Figure 7. Examples of obesity-related genes and functional gene categories showing differential DNA methylation in promoters.

(a) The adipose and muscle B-DMR in FTO promoter. Top panels: top half: CpG methylation. Each point represents methylation level (MeDIP-seq read depth) of a sample at a given CpG site. The curves showed average over the samples. The two vertical dashed lines marked the boundaries of the DMR identified. Lower half: CpG dinucleotides (black tick marks on X axis), CpG density (gray line), TSS (black arrow), exons and introns (filled black and white boxes, respectively). Plus and minus marks denote sense and antisense gene transcription. Second panels: validation of individual CpG methylation by MassArray (mapping to yellow box in upper panel). Third panels: a scatter plot and trend line (Pearson correlation) showing correlation between the log₂ ratios of mRNA expression from microarray and CpG methylation of the DMR from MeDIP-seq. Bottom panels: validation of mRNA expression levels by q-PCR. Bars represent the mean expression level.

(b) The adipose T-DMR in ATP1B1 and COL8A2 promoters.

(c) The adipose S-DMR in miRNAs mir-99b, let-7e and mir-125a promoters.

(d) Top ten GO (Gene Ontology) and pathway categories enriched for adipose B-DMRs in promoters. The enrichment analysis was performed using the DAVID software⁵⁹ (see Supplementary Methods). The EASE score, indicating significance of the comparison, was calculated using Benjamini corrected modified Fisher’s exact test. BP: biological process, MF: molecular function.