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In addition, HSF, STE11, PPAR, NaNog, MAZ, PAX, BR-C binding sites were significantly present (Fig. 2D).
In the next step of the study, TFs and Sigma factors whose binding sites were significantly enriched for GATC were identified (Fig. 1).
TCF/Lef and/or VDR binding sites were significantly enriched in 91 of the 103 genes upregulated more than 3 fold at 7 days of 4OHT treatment when compared with the same number of random promoter regions in the mouse genome (Table S1, S2).
37 The cohesin binding sites were significantly reduced in CdLS samples with mutant SCC2/ NIPBL.
Focusing specifically on ribosomal protein gene promoters, BEAF-32 binding sites were significantly enriched, especially on RBf2-bound genes.
Interestingly, also ARNT binding sites were significantly overexpressed in this gene set (p = 2.33 × 10−6, Table 5A).
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CREB binding sites are significantly overrepresented in SCN-specific prediction lists, presumably due to its dependency on the light input.
This hypothesis is further sustained by the finding that high-confidence miRNA binding sites are significantly enriched in the 3'-UTRs of experimentally determined PUM1 and PUM2 targets.
Statistical analysis (one-way ANOVA) also indicates that the means of binding sites are significantly different among the five SHOX 3'UTR exons (p<0.001) (Table S2a).
Strikingly, we found that PUF motifs are enriched around predicted miRNA binding sites and that high-confidence miRNA binding sites are significantly enriched in the 3'-UTRs of experimentally determined PUM1 and PUM2 targets, strongly suggesting an interaction of human PUM proteins with the miRNA regulatory system.
Indeed, all median unpaired probabilities of predicted binding sites are significantly higher than controls).
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