Genome structure and organization in mouse CD8 T cells [RNA-seq]

Our experiments aimed to investigate the landscape of enhancers and super-enhancers in naïve, effector and memory CD8+ T cells. Here we mapped four histone modification marks and gene expression in naive, effector, and memory cells after viral infection. Our results suggest that the chromatin environment at regulatory DNA sequences in TCM is more permissive than in TN and TE. We further predicted the enhancers and their targets, and constructed transcriptional regulatory networks (TRNs) in three T cell stages. We have identified a highly dynamic repertoire of the enhancers and their targets during CD8 T cell responses, as 77% of the enhancers and 82% of the enhancer-promoter interactions are stage-specific. Our results suggest the dynamic change of enhancer activity during cell stage transition leads to TRN rewiring, which explains the expression change of the key factors of T cell function. We performed RNA-Seq experiments in WT and Tcf1/Lef1 difficient CD8 cells, and performed Hi-C experiments in WT cells.