Fig. 4: OSK target chromatin loops with diminished linker histone.

a, Profile plots of Micro-C ligation junctions around OSK nucleosome arrays (±5 kb) in early (black) and final (blue) reprogramming, H1-KD MEFs (red) and H1-OE MEFs (green). b, Micro-C pileup heat maps of OSK nucleosome arrays (SOX2-motif-direction corrected) in early (right) and final (left) reprogramming. Maps are plotted using bin = 100 bp at log scale. The arrowheads indicate strong interactions across chromatin loops. c, Micro-C contact matrices (bottom), showing 1-kb-resolution interactions around the Nanog locus in early (left) and final (right) reprogramming. Contacts around exemplar OSK nucleosome arrays are indicated by arrows with the corresponding genome browser tracks of ATAC–seq and ChIP–seq shown above and highlighted in yellow. Associated loops called by FitHiChIP (q < 0.01) are shown at the top. d, Schematic of the nucleosome array organization within chromatin loops, illustrating OSK co-binding in early (left) and final (right) reprogramming. OSK binding is highlighted in blue, H1-enrichment in yellow and H3K27 acetylation is indicated by green flags. e, Micro-C decay curves showing internucleosomal contacts in H1-KD MEFs (red), MEFs (black) and H1-OE MEFs (green). Interactions between nucleosome n and n + x in 5′-to-3′ orientation and similar abundance are linked by brackets. f, Cartoon representations of the two-start zig-zag nucleosome fibre that comply with the internucleosomal n and n + x contacts shown in e. The coloured circles indicate the ligated partners between n (star) to n + x (coloured circles) in 5′-to-3′ orientation. g, Micro-C decay curves as in e for OSK nucleosome arrays. Nucleosome repeat-length changes are indicated by dashed lines. h, Profile plots (top) and heat maps (bottom) of ATAC–seq around OSK nucleosome arrays of TNG-KOSM-MEFs (OSKM-0h) or after OSKM induction (OSKM-72h) infected with empty, H1.4-KD or H1.4-OE vectors. i, Quantification of iPS cells (NANOG⁺) generated from TNG-KOSM-MEFs that were infected with empty, H1.4-KD and H1.4-OE vectors. Statistical significance was determined using two-sided unpaired t-tests; ****P < 0.0001, **P = 0.005. Data are mean ± s.d. from biological replicates (n = 11).