Fig. 6: TEs are hypomethylated in skin T_reg cells and blood CCR8⁺ T_reg cells.

a,b, Enrichment of TE classes and subfamilies in regions hypomethylated (a) or hyperaccessible (b) in skin T_reg cells. P values were determined by one-tailed permutation test (n = 298,457 DMRs and 3,192 differential peaks) with a Benjamini–Hochberg correction; RC, rolling circle. c, Methylation of annotated insertion sites (with median) for three TE classes in skin T_reg and blood CD45RA⁺ T_reg cells (blood RA⁺ T_reg cells; left; three donors per cell type; Tissue Donors 7, 10 and 11 and Blood Donors 3–5) and distribution of differences in mean methylation (across the three donors) between skin T_reg and blood CD45RA⁺ T_reg cells for each insertion site (right). The numbers indicate how many insertion sites displayed differences below and above 0; AU, arbitrary units. d, Methylation (donors are as in c) and chromatin accessibility (ATAC Donors 1, 2, 4 and 5) in skin T_reg and blood CD45RA⁺ T_reg cells around selected TE insertion sites. Highlighted regions mark DMRs (methylation tracks), differential peaks (accessibility tracks) and TE insertion sites overlapping with DMRs (only TE subfamilies enriched among the DMRs; gene tracks). Vertical lines at the bottom of the methylation tracks mark CpG sites (CpG sites overlapping with TEs are shown in red). TE labels correspond to TE subfamilies (partly overlaps with Figs. 3 and 5). e,f, Enrichment of TE classes and subfamilies in regions that are hypomethylated (e) or hyperaccessible (f) in skin T_reg cells and defined by specific positionings of blood CCR8⁺ T_reg cells. P values were determined by two-tailed Fisher’s exact test (n = 292,033/2,064 DMRs/peaks ‘closer to skin T_reg’, 6,424/1,128 DMRs/peaks ‘closer to blood CD45RA⁺ T_reg’). g, Methylation of TE insertion sites overlapping with regions hypomethylated in skin T_reg cells (with median) in skin T_reg, blood CCR8⁺ T_reg and blood CD45RA⁺ T_reg cells (top; three donors per cell type; Tissue Donors 7, 10 and 11 and Blood Donors 3–8) and distribution of differences in mean methylation (across the three donors) between any two cell types for each insertion site (bottom). Numbers indicate how many insertion sites displayed differences below and above 0. Data are representative of two or more independent experiments with two or more individual donors.