Fig. 4

Enhancer and promoter signatures of transcriptional permissive marks regulate training in primed microglia. a, b Scatterplots depicting the correlation of differentially expressed genes (logFC) with corresponding differential ATAC peaks (M-value) in KO versus WT, LPS-treated KO versus LPS-treated WT, LPS-treated WT versus WT and LPS-treated KO versus KO microglia (a), and differential H3K4me1, H3K4me3, H3K27ac or H3K27me3 peaks (M-value) in KO versus WT microglia (b). The chromatin peaks are divided into promoters (within 2 kb of the nearest TSS) and enhancers (distal to promoters). Each dot represents a differentially expressed gene that is associated with a significantly differential chromatin peak (FDR < 0.01) in the given comparison. Gray color of dots indicates non-significant gene expression differences (logFC > 1, FDR > 0.01). c, d Transcription factor binding site analysis generated by diffTF to identify critical regulators for different gene sets based on ATAC- and RNA-seq data. Volcano plots depicting weighted mean difference of accessible TFBS between KO-PBS versus WT-PBS (c) and KO-LPS versus WT-LPS (d) microglia. The color of each TF indicates its classification into activator (green), repressor (red) or undetermined (black) based on correlation of TFBS accessibility with RNA expression of the TF. e Gene expression values (CPM, Additional file 6) of selected homeostatic microglia genes in the primed mouse model. Every dot depicts an individual animal (n = 3 per experimental condition). CPM counts per million reads, TF transcription factor, TFBS transcription factor binding site