Fight Aging!

Epigenetic clocks to measure biological age are near all based on the analysis of DNA methylation of the nuclear genome. Epigenetic changes to the nuclear genome, such as whether or not a particular CpG site is decorated with a methyl group, adjust gene expression by altering the structure of packaged DNA, hiding or exposing sequences. The genes in exposed sequences can be transcribed into RNA, those in hidden reaches of the genome cannot. Epigenetic marks are in constant flux, driven by the surrounding environment within and outside the cell. Some of these marks are characteristic of age, however, and in some way reflect specific changes in the cell and its environment that tend to occur with aging. Thus it is possible to construct epigenetic clocks, though it remains a topic for discussion and further research as to exactly which processes of aging give rise to which epigenetic changes.

In today's open access paper, researchers report on progress in understanding DNA methylation of the mitochondrial genome. Mitochondria, the power plants of the cell, are the descendants of ancient symbiotic bacteria, and bear a remnant circular genome. Epigenetics works quite differently in a circular genome, but at the high level, the concept is similar: it adjusts expression of genes. The researchers show that, once more accurately measured than has been possible in the past, a common form of DNA methylation of the mitochondrial genome correlates with the age of the individual bearing that mitochondrion, at least in the laboratory species tested.

N6-Methyladenine Progressively Accumulates in Mitochondrial DNA during Aging

During DNA methylation, a methyl group (-CH3) is added to a specific nucleobase, cytosine or adenine, primarily converting the former to 5-methylcytosine (5mC) and the latter to N6-methyladenine (6mA). These modified nucleobases often alter the activity of the affected genetic locus (in general, 5mC represses, while 6mA promotes, gene expression), and the new DNA methylation pattern can be inherited by daughter cells and offspring for certain generations. Efforts to understand the relationship between 5mC and aging have reached such an advanced stage in the last 10 years that several research groups have managed to set up a so-called epigenetic clock to estimate an individual's age based on CpG methylation distributions in the genome. Although relatively good results have been obtained by predicting biological age from 5-cytosine methylation, the method still relies on a genome-wide methylation profile for which the 5mC pattern of the whole genome or at least significant parts of the genome has to be revealed, and this makes the method cumbersome, costly and slow.

DNA methylation at the N6 position of adenine is the other major type of epigenetic modification, which has been widely recognized in bacteria and plants. A few years ago, DNA 6mA modification was also identified in the genome of a diverse range of animal taxa ranging from worms to mammals. Furthermore, the presence of 6mA was recently detected in mammalian mitochondrial DNA (mtDNA). The mitochondrion, a membrane-bound, energy-converting organelle of eukaryotic cells, is known to be involved in the regulation of the aging process across a wide variety of animal species; Caenorhabditis elegans (nematode), Drosophila melanogaster (insect) and mouse (mammalian) strains with decreased mitochondrial activity exhibit a long-lived phenotype.

Because there is a strong association between the epigenetic modifications of genomic DNA and biological age, epigenetic modifications in the mitochondrial genome may be similarly related to the age of the organism, but this has not yet been investigated and explored. In this study, we present a novel, reliable, PCR-based (i.e., sequence-specific) 6mA detection method that is free of technological artifacts and show in several genetic models that relative 6mA levels at different mtDNA sites (these levels actually show that how many percent of the individual mitochondrial genomes present in a given tissue sample are methylated at a selected adenine nucleobase) are significantly related to the age of the organism. Thus, N6-adenine methylation is an inherent process in the organization of mitochondrial genomes too.

These results suggest that the widely observed age-related decline in mitochondrial function is strongly associated with changing 6mA levels and that biological age can be accurately determined from 6mA levels at certain mtDNA sites in a reliable, fast and cost-effective way. Furthermore, we reveal the enzymatic pathways of the mtDNA N6-adenine methylation and demethylation processes in C. elegans and Drosophila, showing the involvement of DNA N6-adenine methyltransferases and N6-methyladenine demethylases mediating 6mA metabolism in the nuclear genome. Together, these results suggest a fundamental role for mtDNA N6-adenine methylation in aging and reveal an efficient diagnostic technique to determine age using DNA.