Fig. 3

Nanog rewires the pluripotency network. a Representative enrichment profiles (reads per million) of the indicated TFs (ChIP-seq) and chromatin accessibility (ATAC-seq) across an 8 kb-long genomic region (mm9: chr10:33,952,000–33,960,000). In black, average signal from 6 publicly available Nanog datasets. In blue and red, average signal of 44iN cells cultured in the presence or absence of Dox, respectively. The peak highlighted by a green box shows reduced signal in the absence of Dox; note an upstream peak displays increased Sox2 binding. b Heat map of average enrichment levels in each indicated condition (+/−Dox) across 0.5 kb centred on the Nanog peak summit at all Nanog sites (27,782), ranked from high to low Nanog. The regions were split in two groups depending on the presence (co-binding) or absence (Solos) of other TFs. c Plots displaying the -log10 Fisher p-value (Y-axis) of the enrichment of genes upregulated (left) or downregulated (right), at a given distance (X-axis) from specific groups of Nanog binding sites identified in b, d, as indicated in the colour-coded insets. d Heat map corresponding to 8 clusters identified on the basis of TF co-binding and the effects of Dox withdrawal, presented as in b without ranking for Nanog binding levels