Figure 5.

The most enriched TF binding sequences in ESC and NSC chromatin

The top de novo sequence motifs (based on enrichment) detected by XXmotif (see Materials and Methods) in ChIP-Seq data for Oct4 in ESCs, Sox2 in ESCs, Sox2 in NSCs (upper panel), Oct6, Brn1 and Brn2 in NSCs (lower panel). The most enriched motif in Oct4 and Sox2 ChIP-Seq data from ESCs is a composite Oct/Sox motif. This motif is not recovered from ChIP-Seq of NSCs with Sox2 or the multiple POU-TFs shown (see also a more extensive list in Appendix Fig S3). Rather, the top motif recovered from Oct6, Brn1 and Brn2 ChIP-Seq of NSCs is the MORE. Sox2 ChIP recovered a Sox motif as 2^nd and 3^rd most enriched sequence from ESCs and NSCs, respectively. Shown are the position frequency matrices visualised by WebLogo.