Fig. 3

The LPS response in naive and desensitized microglia is defined by enhancer signatures of transcriptional permissive marks. a Scatterplots depicting the correlation of differentially expressed genes (logFC) with corresponding differential ATAC, H3K4me3 or H3K27ac peaks (M-value) at promoters (within 2 kb of the nearest TSS) or enhancers (distal to promoters) between PL versus PP (left panel), LL versus LP (middle panel), PL versus LL (right panel). Each dot represents a differentially expressed gene that is associated with a significant differential chromatin peak (FDR < 0.0)1 in the given comparison. Light gray-colored dots indicate non-significant gene expression differences (FDR > 0.01). b–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 PL versus PP (b), LL versus LP (c), or PL versus LL (d). The color of each TF indicates its classification into an activator (green), a repressor (red) or undetermined (black) based on correlation of TFBS accessibility with RNA expression of the TF. FC fold change, TF transcription factor, TFBS transcription factor binding site