Figure 1

Chromatin structure and gene expression are immune cell type-specific. (A) Normalized read coverage plots of ATAC-seq and RNA-seq libraries at phenotype-defining genes including CD4, CD8A, IFNG, MS4A1 and BCL11B loci in resting CD4⁺ (nCD4⁺), resting CD8⁺ (nCD8⁺), activated CD4⁺ (aCD4⁺), activated CD8⁺ (aCD8⁺) T and resting B (B) cells. (B) In-situ Hi-C contact matrices for a 1 Mb region on chromosome 14 that includes BCL11B, which is known to be expressed in T but not B cells. The top four Hi-C matrices display data from resting and activated T cells and show distinct genome organisation at the gene, while the bottom Hi-C matrix of B cells shows a lack of genome organisation at BCL11B. Color scale indicates number of reads per bin pair and has been scaled within each matrix to facilitate comparisons. (C) Multidimenional scaling (MDS) plots of log-CPM values with samples coloured by cell type and shaped by donors. The log-CPM values were corrected for the donor variable. Distances on the plot correspond to the leading fold-change, which is the average (root-mean-square) log2-fold-change for the 500 genes (RNA-seq), 5000 peaks (ATAC-seq) and 50,000), bin pairs (Hi-C) most divergent between each pair of samples.