Epigenetics and Aging

The previous two articles were only introductions into the main topic of this expert series. In this and the following two articles, we’ll get into the actual topic of epigenetic deregulation during aging. However one could not understand epigenetic deregulation without first understanding epigenetics. So hopefully by now you have a basic understanding of what epigenetics is, why it exists and how it is maintained and established. In this article we’ll get into what exactly happens to the epigenome during aging, why it happens and how we can measure it for our benefit. Firstly let’s talk about how epigenetics plays into the plethora of changes that occur during aging. 

---

This article is part three of a four-part series on epigenetics.

1. Introduction to Epigenetics
2. Epigenetics and Gene Expression
3. Epigenetics and Aging
4. Coming Soon

---

Now if you’ve ever attempted to venture into the field of aging science the first article that you’ll likely stumble upon or find commonly referenced by almost all aging papers is a review article called the “Hallmarks of aging”. This article self-admittedly attempts to replicate the landmark paper “Hallmarks of cancer” for the field of aging. In this article the authors establish nine different aging hallmarks that they argue “…are generally considered to contribute to the aging process and together determine the aging phenotype”.¹ Among these nine hallmarks is epigenetic alterations. However, slightly different from the other hallmarks, epigenetic alterations are among the hallmarks denoted as “primary”. Meaning they are the causes of damage, or places that damage manifests in. Other categories are, antagonistic (responses to damage) and integrative (outcomes of cumulative damage). The primary hallmarks are arguably more important in the sense that their deregulation precedes the other hallmarks and more often than not causes them. Interventions that target the primary hallmarks may also alleviate the symptoms that arise from the other hallmarks. 

Figure 1: The nine key hallmarks of aging as discussed in the review: genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, and altered intercellular communication. Sourced from Lopez-Otin et al.¹

Epigenetics arguably holds an even more important place among the other primary hallmarks of aging because of its analog, complex nature. The other primary hallmarks include genomic damage, telomere attrition and loss of proteostasis. Whereas genomic damage and telomere attrition impact the cellular machinery in a relatively direct manner, epigenetic alterations operate through a more nuanced and multifaceted pathway, influencing gene expression and cellular identity without altering the underlying DNA sequence. This analog and complex mechanism allows epigenetics to exert a broad influence over the biological processes that dictate aging, acting as a master regulator of the cellular response to aging and environmental influences.

Changes in epigenetic modifications during aging

The intricate system that is the epigenome, which includes DNA methylation, histone modifications, non-coding RNAs, and chromatin remodeling, is essentially the maestro of gene expression. With age, this conductor starts changing its tune, leading to shifts in how genes perform. This exploration aims to unpack the nuances of these epigenetic changes and their significant role in the aging process. Before going onto the specific modifications and how they change during aging it would be better to talk about the epigenome as a whole. One common phenomena observed consistently across aging is the erosion of heterochromatin during aging. As mentioned in the previous article heterochromatin is the tightly compacted, generally not expressed parts of chromatin. They naturally differ from cell type to cell type. Keeping genes and pathways that aren’t required silenced. With age the epigenetic marks that denote heterochromatin locations begin to weaken, leading to a less compact and more transcriptionally active state. This loss of heterochromatin integrity allows genes that are normally silenced to become erroneously expressed, contributing to the cellular dysfunction often seen in aging. This understanding of heterochromatin erosion sets the stage for examining specific epigenetic modifications such as DNA methylation, histone changes, and non-coding RNA interactions, and their roles in the aging process.

Transcriptional changes

Transcriptional output, the eventual result of the epigenetic landscape is how age-related epigenetic changes manifest themselves in the phenotype. Numerous studies have identified changes in the expression levels of individual genes and entire pathways associated with aging. For example, a study of gene expression profiles of nearly 15000 individuals identifies around 1500 genes that change significantly with age.² The genes show reduced activity in RNA and protein synthesis, mitochondrial functions, and DNA repair, alongside an upregulation in immune responses and metabolic processes across the studies. 

However, it’s important to understand that aging affects each person differently, making it a very diverse process. Imagine trying to understand what a typical family looks like based on just a few examples; with only three younger and three older individuals’ data, it’s tough to capture the full range of differences that might exist. Just as families vary widely in how many people they have, what they like to do, or where they live, the changes in gene activity as we age can also vary greatly from one person to another.

