Extended Data Fig. 4: Differential Tle3 binding is associated with immune regulation during CD8⁺ T cell responses.

a. Volcano plots showing differential ChrAcc sites between WT and Tle3^–/– T_EM cells (left) and those between WT and Tle3^–/– T_CM cells (right) by a more stringent criteria of ≥3-fold signal strength changes and FDR < 0.05. Values in the plot denote numbers of differential ChrAcc sites in each pairwise comparison. b. Principal component analysis (PCA) of Tle3 CUT&RUN libraries from WT T_N, T_EFF, T_EM and T_CM cells. c. Volcano plots showing differential Tle3 binding sites in comparisons of T_EFF, T_EM and T_CM with T_N cells, where stringent criteria (≥3-fold difference in binding strength, adjusted p value < 0.05 using DESeq2) were used to define dynamic Tle3 binding sites. Values in plots denote numbers of dynamic Tle3 binding sites in each comparison. d,f. Functional annotation of dynamic Tle3 binding sites in TleC1 (d) and TleC3 (f) (as defined in Fig. 4d), using GREAT analysis, with GO terms associated with immune regulation highlighted in orange. Values denote Hyper Observed Gene hits. e,g. Tle3 CUT&RUN sequencing tracks showing TleC1 (e) or TleC3 (g) Tle3 binding sites at select genes as displayed on IGV, with the dynamic Tle3 binding sites marked with open bars and subcluster information labeled. IgG CUT&RUN in T_N cells was used as a negative control. h. Detection frequency of dynamic Tle3 sites within +/–100 kb of TSS of DEGs in the five expression clusters defined in Fig. 3c. Values denote numbers of DEGs that are associated with dynamic Tle3 sites (w/) and those that are not (w/o). i. Distribution of DEG-associated dynamic Tle3 binding sites in genomic regions. From panel h, the DEGs associated with dynamic Tle3 peaks are divided into three categories, based on Tle3 site locations in promoters, distal regulatory regions, or both; and the values denote DEG numbers in each category.