Fig. 2 |. H1 stoichiometry regulates chromatin compaction in spatially defined nuclear compartments.

a, Representative transmission electron microscopy of wild-type and H1cTKO;Vav-iCre spleens. b, Hi-C was performed in CD8⁺ T cells isolated from wild-type and H1cTKO;Vav-iCre mice and a C-score was calculated for each 100-kb genomic segment to define A and B compartments and identify compartment switching, decompaction and compaction upon H1 depletion. c, d, Representative regions illustrating local chromatin decompaction and increased chromatin contacts in H1cTKO;Vav-iCre compared with wild-type CD8⁺ cells. Linear genome browser views of the C-score and chromatin type (see g) at the indicated genomic loci on chromosome 18 (c) and chromosome 6 (d) are shown. e, f, Interacting chromatin regions at 100-kb resolution were identified. The number of regions exhibiting a change (adjusted P < 0.01) in interaction frequency upon H1 depletion (e) and the normalized contact frequency between compartments (f; P < 0.0001, two-tailed t-test) in wild-type and H1cTKO;Vav-iCre CD8⁺ T cells are shown. In box plots, the centre line shows the median, box edges represent quartiles and whiskers extend to 10th and 90th percentiles. g, ATAC-seq fragment lengths and density in wild-type and H1cTKO;Vav-iCre CD8⁺ T cells by chromatin type. Change in nucleosome repeat length and chromatin accessibility are shown for each chromatin state. h, CUT&Tag was performed in wild-type and H1cTKO;Vav-iCre CD8⁺ T cells against the linker histone H1 and core histone H3. The normalized H1 to H3 CUT&Tag read ratios and density are shown for chromatin types 1, 2 and 3.