Fig. 1

Effect of SIV infection on genome-wide DNA methylation of CD4 + T cells. CD4 + T cell subsets were defined in LN based on CD95 and CD28 expression and divided into central memory (Tcm), effector memory (Tem) and naïve T cells for a AGM and b MAC. Individual samples are depicted using stacked bar charts. Circular representation of the c AGM and d MAC genomes, with differentially methylated sites for each of the conditions indicated by dots. Blue and orange dots indicate a hypomethylation and hypermethylation post-infection compared to baseline, respectively. For AGM, the tracks correspond to LN day + 14, LN chronic phase and blood chronic phase from the outside inwards. For MAC, the tracks correspond to LN day + 14, LN chronic phase, blood day + 14 and blood chronic phase from the outside inwards. The numbers of e DMP and f DMG for AGM (blue) and MAC (red) are depicted. Bars depicting LN are filled with dark red and blue, while bars depicting blood are dotted and filled with light red and blue. Hypomethylated sites are shown as negative numbers and hypermethylated as positive numbers. g The percentage of gene-associated and intergenic DMP is shown for AGM and MAC. h The distribution of DMP among gene regions is shown. LN lymph node, DMP differentially methylated probes, DMG differentially methylated genes, TSS transcription start site, UTR untranslated region, AGM African green monkeys (sabaeus), MAC Chinese rhesus macaque. The analyses included for LN and blood, respectively, 5 and 7 MAC at baseline, 4 and 3 MAC in acute infection and 13 and 10 MAC in chronic infection, as well as AGM 5 and 10 AGM at baseline, 4 and 0 in acute infection, and 8 and 9 in chronic infection