This variety means that when researchers only look at a small number of people, they can’t confidently say what typical aging-related changes might look like. They need a lot of data from many different people to see the real patterns of how aging affects gene activity. Therefore, while there are general trends in how aging impacts our genes, pinpointing these trends in small studies can be unreliable due to the high level of natural variation in gene expression among individuals.

DNA methylation

The relationship between DNA methylation and aging, although one of the simplest among epigenetic modifications, is still somewhat complex. DNA methylation, a key epigenetic change, involves the addition of methyl groups to specific DNA regions, primarily at cytosine bases in CpG dinucleotides. This process is crucial for regulating gene activity and plays a significant role in the aging process. As we age, a general trend of DNA methylation loss is observed.³⁴ This may be caused by the changes in the activity levels of the enzymes responsible for DNA methylation, known as DNA methyltransferases (DNMTs). DNMT1, the variant responsible for maintenance of existing DNA methylation marks tends to decrease, reducing overall methylation levels and potentially leading to increased gene activity that was previously suppressed.⁵⁶

While global DNA methylation levels tend to decrease as we age, we can also observe specific and distinct changes within the methylome—the complete set of DNA methylation in our cells. Some sites exhibit gain of methylation with age whereas some sites lose DNA methylation distinct from the global loss.⁷⁸ Moreover, these methylation changes aren’t just random; some are consistent across different species, suggesting a common biological aging phenotype.⁹ In fact we are attempting to uncover and quantify these non-random changes in DNA methylation with machine learning through the use of epigenetic clocks, which we’ll get into later in the article.

Histone related changes

Histone modifications and changes in histone variants are crucial to understanding the epigenetic mechanisms that influence how we age. These processes involve tweaks to the proteins around which DNA is wrapped, affecting gene activity. As we grow older, specific changes in these histone proteins and their modifications can impact how cells function and contribute to the aging process.

Histone variants are special versions of the standard histone proteins that play unique roles in DNA and gene regulation. Unlike regular histones, which are replaced during DNA replication, variants like H3.3 are added to chromosomes independently of replication. This is important for maintaining chromatin structure in cells that no longer divide, such as those in aging tissues. For instance, H3.3 becomes the main form of histone H3 in senescent human cells, highlighting its role in cellular aging.¹⁰¹¹ Additionally, the variant macroH2A, which increases with age, is linked to repressing genes associated with cellular aging and plays a critical role in keeping the chromatin organized during senescence.¹²

Histone modifications—like adding or removing methyl or acetyl groups—can either loosen or tighten DNA packaging, thus influencing whether genes are turned on or off. For example, acetylation usually opens up the chromatin to promote gene activity, while methylation can either activate or silence genes depending on where and how many methyl groups are added. Acetylation at specific sites on histones H3 and H4 (H3 K56Ac and H4 K16Ac) can influence aging in different ways. In yeast H3 K56Ac is linked to improved DNA stability and repair, promoting longevity.¹³ On the other hand, an increase in H4 K16Ac in older cells is associated with aging processes, indicating that a proper balance of acetylation is crucial for a longer life.¹⁴ Methylation changes, especially the trimethylation marks on histones, also play a significant role in aging. More methylation at certain sites might silence genes that need to be active for youthfulness, contributing to age-related decline, while less methylation might activate genes that lead to aging.¹⁵ Changes in histone methylation with age mirrors the loss of heterochromatin, meaning we observe an increase in active histone methylation marks whereas a decrease in repressive histone marks.¹⁶¹⁷ In fact this trend was even shown to be causal in the nematode worm C. elegans. Reducing the active chromatin mark H3K4me3 by decreasing the expression of the proteins that deposit that modification led to an increase in lifespan and conversely the decrease of proteins that remove this mark decreased lifespan.¹⁸

Changes in histone marks, which come in many forms, indicate a loss of heterochromatin. Yet, these changes don’t neatly show the difference between old and young cells. While we’ve pinpointed specific modifications that can impact lifespan, there’s still much we don’t fully understand. Additionally, these findings need to be confirmed in mammals and humans to ensure they’re applicable more broadly. Although our knowledge has gaps, it’s clear that histone modifications play a vital role in aging and disease. 

nc-RNAs

We have explored nc-RNAs and their functions previously. Once a part of the genetic material labeled as “junk DNA”, the body of evidence supporting their roles as key regulators in genetic networks is ever growing. The research on the changing dynamics of nc-RNAs during aging are far less understood compared to other epigenetic modifications. Nonetheless there is a recently growing body of literature that elucidates their changes in aging.

