Re-engineered RNA-Guided FokI-Nucleases for Improved Genome Editing in Human Cells

Mol Ther. 2017 Feb 1;25(2):342-355. doi: 10.1016/j.ymthe.2016.11.007.

Abstract

Clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 enables us to generate targeted sequence changes in the genomes of cells and organisms. However, off-target effects have been a persistent problem hampering the development of therapeutics based on CRISPR/Cas9 and potentially confounding research results. Efforts to improve Cas9 specificity, like the development of RNA-guided FokI-nucleases (RFNs), usually come at the cost of editing efficiency and/or genome targetability. To overcome these limitations, we engineered improved chimeras of RFNs that enable higher cleavage efficiency and provide broader genome targetability, while retaining high fidelity for genome editing in human cells. Furthermore, we developed a new RFN ortholog derived from Staphylococcus aureus Cas9 and characterize its utility for efficient genome engineering. Finally, we demonstrate the feasibility of RFN orthologs to functionally hetero-dimerize to modify endogenous genes, unveiling a new dimension of RFN target design opportunities.

Keywords: CRISPR/Cas9; FokI; RNA-guided FokI nuclease; gene editing.

MeSH terms

  • Bacterial Proteins / metabolism
  • Base Sequence
  • Binding Sites
  • CRISPR-Associated Protein 9
  • CRISPR-Cas Systems
  • Deoxyribonucleases, Type II Site-Specific / chemistry
  • Deoxyribonucleases, Type II Site-Specific / genetics
  • Deoxyribonucleases, Type II Site-Specific / metabolism*
  • Endonucleases / metabolism
  • Gene Editing*
  • Genetic Variation
  • Humans
  • Models, Biological
  • Mutation
  • Pluripotent Stem Cells / metabolism
  • Protein Binding
  • Protein Engineering*
  • Protein Multimerization
  • RNA, Guide, CRISPR-Cas Systems*
  • Regulatory Factor X Transcription Factors / chemistry
  • Regulatory Factor X Transcription Factors / genetics

Substances

  • Bacterial Proteins
  • RNA, Guide, CRISPR-Cas Systems
  • Regulatory Factor X Transcription Factors
  • Rfx6 protein, human
  • CRISPR-Associated Protein 9
  • Cas9 endonuclease Streptococcus pyogenes
  • Endonucleases
  • endodeoxyribonuclease FokI
  • Deoxyribonucleases, Type II Site-Specific