Fast and sensitive detection of indels induced by precise gene targeting

Authors:
Yang Z, Steentoft C, Hauge C, Hansen L, Thomsen AL, Niola F, Vester-Christensen MB, Frödin M, Clausen H, Wandall HH, Bennett EP
In:
Source: Nucleic Acids Res
Publication Date: (2015)
Issue: 43(9): e59
Research Area:
Gene Expression
Basic Research
Molecular Biology
Platform:
Nucleofector® I/II/2b
Experiment
CHO cells were cultured in ex-Cell-CD media (Sigma Aldrich, USA) with 2% L-glutamine. Cells were nucleofected using solution kits T and V (K562) (Lonza, USA) and a Amaxa® Cell Line Nucleofector® device as previously described (15,16) using protocols provided by Lonza (http://www.lonzabio.com/resources/product-instructions/protocols/). In brief, 1 × 106 cells were transfected with 2 µg of ZFN or TALEN plasmid pairs or 2 µg of Dual-GALNT6-ZFN. For CRISPR/Cas9 CHO Cosmc targeting, 2 µg Cas9 and gRNA plasmids were nucleofected, and for pCMV-Cas9-GFP expressing KRAS gRNA 2 µg plasmid was used. Cells were exposed to a cold shock 30°C for 2 days post-transfection, and incubated one day at 37°C after which DNA of the cell pool was prepared using Nucleospin kit as recommended by the supplier (Machery-Nagel, USA). For consecutive targeting of the KRAS locus, K562 cells were subjected to fluorescence-activated cell sorting (FACS) 3 days after nucleofection for isolation of the 2% most highly GFP fluorescent cells that were then cultured for about 1 week. Thereafter, an aliquot of the cell pool was analysed by IDAA (first hit), whereas the rest of the cells were subjected to another two rounds of nucleofection and FACS to produce second and third hit pools, respectively, Furthermore, after the third hit, cells were also single-cell plated in 96-well plates and expanded to clonal cell lines.
Abstract
The nuclease-based gene editing tools are rapidly transforming capabilities for altering the genome of cells and organisms with great precision and in high throughput studies. A major limitation in application of precise gene editing lies in lack of sensitive and fast methods to detect and characterize the induced DNA changes. Precise gene editing induces double-stranded DNA breaks that are repaired by error-prone non-homologous end joining leading to introduction of insertions and deletions (indels) at the target site. These indels are often small and difficult and laborious to detect by traditional methods. Here we present a method for fast, sensitive and simple indel detection that accurately defines indel sizes down to ±1 bp. The method coined IDAA for Indel Detection by Amplicon Analysis is based on tri-primer amplicon labelling and DNA capillary electrophoresis detection, and IDAA is amenable for high throughput analysis.