Extended Data Fig. 6: Three-dimensional changes in chromatin architecture owing to a deficiency of H1C and H1E in GC B cells recapitulate decompaction during iPS cell differentiation.

a, Schematic of a previous study of B cell differentiation to iPS cells³² with time points for HiC analysis. b, Correlation plots comparing shifting to A c-scores in iPS cells (day 2, day 4, day 6, day 8) compared to control B cells versus c-score changes in H1c^−/−H1e^−/− GC B cells. Estimated odds ratios and P values were calculated using Fisher’s exact test. c, GSEA analysis of shifting to A compartments in iPS cells (day 2, day 4, day 6, day 8) against ranked Δ c-scores derived from H1c^−/−H1e^−/− minus wild-type mouse GC B cells (NES and FDR values as implemented by GSEA). d, Violin plots comparing stable and shifting B to A compartments during iPS cell differentiation (day 2, day 4, day 6, day 8 and fully undifferentiated) to the estimated Δ c-score due to deficiency of H1C and H1E in those same regions in GC B cells. (day 2, P < 2.2 × 10⁻¹⁶; day 4, P < 2.2 × 10⁻¹⁶; day 6, P = 0.002; day 8, 0.0001; estimated with two-sided Wilcoxon test). Box plot centre represents median, bounds of box are the first and third quartiles and whiskers extend to 1.5 × the interquartile range. e, v4c analyses on the Klf5 locus (chr14: 99,000,000–100,200,000) anchored on the Klf5 promoter for (top) B cell reprogramming (blue) to iPS cells (red) with four intermediate time states (grey) from a previous study³², as well as GC B cells (bottom) (H1c^−/−H1e^−/− and wild-type H1). IgV tracks below comprise Δ c-score and ATAC–seq signal in H1c^−/−H1e^−/− versus wild-type GC B cells. Gained HiC interactions in H1c^−/−H1e^−/− compared to wild-type GC B cells (shaded in grey 1–3: pval = 0.04; pval = 0.059; pval = 0.02, respectively, two-sided unpaired t-test) have OCT2 motif sequences as shown. f, Schematic of experimental set-up with H1c^−/−H1e^−/− or wild-type littermate mouse embryonic fibroblasts. g, Representative images of alkaline phosphatase (AP)-stained H1c^−/−H1e^−/− and wild-type iPS cell colonies at day 21. h, Per cent iPS cell reprogramming efficiency of H1c^−/−H1e^−/− (n = 5 transfections on two biological replicates) and wild-type (n = 4 transfections on two biological replicates) mouse embryonic fibroblasts determined as the ratio of AP⁺ colonies to the number of seeded mCherry⁺ cells. P = 0.01, two-sided unpaired t-tests. Data are mean ± s.d. Data are representative of three independent experiments.