Skip to main content

Table 2 Effect of A-FOS on GR binding to the GR motif and 1-bp variants

From: Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding

GR Motifs

#in Genome

#in Peaks(%of Peaks with the Motif)

%With AP-1(%in c-Jun Peaks)

+AP-1

---AP-1

    

%A-Fos

%A-Fos

  

Pre-Programmed (5,865 Peaks)

G-ACA---TGT-C

27,176

523 (9%)

23% (80%)

44%

15%

G-ACA---CGT-C

7,394

131 (2%)

23% (80%)

38%

20%

1-bp Variants

575,842

1,719 (30%)

31% (86%)

54%

28%

  

Re-Programmed (1,946 Peaks)

G-ACA---TGT-C

27,176

665 (34%)

14% (44%)

45%

9%

G-ACA---CGT-C

7,394

134 (7%)

10% (23%)

39%

4%

1-bp Variants

575,842

806 (41%)

18% (33%)

50%

11%

  

Un-Programmed (425 Peaks)

G-ACA---TGT-C

27,176

205 (48%)

6% (0%)

58%

8%

G-ACA---CGT-C

7,394

29 (7%)

7% (0%)

50%

4%

1-bp Variants

575,842

186 (44%)

9% (6%)

41%

11%

  1. Effect of A-FOS on GR binding to the GR motif and 1-bp variants depends on the presence of an AP-1 motif within 150-bps. GR ChIP-seq peaks are placed into three groups, pre-programmed, re-programmed, and un-programmed. Column 1: GR motifs. Column 2: # of occurrences of each motif in the genome. Column 3: # of motifs bound by GR. In brackets is the % of peaks that contain the motif. Column 4: % of peaks containing a GR motif containing an AP-1 motif within 150-bps. In brackets is the % of GR motifs contain an AP-1 motif that are bound by c-Jun. Column 5: % of GR motifs containing an AP-1 motif nearby that loses GR binding after inhibition of c-Jun binding by the dominant negative A-FOS. Column 6: % of GR motifs without a nearby AP-1 motif that lose GR binding after inhibition of c-Jun binding by the dominant negative A-FOS.