Human embryonic stem cells have a unique epigenetic signature

Abstract

Human embryonic stem (hES) cells originate during an embryonic period of active epigenetic remodeling. DNA methylation patterns are likely to be critical for their self-renewal and pluripotence. We compared the DNA methylation status of 1536 CpG sites (from 371 genes) in 14 independently isolated hES cell lines with five other cell types: 24 cancer cell lines, four adult stem cell populations, four lymphoblastoid cell lines, five normal human tissues, and an embryonal carcinoma cell line. We found that the DNA methylation profile clearly distinguished the hES cells from all of the other cell types. A subset of 49 CpG sites from 40 genes contributed most to the differences among cell types. Another set of 25 sites from 23 genes distinguished hES cells from normal differentiated cells and can be used as biomarkers to monitor differentiation. Our results indicate that hES cells have a unique epigenetic signature that may contribute to their developmental potential.

Figure 1.

Cluster analysis of human embryonic stem cells, differentiated cells, somatic stem cells, and cancer cell lines based on correlation of methylation profiles of 1536 CpG sites (A) and 36 CpG sites from six X-linked housekeeping genes: EFNB1, ELK1, FMR1, G6PD, GLA, and GPC3 (B).

Figure 2.

Boxplots of methylation levels in three sample groups—hES cells (N = 16), differentiated and somatic stem cells (N = 13), and cancer cell lines (N = 24). (A) Global methylation levels, calculated using all 1536 CpG sites; (B) methylation levels of 146 CpG sites in 33 imprinted genes; (C) methylation levels of 190 CpG sites in 45 tumor suppressor genes; (D) methylation levels of 45 CpG sites in 13 genes from the MHC region. The black bar represents the median methylation level for each cell type, calculated from the means of each individual cell line. The gray box defines quartiles (25% and 75%, respectively). The error bars are 1st and 99th percentiles of the distribution. Dots represent the outliers. P-values were computed using the Kruskal-Wallis test, which indicates the likelihood that all medians are the same.

Figure 3.

Methylation profiles of human embryonic stem cells, differentiated tissues, somatic stem cells, and cancer cell lines for 49 CpG sites from 40 genes that most strongly distinguish between hES cells and the other three cell categories.

Figure 4.

Methylation profiles of human embryonic stem cells, differentiated tissues, and somatic stem cells for 25 CpG sites (from 23 genes) selected for their distinct difference in methylation level between hES cells and normal differentiated tissues and somatic stem cells.