Closer inspection of these binding sites revealed that 3420 83.7%%) of the non-CTCF bound binding sites contained the CTCF motif, indicating that they are either not bound by CTCF in ESCs, even though the binding motif is present or that these sites were not detected during ChIP-sequencing.
CTCF-A motifs constituted the largest fraction of the motifs (57 %), while 24 and 14%% of the CTCF binding sites contained the CTCF-B and CTCF-C motifs, respectively (Fig. 1d).
We found that 190 sites (about 2.9%, 190 out of 6,629 AR binding sites) contain the proliferative AR consensus matrix M00481, M00447 and M00962 (from the Transfac database) with a likelihood (LR) ratio of 500 compared to genomic background.
In contrast, only about 2.9% (190/6,629) of AR binding sites contains the canonical AR matrix M00481, M00447 and M00962 (from the Transfac database), which is derived mostly from AR proliferative responsive genes in androgen dependent cells.
For example, the smallest peak in Fig. 4B is the result of genes whose three binding sites contain the same letter x, and the largest peak is the result of genes with a different letter at each of the three binding sites.
We therefore sought to investigate whether there is functional divergence among CTCF binding sites containing the three different motifs.
Motif analysis in identified binding regions was done using MEME (Bailey et al, 2009); 500 binding sites containing the highest peak counts were used for analysis.
For example, recent ChIP-seq analyses have revealed that not all binding sites contain the 'expected' motif that was derived from in vitro binding studies [ 30, 31].
In this study they demonstrated that both Grb2 binding sites contain the core consensus motif RxxK (with x for any amino acid) [ 42].
This is because motif 12 5 is based on a CCTTTRA consensus sequence, and while all three sites contain the sequence CTTT, none of the three POP-1 binding sites contain the longer consensus sequence.
However, experimental validation is still required for their binding sites containing the 5-HT3B subunit as many of the residues with predicted ligand interactions in B+A− binding sites are known to not effect 5-HT activation or granisetron binding (Lochner and Lummis, 2010; Thompson et al., 2011c).
