Fig. 4
Targeted CpG methylation and expression analysis in representative hypermethylated genes related to immune cell activation. A Methylation peaks in four interesting gene regions are shown. Pink dumbbells also express the loci where primers have been designed. The DMR in the BACH2 gene is located in the second intron of 6 introns, the DMR in the SH2D1A gene is located in TTS, DMR in TXK is located CpG shore promoter, and the DMR in UHRF1 is located in the second exon of 17 exons overlapped with CpG shore. B The methylation validation for 12 CpGs in BACH2 DMR, 7 CpGs in SH2D1A and TXK DMR, and 22 CpGs in UHRF1 DMR by performing targeted bisulfite sequencing using primers listed in Table S10. Methylated CGs are indicated by black circles, and unmethylated CGs are expressed by empty (white) circles. C Violin plots show the distribution of methylated CG (%) between groups. The total percentages of methylated CG were calculated as ‘(The number of methylated CG / The number of total CG in the amplified region) * 100 (%)’ in each CG for every sample. D In contrast to Violin plots in (C), Box plots show the expression levels are significantly down-regulated in Benign and Carcinoma PBMCs versus Normal PBMCs. The y-axis means the log2-transformed (TPM + 1) quantified using RNA-seq