The enzyme Dicer, which plays a key role in cutting small non-coding RNAs, such as miRNAs, into their active forms, shows less activity in older organisms.¹⁹ This suggests a general decrease in ncRNA regulation with age. MiRNAs themselves, which fine-tune gene expression by targeting mRNAs, undergo changes in expression as organisms age. They dramatically affect lifespan and tissue aging, as demonstrated in studies with C. elegans where certain miRNAs enhance longevity while others shorten it.²⁰ Like most early research areas most miRNA – aging relationships have been shown in lower organisms. Among the few that have been shown to affect lifespan in mammalian models there is miR-17. Mice expressing miR-17 observed a 16% increase in lifespan along with decreased cellular senescence.²¹

On the other hand, long non-coding RNAs (lncRNAs) also significantly impact aging by interacting with chromatin and protein complexes, affecting everything from genomic stability to inflammation. For example, higher levels of the lncRNA Gas5 in aged mouse brains have been linked to impaired learning abilities.²² Similarly, H19, another lncRNA, plays a role in regulating gene networks that could lead to age-related diseases like prostate cancer when altered.²³

Yet, despite these insights, our understanding of how ncRNAs regulate cellular processes, including aging, remains incomplete. This gap underscores the need for further research to fully grasp and potentially harness ncRNAs in aging.

Chromatin Remodelling and 3D genome structure

Chromatin, the complex of DNA and proteins found in our cells, isn’t randomly bunched into the nuclei of cells but rather is in an organized three-dimensional structure that is crucial for regulating gene activity. This three-dimensional structure separates the genetic material into compartments for organized epigenetic control and can differ from cell to cell. However, like all epigenetic mechanisms it is also subject to deregulation with age. Sequencing technologies that allow to capture 3D interactions in the genome are relatively recent which makes this area a newly developing field. Most of the information present overlaps with the acquisition of senescence rather than explicitly aging. For example, in senescent human mesenchymal stem cells and fibroblasts, regions marked by H3K27me3 switch from inactive (B) to active (A) compartments, altering gene expression linked to aging.²⁴

Figure 2: As aging progresses, there is a general loss of heterochromatin and a detachment of lamina-associated domains (LADs) from the nuclear lamina. This restructuring of higher-order chromatin is accompanied by shifts in histone modifications, leading to increased chromatin accessibility, activation of repetitive sequences, and dysregulated gene expression. Sourced from Wang et al.²⁵

Epigenetic information maintenance

So epigenetic information is lost with aging. We went over a variety of modifications that change towards a specific direction during aging. There must exist drivers of this change. Phenomena that lead to loss of epigenetic information and there must be a system in cells to oppose this change. A system that aims to maintain and propagate epigenetic information against these “deregulators”. Wherever/whenever the maintenance system comes short some epigenetic information is lost and contributes to the accumulation of loss over the lifespan of an organism which in turn contributes to aging. 

Epigenetic information in the cell cycle

Epigenetic inheritance during cell division is crucial for maintaining cellular identity and function across generations. This process ensures that epigenetic information, such as DNA methylation and histone modifications, is accurately transmitted from mother cells to daughter cells, despite the disruptive nature of cell replication.²⁶ During cell division, accurately replicating DNA’s genetic and epigenetic information is crucial. DNA methyltransferase enzymes play a key role by copying methylation patterns from the parent DNA to the new strands, ensuring that DNA methylation—which typically suppresses gene expression—is preserved in daughter cells.²⁷ Similarly, histone modifications such as methylation and acetylation, which impact chromatin structure and gene activity, are meticulously replicated. Old histones are redistributed between the new DNA molecules, and new histones are added and modified to reflect the original patterns, guided by the original histone ‘template’.²⁸

