Illegitimate translation causes unexpected gene expression from on-target out-of-frame alleles created by CRISPR-Cas9

Sci Rep. 2016 Dec 21;6:39608. doi: 10.1038/srep39608.


CRISPR-Cas9 is efficient enough to knock out both alleles directly by introducing out-of-frame mutations. We succeeded in making biallelic on-target frameshift mutations of the endogenous Gli3 gene; however, the GLI3 protein was expressed in all six of the established cell lines carrying homozygous out-of-frame mutations. We developed a dual-tagged expression vector and proved that illegitimate translation (ITL) was the cause of the unexpected Gli3 expression. Thus, gene expression must be examined even if designed on-target out-of-frame sequences are introduced by genome editing. In addition, it is highly recommended to pre-examine the occurrence of ITL in vitro prior to the design and construction of any genome-editing vectors. In vitro assay systems such as the dual-tagged ITL assay system developed in this study should aid the identification and elucidation of ITL-based human diseases and gene expression.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Animals
  • CRISPR-Cas Systems*
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Frameshift Mutation*
  • Gene Expression
  • Gene Expression Profiling
  • Gene Expression Regulation*
  • Gene Targeting
  • Genetic Vectors
  • Genome
  • HEK293 Cells
  • Homozygote
  • Humans
  • Mice
  • Mice, Transgenic
  • Mutation
  • NIH 3T3 Cells
  • Nerve Tissue Proteins / genetics
  • Open Reading Frames
  • Protein Biosynthesis / genetics*
  • Reading Frames
  • Sequence Analysis, DNA
  • Zinc Finger Protein Gli3 / genetics


  • GLI3 protein, human
  • Gli3 protein, mouse
  • Nerve Tissue Proteins
  • Zinc Finger Protein Gli3