Comparative epigenetic evaluation of human embryonic stem and induced pluripotent cells

Abstract

Histone H3 lysine 9 methylation has been shown to be a critical barrier to efficient cell reprogramming. This discovery allows the assessment of the cell pluripotency state by considering the extent of H3K9 methylation vs. acetylation at the same position. A set of pluripotent and differentiated human cells including embryonic stem cells, their differentiated and reprogrammed counterparts, along with human fibroblasts and their derived reprogrammed cells, were used to evaluate the ratio of total H3K9 methylation over acetylation using a quantitative ELISA-based approach. Also, the occurrence of the H3K4me3 and H3K27me3 bivalent marks was evaluated. Additionally, using ChIP-qPCR the occurrence of these histone marks on the regulatory regions of stemness genes (Nanog, Oct4 and Sox2) as well as on genes indicating fibroblast differentiation (Vim, COL1A1 and THY1) was evaluated. We evidence remarkably high ratios of H3K9ac/K9me2 in ES and iPS cells vs. differentiated cells. In iPSCs, a direct relationship between the ratios of total H3K9ac/H3K9me2 and the ratios of these marks on pluripotency gene regulatory regions and their expression was observed. In differentiated cells, in contrast, the ratios of global H3K9ac/K9me2 is low but the active genes escape this general situation and bear higher amounts of H3K9ac vs. H3K9me. Total H3K4me3/K27me3 ratios presented the same trends, but with reduced amplitudes. We propose that the rapid quantitative measurements of relative amounts of H3K9ac and K9me2 in iPS cells compared to the parental differentiated cells constitute a reliable and convenient criterion to rapidly assess the cell pluripotency potentials and the efficiency of cell reprogramming.