The interplay between DNA methylation and sequence divergence in recent human evolution

Abstract DNA methylation is a key regulatory mechanism in mammalian genomes. Despite the increasing knowledge about this epigenetic modification, the understanding of human epigenome evolution is in its infancy. We used whole genome bisulfite sequencing to study DNA methylation and nucleotide divergence between human and great apes. We identified 360 and 210 differentially hypo- and hypermethylated regions (DMRs) in humans compared to non-human primates and estimated that 20% and 36% of these regions, respectively, were detectable throughout several human tissues. Human DMRs were enriched for specific histone modifications and contrary to expectations, the majority were located distal to transcription start sites, highlighting the importance of regions outside the direct regulatory context. We also found a significant excess of endogenous retrovirus elements in human-specific hypomethylated regions suggesting their association with local epigenetic changes. We also reported for the first time a close interplay between inter-species genetic and epigenetic variation in regions of incomplete lineage sorting, transcription factor binding sites and human differentially hypermethylated regions. Specifically, we observed an excess of human-specific substitutions in transcription factor binding sites located within human DMRs, suggesting that alteration of regulatory motifs underlies some human-specific methylation patterns. We also found that the acquisition of DNA hypermethylation in the human lineage is frequently coupled with a rapid evolution at nucleotide level in the neighborhood of these CpG sites. Taken together, our results reveal new insights into the mechanistic basis of human-specific DNA methylation patterns and the interpretation of inter-species non-coding variation. Author summary Human and great apes, their closest living relatives, differ in numerous morphological and cognitive aspects, however their protein sequences are highly similar. It has long been hypothesized that human specific traits may be explained by changes in regulatory elements rather than by changes in primary sequence. In this context, evolutionary biologists have identified regulatory regions based on nucleotide sequence acceleration or conservation. However, epigenetics adds an extra layer of information that cannot be detected when comparing DNA sequences. The current study provides one of the first genome-wide comparison of genetic and epigenetic variation among humans and our closest living relatives. We identify and describe hundreds of regions presenting a human-specific DNA methylation pattern compared to great apes. We also report a local interplay between DNA methylation changes and the underlying nucleotide sequence in regions of incomplete lineage sorting and in regions of transcription factor binding, suggesting that both phenomena are closely associated.