Fig. 2
Epigenetic landscape of TIM cells. a Venn diagram illustrating the intersection of promoter (left) and enhancer (right) regions in naïve (N) and innate memory (TIM CD8SP cells). b Scatter plots presenting counts of reads per H3K27ac peaks at promoters (left) and enhancers (right) with the indicated number of regions in naïve and TIM samples. Differentially active regions in TIM or naïve cells are shown in red and blue, respectively. c Representative tracks of differentially active H3K27ac peaks on IGV genome browser (highlighted in grey). d H3K27ac read densities on the union of all peaks (left) or centered on the TSS (±5 kb) of differentially expressed genes (DEG) in TIM (middle) and naïve cells (right). Each heatmap is accompanied by a plot showing the normalized cumulative coverage around the centre of the regions. e MA plot of mean log2 ATAC-seq peak atlas showing the differentially open regions (DOR) of TIM (red) and naïve cells (blue) with the indicated number of regions. Histograms indicate the distribution and numbers of DOR at promoters and enhancers. f CiiiDER analysis of putative transcription factors motifs in enhancer-bound DOR. Transcription factors are coloured according to the P-value of their gene coverage and whether they are over- (red) or under- (blue) represented in TIM cells. The size of each point is also proportional to log10 P-value. ChIP-seq was performed on three independent IPs (n = 5 mice per sample). ATAC-seq was performed on 1–3 independent samples (n = 2 mice per sample) from each group
