Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining

Nat Biotechnol. 2015 May;33(5):538-42. doi: 10.1038/nbt.3190. Epub 2015 Mar 23.


Methods to introduce targeted double-strand breaks (DSBs) into DNA enable precise genome editing by increasing the rate at which externally supplied DNA fragments are incorporated into the genome through homologous recombination. The efficiency of these methods is limited by nonhomologous end joining (NHEJ), an alternative DNA repair pathway that competes with homology-directed repair (HDR). To promote HDR at the expense of NHEJ, we targeted DNA ligase IV, a key enzyme in the NHEJ pathway, using the inhibitor Scr7. Scr7 treatment increased the efficiency of HDR-mediated genome editing, using Cas9 in mammalian cell lines and in mice for all four genes examined, up to 19-fold. This approach should be applicable to other customizable endonucleases, such as zinc finger nucleases and transcription activator-like effector nucleases, and to nonmammalian cells with sufficiently conserved mechanisms of NHEJ and HDR.

Publication types

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

MeSH terms

  • Animals
  • CRISPR-Cas Systems / genetics*
  • Cell Line
  • DNA Breaks, Double-Stranded / drug effects
  • DNA End-Joining Repair / genetics*
  • DNA Ligase ATP
  • DNA Ligases / genetics*
  • DNA Repair / genetics
  • Genetic Engineering / methods*
  • Genome
  • Homologous Recombination / genetics
  • Mice
  • Pyrimidines / administration & dosage
  • Schiff Bases / administration & dosage
  • Zinc Fingers / genetics


  • 5,6-bis(benzylideneamino)-2-mercaptopyrimidin-4-ol
  • Pyrimidines
  • Schiff Bases
  • DNA Ligases
  • DNA Ligase ATP

Associated data

  • SRA/SRX950186
  • SRA/SRX950215