CpG array analysis of histone H3 lysine 4 trimethylation in peripheral blood mononuclear cells of uremia patients

Studies of the epigenome have attracted little interest in nephrology, especially in uremia. Several lines of evidence have suggested that there are links between genomic DNA hypomethylation and cardiovascular complications in uremia patients. However, to date, our knowledge about the alterations in histone methylation in uremia is unknown. H3K4me3 variations were analyzed in peripheral blood mononuclear cells from 20 uremia patients and 20 healthy subjects, using chromatin immunoprecipitation microarray (ChIP-chip) approach. ChIP-real-time polymerase chain reaction (PCR) was used to validate the microarray results. mRNA expression and DNA methylation status can be further analyzed by quantitative (q) reverse transcription (RT)-PCR and methyl-DNA immunoprecipitation (MeDIP)-qPCR, respectively. Seven hundred twenty-six increased and 218 decreased H3K4me3 genes displaying significant H3K4me3 differences were found in uremia patients compared with healthy subjects. The results of ChIP-real-time PCR coincided well with microarray results. Expression analysis by qRT-PCR revealed positive correlations between mRNA and H3K4me3 levels. Aberrant DNA methylation can also be found on selected positive genes (CNOT1 PLTP EDG1 TCF3 KIR3DL2). In addition, we even found that there is an inverse relationship between H3K4me3 and promoter DNA methylation in uremia patients. Our studies indicate that there are significant alterations of H3K4me3 in uremia patients; these significant H3K4me3 candidates may help to explain the immunological disturbance and high cardiovascular complications in uremia patients. Such novel findings show the significance of H3K4me3 as a potential biomarker or promising target for epigenetic-based uremia therapies.