Figure 6.

PE-SCAn to combine Hi-C and ChIP-seq data. A PE-SCAn (de Wit et al. 2013) analyzes whether sequences bound by a chromatin factor of interest show preferential long-distance (i.e., TAD-crossing) interactions. The depicted example is reprinted from Krijger et al. (2016) and shows the relationship of Sox2-binding profiles obtained in mESCs and mouse NPCs (neural progenitor cells) and the chromatin interactions detected in NSCs and iPSCs (induced pluripotent stem cells). Note that the Sox2-binding sites detected in ESCs exclusively cluster in iPSCs, whereas the binding sites found in NPCs cluster in NSCs.