Fig. 1: HIRA ensures proper provision of H3.3 and restricts accessibility in compartment A.

a Experimental strategy to assess the effect of disrupting chromatin assembly on higher-order genome organization by constitutive HIRA knock-out (KO). Hi-C was performed in WT and HIRA KO H3.1-SNAP and H3.3-SNAP cells. To compare the 3D folding of chromatin to local state, we obtained H3.1 and H3.3 SNAP ChIP-seq from Gatto et al. (2022)¹⁹ and profiled H3 PTMs by ChIP-seq and accessibility by ATAC-seq. b Left: Representative Hi-C map at 50 kb resolution with A/B compartment track and H3.1 and H3.3 enrichment at 10 kb resolution of chromosome 5q (chr5: 50–170 Mb) from WT cells. Right: Total H3.3 and H3.1 enrichment at 10 kb bins at A (n = 1573) and B (n = 1573) compartment domains from WT HeLa cells, sorted by size and centered at their middle ± 2.5 Mb. c Left: Hi-C map, compartment track and right: H3.1 and H3.3 enrichment shown in A (n = 1582) and B (n = 1588) compartment domains as in (b), for HIRA KO cells. d EV1 (1st eigenvector, indicating compartment) of 50kb-binned Hi-C matrices from HIRA WT vs KO cells. Bins which change from A-to-B (lower right quadrant) or B-to-A (upper left quadrant) in the same direction in both cell lines are coloured red and blue, respectively). e ATAC-seq at 10 kb bins at compartments A and B from WT and HIRA KO HeLa cells, sorted by size and centered at their middle ± 2.5 Mb ATAC-seq is shown as cpm. H3.3 and H3.1 enrichment shown is z-score of log₂ IP/input.