Bisulfite sequence analysis of candidate CpG loci validates IDH1R132H/WT-induced DNA methylation changes. (A) Stripcharts of DNA methylation values (β) in HCT116 parental (WT: black) and IDH1R132H/WT (R132H: gray) cells are shown next to data for the same loci in TCGA GBMs that are IDH1 wild-type (WT: black) or mutated (mut: gray) and LGGs that are G-CIMP negative (CIMP−: black) or positive (CIMP+: gray). P-values are from Welch's two-sided t-test. (B) Bisulfite sequence analysis of the loci shown in A. (Top) The interrogated region is depicted with a schematic of the gene with CpG dinucleotides represented by vertical tick marks on the x-axis. Browser tracks denote CpG islands, the region analyzed by bisulfite sequencing (Bis seq) and CpG loci interrogated by the HumanMethylation27 platform (Inf27). The CpG locus plotted in A is denoted by a black arrowhead above the Inf27 track. (Bottom) Bisulfite sequencing results for the regions denoted in the schematic above. Each row represents a sequenced allele and each dot represents a CpG. (Black dots) Methylated CpGs; (white dots) unmethylated CpGs. The CpG shown in A is denoted with a black arrowhead, and other CpGs interrogated by the assay are shown in gray.
