Fig. 5: ATRX loss of function is associated with perturbation of the chromatin environment and gene expression in a subpopulation of erythroblasts.

a Comparison of the chromatin environment in erythroblasts across the α-globin locus between unaffected donors and ATR-X cases (n = 1). H3K27ac ChIP-seq were performed as ChIP-Rx and normalised based on the Drosophila melanogaster S2 cells spiked in. b–d Tukey based box plots of scATAC-seq data showing the distribution of chromatin accessibility in controls (n = 2: Ctr2 and Ctr3, each of them composed of 4000 cells) and ATR-X cases (n = 2: case1 and case2, each of them composed of 4000 cells). Tukey based box plots showing the 25th and 75th percentiles (lower and upper bounds of the box, respectively), the median (centre line highlighted by an arrow), the minimum value lower than the 25th percentile minus 1.5* inter-quartile range (IQR) (lower whisker) and the maximum value greater than the 75th percentile plus 1.5*IQR (upper whisker), any values beyond the whiskers boundaries are represented as dots. b HBB locus, c HBA locus and d HBM locus. e–h t-SNE analysis of scATAC-seq data showing each individual cell (n = 4: Ctr2, Ctr3, Case1 and Case2) and encircled in red a subpopulation with contrasting chromatin accessibility scores for e HBB, f HBA1, g HBM; in h highlighting the cells belonging to either controls or cases that are included in or surrounding the subpopulation encircled with a red line; in e–g the black arrows point to examples of subpopulations where there are high levels of chromatin accessibility at HBB, HBA and HBM loci. i, j scRNA-seq data showing each individual cell colour based on HBM expression in control (n = 1: Ctr3) and in case (n = 1: Case1) and showing in i the relative gene expression of HBA relative to HBB. and in j the relative gene expression of HBM relative to HBB. k Model of the loss of chromatin integrity observed in ATR-X cases during cell differentiation/locus activity and the associated effect on gene expression.