Figure 1.

TCR/coreceptor signaling alters chromatin accessibility landscapes responsible for Th1 and Th2 cell differentiation. (A) In peripheral T cells, antigen stimulation via TCR/coreceptor signaling is recognized as the priming signal, while environmental cytokines are known as commitment factors. APCs are important for T cells to receive TCR/coreceptor signaling; however, the dissociation of APCs from T cells is considered one of the important commitment factors for differentiation into Th subsets. ATAC-seq was performed with differentiating Th1 and Th2 cells at the indicated time points. Th1 and Th2 cells that received prolonged TCR/coreceptor stimulation throughout the differentiation process (from 0 to 120 h; green dashed line) and those that received regular TCR/coreceptor stimulation (from 0 to 48 h; red dashed line) were prepared. (B) The heatmap demonstrates the level of chromatin accessibility at 38,044 regulatory regions measured by ATAC-seq. Results with two replicates are shown for each time point. Accessible regions were organized in groups by k-means clustering (k = 20). Clusters were assembled into six metaclusters (groups 1–6), depending on their accessibility patterns. (C) The average tag count of each peak of ATAC-seq in differentiating Th1 or Th2 cells. Results with two replicates are shown for each time point. (D) The RNA expression levels of genes whose promoters (i.e., from 5 kb upstream to 2 kb downstream of the transcription start site) have ATAC peaks as shown in C. The mean values of two replicates were used for plotting. FPKM, fragments per kilobase of exon per million reads mapped. (E) The Venn diagram displays the overlap of the enriched motifs among groups 1–6 regions. (F) A list of specific motifs found in each group. (G) Potential proteins binding to the promoters of the group 4 genes were predicted based on a transcription factor enrichment analysis.