Epigenomics as a tool to assess iPSC identity. Chromatin signatures obtained by epigenomic profiling of a cohort of human embryonic stem cell (hESC) lines can be used to generate hESC reference epigenomes (left panels). The extent of reprogramming and differentiation potential of individual induced pluripotent stem cell (iPSC) lines can be assessed by comparing iPSC epigenomes (right panels) to the reference hESC epigenomes. (a-c) Such comparisons should evaluate epigenetic states at regulatory elements of self-renewal genes that are active in hESCs (a), developmental genes that are poised in hESCs (b), and tissue-specific genes that are inactive in hESCs, but are expressed in the cell type of origin used to derive iPSC (c). H3K4me1, methylation of lysine 4 of histone H3; H3K4me3, trimethylation of lysine 4 of histone H3; H3K27ac, acetylation of lysine 27 of histone H3; H3K27me3, trimethylation of lysine 27 of histone H3; meC, methylcytosine.