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We thus compared the potential transcriptionally important CpG sites that we had identified with the E2F1 binding site identified by Qiu et al. [24].
The results of the HscA ATPase assays reported here support the binding site identified by NMR spectroscopy.
It is currently unclear whether the latter binding site is identical to the tight binding site identified by functional studies [43].
To verify SF-1-responsiveness of the binding site identified by ChIP-on-chip, reporter constructs containing different lengths of the CITED2 promoter were designed, and activation by SF-1 was studied in luciferase assays.
We have high confidence in a CTCF binding site identified by the motif-based approach because binding at the exact same motif location is detected in more than 90% of cell lines.
Though the binding site identified by footprinting analysis is much larger, the MazEF module can be expressed by two promoters, namely P2 and P3 occurring at a distance of 13 base pairs (Marianovsky et al. 2001).
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While there is an overlap between the DaliLite alignment of PrgI with Bcl-xL and the protein ligand binding sites identified by CPASS, these sites are not identical.
By contrast MEME was unable to detect an enriched sequence motif within the intronic pool of binding sites identified by CLIP.
Also, locations of binding sites identified by ChIP-chip or ChIP-seq are often overrepresented in the TSS vicinity (data not shown).
In contrast to the STAT binding sites, the putative FoxO1 binding sites identified by Kitamura and colleagues, which are located between to the IREs and STAT binding sites, are not well-conserved (Figure 2B).
In addition to potential binding sites identified by Patser, we designed primers to amplify sequences approximately every 350 base pairs to test potential non-consensus binding across the entire 35S rDNA transcription unit (sites 5 17, 19 20, 22 27).
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