The novel dimeric motifs are almost identical to the known SOX9 motif complex, except that the spacing between the monomer binding sites is increased or decreased by a single basepair.
The activity of each alternative promoter A, B and C, mutated or not in the NF-Kappa B binding sites, was increased in Nter-142Q compared to Nter-15Q neuronal-like cells.
Interestingly, the number of SUMO-2/3 specific binding sites was increased by 12% (from ~27 k to ~57 k) while the number of SUMO-1 specific binding sites was decreased by 11% (from ~13 k to ~10 k) during viral reactivation.
In addition, the local concentration of the binding interfaces near their target site is increased, which promotes their interaction (40).
The analysis revealed that in the case of three isoforms (smTM, TM1b9a and TM5a) the affinity to an isolated binding site (Ko) was reduced and binding to a contiguous site was increased by modification of the actin C-terminus.
The amount of RbAp46 and HDAC1 on the complex binding to the Sp1 site was increased when the RbAp46 expression level was increased either by increased Ras expression or by increased RbAp46 expression.
In response to TNFα however, p65 binding to bona fide κB sites is increased [29].
In support of this, we find that retention of both C/EBPα and PPARγ binding is increased, when the binding sites overlap with a binding site of the other factor, suggesting that a potential synergy between these two factors is of such significance that selective pressure on these overlapping sites is increased.
As shown in Figure 7E (left panel), in the presence of CTCFL, binding of CTCF was reduced on ~1,100 sites, whereas binding on ~100 sites was increased.
