(A) Significance of chromatin changes is plotted against the magnitude of the change. Significantly open or closed chromatin regions at a FDR of 5% are represented by red or blue dots, respectively. Counts of DOC regions are given at the top. Vertical dashed lines indicate the minimum log₂FC of 0.2 on the x axis. For HC subjects, 23.3% of the tested regions displayed significant chromatin remodelling in response to M. tuberculosis, whereas PLWH and PrEP subjects lacked significant chromatin changes. The raw P value significance cut-off for FDR less than 5% varies as the FDR procedure is based on the P value distributions that are intrinsic to each tested group. (B) Density of the absolute log₂FC for 12,360 DOC regions is shown for HC, PrEP, and PLWH groups in blue, green, and red, respectively. Mean log₂FC for each group is highlighted by horizontal lines. PrEP and PLWH groups showed strongly impaired chromatin remodelling in response to M. tuberculosis compared with the HC group. (C) Pathway/GO term enrichment analysis of genes assigned to DOC regions for the HC response to M. tuberculosis. GO biological process (BP), KEGG, and Reactome pathways to which at least 5 genes had been assigned are plotted against the negative log₁₀ FDR. In total, 724 of the 8066 tested terms were significant. Enrichment analysis indicated that M. tuberculosis challenge promoted chromatin remodelling in regions assigned to genes belonging to IFN and TNF signaling pathways as well as response to viral and bacterial pathogens. (D) Rank plot of selected terms. DOC regions tagged genes assigned to “I−kappaB kinase/NF−kappaB signaling,” “TNF signaling,” and “Interferon signaling” pathways. DOCs are plotted according to their log₂FC on the x axis and ranked according to the magnitude of change on the y axis. Genes corresponding to opening or closing DOC regions are shown in red and blue, respectively. Horizontal lines indicate the 0.2 log₂FC cut off.