Fig. 3. CH hypermethylation is significantly higher in human neurons compared to other primates.

a Differences in the proportions of sites with neuronal CH methylation between species. b Mean methylation levels of human-specific CH DMRs demonstrate pronounced hypermethylation of human neurons. c CH methylation between humans and chimpanzees strongly predicts gene expression difference. The shaded band represents the 95% confidence interval for the fitted regression line. d Gene expression fold-change between human and macaque in CH DMR genes across developmental time points (Human CH DMR genes, n = 450 and Chimpanzee CH DMR genes, n = 144). Macaque samples were age-matched to human developmental time points in a previous study¹⁴. Statistical significance was computed using Kruskal–Wallis test (two-sided). e Enrichment of human and chimpanzee CH DMR genes in specific cell-types. Human CH DMR genes are enriched in inhibitory neurons, whereas chimpanzee CH DMR genes are enriched in excitatory neurons. In each gene set, genes expressed in at least 50% of the cells that are statistically significant (FDR < 0.05 and log₂FC > 0.3) are included. Cell-type data are from human medial temporal gyrus (MTG)³⁶. f CH methylation of neuronal subtypes for CH DMR genes using methylation of single nuclei from the human frontal cortex¹². Human CH DMR genes are hypomethylated in inhibitory neurons, whereas chimpanzee CH DMR genes are hypomethylated in excitatory neurons (excitatory neurons, n = 1879 and inhibitory neurons, n = 861). Statistical significance was computed using two-sided Mann–Whitney U-test. Box represents a range from the first quartile to the third quartile. The line in the box indicates the median value. The minima and maxima are within 1.5 times the distance between the first and third quartiles from box. Source data are provided as a Source Data file. Cell-type images were color modified from the original image, which was created by Akiyao and available at the Wikimedia Commons under the Creative Commons license (https://creativecommons.org/licenses/by-sa/3.0/deed.en).