Figure S2.

Integration of dynamic CTCF binding with transcriptomic and ChrAcc changes during T_N to T_EFF cell differentiation. (A) PCA of the ChrAcc profiles of WT T_N, WT and Ctcf^−/− early T_EFF cells, where normalized ATAC-seq signals on merged peaks were used as input data. (B) Volcano plot showing differential ChrAcc sites between WT T_N and early T_EFF cells, where values denote numbers of differential ChrAcc sites. FC, fold change. (C) PCA of transcriptomic profiles in WT T_N, WT and Ctcf^−/− early T_EFF cells, where TPM for each gene in different samples were used as the input data. (D) Volcano plot showing DEGs between WT T_N and early T_EFF cells, where values denote numbers of DEGs. (E) Functional annotation of DEGs associated with concordant changes in CTCF binding and ChrAcc changes. DEGs from WT T_N vs. early T_EFF comparison were grouped into A–D based on association with concordantly acquired or lost CTCF + ChrAcc sites (as illustrated in Fig. 1 F), with gene and site numbers listed. DEGs in each group was analyzed with DAVID for functional annotation, and select GO terms of interest were displayed along with gene numbers and enrichment scores. All genes in the listed GO terms were visualized in gene expression heatmaps, and the gene-associated CTCF binding and ChrAcc changes are shown in heatmaps as parallel panels in Fig. 1 F. (F) Tracks of CTCF CUT&RUN and ATAC-seq in WT T_N and T_EFF cells at select genes in group B, which are associated with concordantly lost CTCF + ChrAcc sites (denoted with blue bars). Note that these CTCF binding sites may function as transcriptional silencers in T_N cells, and their eviction in T_EFF cells results in target gene induction. (G) Tracks of CTCF CUT&RUN and ATAC-seq in WT T_N and T_EFF cells at select genes in group D, which are associated with concordantly acquired CTCF + ChrAcc sites (denoted with orange bars). Note that these acquired CTCF binding sites may function as transcriptional silencers in T_EFF cells.