Filling in the blanks

The epigenome, a complex network of modifications that cells utilize during both development and normal functioning of terminally differentiated cells, exhibits a significant feature: the crosstalk between different modifications. These relationships are intricate and multifaceted. For instance, it’s well-documented that DNA methylation often co-locates with a specific histone modification, H3K9me3.²⁹ Another detailed example shows that two different histone modifications can be connected through a transcription factor that recognizes one modification and establishes the other.³⁰

Such examples are abundant across the epigenome. These interactions are what make Waddington’s epigenetic landscape analogy particularly apt. In this model, epigenetic states are akin to a ball’s position on a landscape, settling naturally into valleys which represent stable states. Due to the reinforcing nature of these interactions, a mere alteration of a single modification is generally insufficient to shift an epigenetic state. The surrounding epigenetic architecture compensates for this change, pulling the state back to its original ‘valley’ through the influence of existing modifications. To effectively alter an epigenetic state, multiple modifications need to be targeted simultaneously across different genomic locations. This introduces a level of redundancy to the epigenome, ensuring stability and resilience in gene regulation.

Drivers of epigenetic deregulation

Okay so the epigenome changes with age. We know a little about these changes. Some of the sites where they happen and in which conditions they happen. But why? Is it planned or does it just happen? We must understand the mechanisms and pathways that drive epigenetic deregulation to identify interventions that can halt or reverse it. 

External / internal damage – general loss with time

This is the most fundamental of all the various drivers of epigenetic information loss. Basically what it amounts to is entropy. The epigenome is an ordered construct that contains information. The medium in which this information is stored is subject to the natural processes of decay and disruption over time. There are internal and external damages that the epigenome among other things in the cell has to survive. Internal damagers like cellular inflammation and metabolic byproducts can disrupt epigenetic markers, altering gene expression and cellular behavior.³¹ External damagers, such as ultraviolet (UV) radiation, environmental pollutants, and reactive oxygen species (ROS), further challenge the epigenome’s integrity.³²³³ These factors introduce errors and modifications to the DNA and associated proteins, leading to a gradual degradation of the epigenetic landscape though single epigenetic mutations termed “epimutations”.³⁴ This entropy not only impacts the function of individual cells but can also contribute to broader organismal aging and the onset of disease.

DNA replication and cell divisions

One of the main challenges the epigenome has to overcome is the compaction of chromatin during cell division. The cell has numerous established pathways to transmit epigenetic information to daughter cells as mentioned above. Despite these sophisticated mechanisms, the process isn’t foolproof. Errors can occur, DNA methylation patterns can be incompletely copied during cell division, leading to methylation loss.³⁵ Similarly, errors in the placement of histone modifications, regulatory proteins, and RNAs may also occur. These errors can accumulate over successive cell divisions, leading to changes in the epigenetic landscape that may alter gene expression and cellular function.³⁶ This gradual epigenetic drift contributes to aging and various diseases, highlighting the complex and somewhat vulnerable nature of cellular inheritance.

DNA damage response

There is one thing in the cell whose maintenance is unarguably more important for regular cellular function than epigenetic information and that is the genetic information. Thus, the cell has a very speedy and acute solution to DNA damage. Upon DNA damage machinery to repair the damage is recruited to the damage site within minutes.³⁷ Among the DNA repair machinery that is recruited to the damage site there are chromatin remodelers. As can be understood from the name their functions are to remodel chromatin for any subsequent processes. However in the haste of repairing genetic damage the cell loses epigenetic information at the site of DNA damage.³⁸

In fact this DNA damage response can result in so much epigenetic information loss that when DNA damage is artificially induced in the cells of an organism they exhibit accelerated aging. Researchers use an enzyme that cuts the mouse genome at 20 different sites 19 of which don’t code for proteins. Expressing this protein which leads to these DNA cuts results in a constant DNA damage response which recruits chromatin remodelers to the damage site and leads to epigenetic information loss. These mice, which are termed “inducible changes to the epigenome” (ICE) mice, exhibit increased hallmarks of aging both at a cellular and physiological level.³⁹

