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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
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