This six nucleotide deletion destroys the SP1-binding site which reduces the caspase-8 expression and thereby decreasing the apoptotic activity of the caspase-cascade [ 31].
In contrast, when DNA was biotinylated, the remodeler was not disruptive and instead repositioned nucleosomes on top of the biotinylated DNA sites, which reduced nucleosome binding affinity.
Jiang et al. also demonstrated that, in macrophages, neither COX-2 protein or mRNA expression was affected by tocopherol treatment, leading to the speculation that RRR-γ-tocopherol may compete for the arachidonic acid binding site which leads to protein inhibition and reduced activity [ 13].
Sum1 binds a DNA binding site which resembles, and partly overlaps, the binding site of Ndt80 [ 23], [ 18].
The A247E mutation located within the receptor-binding site, which causes reduced killing of target cells (Supplementary Figure S1A and Del-Rey et al)., displays reduced FasL processing.
Among many other binding sites lost in the –673 construct were an E-box, a STAT binding site which forms a sequence model (Genomatix modelInspector) together with an ets binding site, and a Myc associated zinc finger binding site (MAZF).
Any binding site which had a p < 0.01 was annotated as a potential miRNA binding site.
When binding to DNA, LysR protein forms a homodimer and targets two specific binding sites, a regulatory binding site, which has the conserved T-N11-A/TTA-N7/8-GAA T-N11-A/TTA-N7/8-GAA T-N11-A/TTA-N7/8-GAA T-N11-A/TTA-N7/8-GAA T-N11-A/TTA-N7/8-GAAig. 2b).
Furthermore, no existing model incorporates information about the co-localization of TF binding sites, which may help reduce the number of non-relevant TF predictors in the model.
