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PubMed Central, Figure 2: Oncogene. 2016 Nov 3; 35(44): 5781–5794. Published online 2016 May 2. doi:  10.1038/onc.2016.112
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Oncogene. Author manuscript; available in PMC 2016 Nov 7.
Published in final edited form as:
Oncogene. 2016 Nov 3; 35(44): 5781–5794.
Published online 2016 May 2. doi:  10.1038/onc.2016.112

Figure 2

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De novo motif search identified TP53 and AP-1 consensus sequences

The motifs most frequently bound by p63, TAp73 and c-REL transcription factors were identified by MEME-ChIP (55) or Gibbs Motif Sampler (54). They are shown as the sequence logos with known consensus (A-D left). (A, left) The predominant TP53/p63 motifs consistent with the TP53.02 consensus sequences were identified in basal binding of TAp73. (B, left) The predominant motif of TP63 was identified by TP63α binding activities after TNF-α treatment. (C, left) AP-1 motif was identified in basal cREL binding. (D, left) The AP-1 motif was observed in TNF-α induced TAp73 binding. (A-D, right) Distance relationships between different motifs detected by ChIP-Seq were examined. Motifs are considered to be intersecting if they are located within 1 kb distance. The corresponding motifs were mapped back to peak sequences. Motif density (y axis) was plotted against the distance from the center of the binding peak (x axis), showing the distribution pattern of specific motifs in peaks (scales are labeled as ×102). (E) The relative interaction on the TP53 motif (y axis) was plotted against the distance of basal TAp73 binding vs. TP63α after TNF-α treatment. Under TNF treated condition, the relative interaction (x axis) of TP63 binding on TP53 motifs and TAp73 binding on AP-1 motif was plotted against the distance between the two binding motifs (x axis, right). (F) Sedimentation coefficient distribution of purified cRel Rel homology domain (RHD, left) and p73 DNA binding domain (DBD, right) binding to fluorescein-labeled AP-1 (black), cREL (red) and TP53 (blue) response elements (REs). Fluorescein absorbance was detected at 488 nm. The peaks corresponding to the protein dimers and tetramers are indicated. No tetrameric binding of p73 DBD was observed to the AP-1 and cREL REs. For clarity the peak at 2 S for the unbound DNA species is not displayed.

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