A versatile reporter system for CRISPR-mediated chromosomal rearrangements

Although chromosomal deletions and inversions are important in cancer, conventional methods for detecting DNA rearrangements require laborious indirect assays. Here we develop fluorescent reporters to rapidly quantify CRISPR/Cas9-mediated deletions and inversions. We find that inversion depends on the non-homologous end-joining enzyme LIG4. We also engineer deletions and inversions for a 50 kb Pten genomic region in mouse liver. We discover diverse yet sequence-specific indels at the rearrangement fusion sites. Moreover, we detect Cas9 cleavage at the fourth nucleotide on the non-complementary strand, leading to staggered instead of blunt DNA breaks. These reporters allow mechanisms of chromosomal rearrangements to be investigated.National Institutes of Health (U.S.) (Grant 2-PO1-CA42063)National Institutes of Health (U.S.) (Grant RO1-EB000244)National Institutes of Health (U.S.) (Grant RO1-CA115527)National Institutes of Health (U.S.) (Grant RO1-CA132091)National Cancer Institute (U.S.) (Cancer Center Support (Core) Grant P30-CA14051)MIT Skoltech InitiativeNational Institutes of Health (U.S.) (Centers for Cancer Nanotechnology Excellence 5-U54-CA151884-04)MIT-Harvard Center of Cancer Nanotechnology Excellenc