-scale tests of the targeting range of the gRNA/Cas9 system, as has been done recently with TALENs in human cells¹³, and at understanding why some gRNAs fail to mediate efficient sequence alterations (e.g.—the two failed gRNAs among the 11 we tested) and whether such failures can be predicted in advance.

It is important to emphasize that the modified CRISPR/Cas platform described here can be rapidly adopted by any researcher seeking to modify the genome of any organism into which RNA can be introduced. Our plasmids expressing short ~100 nt gRNAs with customized targeting regions can be easily and rapidly assembled simply by ligating pairs of short annealed oligonucleotides into our T7 promoter-based gRNA vector (Methods). This process is considerably simpler than other publicly available methods for assembling TALEN- or ZFN-encoding plasmids⁹ and therefore should be readily amenable to automation and high-throughput use. The cost of making gRNA expression plasmids will be relatively lower than even that of making TALENs since oligonucleotides can be commercially ordered in large-scale at low cost and only a simple ligation reaction is required. In addition to facilitating target site identification, the updated ZiFiT Targeter program also provides the sequences of oligonucleotides required to construct customized gRNAs. All plasmids described in this report will be available through the non-profit reagent distribution service Addgene (http://www.addgene.org/crispr-cas).

Previous studies from our groups and others have shown efficient germline transmission occurs for all engineered ZFNs and TALENs that exhibit somatic mutation rates of 2% or greater in the embryos that develop normally after microinjection^14–17. We note that all of the active gRNA/Cas9 nuclease combinations described in this report exhibit somatic mutation rates well above 10% and that these alterations were detected in normally developing embryos. Therefore, we expect that germline transmission of Cas9-induced mutations will be as efficient as those induced by ZFNs or TALENs.

Another important question to address in future studies will be the genome-wide specificity of RNA-guided Cas9 nucleases. A previous in vitro study has suggested that the 3’ end of the gRNA target recognition sequence may be the most critical for specificity⁶ but whether this will also be true in cells or in vivo remains to be determined. We note that the toxicity induced by gRNA/Cas9-encoding mRNA in zebrafish (as judged by the numbers of deformed and dead embryos; Supplementary Figure 4) appeared to be variable among the different gRNAs tested with no direct correlation to their abilities to induce indels at the intended target sites, a phenomenon we have also observed with ZFNs and TALENs in previous studies^{14, 16, 18, 19}. The frequencies of deformed or dead embryos are comparable to what we have observed in previous experiments using ZFNs^{14, 19} and TALENs^{16, 18}.

Our results provide the largest set of endogenous genes modified by RNA-guided Cas9 nucleases to date and demonstrate the robustness of this platform in vivo for facile and efficient genetic modification of zebrafish. In addition, the small size of gRNAs and the need for only a single monomeric Cas9 nuclease (rather than pairs of dimeric ZFNs or TALENs) are characteristics that make this system potentially ideal for performing multiplex genome editing. The demonstration that customized RNA-guided nucleases can be used to efficiently induce site-specific modifications in vivo in zebrafish will encourage wider use of this robust and easy-to-use technology in a broad range of other whole organisms.