Transposable elements

Transposable elements are genetic elements that form a major part of eukaryotic genomes. They comprise about half of the mammalian genome. They are one side of an ancient evolutionary battle to survive. Transposable elements are nucleic acid sequences that can move or copy themselves to new positions within the genome. Because of this ability they are sometimes referred to as “jumping genes”. They hijack cellular transcription machinery to carry out their needs. These transposable elements are abundant and very old. Thus, through evolution our biology has found ways to utilize them for our purposes as well. For example certain transposable elements play an important role in development. Thus, not all are transposable elements are equal.⁴⁰

However, similar to the DNA damage response machinery, their action of cutting / copying and pasting themselves into the genome may lead to the loss of some epigenetic information through the remodeling of chromatin. Most of the transposable elements are silenced after development through the attachment of heterochromatin (silenced chromatin) markers.⁴¹ However with age these markers are eroded leading to the expression of some transposable elements. Their expression leads to collateral damage, including the loss of epigenetic information. This loss is partly caused by the induction of the DNA damage response, which in turn contributes further to the erosion of epigenetic information.⁴² In fact the inhibition of a specific type of transposable element led to the reversal of various hallmarks of aging in mouse and human cells with accelerated aging syndromes. In addition preventing the actions of this transposable element led to increases in lifespan of mice with an accelerated aging syndrome.⁴³ 

Epigenetic Drift

Over time, the combined effects of various factors that disrupt epigenetic regulation gradually blur the once clear and specific epigenetic states of cells, leading to what is known as epigenetic drift. This drift results from the buildup of small changes in epigenetic modifications that occur without a specific plan, making them unpredictable and challenging to measure. Because of this drift, as cells age, they start to wander from their ideal epigenetic states. This epigenetic drift can be prevented by targeting the drivers of epigenetic deregulation and can be even reversed with interventions such as partial reprogramming as can be seen from figure 3. 

Figure 3: The epigenetic landscape, starting with pluripotent cells at the peak and progressing to differentiated states through development, dictated by changes like DNA methylation and histone modifications. As aging occurs, DNA damage and other stresses alter this landscape, leading to cell identity drift and functional decline, while partial epigenetic reprogramming shows potential in restoring youthful characteristics and extending lifespan. Sourced from Lu et al.⁴⁴

As cells deviate from their optimal epigenetic states due to epigenetic drift, the effects of aging become increasingly varied. This variability is evident not only across different individuals but also among the cells within a single person. Such diversity in the aging process introduces significant challenges in understanding and tracking how we age, complicating efforts to identify consistent biological markers or develop uniform treatments for age-related conditions. Given this complexity, there is a clear need for sophisticated tools that can measure and analyze the multifaceted nature of epigenetic changes. Such tools would help us quantify the impact of aging on the epigenome and assess the effectiveness of various interventions aimed at mitigating age-related changes.

Epigenetic Clocks: An Attempt at Measuring & Tracking Epigenetic Deregulation

One attempt to deconvolute the changes in the epigenome into a quantifiable measure are epigenetic clocks. These clocks help us quantify the complex changes happening within our epigenome as we age—a task made challenging due to the diverse and intricate nature of these changes. Every individual’s epigenome reacts uniquely to their environment, leading to subtle variations in how we age, which is why a one-size-fits-all approach to studying aging has always fallen short. With the advent of machine learning, we now have the capability to analyze immense amounts of data to uncover patterns in these epigenetic changes. 

The first iterations of epigenetic clocks were introduced in 2013 by two separate research teams: Hannum et al. and Horvath et al.⁴⁵⁴⁶ Hannum et al. focused on developing their clock using blood samples, while Horvath’s approach utilized samples from multiple tissues, allowing for broader applications across different types of biological materials. The Horvath clock’s edge was in its versatility, it was able to predict biological age regardless of the source of cells. The generation process of the Horvath clock requires two inputs for each sample: the DNA methylation data for around 20,000 methylation sites across the genome and the age of the patient from which the sample was derived. Then through several iterations of machine learning magic the algorithm sifts through the noise and identifies methylation site patterns that seem to be correlated with age. The Horvath clock specifically uses 353 specific sites, some positively correlated, some negatively correlated with age at different weights. Only by looking at these methylation sites the horvath clock is able to predict their chronological ages with remarkable accuracy. 

