Figure 2.

Transcriptome up- and down-regulation can co-exist with CpG hyper- or hypo-methylation in the promoter and gene body. An integrated transcriptome-methylome analysis supported a negative finding, notably the absence of any tight correlation between transcriptome- and methylome alterations following SNL. Shown is the direction of CpG methylation change and gene expression change following nerve injury. Genes were divided into 2 groups: high CpG promoter (HCP; panel A and B) and low CpG promoter (LCP) genes (panel C and D). Promoter- (left, panel A and C) and gene body methylation (right, panel B and D) were analyzed separately. The methylation values of dDMCs (x-axis) were plotted against the expression value of their corresponding gene (y-axis). Each circle represents a differentially methylated CpG (dDMC), thereby allowing multiple pairings of individual dDMCs with the same gene. The analysis was performed on significantly changed CpG sites located in genes that underwent a significant change in expression. The results shown demonstrate that all possible scenarios exist: hyper- and hypo-methylation of CpG associated with increase or decrease in RNA levels from the same gene. Red: hypermethylated dDMC, blue: hypomethylated dDMC.