Towards a Universal Epigenetic Clock for Mammals
Epigenetic marks are constantly added to and removed from CpG sites on the genome, controlling gene expression and thus cell behavior. The pattern of epigenetic marks in any given cell shifts in response to environment and circumstances, and some of those changes are characteristic of the presence of the underlying molecular damage of aging. Epigenetic clocks can thus be constructed from weighted combinations of epigenetic mark status at various CpG sites in order to measure biological age. Existing epigenetic clocks are specific to a given species, but here researchers process an enormous amount of data from many species to produce epigenetic clocks that are universal to all placental mammals. If this result holds up well in further testing, then such universal clocks could help to speed up the development of therapies that target the mechanisms of aging.
Aging is often perceived as a degenerative process caused by random accrual of cellular damage over time. In spite of this, age can be accurately estimated by epigenetic clocks based on DNA methylation profiles from almost any tissue of the body. Since such pan-tissue epigenetic clocks have been successfully developed for several different species, it is difficult to ignore the likelihood that a defined and shared mechanism instead underlies the aging process.
To address this, we generated 10,000 methylation arrays, each profiling up to 37,000 cytosines in highly-conserved stretches of DNA, from over 59 tissue-types derived from 128 mammalian species. From these, we identified and characterized specific cytosines, whose methylation levels change with age across mammalian species. Genes associated with these cytosines are greatly enriched in mammalian developmental processes and implicated in age-associated diseases.
From the methylation profiles of these age-related cytosines, we successfully constructed three highly accurate universal mammalian clocks for eutherians, and one universal clock for marsupials. The universal clocks for eutherians are similarly accurate for estimating ages of any mammalian species and tissue with a single mathematical formula. Collectively, these new observations support the notion that aging is indeed evolutionarily conserved and coupled to developmental processes across all mammalian species - a notion that was long-debated without the benefit of this new and compelling evidence.