Extended Data Fig. 8: GET recognize motif-dense and highly inter-connected nucleosome arrays enriched for H1.

a, Histograms showing size distribution of GET nucleosome arrays (grey bars) compared to arrays targeted by GET individually (blue, red, magenta, respectively). OSK nucleosome arrays are also shown for comparison (grey line). b, Profile plots showing GET motif distribution on top (red) and bottom (blue) DNA strands around the centre of GET nucleosome arrays (highlighted in yellow), with borders indicated in dotted lines. c, Histograms showing GET motif frequency distribution within GET nucleosome arrays in early reprogramming. d, Motif density heatmaps on both DNA strands (red and blue) around the left border (left panel) and right border (right panel) of GET nucleosome arrays containing TFAP2C motif on the right border. The arrays were rank-ordered based on size and motifs scored by the colour gradient scale at the bottom. Number of arrays (n) is indicated on the side. e, TFAP2C motifs are enriched in either the left or right border of the GET nucleosome arrays. Bar plot showing the count of TFAP2C motifs within each border of GET nucleosome arrays. f, profile plot showing the enrichment of H1 within GET nucleosome arrays in early reprogramming (red) in contrast to OSK nucleosome arrays (blue). Average GET nucleosome array size highlighted in yellow. GEO access codes of H1 ChIP-seq is indicated. g, Micro-C pile-up heatmaps of nucleosome arrays targeted by GET in early reprogramming (left) and in iTSCs (right) showing the increase of long-range interactions (indicated by arrow) after the completion of reprogramming. Bins = 2,000 bp and log enrichment scale is indicated at the bottom. h, Corner stripe stackup profiles (top) and heatmaps (bottom) showing the diffusion of borders around GET nucleosome arrays from early (left panels) to full reprogramming (right panels) at 2 kb resolution. Only GET nucleosome arrays with TFAP2C motif on the left border are shown (n = 11,501). i, GET translocate across interconnected nucleosome arrays during reprogramming. Arch representations of peak to peak (P2P) loops (magenta) showing interactions of exemplar nucleosome array bound by GET in early (blue) and final reprogramming (red). Genome browser tracks of ChIP-seq corresponding to GET nucleosome arrays highlighted in yellow. P2P loops are called by FitHiChIP with Q<0.01 threshold. j, GET nucleosome arrays in early reprogramming are not enriched for Cohesin and CTCF in MEFs. Line plots showing that histone marks and co-factors associated with open chromatin are depleted within GET nucleosome arrays in MEFs. The GEO access codes of the data used are indicated.