Fig. 2: Motif readout on nucleosome arrays deciphers OSK combinatorial binding.

a, Density heat maps showing the MNase–seq (purple), OSK ChIP–seq (blue) and ATAC–seq (red) signal, spanning ±5 kb around OSK nucleosome arrays during early reprogramming. The arrays within open (top) and closed (bottom) chromatin were separated according to ATAC–seq in MEFs and rank ordered based on size. The number of nucleosome arrays (n) is indicated. b, Profile plots of motif enrichment on both DNA strands (red and blue) around OSK nucleosome arrays (±5 kb) during early reprogramming. The average array size is highlighted in yellow. The dashed lines indicate near and far borders. c, Density heat maps showing OSK motif distribution (logos on top) around the OSK nucleosome array midpoints (±5 kb) during early reprogramming within closed chromatin and containing ≥7 SOX2 motifs per kb on the bottom strand. The motif density is scored on the top (red) and bottom (blue) strands, as indicated by the colour gradient scale shown at the bottom. MNase–seq read density heat maps (purple) are also shown. The arrays were rank ordered based on size, and those within 0.8–2.8 kb are indicated by arrowheads, dashed lines and number (n). d, Profile plots of OSK motifs centred around the near border (dashed line) of OSK nucleosome arrays (0.8–2.8 kb in size) as shown in c. The average array size is highlighted in yellow. e, The same as in d, but showing MNase–seq (top) and H1 ChIP–seq (bottom) in MEFs (blue) and ES cells (orange). f, The same as d, but showing the OSK occupancy (ChIP–seq). g, Genome browser screenshot around an exemplar OSK nucleosome array targeted in early and final reprogramming, showing MNase–seq, ATAC–seq and OSK ChIP–seq. The near and far borders are indicated by dashed lines, with the direction of KLF4 motifs on top. h, The same as d, but showing ATAC–seq (top) and H3K27ac ChIP–seq (bottom). i,j, The same as in d, but showing OSK ChIP–seq data from two independent studies ((i)¹¹ and (j)¹⁰). RPGC, reads per genome coverage.