(a) Conventional 4C-Seq analysis (representative experiment shown) of the Dppa3-Nanog locus at early reprogramming timepoints using the Nanog promoter as a viewpoint. Border region defined by Hi-C and superenhancer (SE) are indicated in blue. (b) 2.25 Mb in-situ Hi-C contact maps (50 kb resolution) centered on the Sox2 gene and its superenhancer (SE) for both independent biological replicate reprogramming experiments. TAD border calls per timepoint are indicated by black arrows. Note the progressive insulation of Sox2 and its SE into a smaller domain as the gene is activated (indicated by a black arrow in the PSC maps). (c-e) Kinetics of mean H3K4Me2 (panel c), D-score (panel d) and PC1 (panel e) changes at dynamic borders harboring genes that are either upregulated (n = 22) or downregulated (n = 21) after I-score changes are initiated. Shading denotes SEM.