Extended Data Figure 2: Methylation pattern analysis defines epigenomic heterogeneity in stem cells and fibroblasts.

a, Quantification of average methylation for individual CpGs in regions with low (<1.5%), medium (1.5–5%) and high CpG (>5%) content reconfirms the known bipolar epigenomic organization in ES cells. Low CpG content regions are always methylated to near completeness, and high CpG content regions are strongly biased to low methylation levels. Regions with 20–80% average methylation are rare in ES cells. b, A similar analysis for fibroblasts shows that although the overall bipolar organization is retained, a proportion of the genome develops intermediate methylation levels. c, Colour-coded density map shows comparison of regional (MspI fragment) methylation average between ES cells and fibroblasts. Regions developing intermediate methylation in fibroblasts are typically fully methylated in ES cells. d, Methylation pattern analysis is based on estimating frequencies of patterns at loci. For each genomic locus with adequate coverage, we identify the most common pattern, other frequent patterns (if such exist), and all rare (<20%) patterns. The most frequent pattern (11/20) in this example is the unmethylated pattern, with a second pattern observed in five molecules and an additional four rare patterns. e, Fraction of loci dominated by unmethylated, partially methylated or methylated patterns, in ES cells (left) and fibroblasts (right). Note that fractions are computed relative to the pool of MspI fragments that are covered in both libraries. f, Shown are the distributions of total frequencies of rare patterns at loci dominated by methylated, partially methylated and unmethylated patterns. g, Comparison of the entropy of methylation pattern distributions between polyclonal human ES-cell (H1/H9) populations and non-clonal WI38 populations. Regions that are of generally high entropy are more heterogeneous in fibroblasts, while regions with generally low entropy are more heterogeneous in ES cells. h, Similar to g, but using epipolymorphism (the probability that two random epialleles are not the same). i, For each of four ES-cell clonal populations (two from H1 and two from H9), we compare the frequency of patterns in the clonal population (y-axis) to the frequency of the same pattern in the matching polyclonal ES-cell population. No notable differences are apparent. j, Similar to i, but using data on six WI38 fibroblasts clonal populations. For each clonal population we observe an independent group of patterns that appear at a frequency of approximately 50% but are rare in the founding polyclonal population.