Epigenetic age prediction using N6-methyladenine in the bumblebee Bombus terrestris

Epigenetic alterations are a hallmark of aging. Age-specific DNA methylation patterns can be used to create epigenetic clocks--machine-learning algorithms that use methylation data from multiple genomic sites to predict an organisms chronological age (i.e., the number of years or time passed since birth) or biological age (i.e., a measure of an organisms health and functional status). Epigenetic clocks have been developed for mammals and, to a lesser extent, for birds, fish, amphibians, crustaceans, and insects. At present, all epigenetic clocks utilise C5-methylcytosine (5mC), a prevalent DNA methylation mark in vertebrates. However, in some species, 5mC marks are rare or even undetectable. Here, we describe epigenetic clocks based on N6-methyladenine (6mA), a DNA methylation mark whose role in aging has remained unexplored. Using Oxford Nanopore Technology (ONT) sequencing, we measured genome-wide base-resolution levels of 6mA and 5mC in males of the buff-tailed bumblebee Bombus terrestris (n = 24). We constructed a series of epigenetic clocks using age-specific patterns in 6mA or 5mC. For each clock, predicted epigenetic age and chronological age were highly correlated. Furthermore, we pharmacologically increased individual lifespan with pharmacological agents and showed that, for individuals whose lifespan had been pharmacologically increased, each clock predicted younger epigenetic age than chronological age, indicating that the clocks captured signals of biological aging. Our results demonstrate that 6mA patterns can be used to build epigenetic clocks that accurately predict both chronological and biological age in animals, paving the way toward the use of 6mA as a reliable biomarker of aging.