Recombineering in C. elegans: genome editing using in vivo assembly of linear DNAs

Abstract

Recombineering, the use of endogenous homologous recombination systems to recombine DNA in vivo, is a commonly used technique for genome editing in microbes. Recombineering has not yet been developed for animals, where non-homology-based mechanisms have been thought to dominate DNA repair. Here, we demonstrate that homology-dependent repair (HDR) is robust in C. elegans using linear templates with short homologies (~35 bases). Templates with homology to only one side of a double-strand break initiate repair efficiently, and short overlaps between templates support template switching. We demonstrate the use of single-stranded, bridging oligonucleotides (ssODNs) to target PCR fragments precisely to DSBs induced by CRISPR/Cas9 on chromosomes. Based on these findings, we develop recombineering strategies for genome editing that expand the utility of ssODNs and eliminate in vitro cloning steps for template construction. We apply these methods to the generation of GFP knock-in alleles and gene replacements without co-integrated markers. We conclude that, like microbes, metazoans possess robust homology-dependent repair mechanisms that can be harnessed for recombineering and genome editing.