Extended Data Figure 8 AOA and R-2-HG selectively affected DNA hydroxymethylation and methylation at FOXP3 locus, but not other important lineage specific signature gene loci examined by (h)MeDIP-seq. a, and b, Exogenous addition of dimethyl R-2-HG selectively decreases 5hmC signal and increase 5mC signal at FOXP3 locus. DNA extracted from differentiating TH17 cells (day 4) in the absence or presence of 0.75 mM dimethyl R-2-HG were immunoprecipitated with antibodies to 5hmC (a) or 5 mC (b), followed by deep sequencing. The sequence data were analyzed as described in method, and differential peaks from hMeDIP were plotted in a. 5hmC peaks located in FOXP3 conservative region or in other conservative regions at Il4, Il5, Il13, Il10, IFNγ, Rorc, etc. were highlighted. Peak 1,2,11 were located in Gata3; peak 3 in Rorc, peak 4 in Il4, peak 5,16 in Il10, peak 6 in IFNγ, peak 7 and 10 in Il5, peak 8, and 9 in Tbx21, peak 12 in Il13, peak 13,15 in Il17a, peak 14 in Il17f. Among 330, 582 peaks detected, R-2-HG decreased 5hmC signal in 17,676 peaks, however, R-2-HG did not decrease DNA hydroxymethylation at Il4, Il5, Il10, Il13, Il17a/f, IFNγ, Rorc, Tbx21 loci. b, Further analysis of 5mC signal in these 17,676 peaks, 3,402 peaks exhibited increased 5mC signal. Apparently, R-2-HG indeed selectively decreased 5hmC signal and increased 5mC signal at FOXP3 promoter and CNS2 region, but did not affect 5hmC or 5mC signal at IFNg, Il4/5/10/13, Il17a/f, Tbx21, Rorc. Notably, exogenous dimethyl R-2-HG did not affect 5hmC or 5mC signal only at FOXP3 locus, rather it had a more broad effect at many loci. c, and d, AOA treatment selectively affect DNA hydroxymethylation and methylation at FOXP3 locus. DNA extracted from TH17 culture in the absence or presence of 0.75 mM AOA were immunoprecipitated with antibodies to 5hmC (c) or 5mC (d), followed by deep sequencing. The sequence data were analyzed as described, and differential peaks were plotted. 5hmC peaks located in FOXP3 conservative region or in other conservative regions at Il4, Il5,Il13, Il10, IFNγ, Rorc, etc. were highlighted, the labels are the same as in a. Among 330, 582 peaks detected, AOA increased 5hmC signal in 11,896 peaks. Consistently, AOA increase hydroxymethylation at FOXP3 promoter and CNS2 region, but AOA did not affect DNA hydroxymethylation at IFNү, Il4, Il5, Il10, Il13, Rorc, Tbx21, etc. Notably, AOA treatment reduced 5hmC signal at Il17a/f loci, probably due to the antagonistic effect of FOXP3 on Rorүt to recruit Tet proteins to Il17a/f loci. d, Further analysis of 5mC signal in these 11,896 peaks, 1643 peaks exhibited increased 5mC signal. Apparently, AOA indeed decreased 5mC signal at FOXP3 promoter. Notably, the changes in 5mC signal at FOXP3 CNS2 region was unable to be detected, probably due to the fact that CNS2 region is largely methylated (around 70–80% of it is methylated in iTregs), and changes in 5mC is more subtle and difficult to be detected than 5hmC. Notably, both AOA and 2-HG affected 5hmC signal, but not 5mC signal at Gata3, indicating that AOA and 2-HG indeed have a minimal effect on DNA methylation at Gata3 locus. However, Gata3 expression is not regulated by DNA hydroxymethylation as shown in previous study, therefore 2-HG and AOA are unlikely to affect Gata3 expression. e, 17,676 peaks with increased 5hmC signal by AOA (from a, blue) is overlapped with 11,896 peaks with decreased 5hmC signal by 2-HG (from c, green). f, 3402 peaks with increased 5mC by 2-HG (from b, purple) overlapped with 1643 peaks with decreased 5mC signal by AOA (from d, red). These epigenetics analysis clearly showed that the effect of AOA and 2-HG on Foxp3 vs. other T-lineage related genes is highly selective, despite their more broad effects on genome-wide DNA methylation and hydroxymethylation. Although demethylation at FOXP3 locus promotes FOXP3 expression, expression of many other genes is not regulated by DNA demethylation, such as Rorc, Gata3. Treatment of T cells with AOA under TH17 condition stabilizes FOXP3 expression, while not having much effect on the expression of other lineage-specific transcription factors, such as Gata3, Rorc. FOXP3 can antagonize the function of RORγt to suppress expression of TH17 signature genes as well as recruit Dnmt1 to the gene loci of proinflammatory cytokines or signature genes to promote methylation at these loci, suppressing their expression. In addition, FOXP3 functions as both a transcriptional activator to directly activate its target genes required for ITreg cell differentiation/function, and a transcriptional repressor to directly suppress the genes associated with effector T cell function, resulting in ITreg cell fate.