Fig. 7: Correlation between expression of switch-like genes and methylation at nearby CpG sites.
A A schematic showing that methylation at CpG sites in gene promoters typically represses transcription. B Correlation in the prostate between expression of tissue-specific switch-like gene TBX4 and methylation at a CpG site close to the transcription start site for the gene. C Correlation in the breast between expression of tissue-specific switch-like gene KRT6B and methylation at a CpG site close to the transcription start site for the gene. D A schematic showing how the polymorphic deletion of a gene and a nearby unmethylated CpG site can lead to a negative correlation between the expression level of the gene and the methylation level at the CpG site across individuals. This mechanism is not an example of epigenetic silencing. E The expression of GSTM1 is negatively correlated with methylation levels at a nearby CpG site across individuals in multiple tissues because of a polymorphic deletion affecting both the gene and the CpG site. F The genetic variant rs393329 (T- > C) represses NPIPB2 expression across tissues via cg16495772 (a CpG site in the vicinity of NPIPB2) methylation. The x-axis represents genotypes of the variant. The figure on the left shows methylation level distributions of cg16495772 for each genotype in six tissues. The figure on the right shows expression level distributions of NPIPB2 for each genotype in six tissues. In each violin, data points below the 1st percentile and above the 99th percentile were excluded to minimize the impact of outliers on the distribution. In B, C, E, and F, log(TPM + 1)C refers to the values of log(TPM + 1) corrected for the effects of technical confounders. A and D were designed entirely with BioRender. All panels were assembled as Fig. 7 in BioRender. Aqil, A. (2025) https://BioRender.com/eet7v3w. Source data are provided as a Source Data file.
