Effects of DNA methylation and histone modification on differentiation-associated gene expression in ES, NIH3T3, and NIT-1

Summary The effects of epigenetic modification on the differentiation of islet cells and the expression of associated genes (Pdx-1, Pax4, MafA, and Nkx6.1, etc) were investigated. The promoter methylation status of islet differentiation-associated genes (Pdx-1, Pax4, MafA and Nkx6.1), Oct4 and MLH1 genes of mouse embryonic stem cells, NIH3T3 cells and NIT-1 cells were profiled by methylated DNA immunoprecipitation, real-time quantitative PCR (MeDIP-qPCR) techniques. The histone modification status of these genes promoter region in different cell types was also measured by using chromatin immunoprecipitation real-time quantitative PCR methods. The expression of these genes in these cells was detected by using real-time quantitative PCR. The relationship between the epigenetic modification (DNA methylation, H3 acetylation, H3K4m3 and H3K9m3) of these genes and their expression was analyzed. The results showed that: (1) the transcription-initiation-sites of Pdx-1, MafA and Nkx6.1 were highly methylated in NIH3T3 cells; (2) NIH3T3 cells showed a significantly higher level of DNA methylation modification in the transcription-initiation-site of Pdx-1, Pax4, MafA and Nkx6.1 genes than that in mES cells and NIT-1 cells ( P <0.05); (3) NIT-1 cells had a significantly higher level of H3K4m3 modification in the transcription-initiation-site of Pdx-1, Pax4, MafA and Nkx6.1 genes than that in mES cells and NIH3T3 cells ( P <0.05), with significantly increased level of gene expression; (4) NIH3T3 cell had a significantly higher level of H3K9m3 modification in the transcription-initiation-site of Pdx-1, Pax4, MafA and Nkx6.1 genes than that in mES cells and with NIT-1 cell ( P <0.05), with no detectable mRNA expression of these genes. It was concluded that histone modification (H3K4m3 and H3K9m3) and DNA methylation might have an intimate communication between each other in the differentiation process from embryonic stem cells into islet cells.