Targeted gene addition to a predetermined site in the human genome using a ZFN-based nicking enzyme

Genome Res. 2012 Jul;22(7):1316-26. doi: 10.1101/gr.122879.111. Epub 2012 Mar 20.

Abstract

Zinc-finger nucleases (ZFNs) drive highly efficient genome editing by generating a site-specific DNA double-strand break (DSB) at a predetermined site in the genome. Subsequent repair of this break via the nonhomologous end-joining (NHEJ) or homology-directed repair (HDR) pathways results in targeted gene disruption or gene addition, respectively. Here, we report that ZFNs can be engineered to induce a site-specific DNA single-strand break (SSB) or nick. Using the CCR5-specific ZFNs as a model system, we show that introduction of a nick at this target site stimulates gene addition using a homologous donor template but fails to induce significant levels of the small insertions and deletions (indels) characteristic of repair via NHEJ. Gene addition by these CCR5-targeted zinc finger nickases (ZFNickases) occurs in both transformed and primary human cells at efficiencies of up to ∼1%-8%. Interestingly, ZFNickases targeting the AAVS1 "safe harbor" locus revealed similar in vitro nicking activity, a marked reduction of indels characteristic of NHEJ, but stimulated far lower levels of gene addition-suggesting that other, yet to be identified mediators of nick-induced gene targeting exist. Introduction of site-specific nicks at distinct endogenous loci provide an important tool for the study of DNA repair. Moreover, the potential for a SSB to direct repair pathway choice (i.e., HDR but not NHEJ) may prove advantageous for certain therapeutic applications such as the targeted correction of human disease-causing mutations.

MeSH terms

  • Amino Acid Sequence
  • Catalytic Domain
  • Cell Line, Transformed
  • Cell Line, Tumor
  • Cloning, Molecular
  • DNA Breaks, Double-Stranded
  • DNA Breaks, Single-Stranded
  • DNA End-Joining Repair
  • Deoxyribonucleases, Type II Site-Specific / genetics
  • Deoxyribonucleases, Type II Site-Specific / metabolism*
  • Fibroblasts / cytology
  • Fibroblasts / metabolism
  • Gene Targeting / methods*
  • Genetic Vectors
  • Genome, Human*
  • Histones / metabolism
  • Humans
  • INDEL Mutation
  • Molecular Sequence Data
  • Protein Engineering / methods
  • Receptors, CCR5 / genetics
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism*
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Transformation, Genetic
  • Zinc Fingers*

Substances

  • Histones
  • Receptors, CCR5
  • Recombinant Fusion Proteins
  • endodeoxyribonuclease FokI
  • Deoxyribonucleases, Type II Site-Specific