Fig. 3

Enhancers that acquire transcriptional activity de novo upon M.tb infection. a and (b) show presumable changes in gene regulation upon infection: (a) In non-infected macrophages, a transcriptionally inactive enhancer loops towards its target gene, (b) Upon M.tb infection, the enhancer acquires transcriptional activity; an additional loop is formed de novo for another acquired transcribed enhancer; the gene expression is induced. c eRNA expression of 356 acquired enhancers (left) and their 526 target genes (right); dashed line shows median gene expression prior to the infection, expression in TPM was averaged across replicates, p-values of Wilcoxon two-sided rank sum tests are shown. d Top 5 KEGG pathway maps with the lowest FDR enriched for 526 target genes of the acquired enhancers; next to the bars are the numbers of genes in the KEGG term covered by our gene list; dashed line indicates FDR = 0.05