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Table 3 Predicted transcription factor binding sites in the HIV-1 LTR

From: Utilization of HIV-1 envelope V3 to identify X4- and R5-specific Tat and LTR sequence signatures

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
  1. 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