Fig. 2

DNA methylation changes in iPSC neural derivatives with T21. a Heat map of 500 differentially methylated CpG sites in T21 and euploid neural cell lines. Hierarchical clustering of the 500 CpGs in euploid (Ctrl) and trisomic (DS) neural lines at the NPC and DiffNPC differentiation stages, respectively (differences > 15% of average beta values in Ctrl vs. DS lines). Methylation values are color-coded according to legend. b Bar chart represents the distribution of hypermethylated (orange bars) and hypomethylated DMPs (blue bars) among all 500 DMPs in T21 lines. An enrichment of hypomethylation in T21 neural lines is examined (p = 0.049). c Chromosomal distribution of hyper-and hypomethylated DMPs in T21 neural lines. White bars represent percentages of CpG sites queried on a particular chromosome, orange bars percentages of hypermethylated DMPs and blue bars the percentages of hypomethylated DMPs. Chromosome 1 is significantly (*p < 0.05) enriched for hypermethylated DMPs. Chromosome 17 is depleted of hypermethylated DMPs and chromosomes 2, 8, 19, 21, and 22 are enriched for hypomethylated sites (**p < 0.005). d The positions of CpGs called by DMPs are illustrated relative to CpG islands (CGIs) and flanking genomic regions compared to the average of 450K array. Bars represent distribution of hypermethylated DMPs (orange; n = 218), hypomethylated DMPs (blue; n = 282), all DMPs (black; n = 500) and 450K array coverage (white) in different genomic regions. Individual CpGs (grey and white circles) were classified based on their location relative to a CpG island (bottom). The proportion of differentially methylated probes in north shores are overrepresented (p = 0.016) and preferentially hypomethylated (p = 0.0003) when compared to the genome average. In contrast, CpG islands are enriched in hypermethylated CpGs (p = 0.034). e Euler diagram illustrates 500 DMPs in T21 neural iPSCs comprising 323 DMPs located within or close to a CpG island (CGI+) of which 234 DMPs are assigned to a gene