Although IDEF1, IDEF2, and OsIRO2 regulate the expression of MAs-related genes and other Fe deficiency-inducible genes, their binding sequences are not consistently present in upstream regions of the genes that showed similar expression patterns in the current work (Table 2).
Interestingly, Efg1 binding sequences are not identical but overlap partially with the sequences bound by Tpk2.
This indicated that NFI binding sequences are not significantly enriched at mouse promoters as compared to intergenic and transcribed regions, but that it is the association to the binding sites per se that occurs preferentially at promoters.
DNA binding by a C-terminal deletion mutant of p53, p5382 360, which lacks the USP7 binding sequences, was not stimulated by USP7, suggesting that binding to USP7 is required for this effect.
Although the role of PDZ-domain-dependent targeting in PTEN function is rather unclear, it is known that the PDZ binding sequence is not required for the general regulation of cellular PtdIns 3,4,5 P3 levels and PKB/Akt activity ([25, 26] and confirmed during this study [data not shown]).
First, in this analysis, type-I AdpA binding, in which both subunits of the AdpA dimer bind each of the two divergent AdpA-binding sequences, was not considered, because we could not conclusively identify type-I-binding sites without DNase I footprinting.
These facts support the idea that these DNA-binding compatible sequences are not found in error, but rather that this is their true distribution and density within the genome.
The binding affinities of these negative sequences are not always available, so we use some value below the lowest binding affinity among all bound sequences, as the substitute of measurements.
The narrow extent of reactivation implies that the majority of transcription factor recognition sequences are not competent for binding even in the absence of methylation, and that methylation accounts for only a modest fraction of cell-selective binding.
However, many of their binding sequences are also distinct (the TF spheres appear not to overlap completely).
When the positions of the bipartite motifs within the binding sequences are depicted, the motifs are usually located in the middle of the binding sequences, but some are not centrally located in the long binding sequences (Fig. 4C, Supplementary Table S3).
