Fig. 5: Demethylation of hemi-methylated CpG sites up-regulates pluripotent genes. | Cell Discovery

Fig. 5: Demethylation of hemi-methylated CpG sites up-regulates pluripotent genes.

From: Hemi-methylated CpG sites connect Dnmt1-knockdown-induced and Tet1-induced DNA demethylation during somatic cell reprogramming

Fig. 5

a–c Approximately 20,000 protein-coding genes were divided into different groups based on their methylation levels and CpG densities near TSS (−1.5 ~ + 2.0 kb). The number of genes in the different groups were summarized in a. Genes with 42–83 CpG sites near their TSS (−1.5 ~ + 2.0 kb) were highlighted as in Zone I in a. Of the genes in Zone I, the genes with methylation levels between 40 and 60% were highlighted in Zone II. The changes in methylation of approximately 14,500 genes detected in the current RRBS were summarized in b, while the changes in the expression of approximately 11,000 genes detected in the current RNA-seq were summarized in c. Groups with less than 50 genes detected in RRBS or RNA-seq were not listed in b and c. d–f Demethylation of genes highlighted in Zone I and Zone II in a were compared to the average demethylation of all genes in d, e. The expression changes of 698 genes in Zone II were compared to the expression changes of all genes (f). g–i GO analysis results of the 698 genes in Zone II (g). The 22 genes that undergo significant up-regulation were selected and their demethylation was listed in h. Of these 22 genes, the expression changes of 6 pluripotent genes were determined by qPCR (i)

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