Fig. 3: Changes in histone mark patterns between CD8 + T cell subsets occur in high transcript abundance genes without changes in transcript.
A Heatmaps summarising the number of genes that occur within each histone mark pattern (H3K4me2 = K4m2; H3K27me3 = K27m3) when comparing a less differentiated cell type (x axis) to a more differentiated cell type (y axis) for naïve vs central memory (CM), CM vs effector memory (EM), and naïve vs EM. Most genes tend to maintain RNAhi or RNAlo status and the same histone mark pattern between subsets. The number of genes is indicated by the colour-coding (maximum depicted colour-coded count, 500 genes). B, C. Sub-analyses of the heatmap from the top left corner of each comparative heatmap in A comparing a less differentiated cell type to a more differentiated cell type for naïve vs CM, CM vs EM and naïve vs EM. These analyses include RNAhi genes that do not (B) or do (C) show a significant change in transcript expression by limma (LogFC > 1, adjusted P < 0.05 by Benjamini-Hochberg procedure) between compared subsets. Genes on the diagonal (top left to bottom right of each plot) do not change histone mark pattern between subsets. Genes within red boxes show changes in histone mark patterns that indicate enrichment in the more differentiated cell types. Genes within white boxes show changes in histone mark patterns that indicate enrichment in the less differentiated cell types. Most genes that change histone mark patterns between subsets are not identified by differential gene expression analyses of RNA-seq data (compare B to C).
