Supplementary Figure 3: Tcf1 and Lef1 deficiency perturbs the lineage integrity of naive CD8⁺ T cells.

WT CD4⁺ and CD8⁺, Tcf7^–/–Lef1^–/– CD8⁺ mature thymocytes were sort-purified and analyzed for H3K4me3, H3K27me3, and H3K27Ac by ChIP-Seq. (a) Analysis of H3K4me3 and H3K27me3 at the 108 CD4⁺ characteristic genes. Normalized read counts of H3K4me3 and H3K27me3 signals surrounding the TSSs of the 108 genes in the CD4⁺ T cell gene set were plotted.

(b) H3K27Ac ChIP-Seq tracks at the St8sia6, Cd40lg, and Lgmn genes. Gene structures and transcriptional orientations were marked on top of each panel. These CD4⁺ signature genes were associated with strong H3K27Ac signals in WT CD4⁺ T cells, which were absent in WT CD8⁺ T cells. Tcf7^–/–Lef1^–/– CD8⁺ T cells, however, showed strong H3K27Ac signals similar to WT CD4⁺ T cells.

(c) Analysis of H3K4me3 and H3K27me3 at the 472 upregulated genes in Tcf7^–/–Lef1^–/– CD8⁺ T cells. Normalized read counts of H3K4me3 and H3K27me3 signals surrounding the TSSs of the 472 upregulated genes in Tcf7^–/–Lef1^–/– CD8⁺ T cells were plotted.

(d) H3K27Ac ChIP-Seq tracks at the Foxp3 and Rorc genes. Gene structures and transcriptional orientations were marked on top of each panel. Compared with WT CD8⁺ T cells, Tcf7^–/–Lef1^–/– CD8⁺ T cells showed increased H3K27Ac signals at the 5’-regulatory region of Foxp3 and the gene body of Rorc. In b and d, also shown are the Tcf1 ChIP-Seq tracks in splenic CD8⁺ T cells, with the MACS-called Tcf1 binding peaks marked by green rectangles.