Extended Data Fig. 8 |. Changes in activation marks H3K4me3 and H3K27ac and repressive marks H3K9me2 and H3K9me3 in H1-deficient GCB-cells are associated with compartment B decompaction.

a, Genes defined as type Groups 3 and 4 (n=108 genes) and Group 5 (n=152 genes) manifest transcriptional activation and significant upregulation in H1c^−/−/e^−/−GCB-cells compared to WT GCB-cells. Paired Wilcoxon test. Boxplot center represents median, bounds of box are 1^stand 3^rdquartile and whiskers extend out 1.5*interquartile range from the box. b, Top: Expression of the genes defined as type Groups 3–5 was plotted for each cell on the Y axis. Average expression is represented by the different colored spline curves for each genotype as indicated. Bottom: Differential expression between H1c^−/−/e^−/− and wild type cells were represented as the delta spline plot across pseudotime. Cells are divided by pseudotime into bins of equal cell number (gray vertical dashed lines) and tested for signature enrichment compared to WT GCB-cells by two-sided Wilcoxon (P < 6.81⁻⁵⁰). c, Fraction of histone peak coverage for H3K4me3 and H3K27Ac within 100kb compartments across HiC compartment score (X axis) for wild-type H1 GC B-cells. Cubic smoothing spline of data is presented with error bars as shaded regions indicate 99% confidence intervals. d, GSEA with genes marked with gain in H3K4me3 (top) or H3K27Ac (bottom) on their promoters (TSS +/−500 bp) using the ranked log2 fold-change in murine H1c^−/−/e^−/−GCB-cells. e, Fraction of histone peak coverage (for H3K9me2 and H3K9me3) within 100kb compartments across HiC compartment score (X axis) for wild-type H1 GC B-cells. Cubic smoothing spline of data is presented with error bars as shaded regions indicate 99% confidence intervals. f, CUT&RUN peaks for H3K9me2 and H3K9me3 show altered abundance between H1c^−/−/e^−/− compared to WT GC B-cells (FC>1.5, n=5277 gained and n=4717 lost H3K9me2 and n=2511 gained and n=7529 lost H3K9me3 peaks). g, Genome wide correlation plot of log2 fold H3K9me2 (left) and H3K9me3 (right) (H1c^−/−/e^−/−vs wild-type H1) peaks versus delta compartment score (H1c^−/−/e^−/−- wild-type H1). Both H3K9me2 and H3K9me3 changes were largely loss and were anti-correlated with compartment decompaction (Pearson correlation coefficient R=−0.438, P<1e-16 and R=−0.543, P<1e-16, respectively). h-i, Heatmaps of H39me2 and H3k9me3 centered within shifting B to A compartments (100kb) and surrounding 300kb for H1c^−/−/e^−/−and WT GCB-cells for compartment “extensions” (h) and “islands” (i). j, Fraction peak (H3K9me2 and H3K9me3) coverage of regions within shifting compartment groups 1–2 in H1c^−/−/e^−/−and WT GCB-cells. Paired Wilcoxon test, Group 1: H3K9me2, P<1e-16, H3K9me3, P<1e-16; Group 2: H3K9me2, P<1e-16; H3K9me3, P<1e-16 ; Boxplot center represents median, bounds of box are 1^st and 3^rdquartile and whiskers extend out 1.5*interquartile range from the box.