UEA1+CD45−mTECs and UEA1−CD45−thymic stromal cells display distinct DNA methylation levels at mTECany2-T-DMRs. DNA methylation levels at the mTECany2-T-DMRs in mTECs and stromal cells isolated from Aire+/+ and Aire−/− littermate mice, as detected by COBRA. The levels of DNA methylation at CpGs within the HpyCH4IV site are indicated by the vertical axis. For Aire and CD80 genes—containing 2 HpyCH4IV sites inside the investigated region—the DNA methylation rate was calculated when any 1 of the CpGs was methylated. For the remaining genes, the levels represent DNA methylation levels at a single CpG. Bar graphs indicate means ± standard errors of the data from at least 3 independent bisulfite PCRs using independently isolated cells from 3 Aire+/+ mice and 3 Aire−/− mice.