Fig. 3

Differential non-CpG methylation across functionally distinct brain regions. a Principal component analysis of distances derived from average autosomal, plus strand CA (mCA+) methylation in 1-kb bins. b Heatmap representing log2 enrichment of CA, CT, and CC within CH-DMRs compared to the rest of the genome for indicated features including CG-DMRs identified in this study. Gene models from GENCODEv26 (promoters, intronic, exonic, 5′UTR, 3′UTR, intergenic), CpG islands (CGIs) and related features from UCSC (shores, shelves, OpenSea), putative enhancer regions (enhancers and high confidence enhancers from PsychENCODE [18] and H3K27ac [19]). 5-group = CH-DMRs between all 5 groups; 5-group > 10% = 3195 CH-DMRs from 5-group comparison with mean CA-DMR methylation difference > 10%. c As in b, showing enrichment in regions of open chromatin in NeuN− and NeuN+ nuclei and NeuN+ nuclei isolated from the indicated brain regions (PV cortex, primary visual cortex; Med. thalamus, mediodorsal thalamus) from [10]. d Hierarchical clustering of samples based on the average CA(+) methylation per sample in the CA-DMRs with > 10% methylation difference among the 5 tissue groups. e Venn diagrams illustrating intersections between CH- and CG-DMRs identified between different analyses. f Example CA-DMR over NRGN with both strands and CG-DMRs (mCG(S); obtained from small smoothing window) and blocks (mCG(L); obtained from large smoothing window). Average methylation values calculated from NeuN+ nuclei isolated from indicated tissue groups. Regions of differential methylation are shaded in pink