Table 3.
Predicted transcription factor binding sites in the HIV-1 LTR
| Transcription factor | JASPAR matrix | In vitro confirmed | HXB2 index | Strand direction | X4 mean score | R5 mean score | P value |
|---|---|---|---|---|---|---|---|
| C/EBP | MA0102.1-CEBPA | 76 | Reverse | 4.55 | 4.06 | 0.3860 | |
| MA0102.2-CEBPA | 79 | Reverse | 4.94 | 4.41 | 0.3860 | ||
| MA0102.2-CEBPA | 81 | Forward | 4.24 | 3.12 | 0.2304 | ||
| MA0102.1-CEBPA | 150 | Reverse | 5.16 | 3.39 | <0.0001 | ||
| MA0102.2-CEBPA | 153 | Reverse | 6.35 | 4.58 | <0.0001 | ||
| MA0102.2-CEBPA | 154 | Forward | 4.53 | 1.83 | <0.0001 | ||
| MA0102.1-CEBPA | 197 | Reverse | 5.27 | 4.63 | 0.0092 | ||
| MA0102.2-CEBPA | 200 | Reverse | 4.33 | 4.34 | 0.0063 | ||
| MA0102.1-CEBPA | C/EBP II | 278 | Reverse | 5.84 | 6.29 | 0.0005 | |
| MA0102.2-CEBPA | C/EBP II | 281 | Reverse | 5.26 | 5.70 | 0.0010 | |
| MA0102.3-CEBPA | C/EBP II | 281 | Forward | 7.65 | 9.67 | 0.0008 | |
| MA0102.2-CEBPA | C/EBP I | 342 | Forward | 5.26 | 4.65 | <0.0001 | |
| CREB | MA0018.2-CREB1 | 173 | Forward | 4.74 | 3.93 | 0.1020 | |
| MA0018.2-CREB1 | ATF/CREB | 330 | Forward | 5.25 | 5.63 | 0.4547 | |
| MA0018.2-CREB1 | 410 | Reverse | 4.43 | 4.68 | 0.8684 | ||
| NF-kB | MA0105.1-NFKB1 | NF-kB II | 350 | Forward | 13.66 | 14.52 | 0.9605 |
| MA0105.1-NFKB1 | NF-kB II | 350 | Reverse | 7.43 | 8.30 | 0.9605 | |
| MA0105.2-NFKB1 | NF-kB II | 350 | Forward | 6.67 | 7.41 | 0.9605 | |
| MA0105.3-NFKB1 | NF-kB II | 350 | Forward | 12.37 | 13.41 | 0.9722 | |
| MA0105.1-NFKB1 | NF-kB II | 351 | Reverse | 4.85 | 5.31 | 0.9813 | |
| MA0105.1-NFKB1 | NF-kB I | 363 | Forward | 6.18 | 6.77 | 0.8062 | |
| MA0105.2-NFKB1 | NF-kB I | 363 | Forward | 8.20 | 8.62 | 0.8062 | |
| MA0105.2-NFKB1 | NF-kB I | 363 | Reverse | 7.60 | 7.88 | 0.8345 | |
| MA0105.1-NFKB1 | NF-kB I | 364 | Forward | 14.55 | 14.35 | 1.0000 | |
| MA0105.1-NFKB1 | NF-kB I | 364 | Reverse | 8.33 | 8.26 | 1.0000 | |
| MA0105.2-NFKB1 | NF-kB I | 364 | Forward | 7.44 | 7.29 | 1.0000 | |
| MA0105.3-NFKB1 | NF-kB I | 364 | Forward | 15.66 | 15.15 | 0.8907 | |
| MA0105.1-NFKB1 | NF-kB I | 365 | Reverse | 5.34 | 5.15 | 1.0000 | |
| MA0105.2-NFKB1 | NF-kB | 504 | Forward | 6.09 | 6.46 | 0.9850 | |
| MA0105.2-NFKB1 | NF-kB | 504 | Reverse | 8.56 | 8.83 | 0.9881 | |
| MA0105.1-NFKB1 | NF-kB | 505 | Reverse | 6.01 | 6.30 | 0.9850 | |
| Sp | MA0079.2-SP1 | 98 | Reverse | 4.68 | 5.68 | 0.0093 | |
| MA0079.1-SP1 | 99 | Forward | 5.01 | 5.35 | 0.0093 | ||
| MA0079.1-SP1 | 223 | Forward | 4.35 | 3.31 | <0.0001 | ||
| MA0079.1-SP1 | 224 | Forward | 4.57 | 2.05 | <0.0001 | ||
| MA0079.1-SP1 | 266 | Reverse | 4.36 | 3.37 | 0.1034 | ||
| MA0079.2-SP1 | Sp-III | 373 | Reverse | 5.30 | 5.86 | 0.5696 | |
| MA0079.1-SP1 | Sp-III | 374 | Forward | 4.12 | 4.82 | 0.0755 | |
| MA0079.2-SP1 | Sp-III | 376 | Reverse | 5.22 | 6.46 | <0.0001 | |
| MA0079.1-SP1 | Sp-III | 377 | Forward | 3.86 | 5.56 | <0.0001 | |
| MA0079.2-SP1 | Sp-III | 382 | Reverse | 4.71 | 5.81 | <0.0001 | |
| MA0079.2-SP1 | Sp-II | 387 | Reverse | 6.72 | 7.11 | 0.7894 | |
| MA0079.3-SP1 | Sp-II | 387 | Reverse | 10.11 | 10.46 | 0.6982 | |
| MA0079.1-SP1 | Sp-II | 388 | Forward | 5.78 | 6.14 | 0.2648 | |
| MA0079.2-SP1 | Sp-II | 392 | Reverse | 6.62 | 7.07 | 0.1179 | |
| MA0079.2-SP1 | Sp-II | 393 | Reverse | 5.51 | 6.81 | 0.0168 | |
| MA0079.1-SP1 | Sp-I | 398 | Forward | 4.35 | 4.35 | 0.6176 | |
| MA0079.2-SP1 | Sp-I | 398 | Reverse | 6.69 | 7.21 | 0.5383 | |
| MA0079.1-SP1 | Sp-I | 399 | Forward | 4.30 | 4.47 | 0.5539 | |
| MA0079.2-SP1 | Sp-I | 400 | Reverse | 5.78 | 5.83 | 1.0000 | |
| MA0079.1-SP1 | 479 | Forward | 5.21 | 5.02 | 0.9279 |
LTR sequences classified as either R5 or X4 based on their co-linear Env-V3 sequence were scanned for potential transcription factor binding sites. All binding sites with a percentile score >0.3 in either of the two groups were included in this analysis. The overall score distribution of R5 and X4 binding sites was compared using a KS-test, and multiple testing was accounted for using the Benjamini–Hochberg procedure. Statistically significant sites (P < 0.01) are highlighted in italics