One aspect in which the Horvath clock falls short is that it was trained solely on chronological age to interpret complex DNA methylation data. Thus, it must assume that the chronological age and biological age of the patients from whom the training DNA methylation data was obtained are equivalent. After the discovery of the Horvath clock, other DNA methylation clocks have been developed to address a significant limitation. The Horvath clock, trained solely on chronological age, relies on the assumption that the chronological and biological ages of the training samples align perfectly—an assumption that is not always valid. To provide a more accurate measure of biological aging, newer generation clocks, such as the DNAm PhenoAge, have shifted their focus. Unlike the Horvath clock, the DNAm PhenoAge is not trained solely on chronological age but on phenotypic markers of aging such as, blood glucose, blood albumin, white blood cell count and more.⁴⁷ There are other clocks that further build upon this and train on parameters such as remaining lifespan.⁴⁸ This approach helps these newer clocks more accurately reflect an individual’s biological age by incorporating broader health and lifespan indicators, thereby improving predictions of aging outcomes and allowing interventions to be applied more effectively.

Figure 4: The three epigenetic clocks—Horvath’s Clock (blue line), DNAm PhenoAge (green line), and Hannum’s Clock (red line)—in their ability to determine age acceleration and prediction capabilities across various situations. Horvath’s Clock excels in estimating age accurately across multiple tissues and age groups, including supercentenarians but underperforms in phenotypic changes like smoking and time to death (left side). DNAm PhenoAge is noted for its strong predictive accuracy for mortality, its correlation with smoking status, and links to markers of immune aging. Hannum’s Clock, primarily used for blood samples, is effective in predicting lifespan. However, both perform under the multi-tissue clock when it comes to basic age from various ages and tissues (right side). “AA” indicates age acceleration, with ‘AA blood’ specifically measuring it in blood samples. Sourced from Horvath et al.⁴⁹

Besides DNA methylation clocks, scientists have explored various other epigenetic clocks such as, based on histone modifications and DNA accessibility.⁵⁰⁵¹ While these alternative approaches are intriguing and add depth to our understanding of aging, they don’t yet have the same level of widespread validation or extensive research backing that DNA methylation clocks do. As it stands, DNA methylation clocks are the most trusted and well-established tools in the field, celebrated for their consistent accuracy in predicting biological age and evaluating the effectiveness of aging interventions.

While epigenetic clocks are revolutionary in aging research, they face several limitations and challenges. One major concern is their reliance on the assumption that chronological and biological ages align, which isn’t always true due to individual lifestyle and health differences (this problem is addressed with newer generation clocks). They also tend to be trained on specific sample types, which may not represent the entire population or all tissue types, limiting their universal applicability. Furthermore, the biological mechanisms underlying the epigenetic changes these clocks measure are not fully understood, complicating their use in clinical settings where the cause and effect of aging need to be clear.⁵²

Conclusion

In conclusion, the intricate relationship between epigenetics and aging is unveiling new layers of complexity in our understanding of biological aging processes. Ongoing research in this area not only deepens our grasp of how epigenetic mechanisms influence aging but also brings forth innovative tools like epigenetic clocks. These tools hold the potential to predict and perhaps even modify the aging trajectory. In the next article, we will explore existing epigenetic interventions, those under development, and potential future strategies.

