Figure 3. Chromatin accessibility profiles of T_conv cells with or without PPP2R2D expression using ATAC-seq analysis.

CD4⁺ T_conv cells were sorted out from spleens of R2D^fl/fl or Lck^CreR2D^fl/fl mice (n = 2 mice/group) and ex vivo stimulated by plate-bound CD3 and CD28 antibodies for 4 hours before being subjected to ATAC-seq. (A) Correlation heatmap indicating cross-correlation between each replicate or each group. (B) Histogram showing the distance from the nearest transcription start site (TSS) for all ATAC-seq peaks. (C) Volcano plot showing differential chromatin accessibility in CD4⁺ T_conv cells isolated from R2D^fl/fl (WT) and Lck^CreR2D^fl/fl (KO) mice. Fold change (FC) is calculated as log₂ (Lck^CreR2D^fl/fl/R2D^fl/fl). Red indicates sites that were significantly different (adjusted P ≤ 0.01, FC ≥ 4). (D) Transcription factor (TF) family binding motifs enriched in loci more accessible in Lck^CreR2D^fl/fl or R2D^fl/fl T_conv cells; the x axis shows the enrichment factor (ratio of the percentage of differential sites with motifs to the percentage of nondifferential sites with motifs), and the y axis shows the significance level of enrichment. TF families are indicated by color. (E) Accessibility tracks for selected gene loci (IL-2, Fos, Jun, Nfatc1, Nfkb1, and Rela) in R2D^fl/fl (up) and Lck^CreR2D^fl/fl (down) T_conv cells were plotted using the integrative genomics viewer (IGV). ATAC-seq data are average of 2 biological replicates at each cell type.