Supplementary Figure 1: Characteristics of SEs in T_reg and T_conv cells.

(a) Patterns of indicated transcription factor-binding at SEs and surrounding regions in T_reg and T_conv cells. Average normalized ChIP-seq signals of global T_reg-SEs, common-SEs or T_conv-SEs were plotted for merged SE regions ± 20 kb. Merged ends of SEs are marked as S (start) and E (end). (b) Frequency of sites co-occupied by Smc1a and Med1 within indicated regions in T_reg and T_conv cells. (c) H3K27ac, H3K4me1 and H3K27me3, ATAC-seq, and MBD-seq signals at global common-SE and T_conv-SE regions and H3K4me3 signal around transcription start sites (TSS) of common- or T_conv-SE-associated genes in T_reg and T_conv cells. Average normalized ChIP-seq density of common- or T_conv-SEs is plotted for merged SE regions ± 20 kb or TSS ± 5 kb. Merged ends of SEs are marked as S (start) and E (end). (d) Heatmap showing the expression of genes associated with T_reg-SE, common-SE or T_conv-SE in indicated immune cells. LT-HSC: long-term hematopoietic stem cell, ST-HSC: short-term hematopoietic stem cell, MPP: multipotent progenitor, CMP: common myeloid progenitor, MEP: megakaryocyte-erythrocyte progenitor, GMP: granulocyte-monocyte progenitor, and CLP: common lymphoid progenitor. (e) Expression of genes associated with common-SEs (334 genes) or -TEs (3516 genes) (left) and with T_conv-SEs (19 genes) or -TEs (146 genes) (right) in T_reg and T_conv cells. Average of two independent RNA-seq experiments are plotted in box-and-whisker plot (median and 10-90 percentiles are shown). ns P > 0.05, * P ≤ 0.1, *** P ≤ 0.001, and **** P ≤ 0.0001 (Kruskal-Wallis test, followed by Dunn’s multiple comparisons test). Data are from one experiment (transcription factor ChIP-seq, ATAC-seq, H3K4me1 and H3K27me3 ChIP-seq), representative of two independent experiments (H3K27ac ChIP-seq, H3K4me3 ChIP-seq and MBD-seq) (a-c), or are average of two independent experiments (RNA-seq) (d,e).