Gene body cytosine methylation changes drive gene expression differences. RUNX1 methylation and gene expression were examined only (A, B) In the original discovery dataset, the gene body region of RUNX1 was hypomethylated (A) and the corresponding transcript level was increased (B) in the CKD (discovery) dataset. CTL, control. (C,D) The differential methylation (C) and expression (D) of RUNX1 in the DKD replication dataset. (E,F) Transcript levels are increased (F) in vitro in cultured tubules after decreasing the methylation level of the locus following 0.5 μM decitabine (DAC) treatment (E). (G) Genomic representation of the RUNX1 locus showing DMRs in the DKD dataset and in the CKD dataset. Different tracks are shown for the RUNX1 locus, including RefSeq gene, DMRs in the DKD dataset, DMRs in the CKD cells, and histone ChIP-seq data for H3K4me1 and H3K4me3 for adult kidney cortex and DHS sites from fetal kidneys. In addition, ENCODE-based transcription factor binding sites are also shown.