Genome-wide analysis of histone H3 lysine 4 trimethylation by ChIP-chip in peripheral blood mononuclear cells of systemic lupus erythematosus patients

Abstract

Objectives: Histone H3 lysine 4 trimethylation(H3K4me3) is an important epigenetic modification and associated with active transcription in multiple organisms. In systemic lupus erythematosus (SLE), global and gene-specific DNA methylation changes have been demonstrated to occur. However, to date, our knowledge about the alterations in the histone lysine methylation in SLE is known little. This study aimed to investigate the variations in H3K4me3 in CpG island regions in the peripheral blood mononuclear cells (PBMCs) of SLE patients and the controls, including rheumatoid arthritis patients and healthy subjects.

Methods: PBMCs were isolated by density gradient centrifugation from 10 active SLE patients, 7 inactive SLE patients, 8 rheumatoid arthritis patients and 8 healthy volunteers. H3K4me3 variations were analysed by using chromatin immunoprecipitation linked to the microarray (ChIP-chip) approach. ChIP-real time PCR was used to validate the microrray results. Expression analysis by qRT-PCR revealed correlations between mRNA and H3K4me3 levels. In addition, DNA methylation status was also further analysed by Methyl-DNA immunoprecipitation-quantitative PCR.

Results: Many key relevant candidate genes (such as PTPN22, LRP1B etc.) displaying differential changes in H3K4me3 in SLE versus controls (rheumatoid arthritis patients, healthy subjects) were identified. The results of ChIP-real time PCR were coincided well with those of microarray. Aberrant DNA methylation can also be found on selected randomly positive genes (WDR5, SLC24A3, PTPN22, LRP1B METT10D and CDH13).

Conclusions: Our results first indicate that there are significant alterations of H3K4me3 in PBMCs of SLE patients, and H3K4me3 alterations are associated with the pathogenesis of the SLE. Such novel findings show the significance of H3K4me3 as a potential biomarker or promising target for epigenetic-based lupus therapies.