CRISPR-READI: Efficient Generation of Knockin Mice by CRISPR RNP Electroporation and AAV Donor Infection

Abstract

Genetically engineered mouse models harboring large sequence insertions or modifications are critical for a wide range of applications including endogenous gene tagging, conditional knockout, site-specific transgene insertion, and gene replacement; however, existing methods to generate such animals remain laborious and costly. To address this, we developed an approach called CRISPR-READI (CRISPR RNP electroporation and AAV donor infection), combining adeno-associated virus (AAV)-mediated HDR donor delivery with Cas9/sgRNA RNP electroporation to engineer large site-specific modifications in the mouse genome with high efficiency and throughput. We successfully targeted a 774 bp fluorescent reporter, a 2.1 kb CreERT2 driver, and a 3.3 kb expression cassette into endogenous loci in both embryos and live mice. CRISPR-READI is applicable to most widely used knockin schemes requiring donor lengths within the 4.9 kb AAV packaging capacity. Altogether, CRISPR-READI is an efficient, high-throughput, microinjection-free approach for sophisticated mouse genome engineering with potential applications in other mammalian species.

Keywords: AAV; CRISPR; CRISPR-EZ; HDR editing; electroporation; genome editing; knockin; mouse models.

Figure 1

CRISPR-READI optimization for efficient HDR editing in mouse embryos. a Zygotes were transduced with a panel of AAV serotypes harboring a CMV-eGFP reporter and imaged by fluorescent microscopy 48 hours post-transduction. Representative embryos transduced with scAAV1-CMV-eGFP are shown (left), and mean fluorescence intensity per embryo was quantified for each serotype (right). Scale bars = 50 μm. b Cartoon depiction of CRISPR-READI workflow. Embryos are collected from superovulated female mice, transduced with rAAV1 harboring the donor template, electroporated with Cas9/sgRNA RNPs, and implanted into pseudopregnant females to generate edited mice. c Schematic of Tyr targeting strategy. The scAAV1-Tyr donor creates an EcoRI restriction site in exon 1 of the Tyr locus upon HDR editing. ITR: inverted terminal repeat, HA: homology arm, F/R: forward/reverse primers for RFLP analysis. d Optimization of rAAV1 dosage for HDR editing. Zygotes were transduced with scAAV1-Tyr at a dose of 1.1×10⁸, 4.2×10⁸, or 1.7×10⁹ GCs, electroporated with RNPs 5 hours post-transduction, and then returned to rAAV1 incubation for another 19 hours. Treated embryos were cultured to the morula stage and genotyped by restriction fragment length polymorphism (RFLP) analysis (shown for dose of 1.7×10⁹ GCs). Edited embryos yield 650 bp and 420 bp bands upon EcoRI digestion of the PCR amplicon (top, black arrows). HDR rate was quantified by RFLP analysis for each dose (bottom left), and embryo viability was scored as percentage of cultured embryos that reached the morula stage (bottom right). e Optimization of RNP electroporation timing relative to rAAV transduction. Zygotes were transduced with scAAV1-Tyr, electroporated at varying time points post-transduction (2, 4, 6, 8, or 10 hours), and returned to rAAV incubation for a total of 24 hours. Treated embryos were cultured to the morula stage, lysed, and assessed by RFLP analysis (right). 6 hours (*) was identified as the optimal time of RNP electroporation for maximal editing efficiency.

