Fig. 2

Both TNF-α-PMA and SAHA stimulation increase DNA methylation of the latent HIV-1 5’ LTR in the H12 cell line. a The CpG methylation profiles of the 5’ LTR in non-stimulated H12 cells and EGFP-negative H12 cells selected after a 24-h stimulation with TNF-α and PMA or with SAHA. A schematic representation of CpG dinucleotide distribution in the 5’ LTR of the pEV731 vector together with the corresponding transcription factor binding sites is shown. An analysis of the promoter molecules is shown as a linear array of open circles representing non-methylated CpG residues and closed circles representing methylated CpG residues. Each line represents one sequenced molecule of the 5’ LTR. The methylation levels are presented as a mean percentage of methylated CpGs (mCpGs) in HIV-1 promoters. The p values were calculated by the non-parametric Kruskal-Wallis test. Significance *** was assigned for p values <0.001. b Distribution of the 5’ LTR molecules according to the proportion of methylated CpGs contained within. Non-stimulated H12 cells and EGFP-negative H12 cells selected after a 24-h stimulation with TNF-α and PMA or with SAHA are depicted. The percentage of respective molecules is shown on the x-axis. The total counts of methylated CpGs per molecule are shown on the y-axis. c Percentage of methylated CpGs within individual positions of CpGs. Non-stimulated H12 cells and EGFP-negative H12 cells selected after a 24-h stimulation with TNF-α and PMA or with SAHA are depicted. Individual CpG positions are shown on the x-axis; a schematic representation of CpG dinucleotides in the 5’ LTR of the pEV731 vector together with the corresponding transcription factor binding sites is shown below the x-axis. The percentage of methylated CpGs is shown on the y-axis. The p values were calculated by Fisher’s exact test. Significance was assigned as follows: * for p values <0.05, ** for p values <0.01