Homology arms of targeting vectors for gene insertions and CRISPR/Cas9 technology: size does not matter; quality control of targeted clones does

Cell Mol Biol Lett. 2015 Dec;20(5):773-87. doi: 10.1515/cmble-2015-0047.


Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) technology has brought rapid progress in mammalian genome editing (adding, disrupting or changing the sequence of specific sites) by increasing the frequency of targeted events. However, gene knock-in of DNA cassettes by homologous recombination still remains difficult due to the construction of targeting vectors possessing large homology arms (from 2 up to 5 kb). Here, we demonstrate that in mouse embryonic stem cells the combination of CRISPR/Cas9 technology and targeting vectors with short homology arms (~ 0.3 kb) provides sufficient specificity for insertion of fluorescent reporter cassettes into endogenous genes with similar efficiency as those with large conventional vectors. Importantly, we emphasize the necessity of thorough quality control of recombinant clones by combination of the PCR method, Southern hybridization assay and sequencing to exclude undesired mutations. In conclusion, our approach facilitates programmed integration of exogenous DNA sequences at a target locus and thus could serve as a basis for more sophisticated genome engineering approaches, such as generation of reporters and conditional knock-out alleles.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Animals
  • Base Sequence
  • Basic Helix-Loop-Helix Transcription Factors / genetics
  • Basic Helix-Loop-Helix Transcription Factors / metabolism
  • CRISPR-Cas Systems / genetics*
  • Cell Line
  • Gene Knock-In Techniques / standards
  • Genetic Vectors / genetics
  • Genetic Vectors / metabolism*
  • Hepatocyte Nuclear Factor 4 / genetics
  • Hepatocyte Nuclear Factor 4 / metabolism
  • Mice
  • Mice, Inbred C57BL
  • Molecular Sequence Data
  • Mouse Embryonic Stem Cells
  • Mutagenesis, Insertional
  • Nerve Tissue Proteins / genetics
  • Nerve Tissue Proteins / metabolism
  • Quality Control
  • Transcription Factor 7-Like 2 Protein / genetics
  • Transcription Factor 7-Like 2 Protein / metabolism


  • Basic Helix-Loop-Helix Transcription Factors
  • Hepatocyte Nuclear Factor 4
  • Hnf4a protein, mouse
  • Nerve Tissue Proteins
  • Neurog3 protein, mouse
  • Tcf7l2 protein, mouse
  • Transcription Factor 7-Like 2 Protein