In contrast, nuclear extracts from MCF-7TXT9 and MCF-7TXT10 cells exhibited more than threefold higher levels of subunit binding to the NF-κB sequence compared with equivalent extracts from MCF-7CC cells (P < 0.05).
By comparing the effectiveness of the de novo and selex sequences to compete for binding, we established that NKX2-5 has a much higher affinity for the selex sequence compared with the de novo motif.
Despite the increasing number of structural information on longer DNA telomeric sequences, very few data are available on the binding properties of these sequences compared with the shorter DNA telomeric sequences.
Figure 4 shows that there is a significant enrichment of binding sites in orthologous intergenic sequences compared with randomized and simulated intergenic sequences for each species.
Group F proteins contain divergent sequences compared with other groups and another domain for dimerization and DNA binding [ 16].
Group F consists of the COE domain; they have diverse sequences compared with other groups and another domain for dimerization and DNA binding [ 2, 14, 15].
In addition, the sets of differentially expressed genes were not enriched in any functional categories (not shown), and the promoters of these genes showed neither enrichment in direct E2f4 occupancy (Figure 3A) nor enrichment in the presence of E2f4 binding sequences when compared with the DNA present on the promoter arrays (Figure S4).
No specific co-factors for Mash1 were identified in this analysis, whereas cAMP response element (CRE; bound by CRE binding protein (Creb)), Yy1, and Nkx binding sites were significantly enriched near Ngn2 binding sites when compared with the sequence around Mash1 binding sites).
Similar data were observed for ROCK2, showing that the forced expression of miR-200b/c in TFK-1 cells results in a decrease in luciferase activity using conserved wild-type binding sites compared with a mutant sequence and also indicating that the conserved predicted binding sites of miR-200b/c in the 3′-UTR of ROCK2 were functional.
However, our results suggest that Cry1Aa activity does not depend on conserved amino-acid sequences in loops, indicating an unusual binding character compared with other proteins.
