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

Abstract

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.

Body weight at young adulthood and association with epigenetic aging and lifespan in the BXD murine family

“…The genes represented by the age-DMRs included a few notable members such as Cyp46a1 and Abca7, which are involved in cholesterol metabolism and implicated in Alzheimer’s disease 32 , and few members of the WNT-signaling and mesenchyme developmental pathways (e.g., Fzd1, Fzd8, Wnt5a, Jak3, Ptk7, Nrp2 ). Thecurrent data replicated the CpG islands in C1ql3 and Ptk7 , which we previously reported as age-hypermethylated sites in the BXD parental strains, B6 and D2 33 . A region-based functional annotation analysis revealed a significant enrichment in genes involved in cell polarity, an aspect of cells that is established during development through interaction with the WNT polarity signaling pathway, and which becomes dysregulated during aging 34,35 .…”

Profiling DNA Methylation Differences Between Inbred Mouse Strains on the Illumina Human Infinium MethylationEPIC Microarray

“…We then performed a reverse comparison are associated with an increase in methylation with age. Most occur in CGIs that have been reported previously [20]. Out of these seven age-DMRs, six corresponding EPIC of 0.05 ( Table 4).…”

“…The mouse samples we report here were previously assayed for DNA methylation using 1 4 4 MBD-seq [20]. This is an affinity-based enrichment of methylated CpGs using the 1 4 5 methyl binding domain (MBD) of methyl-CpG-binding protein 2, followed by high 1 4 6 throughput sequencing (MBD-seq) [22][23][24].…”

“…For conserved sequences, there is high correspondence in functional and genomic 9 9 features between mouse and human genomes and we referred to the human probe Data S1). To evaluate if the conserved set is enriched in specific features relative to the 1 0 3 full background set, we performed a hypergeometric test using the phyper function in R. Tissues samples were derived from mice that were part of an aging cohort maintained on animal rearing and sample collection are described in Mozhui and Pandey 2017 [20]. All animal procedures were approved by the UTHSC Animal Care and Use Committee.…”

Expression of Xenobiotic Biomarkers CYP1 Family in Preputial Tissue of Patients with Hypospadias and Phimosis and Its Association with DNA Methylation Level of SRD5A2 Minimal Promoter

“…Furthermore, it has been reported that perinatal-stage TCDD exposure increased the basal level of SRD5A2 and decreased androgen receptor (AR) mRNA expression levels alongside upon CYP1 family transcriptional induction in the rat prostate (Theobald et al 2000 ; Ohsako et al 2001 ). Although the mechanism underlying this increase in SRD5A2 expression level is as yet unclear, epigenetic alteration in SRD5A2 may be a plausible explanation for the disorders of the male reproductive system (Horning et al 2015 ; Skakkebaek et al 2016 ; Mozhui and Pandey 2017 ). This suggests that the SRD5A2 mRNA expression level in the postnatal male genitalia may increase in the human population exposed to endocrine disrupting chemicals during the fetal or neonatal period.…”