1. López-Otín, C., Blasco, M. A., Partridge, L., Serrano, M. & Kroemer, G. The Hallmarks of Aging. Cell 153, 1194–1217 (2013). ↩︎
2. Peters, M. J. et al. The transcriptional landscape of age in human peripheral blood. Nat. Commun. 6, 8570 (2015). ↩︎
3. Wilson, V. L., Smith, R. A., Ma, S. & Cutler, R. G. Genomic 5-methyldeoxycytidine decreases with age. J. Biol. Chem. 262, 9948–9951 (1987). ↩︎
4. Heyn, H. et al. Distinct DNA methylomes of newborns and centenarians. Proc. Natl. Acad. Sci. 109, 10522–10527 (2012). ↩︎
5. Casillas, M. A., Lopatina, N., Andrews, L. G. & Tollefsbol, T. O. Transcriptional control of the DNA methyltransferases is altered in aging and neoplastically-transformed human fibroblasts. Mol. Cell. Biochem. 252, 33–43 (2003). ↩︎
6. Ciccarone, F. et al. Age‐dependent expression of DNMT1 and DNMT3B in PBMCs from a large European population enrolled in the MARK‐AGE study. Aging Cell 15, 755–765 (2016).
   ↩︎
7. Rakyan, V. K. et al. Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res. 20, 434–439 (2010). ↩︎
8. Jintaridth, P. & Mutirangura, A. Distinctive patterns of age-dependent hypomethylation in interspersed repetitive sequences. Physiol. Genomics 41, 194–200 (2010). ↩︎
9. Lu, A. T. et al. Universal DNA methylation age across mammalian tissues. Nat. Aging 3, 1144–1166 (2023). ↩︎
10. Skene, P. J. & Henikoff, S. Histone variants in pluripotency and disease. Development 140, 2513–2524 (2013). ↩︎
11. Duarte, L. F. et al. Histone H3.3 and its proteolytically processed form drive a cellular senescence programme. Nat. Commun. 5, 5210 (2014). ↩︎
12. Zhang, R. et al. Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA. Dev. Cell 8, 19–30 (2005). ↩︎
13. Feser, J. et al. Elevated histone expression promotes lifespan extension. Mol. Cell 39, 724–735 (2010). ↩︎
14. Dang, W. et al. Histone H4 lysine 16 acetylation regulates cellular lifespan. Nature 459, 802–807 (2009). ↩︎
15. Pal, S. & Tyler, J. K. Epigenetics and aging. Sci. Adv. 2, e1600584 (2016). ↩︎
16. Sun, D. et al. Epigenomic Profiling of Young and Aged HSCs Reveals Concerted Changes during Aging that Reinforce Self-Renewal. Cell Stem Cell 14, 673–688 (2014). ↩︎
17. Lee, J.-H., Kim, E. W., Croteau, D. L. & Bohr, V. A. Heterochromatin: an epigenetic point of view in aging. Exp. Mol. Med. 52, 1466–1474 (2020). ↩︎
18. Greer, E. L. et al. Members of the H3K4 trimethylation complex regulate lifespan in a germline-dependent manner in C. elegans. Nature 466, 383–387 (2010). ↩︎
19. Mori, M. A. et al. Role of MicroRNA Processing in Adipose Tissue in Stress Defense and Longevity. Cell Metab. 16, 336–347 (2012). ↩︎
20. A Developmental Timing MicroRNA and Its Target Regulate Life Span in C. elegans | Science. https://www.science.org/doi/10.1126/science.1115596. ↩︎
21. Du, W. W. et al. miR-17 extends mouse lifespan by inhibiting senescence signaling mediated by MKP7. Cell Death Dis. 5, e1355–e1355 (2014). ↩︎
22. Meier, I., Fellini, L., Jakovcevski, M., Schachner, M. & Morellini, F. Expression of the snoRNA host gene gas5 in the hippocampus is upregulated by age and psychogenic stress and correlates with reduced novelty-induced behavior in C57BL/6 mice. Hippocampus 20, 1027–1036 (2010). ↩︎
23. Monnier, P. et al. H19 lncRNA controls gene expression of the Imprinted Gene Network by recruiting MBD1. Proc. Natl. Acad. Sci. 110, 20693–20698 (2013). ↩︎
24. Criscione, S. W. et al. Reorganization of chromosome architecture in replicative cellular senescence. Sci. Adv. 2, e1500882 (2016). ↩︎
25. Wang, K. et al. Epigenetic regulation of aging: implications for interventions of aging and diseases. Signal Transduct. Target. Ther. 7, 374 (2022). ↩︎