Figure 2

CRISPR-READI enables efficient knock-in of fluorescent reporters in embryos and animals. a Schematic of strategy to engineer an mStrawberry fluorescent reporter downstream of the endogenous Sox2 locus. The scAAV1-Sox2-mStr vector contains a 774 bp P2A-mStrawberry cassette flanked by ~480 bp homology arms that mediate insertion at the 3’ terminus of the Sox2 ORF upon HDR editing. ITR: inverted terminal repeat, HA: homology arm. b CRISPR-READI efficiently generates embryos with an mStrawberry reporter driven by the endogenous Sox2 promoter. Embryos were treated with scAAV1-Sox2-mStr at a dose of 3.2×10⁷, 1.3×10⁸, or 5.0×10⁸ GCs. Treated embryos were cultured to the late blastocyst stage and imaged by fluorescent microscopy. In edited blastocysts, merged brightfield and fluorescent images show localization of mStrawberry fluorescence to the inner cell mass, recapitulating the endogenous Sox2 expression pattern (top). HDR rate was quantified for each dose by the percentage of mStrawberry-positive embryos (bottom). Scale bars: 50 μm. c CRISPR-READI efficiently generates Sox2-P2A-mStrawberry knock-in mice. PCR genotyping confirmed correctly edited 5’ and 3’ junctions of the modified Sox2 locus in 2 out of 11 mice generated by CRISPR-READI, as indicated by black arrows. We also identified two animals harboring the 5’ but not the 3’ end of the donor sequence, which is likely due to incomplete HDR (lanes 4 and 5). Primers were designed such that one primer binds outside the homology arm and the other primer binds within the P2A-mStrawberry cassette. 5’ expected band size: 1,088 bp, 3’ expected band size: 836 bp. d Representative Sanger sequencing and chromatograms for correctly edited mice. 5’ F/R: forward/reverse primers for 5’ junction genotyping, 3’ F/R: forward/reverse primers for 3’ junction genotyping.

Figure 3

CRISPR-READI efficiently engineers an inducible CreERT2 reporter driven by its endogenous promoter. a Schematic of strategy to create a Sox2-driven inducible CreERT2 reporter. The ssAAV1-Sox2-CreERT2 vector contains a 2112 bp P2A-CreERT2 cassette flanked by ~480 bp homology arms that mediate P2A-CreERT2 insertion at the 3’ terminus of the Sox2 ORF upon successful HDR editing. ITR: inverted terminal repeat, HA: homology arm. b CRISPR-READI efficiently produces embryos with an inducible CreERT2 reporter driven by the endogenous Sox2 promoter. PCR genotyping confirmed the correctly edited 5’ and 3’ junctions of the modified Sox2 locus in 22 out of 32 embryos, as indicated by black arrows. Primers were designed such that one primer binds outside the homology arm and the other primer binds within the CreERT2 cassette. 5’ expected band size: 658 bp, 3’ expected band size: 666 bp. c CRISPR-READI efficiently generates Sox2-P2A-CreERT2 mice. PCR genotyping confirmed correctly edited 5’ and 3’ junctions of the modified Sox2 locus in 2 out of 5 mice with previously described primers. d Representative Sanger sequencing and chromatograms for correctly edited mice. 5’ F/R: forward/reverse primers for 5’ junction genotyping, 3’ F/R: forward/reverse primers for 3’ junction genotyping.

Figure 4

CRISPR-READI enables efficient site-specific insertion of a large expression cassette. a Schematic of strategy to knock a CAG-FLEX-mStrawberry cassette into the Rosa26 locus. The ssAAV1-R26-FLEX-mStr vector contains a splice acceptor + polyA element, a CAG promoter, an inverted mStrawberry ORF flanked by loxP and lox2272 sites, chimeric SV40/bGH polyA signal, and ~500 bp homology arms that direct targeting to the first Rosa26 intron. Upon Cre-mediated recombination, the mStrawberry ORF is irreversibly inverted, leading to robust mStrawberry expression. ITR: inverted terminal repeat, HA: homology arm, SA: splice acceptor. b Representative fluorescent image of CMV-Cre embryos treated with ssAAV1-R26-FLEX-mStr. Successful editing and Cre-mediated recombination lead to robust mStrawberry expression by the morula stage. Scale bar: 50 μm. c PCR genotyping confirmed the correctly edited 5’ and 3’ junctions of the modified Rosa26 locus in 9 out of 26 embryos, as indicated by black arrows. Primers were designed such that one primer binds outside the homology arm and one primer binds within the ssAAV1-R26-FLEX-mStr cassette. 5’ expected band size: 608 bp, 3’ expected band size: 626 bp. d CRISPR-READI efficiently generates Rosa-FLEX-mStr mice. PCR genotyping confirmed correctly edited 5’ and 3’ junctions of the modified Rosa26 locus in 3 out of 11 mice with previously described primers. Notably, we also detected two animals exhibiting partial sequence insertion, similar to our Sox2-P2A-mStr animals (lanes 8 and 9). e Representative Sanger sequencing and chromatograms for correctly edited mice. 5’ F/R: forward/reverse primers used for 5’ junction genotyping, 3’ F/R: forward/reverse primers used for 3’ junction genotyping.