Early Notch signaling programs effector CD8+ T cell differentiation [ATAC-Seq]

A better understanding of the mechanisms regulating CD8+ T cell differentiation is essential to develop new strategies to fight infections and cancer. Using genetic mouse models and blocking antibodies, we uncovered cellular and molecular mechanisms by which Notch signaling favors efficient generation of effector CD8+ T cells. Using transcriptional and epigenetic studies, we identified a unique Notch-driven T cell-specific signature. Early Notch signals were associated with chromatin opening in regions occupied by bZIP transcription factors, specifically BATF, known to be important for CD8+ T cell differentiation. Overall, we show that the delivery of early Notch signals controls the molecular and functional fate of CD8+ T cells after infection. For ATAC-seq, B6-CD45.1 mice were adoptively transferred with WT vs Notch1/2 KO OT-I cells and infected with Lm-OVA. 72h post-infection, splenocytes were purified by negative selection using anti-CD4 and anti-CD19 biotinylated antibodies and streptavidin-conjugated magnetic beads (EasySep Streptavidin RapidSpheres, StemCell Technologies). Activated OT-I cells (Zombie dye− CD8+ CD45.2+CD44+) were then sorted and nuclei isolation was performed.