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As shown in Figure 1, the distribution of various binding motifs shares the same sequences in Alu repeats, and, additionally, most RNA Pol IITF binding motifs cluster in the RNA Pol III promoter sequences, which provoke the thinking of the competition and cooperation among these binding proteins.
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To categorically validate the functional significance of the various transcription factor binding motifs within the hres gene promoter, ChIP (Chromatin Immuno-precipitation assay) was carried out.
The promoter region contains various transcription factor binding motifs with numerous CpG dinucleotides.
Dmp53 shows only 24% sequence identity to human p53 [ 42], with significant differences in the various DNA-binding motifs.
A recent analysis mapped DNAse1 sensitivity sites that harbor binding motifs of various TFs throughout the human mtDNA (Mercer et al. 2011).
For example, using computational tools to search for over-represented binding motifs in various groups of genes in S. cerevisiae, Hughes et al. [ 4] found that TFBSs are highly enriched in the region approximately between 50 and 150 bp upstream of the translation start site.
An important point is that the predictions were accomplished by using the information about the patterns of fragment interactions that are common among various proteins, as well as the binding motifs.
As seen in Table 3 and Text S2.D, several sets of direct targets of MYC derived from various experimental and tumor systems, genes containing MYC binding motifs and MYC-induced genes, were enriched in ER− tumors.
It is known that HNRNP I represses exon splicing by looping out exons between its binding motifs, which has been found in various kinds of tissues (reviewed in [ 31- 34]).
This observation is further supported by a comparison of the frequency of various triangular network motifs (not to be confused with the "binding motifs" in the text), as provided in Text S1.
To investigate and confirm the functional roles of the relevant binding motifs in regulating SPAK promoter activity, we generated various Sp1- and NF-κB-binding mutants (Fig. 5C).
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