Biomarkers of aging

A new epigenetic mark found in studies of aging cells is the loss of histones. Most of the evidence shows that loss of histones is linked to cell division. In aging and dividing yeast MNase-seq (Micrococcal Nuclease sequencing) showed a loss of nucleosomes of ~50%. Proper histone dosage is important in yeast as shown from the extended lifespans seen in strains that are overexpressing histones.[10] A consequence of histone loss in yeast is the amplification of transcription. In younger cells, genes that are most induced with age have specific chromatin structures, such as fuzzy nuclear positioning, lack of a nucleosome depleted region (NDR) at the promoter, weak chromatin phasing, a higher frequency of TATA elements, and higher occupancy of repressive chromatin factors. In older cells, however, the same genes nucleosome loss at the promoter is more prevalent which leads to higher transcription of these genes.[10]

This phenomenon is not only seen in yeast, but has also been seen in aging worms, during aging of human diploid primary fibroblasts, and in senescent human cells. In human primary fibroblasts, reduced synthesis of new histones was seen to be a consequence of shortened telomeres that activate the DNA damage response. Loss of core histones may be a general epigenetic mark of aging across many organisms.[11]

In addition to the core histones, H2A, H2B, H3, and H4, there are other versions of the histone proteins that can be significantly different in their sequence and are important for regulating chromatin dynamics. Histone H3.3 is a variant of histone H3 that is incorporated into the genome independent of replication. It is the major form of histone H3 seen in the chromatin of senescent human cells, and it appears that excess H3.3 can drive senescence.[11]

There are multiple variants of histone 2, the one most notably implicated in aging is macroH2A. The function of macroH2A has generally been assumed to be transcriptional silencing; most recently, it has been suggested that macroH2A is important in repressing transcription at Senescence-Associated Heterochromatin Foci (SAHF).[11] Chromatin that contains macroH2A is impervious to ATP-dependent remodeling proteins and to the binding of transcription factors.[12]

Increased acetylation of histones contributes to chromatin taking a more euchromatic state as an organism ages, similar to the increased transcription seen due to the loss of histones.[13] There is also a reduction in the levels of H3K56ac during aging and an increase in the levels of H4K16ac.[10] Increased H4K16ac in old yeast cells is associated with the decline in levels of the HDAC Sir2, which can increase the life span when overexpressed.[10]

Methylation of histones has been tied to life span regulation in many organisms, specifically H3K4me3, an activating mark, and H4K27me3, a repressing mark. In C. elegans, the loss of any of the three Trithorax proteins that catalyze the trimethylation of H3K4 such as, WDR-5 and the methyltransferases SET-2 and ASH-2, lowers the levels of H3K4me3 and increases lifespan. Loss of the enzyme that demethylates H3K4me3, RB-2, increases H3K4me3 levels in C. elegans and decreases their life spans.[13] In the rhesus macaque brain prefrontal cortex, H3K4me2 increases at promoters and enhancers during postnatal development and aging.[14] These increases reflect progressively more active and transcriptionally accessible (or open) chromatin structures that are often associated with stress responses such as the DNA damage response. These changes may form an epigenetic memory of stresses and damages experienced by the organism as it develops and ages.[14]

UTX-1, a H3K27me3 demethylase, plays a critical role in the aging of C.elegans: increased utx-1 expression correlates with a decrease in H3K27me3 and a decrease in lifespan. Utx-1 knockdowns showed an increase in lifespan[13] Changes in H3K27me3 levels also have affects on aging cells in Drosophila and humans.

Methylation of DNA is a common modification in mammalian cells. The cytosine base is methylated and becomes 5-methylcytosine, most often when in the CpG context. Hypermethylation of CpG islands is associated with transcriptional repression and hypomethylation of these sites is associated with transcriptional activation. Many studies have shown that there is a loss of DNA methylation during ageing in many species such as, rats, mice, cows, hamsters, and humans. It has also been shown that DNMT1 and DNMT3a decrease with aging and DNMT3b increases.[15]

Hypomethylation of DNA can lower genomic stability, induce the reactivation of transposable elements, and cause the loss of imprinting, all of which can contribute to cancer progression and pathogenesis.[15]