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Two of the SNPs are within 200 bp of transcription factor binding sites and would be predicted to have an effect on transcriptional regulation (Table 5).
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Both zebrafish aromatase promoters contain CREB binding sites and would therefore be responsive to cAMP signaling.
If this holds, positional preferences defining a mutual exclusion between transcription factor binding sites and nucleosomes would be expected.
As shown in Figure 4D and 4E, several hydrogen bonds are formed between quercetin, hematin and the amino acid residues in the binding sites, which would be in line with its high binding affinity for the COX enzymes.
For sequencing data, to check for splicing and novel transcripts or detect peaks for transcript factor binding sites, one would be interested in distinguishing the true expression signal from the background.
It is conceivable that the 4 kb region considered is not sufficient since binding sites that would be more distal to the TSS will be missed by this approach.
CTCF only binds non-methylated sequences, so we assumed that the somatic DMRs that were hypermethylated in liver (n = 10) could still have CTCF binding sites that would be occupied in other tissues but be negative in liver.
"Figure 4 Regarding figure 4 : since spanions and tiRNAs are approxiamately in the same size (whereas spanions are much smaller the polII binding sites) it would be much comprehensible if the distance between these elements would be presented as the distance between the 5' edges of both element types.
The higher geometric mean ratios and apparent lower plasma exposure of SU012662 could potentially have been related to low-capacity tight/target tissue binding sites, which would be only present after the first dose at very low concentrations with limited sampling.
If the Sox2 stable binding sites only reflected random non-specific interactions, the clustering behavior of short lived binding sites would be the same as that of the long lived binding sites.
The binding of Sam68 to its two binding sites would be necessary for efficient complex formation, involving the recruitment of U2AF, and so could determine the overall level of v5 exon inclusion.
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