Fig. 5

Genes proximal to super-enhancers change their nuclear positioning upon T cell activation. Three-dimensional immuno-DNA FISH of nine RIGs in resting and activated (anti-CD3/anti-CD28 beads, IL-2 for 48 h) CD4⁺ T cells (green: BAC/gene probe, red: lamin B1, blue: DNA staining with Hoechst 33342, scale bar represents 2 μm). Cumulative frequency plots show combined data from both experiments (n = 100, black: resting cells, red: activated cells). The p values of the Kolmogorov–Smirnov tests are indicated. Box plots represent minimized distances (5th−95th percentile) for the analyzed gene combinations in resting (white) and activated (gray) CD4⁺ T cells, obtained by high-throughput imaging and subsequent computational measurements. In the box plots, the center line represents the median, the bounds of the box span from 25% to 75% percentile, and the whiskers visualize 5% and 95% of the data points. Representative images for a FOXP1, STAT5B, NFATC3, and MKL2; b KDM2A and PACS1; and c GRB2, RNF157, and TNRC6C. d Allele fraction density plot for all resting and activated alleles that displayed peripheral repositioning. The y-axis shows the allele fraction density for genes FOXP1, STAT5B, NFATC3, MKL2, KDM2A, PACS, GRB2, RNF157, and TNRC6C. The x-axis represents ratios of distance from nuclear envelope (lamin B1 staining) and radius (signal to radius ratio) for alleles in resting cells (n = 1700) and activated cells (n = 1690 alleles). Binning into three equal concentric zones of the nucleus is performed as in ref. ¹⁸. e Schematic representation of chromosomal region 11q13.2 within 10 Mb: RIGs (bold red) and single HIV-1 integration sites (plain gray) and HTI of KDM2A and PACS1. f Schematic representation of chromosomal region 17q25.1-3 within 20 Mb: RIGs (bold red) and single HIV-1 integration sites (plain gray) and HTI of GRB2, RNF157, and TNRC6C