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Fig. 5 | Genome Biology

Fig. 5

From: Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells

Fig. 5

The Il4 locus is concordantly demethylated during Th2 cell differentiation. A Genome browser view of part of the Il4 locus, with amplicons indicated as in Fig. 1C. B Positions of CpGs in the first amplicon of Il4 CNS1 (CpGs 1–8), and the amplicons for Exon 1 (CpGs 22–28) and Intron 1-Exon 2 (29–37). C Methylation profiles for CNS1 (CpGs 1–8), Exon 1, and Intron 1-Exon 2 amplicons in Th2 cells after the first (upper) and second (lower) cycles of differentiation. Each row represents one read. Black indicates methylation (5mC + 5hmC) and white indicates the presence of unmodified C, 5fC, or 5caC at the indicated CpG. Note that demethylation occurs progressively between the first and second cycles of differentiation at all CpGs in the first amplicon of Il4 CNS1 (CpGs 1–8), with the most extensive demethylation at CpGs 3–8; similarly, demethylation occurs progressively at the GATA3-binding intronic enhancer, with the most extensive demethylation occurring at CpGs 27–29 near the peak of GATA3 occupancy (see Fig. 4A). D Matrix showing odds ratio of any two CpGs as a measure of concordant modification in Th2 cells after the first (upper) and second (lower) cycles of differentiation. The brighter the red color, the more similar the methylation status of the CpGs being compared. The highest levels of concordant demethylation are observed at CpGs 3–8 of Il4 CNS1, CpGs 25–28 of exon 1, and CpGs 29–31 of intron 1-exon 2. E For all possible pairs of CpGs, the odds ratio for a pair of CpGs is plotted against the distance between that pair of CpGs. Note that the odds Ratio (concordant methylation status) is higher the closer the CpGs

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