Reduced direct joining and increased use of microhomology in a plasmid-based end-joining assay in NIPBL-deficient cellsa
| Direct joining | 6-bp MH | Deletion + MH | Deletion only | Insertion | Total no. of junctions | |
| % | % | % | % | % | ||
| Controlb | 73.0 | 6.3 | 7.9 | 11.9 | 0.8 | 126 |
| Artemis−/− p with control | 59.5 0.099 | 11.9 0.243 | 14.3 0.225 | 11.9 1.000 | 2.4 0.411 | 42 |
| Cernunnos−/− p with control | 4.4 7.5 × 10−20 | 80.9 3.8 × 10−26 | 14.7 0.139 | 0 3.1 × 10−3 | 0 0.461 | 68 |
| NIPBL+/−(P7+P10) p with control | 45.8 6.1 × 10−6 | 20.8 6.4 × 10−4 | 22.9 7.9 × 10−4 | 10.4 0.698 | 0 0.284 | 144 |
| NIPBL+/− (P7), G1 arrested p with control | 43.1 1.7 × 10−4 | 27.5 1.2 x10−4 | 21.6 0.011 | 7.8 0.429 | 0 0.523 | 51 |
| Control+ siCTRL p with control | 68.6 0.509 | 8.6 0.563 | 10.0 0.623 | 12.9 0.846 | 0 0.455 | 70 |
| Control + siNIPBL p with control p with siCTRL | 52.1 0.003 0.044 | 16.4 0.022 0.156 | 19.2 0.019 0.121 | 12.3 0.930 0.924 | 0 0.445 | 73 |
| Direct joining | 6-bp MH | Deletion + MH | Deletion only | Insertion | Total no. of junctions | |
| % | % | % | % | % | ||
| Controlb | 73.0 | 6.3 | 7.9 | 11.9 | 0.8 | 126 |
| Artemis−/− p with control | 59.5 0.099 | 11.9 0.243 | 14.3 0.225 | 11.9 1.000 | 2.4 0.411 | 42 |
| Cernunnos−/− p with control | 4.4 7.5 × 10−20 | 80.9 3.8 × 10−26 | 14.7 0.139 | 0 3.1 × 10−3 | 0 0.461 | 68 |
| NIPBL+/−(P7+P10) p with control | 45.8 6.1 × 10−6 | 20.8 6.4 × 10−4 | 22.9 7.9 × 10−4 | 10.4 0.698 | 0 0.284 | 144 |
| NIPBL+/− (P7), G1 arrested p with control | 43.1 1.7 × 10−4 | 27.5 1.2 x10−4 | 21.6 0.011 | 7.8 0.429 | 0 0.523 | 51 |
| Control+ siCTRL p with control | 68.6 0.509 | 8.6 0.563 | 10.0 0.623 | 12.9 0.846 | 0 0.455 | 70 |
| Control + siNIPBL p with control p with siCTRL | 52.1 0.003 0.044 | 16.4 0.022 0.156 | 19.2 0.019 0.121 | 12.3 0.930 0.924 | 0 0.445 | 73 |
Linearized pDVG94 plasmid was transfected into FBs derived from NIPBL, Artemis and Cernunnos deficient patients and one control. At least two independent experiments are summarized.
Part of the control data (n = 106) as well as the junctions derived from Cernunnos deficient cells have been described previously (Du et al., 2012). The two sets of controls showed very similar pattern and were thus merged in the summary. Statistical analysis was performed using χ2 test.