Table 2.
Global integration patterns of wild-type MLV vector and mutants with ZFD insertion
| Genomic feature | WT (n = 107) | 17.IN.zfd1 (n = 10) | 273.IN.zfd2 (n = 22) | 273.IN.zfd3 (n = 9) | 375.RT.zfd2 (n = 14) | Hypothetical random integration |
| Within genes | 39.3% (0.0843) | 10.0% (0.1433/0.0578) | 54.6% (0.2000/0.1432) | 44.4% (0.4032/0.7520) | 50.0% (0.1362/0.4124) | 22.4%–34.3% (31.5%) |
| Within ±5 kb of the transcriptional start | 34.6% (1.392 × 10-49) | 0.0% (0.4874/0.0214) | 9.1% (0.3146/0.0120) | 11.1% (0.3511/0.1385) | 7.1% (0.6497/0.0308) | 3.0%–5.9% (4.6%) |
| Inside or within 1 kb of CpG | 36.5% (4.926 × 10-151) | 10.0% (0.0606/0.0817) | 0.0% (0.5139/0.0004) | 11.1% (0.0430/0.1136) | 0.0% (0.6026/0.0046) | 1.0%–2.6% (1.9%) |
| LINE | 10.3% (0.0127) | 10.0% (0.4330/0.9751) | 4.6% (0.0713/0.3745) | 11.1% (0.5090/0.9362) | 28.6% (0.4164/0.0245) | 19.7%–20.0% (19.9%) |
| SINE | 11.2% (0.5441) | 0.0% (0.2175/0.2614) | 0.0% (0.0674/0.0958) | 0.0% (0.2420/0.2867) | 21.4% (0.3630/0.2249) | 12.9%–13.5% (13.2%) |
| DNA | 0.9% (0.2104) | 20.0% (0.0016/1.600 × 10-10) | 13.6% (0.0034/2.5232 × 10-10) | 0.0% (0.5978/0.7750) | 0.0% (0.5105/0.7214) | 2.8%–3.2% (3.0%) |
| LTR | 2.8% (0.0325) | 20.0% (0.1985/9.773 × 10-4) | 4.6% (0.4976/0.6197) | 33.3% (0.0081/2.8172 × 10-8) | 7.1% (0.8458/0.3246) | 8.4%–8.8% (8.6%) |
| Total repeats (LINE + SINE + DNA + LTR) | 25.2% (5.575 × 10-5) | 50.0% (0.7312/0.0709) | 22.7% (0.0390/0.7894) | 44.4% (0.9925/0.1836) | 57.1% (0.3451/0.0059) | 44.6% |
The frequencies (%) of integrations within featured genomic regions are shown. The relevant P values (chi-square test), calculated by comparison to the data of hypothetical random integration, are shown in parentheses. Additionally, for the mutants the P values (chi-square test) obtained by comparison of the mutant and wild-type integration patterns are shown after a slash (/) in parentheses. The ranges of frequencies for hypothetical random integration, shown in the right-most column, are based on prior work (5, 8, 28–30), and the averages of these reported frequencies are shown in parentheses. For wild-type MLV Gag-Pol, 17.IN.zfd1, 273.IN.zfd2, 273.IN.zfd3, and 375.RT.zfd2, 294, 76, 197, 101, and 93 virus-host genome junctions were sequenced (Table S1), respectively, and only the junctions that matched a single location on the human genome are considered in this table (n in the top row indicates the number of unique junctions identified and statistically considered for each variant). Multiple junctions with the same sequence were counted once for the analysis in this table, and junctions that matched multiple locations on the human genome were not considered for this analysis. RefSeq genes (http://www.ncbi.nlm.nih.gov/RefSeq/) were considered in our analysis. LINE and SINE are long and short interspersed nuclear elements, respectively. DNA and LTR are DNA transposon and long terminal repeat retrotransposon elements, respectively.