Linking evolution to aging through DNA methylation and CpG density by examining twelve mammalian species

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Project Summary As organisms age, gene regulation becomes increasingly unstable along with changes in the epigenome. Within the genome, a principle epigenetic mark, DNA methylation, occurs at CpG dinucleotides generally causing gene repression. Thus, CpG sites act as genetic control switches depending on their methylation status. As we age, CpG sites gain methylation at gene promoters and drifting methylation levels cause variation between cells and individuals. Methylated CpG sites are also highly mutagenic, so over evolutionary time there has been a depletion of CpG dinucleotides in mammalian species. Together these facts raise a fundamental question. Is the aging process linked to the evolution of a species by the selection of CpG sites at specific genes? Across one hundred thirty-one mammal species, many of them separated by tens of millions of years of evolutionary history, we revealed that in about 1000 genes, CpG density in promoters was positively correlated with species’ lifespans. These genes showed increased CpG density concomitant with increased lifespan and are indicative of an underlying biological signal, one that merits further exploration in order to elucidate insights into the genetic basis of aging. Our main hypothesis is that increased CpG density buffers the impacts of increased methylation during aging. This proposal aims to address two fundamental questions in biology: 1) Have these genes become targets for evolution, increasing in CpG density in long-lived species to maintain epigenetic integrity and preserve gene expression during aging? 2) Does the epigenome drift less in these genes, resulting in more stable gene expression over time in long-lived species? To address these questions, we will examine the epigenomes of individuals from twelve different mammalian species (8 primates, 4 rodents) in three age cohorts (juveniles, sexually mature adults, elder individuals). Using genome- wide reduced-representation bisulfite sequencing, we will compare gene promoter DNA methylation over time and across species. Aim 1 will explore how natural selection impacts DNA methylation differently in long-lived vs. short lived species. Aim 2 will examine how genes become unstable over time and how natural selection selects against that instability. Through these studies we hope to uncover whether epigenetic marks at specific genes are important drivers of aging, therefore providing interventional targets and a molecular mechanism of evolutionary innovation for long lifespan. Currently, this idea is supported by computational comparative genomics, yet does not have a clear molecular explanation. Laboratory validation of the link between the aging epigenome and the evolution of CpG density with lifespan could have broad impact on our understanding of how we age.