Conserved effect of aging on DNA methylation and association with EZH2 polycomb protein in mice and humans

•We performed cross-species comparison of DNA methylation and aging in mice and humans.•DNA methylation was assayed in aging mouse liver using affinity-based enrichment and high-throughput sequencing.•Age-dependent methylation occur at highly conserved CpG islands of genes such as C1ql3, Srd5a2 and Ptk7, which are implicated in cancers.•Comparison with microarray-based data from humans shows consistent age-dependent methylation patterns.•ChIP assay confirms that member of the polycomb repressive complex 2, EZH2, binds to these conserved age-dependent sites. In humans, DNA methylation at specific CpG sites can be used to estimate the ‘epigenetic clock’, a biomarker of aging and health. The mechanisms that regulate the aging epigenome and level of conservation are not entirely clear. We performed affinity-based enrichment with methyl-CpG binding domain protein followed by high-throughput sequencing (MBD-seq) to assay DNA methylation in mouse samples. Consistent with previous reports, aging is associated with increase in methylation at CpG islands that likely overlap regulatory regions of genes that have been implicated in cancers (e.g., C1ql3, Srd5a2 and Ptk7). The differentially methylated regions in mice have high sequence conservation in humans and the pattern of methylation is also largely conserved between the two species. Based on human ENCODE data, these sites are targeted by polycomb proteins, including EZH2. Chromatin immunoprecipitation confirmed that these regions interact with EZH2 in mice as well, and there may be reduction in EZH2 occupancy with age at C1ql3. This adds to the growing evidence that EZH2 is part of the protein machinery that shapes the aging epigenome. The conservation in both sequence and methylation patterns of the age-dependent CpGs indicate that the epigenetic clock is a fundamental feature of aging in mammals.