A versatile reporter system for CRISPR-mediated chromosomal rearrangements

Genome Biol. 2015 May 28;16(1):111. doi: 10.1186/s13059-015-0680-7.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • CRISPR-Cas Systems*
  • Chromosome Deletion
  • Chromosome Inversion
  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • Female
  • Gene Rearrangement*
  • Genomics / methods
  • HEK293 Cells
  • High-Throughput Nucleotide Sequencing
  • Humans
  • INDEL Mutation
  • Liver / metabolism
  • Mice
  • Mice, Inbred Strains
  • Plasmids