Fig. 2

Loss of methylation at the protocadherin γ (PCDHG) cluster of neuroepithelial identity genes. a Structure of the PCDHG cluster showing the 5′ variable exons (A, B and C classes) which are spliced to the 3′ constant exons (right). The top track (amber) shows absolute β values in the WT fibroblast cells from the 450K array, which range from 1(fully methylated) to zero (unmethylated). Only the sites showing significant differences from WT (FDR < 0.05) in each cell line are shown in the three tracks below, with decreases in red representing loss of methylation, and gains in blue. The size of the bar is proportional to the magnitude of change: maxima and minima are indicated on the scales at left. The locations of CpG islands (CGI) are also shown. Pyroassay locations are boxed. b Median β values for all variable exons. Significant differences (Mann–Whitney U) are indicated: *p < 0.05; **p < 0.1; n.s., not significant. c Methylation at each exon in WT and d16 cells obtained by taking the median of the absolute β value for all probes at that exon. The variable class C exons are underlined. d Average methylation values in WT and KD cells obtained from a pyrosequencing assay (pyroassay) designed to cover CpGs in the A2 exon. Bars represent SEM; ***p < 0.001, t-test. e Methylation at the C4 variable exon by pyroassay, shown as a control