Cis -regulation and natural selection in the evolution of human DNA methylation

The vast collection of human-specific traits- such as our unique morphology, cognition, behavior, and diseases- has long been attributed to gene expression divergence between us and our closest living relatives, chimpanzees. Theory suggests that changes to cis -regulatory elements such as promoters and enhancers may drive evolutionary adaptation, and DNA methylation is a key factor in transcriptional cis -regulation. However, we still lack an understanding of 1) how species-specific methylation patterns arise; 2) their downstream effects; and 3) whether they are a common target of natural selection. In this study, we investigated these three questions. By combining a novel hypothesis testing framework with DNA methylation data from six human and chimpanzee cell types, as well as fused interspecies hybrid cells, we disentangled cis - vs. trans -acting methylation divergence across the genome. Across cell types, we found that methylation divergence is primarily driven in cis , which can be linked in some cases to nearby sequence variants such as CpG gains and losses. Although less common, regions with trans -acting methylation divergence were enriched for specific transcription factor (TF) binding motifs, suggesting a role of TFs such as FOXM1 in these differences. Having established these causes of methylation divergence, we then examined the functional consequences of differential methylation. Although methylation lacks a consistent relationship with transcription, we observed that associations between methylation and gene expression are stronger for genes with cis -regulatory divergence. Moreover, we identified lineage-specific selection shaping promoter methylation at the level of entire pathways including those associated with human-specific traits such as speech, cognition, and susceptibility to infection with hepatitis C. Collectively, our findings provide a mechanistic framework suggesting that DNA methylation may occupy a key position, mediating the effects of both cis - and trans -acting factors on transcriptional networks, including those contributing to human-specific traits.