Although further studies are needed, it is possible that ELK4 facilitates TR4 binding to promoter regions that do not contain the DR1 motif, suggesting the presence of ELK4 dependent and ELK4 independent modes of TR4 action.
In contrast, a clear over-representation of ETS family binding motifs was observed in the EWS-FLI1-specific regions that do not contain microsatellite sequences (Table 2).
14 additional sequences belonging to this subfamily possess shorter N-terminal regions that do not contain any explicitly recognizable domains while bearing INSL3/Relaxin binding GPCR-like TM regions [Additional data file 3].
Rather, they are spatially removed from those regions that do, namely, the PPIase domain catalytic site and the WW domain substrate binding Loop I (S16 R21).
Finally, the performance of the peak detection algorithms was evaluated with respect to regions that were confirmed in independent qPCR experiments to be bound by the particular transcription factor (true positives) as well as regions that did not show binding (true negatives) in these experiments.
Moreover, ChIP-NANOG regions that did not overlap with any ChIP-POU5F1 regions also had an increased abundance of OCT-SOX composite binding motifs (Additional file 7).
All D0 MLL4 regions, D2 MLL4 regions that did not overlap with D0 regions, D7 MLL4 regions that didn't overlap with either D0 or D2, and identified MLL4 peaks in myocytes but not in preadipocytes, were regarded as emergent MLL4 binding sites.
All the samples where analysed by real-time PCR using SYBR Green PCR master mix (Applied Biosystems) and specific pairs of primers for two regions of each promoter that contained VDRE and/or TCF/Lef binding sites, one region that does not contain any of these sites, and a completely unrelated region of the genome as a negative control (Table S3).
10 Most enriched DNA motifs found within the 500 bp regions on either side of CUX1 binding sites that do not contain the ATCRAT CUX1 Consensus.
Our search also identified several potential a1- α2 binding sites in the promoter regions of genes that do not appear to be repressed in diploid cells (Table 4).
