Genome-wide analysis of histone H3 lysine 4 trimethylation in peripheral blood mononuclear cells of minimal change nephrotic syndrome patients

Am J Nephrol. 2009;30(6):505-13. doi: 10.1159/000243811. Epub 2009 Oct 1.


Background: Studies of the epigenome have attracted some interest in nephrology. However, to date, our knowledge about the alterations in histone modification in minimal change nephrotic syndrome (MCNS) is unknown. This study aimed to investigate the variations in histone H3 lysine 4 trimethylation (H3K4me3) in peripheral blood mononuclear cells of patients with MCNS.

Methods: H3K4me3 variations were analyzed in peripheral blood mononuclear cells, from 15 MCNS patients and 15 healthy subjects, using the ChIP-chip approach. ChIP real-time PCR is used to validate the microarray results. In addition, mRNA expression and DNA methylation status can also be further analyzed by quantitative (q) RT-PCR and methyl-DNA immunoprecipitation-q PCR, respectively.

Results: 848 increased and 231 decreased H3K4me3 probes displaying significant H3K4me3 differences were found in MCNS patients compared with healthy subjects. The results of ChIP real-time PCR coincided well with the microarray. Expression analysis by qRT-PCR revealed positive correlations between mRNA and H3K4me3 levels. DNA methylation alterations were found on selected positive genes (IL4R, HIVEP3, HPSE2, CDH13 and PRKD2). In addition, we also found that there is an inverse relationship between H3K4me3 and promoter DNA methylation in MCNS patients.

Conclusion: Our studies indicate that there are significant alterations of H3K4me3 in MCNS patients. These significant H3K4me3 candidates may help to explain the immunological disturbance involved in MCNS patients.

MeSH terms

  • Aged
  • CpG Islands / genetics
  • DNA Methylation / physiology*
  • Epigenesis, Genetic / genetics
  • Female
  • Genome-Wide Association Study
  • Histones / genetics*
  • Histones / metabolism*
  • Humans
  • Leukocytes, Mononuclear / physiology*
  • Lysine / metabolism
  • Male
  • Middle Aged
  • Nephrosis, Lipoid / genetics*
  • Nephrosis, Lipoid / metabolism*
  • Oligonucleotide Array Sequence Analysis


  • Histones
  • Lysine