Fig. 2

Divergent patterns of DNA methylation in NeuN⁺ and OLIG2⁺ cell types in the human brain. a Clustering analysis based on whole-genome CpG methylation values completely discriminated between NeuN⁺ (N = 25) and OLIG2⁺ (N = 20) methylomes. Additional NeuN⁺ (colored in turquoise) and those labeled as NeuN⁻ (pink) are from [27]. b Density plots showing the distribution of fractional methylation differences between OLIG2⁺ and NeuN⁺ at differentially methylated positions (DMPs) and other CpGs (non-DMPs). We observed a significant excess of NeuN⁺-hypermethylated DMPs compared to OLIG2⁺ (binomial test with expected probability = 0.5, P < 10⁻¹⁵). c Heatmap of the top 1000 most significant DMRs between OLIG2⁺ and NeuN⁺. Fractional methylation values per individual (column) and DMR (row) show substantial differences in DNA methylation and clear cell type clustering. d Genic annotation of DMRs and coverage with Illumina 450K Methylation Arrays. Counts of different genic positions of DMRs are shown. DMRs containing at least one CpG covered by a probe in the array are indicated. Only 20.8% of the DMRs contain one or more CpG targeted by Illumina 450K Array probes. e DMRs are enriched for brain enhancers. Enrichment of enhancer states at DMRs compared to the 100 matched control DMR sets from 127 tissues [28]. Random sets are regions with similar characteristics as, including the total number of regions, length, chromosome, and CG content. f Correspondence between cell type-specific methylation sites in NeuN⁺ and OLIG2⁺ with NeuN⁺ and NeuN⁻ ChIP-seq datasets [9]. Neuron-specific ChIP-seq peaks show an excess of sites with NeuN⁺-specific hypomethylated sites (positive DSS statistic, see the “Methods” section) whereas non-neuron peaks showed significant enrichment for sites specifically hypomethylated in OLIG2⁺ (negative DSS statistic). g Distribution of cell type-specific methylation differences at CpGs within H3K27ac ChIP-seq peaks in NeuN⁺ and NeuN⁻ nuclei. Positive values of DSS statistic indicate hypomethylation in NeuN⁺ compared to OLIG2⁺, whereas negative values indicate hypermethylation (see the “Methods” section). Dashed lines indicate the significance level for DSS analyses