Differential intragenic CGI methylation negatively correlates with gene expression. Genes showing both a change in DNA methylation at an intragenic CGI and a change in gene expression were plotted. (A) All immune cell comparisons where (+) denotes an increase and (-) denotes a decrease in expression or methylation. (B) The percentage of methylation changes showing a positive or negative correlation with gene expression in immune cells. (C) Brain compared with CD4 cells. (+) denotes an increase and (-) a decrease in expression or methylation. (D) The percentage of methylation changes between brain and CD4 cells showing a positive or negative correlation with gene expression. (E) Expression of Gata3 (relative to Eef1A1) in Th1 and Th2 cells verified by qRT-PCR. (F) MAP-seq read density profile (red) showing differential methylation at an intragenic CGI (asterisk) in the Gata3 gene. CGIs are shown in blue. The arrow indicates the origin and direction of transcription. (G) Confirmation of Gata3 methylation by bisulfite sequencing of in vitro differentiated Th1 and Th2 cells as well as Th2 cells isolated from a Schistosoma mansoni infection. The gray bar on the MAP-seq profile (panel F) indicates the region interrogated. (Filled circles) Methylated CpGs. (Empty circles) Unmethylated CpGs.
