Li, YingxiangPark, Angela I.Mou, HaiweiColpan, CansuBizhanova, AizhanAkama-Garren, ElliotJoshi, NikHendrickson, Eric A.Feldser, DavidYin, HaoAnderson, DanielJacks, TylerWeng, ZhipingXue, Wen2015-07-132015Li, Y., A. I. Park, H. Mou, C. Colpan, A. Bizhanova, E. Akama-Garren, N. Joshi, et al. 2015. “A versatile reporter system for CRISPR-mediated chromosomal rearrangements.” Genome Biology 16 (1): 111. doi:10.1186/s13059-015-0680-7. http://dx.doi.org/10.1186/s13059-015-0680-7.1465-6906http://nrs.harvard.edu/urn-3:HUL.InstRepos:17295772Although 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. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0680-7) contains supplementary material, which is available to authorized users.en-USJournal Article2015-07-1310.1186/s13059-015-0680-7