CRISPR/Cas9 Induced Duplications, Deletions and Inversions in Mouse Zygotes Lead to Karyotype Instability

CRISPR/Cas9 technology has been widely used for targeted modification of the mammalian genomes. We have analyzed the karyotype of 18 mouse fibroblast cell lines with Cntn6 gene rearrangements introduced by CRISPR/Cas9. We have produced cell lines with 2374 kb Cntn6 gene duplications, 1137 kb deletions and inversions of similar size. In addition, we have performed cytogenetic analysis for five control mouse embryonic fibroblasts with the intact Cntn6 gene alleles. The cell lines heterozygous for Cntn6 gene inversion and homozygous and heterozygous for Cntn6 gene duplication had a high level of polyploidy (20–46%), as well as chromosome 6 monosomy (1–9%) and trisomy (1–8%). No trisomy was detected in the four cell lines with the deletion and duplication of the Cntn6 gene in the compound, and the proportion of polyploid cells was minimal (1.5–5.7%). Thus, we have shown the karyotype destabilization in the cell lines that have undergone genome editing using CRISPR/Cas9 system.