A versatile reporter system for CRISPR-mediated chromosomal rearrangements

Yingxiang Li, Angela I. Park, Haiwei Mou, Cansu Colpan, Aizhan Bizhanova, Elliot Akama-Garren, Nik Joshi, Eric A. Hendrickson, David Feldser, Hao Yin, Daniel G. Anderson, Tyler Jacks, Zhiping Weng, Wen Xue

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31 Scopus citations


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.

Original languageEnglish (US)
Article number111
JournalGenome biology
Issue number1
StatePublished - May 28 2015


Cite this

Li, Y., Park, A. I., Mou, H., Colpan, C., Bizhanova, A., Akama-Garren, E., Joshi, N., Hendrickson, E. A., Feldser, D., Yin, H., Anderson, D. G., Jacks, T., Weng, Z., & Xue, W. (2015). A versatile reporter system for CRISPR-mediated chromosomal rearrangements. Genome biology, 16(1), [111]. https://doi.org/10.1186/s13059-015-0680-7