Figure 5.

DNA methylation profiling of lung CD4⁺ T-cells. A, principal component analysis of 44,119 differentially methylated CpGs (DMCs) identified from a beta-binomial regression model with an arcsine link function fitted using the generalized least square method and Wald-test FDR q-value ≤ 0.05. Ellipses represent normal contour lines with one S.D. probability. B, Pearson correlation distance clustering. C, frequency histogram (bin size of 500 bp) showing the distribution of CpGs in relation to transcriptional start sites (TSSs) for both DMCs and non-DMCs. D, frequency histogram (bin size of 500 bp) showing the distribution of CpGs in relation to the middle of CpG islands (CpGis) for both DMCs and non-DMCs. Inset shows zoomed view from ± 1.5 kbp of the center of CpGis. Rectangle denotes 850 bp, the average length of CpGis in the mouse genome (42). E, box-and-whisker plot correlating tertiles of gene expression (log₂-transformed read counts per million) for differentially expressed genes (DEGs) (those with FDR q-value ≤ 0.05) with percent CpG methylation in their gene promoters (TSS ± 1 kbp). Well-observed CpGs from the DSS procedure are shown along with a p-value resulting from a one-way ANOVA post-test for linear trend (F(DFn, DFd) = F(1, 772) 22.86). F, Manhattan plot of the distribution of DMCs with FDR q-value ≤ 0.05. Gray points represent all DMCs; purple points represent DMCs within 2 kbp of differentially expressed gene bodies (inclusive). G, Venn diagram partitioning genes associated with DMCs within 2 kbp of their gene bodies (inclusive) and DEGs, all with FDR q-value ≤ 0.05. p-value resulting from a hypergeometric test is shown. Data are from three replicates per group, each representing pooled cells from three neonatal and two juvenile mice per replicate.