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The CRISPR-Cas system is a powerful tool for generating genetically modified animals; however, targeted knock-in (KI) via homologous recombination remains difficult in zygotes. Here we show efficient gene KI in rats by combining CRISPR-Cas with single-stranded oligodeoxynucleotides (ssODNs). First, a 1-kb ssODN co-injected with guide RNA (gRNA) and Cas9 messenger RNA produce GFP-KI at the rat  Thy1  locus. Then, two gRNAs with two 80-bp ssODNs direct efficient integration of a 5.5-kb CAG-GFP vector into the  Rosa26  locus via ssODN-mediated end joining. This protocol also achieves KI of a 200-kb BAC containing the human  SIRPA  locus, concomitantly knocking out the rat  Sirpa  gene. Finally, three gRNAs and two ssODNs replace 58-kb of the rat  Cyp2d  cluster with a 6.2-kb human  CYP2D6  gene. These ssODN-mediated KI protocols can be applied to any target site with any donor vector without the need to construct homology arms, thus simplifying genome engineering in living organisms.

ssODN-mediated knock-in with CRISPR-Cas for large genomic regions in zygotes