Unexpected genomic rearrangements at targeted loci associated with CRISPR/Cas9-mediated knock-in

The CRISPR/ Cas9gene editing tool enables accessible and efficient modifications which (re)ignited molecular research in certain species. However, targeted integration of large DNA fragmentsusing CRISPR/ Cas9can still be challenging in numerous models. To systematically compare CRISPR/ Cas9’s efficiency to classical homologous recombination(cHR) for insertion of large DNA fragments, we thoroughly performed and analyzed 221 experiments targeting 128 loci in mouse ES cells. Although both technologies proved efficient, CRISPR/ Cas9yielded significantly more positive clones as detected by overlapping PCRs. It also induced unexpected rearrangements around the targeted site, ultimately rendering CRISPR/ Cas9less efficient than cHR for the production of fully validated clones. These data show that CRISPR/ Cas9-mediated recombination can induce complex long-range modifications at targeted loci, thus emphasizing the need for thorough characterization of any genetically modified material obtained through CRISPR-mediated gene editing before further functional studies or therapeutic use.