Notch signaling increases chromatin accessibility of bZIP transcription factors during effector CD8 ⁺ T cell differentiation. (A) 3 days after infection by Lm-OVA, Notch WT and KO OT-I CD44⁺ cells were collected for ATAC-seq. DARs were identified and distributed according to their genotype (left) or genomic location (right). (B) DARs were associated with genes using the HOMER annotation tool before being distributed by distance from their TSS. (C) Common DEGs from our RNA-seq and gene-associated DARs (using HOMER and GREAT annotation tools) from our ATAC-seq were identified while conserving the directionality of the data. (D) Several Notch-regulated genes common to our RNA-seq and ATAC-seq and important for SLEC/MPEC differentiation or function are plotted. (E) Transcription factor (TF) footprinting analysis was performed on all identified ATAC-seq peaks using HINT-ATAC, and statistically significative enrichment (P < 0.05) in either Notch WT or KO was illustrated. Members of the bZIP family are represented in orange. (F) Notch DARs (this paper) were distributed in DAR clusters defined by Scott-Browne et al. (2016). bZIP motif enrichment, calculated by Scott-Browne et al. on their clusters, is also represented. (G) GSEA was performed on Notch DEGs and DARs. Several immunological signatures of naïve versus effector (eff.) CD8⁺ T cells were enriched (P < 0.05). ATAC-seq experiment was performed in two independent adoptive transfers and infections (A–G).