26. Probst, A. V., Dunleavy, E. & Almouzni, G. Epigenetic inheritance during the cell cycle. Nat. Rev. Mol. Cell Biol. 10, 192–206 (2009). ↩︎
27. Law, J. A. & Jacobsen, S. E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204–220 (2010). ↩︎
28. Bar-Ziv, R., Voichek, Y. & Barkai, N. Chromatin dynamics during DNA replication. Genome Res. 26, 1245–1256 (2016). ↩︎
29. Du, J., Johnson, L. M., Jacobsen, S. E. & Patel, D. J. DNA methylation pathways and their crosstalk with histone methylation. Nat. Rev. Mol. Cell Biol. 16, 519–532 (2015). ↩︎
30. Worden, E. J., Hoffmann, N. A., Hicks, C. W. & Wolberger, C. Mechanism of Cross-talk between H2B Ubiquitination and H3 Methylation by Dot1L. Cell 176, 1490-1501.e12 (2019). ↩︎
31. Zhu, X. et al. Inflammation, epigenetics, and metabolism converge to cell senescence and ageing: the regulation and intervention. Signal Transduct. Target. Ther. 6, 1–29 (2021). ↩︎
32. Shrishrimal, S., Kosmacek, E. A. & Oberley-Deegan, R. E. Reactive Oxygen Species Drive Epigenetic Changes in Radiation-Induced Fibrosis. Oxid. Med. Cell. Longev. 2019, 4278658 (2019). ↩︎
33. Shen, Y., Stanislauskas, M., Li, G., Zheng, D. & Liu, L. Epigenetic and genetic dissections of UV-induced global gene dysregulation in skin cells through multi-omics analyses. Sci. Rep. 7, 42646 (2017). ↩︎
34. Oey, H. & Whitelaw, E. On the meaning of the word ‘epimutation’. Trends Genet. 30, 519–520 (2014). ↩︎
35. Endicott, J. L., Nolte, P. A., Shen, H. & Laird, P. W. Cell division drives DNA methylation loss in late-replicating domains in primary human cells. Nat. Commun. 13, 6659 (2022). ↩︎
36. Owen, J. A., Osmanović, D. & Mirny, L. Design principles of 3D epigenetic memory systems. Science 382, eadg3053 (2023). ↩︎
37. Jakob, B. et al. Differential Repair Protein Recruitment at Sites of Clustered and Isolated DNA Double-Strand Breaks Produced by High-Energy Heavy Ions. Sci. Rep. 10, 1443 (2020). ↩︎
38. Soto-Palma, C., Niedernhofer, L. J., Faulk, C. D. & Dong, X. Epigenetics, DNA damage, and aging. J. Clin. Invest. 132, e158446. ↩︎
39. Yang, J.-H. et al. Loss of epigenetic information as a cause of mammalian aging. Cell 186, 305-326.e27 (2023). ↩︎
40. Bourque, G. et al. Ten things you should know about transposable elements. Genome Biol. 19, 1–12 (2018). ↩︎
41. Slotkin, R. K. & Martienssen, R. Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 8, 272–285 (2007). ↩︎
42. Gorbunova, V. et al. The role of retrotransposable elements in ageing and age-associated diseases. Nature 596, 43–53 (2021). ↩︎
43. Della Valle, F. et al. LINE-1 RNA causes heterochromatin erosion and is a target for amelioration of senescent phenotypes in progeroid syndromes. Sci. Transl. Med. 14, eabl6057 (2022). ↩︎
44. Lu, Y. R., Tian, X. & Sinclair, D. A. The Information Theory of Aging. Nat. Aging 3, 1486–1499 (2023). ↩︎
45. Hannum, G. et al. Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates. Mol. Cell 49, 359–367 (2013). ↩︎
46. Horvath, S. DNA methylation age of human tissues and cell types. Genome Biol. 14, 1–20 (2013). ↩︎
47. Levine, M. E. et al. An epigenetic biomarker of aging for lifespan and healthspan. Aging 10, 573–591 (2018). ↩︎
48. Lu, A. T. et al. DNA methylation GrimAge strongly predicts lifespan and healthspan. Aging 11, 303–327 (2019). ↩︎
49. Horvath, S. & Raj, K. DNA methylation-based biomarkers and the epigenetic clock theory of ageing. Nat. Rev. Genet. 19, 371–384 (2018). ↩︎
50. Morandini, F. et al. ATAC-clock: An aging clock based on chromatin accessibility. GeroScience 46, 1789–1806 (2024). ↩︎
51. Camillo, L. P. de L., Asif, M. H., Horvath, S., Larschan, E. & Singh, R. Histone mark age of human tissues and cells. 2023.08.21.554165 Preprint at https://doi.org/10.1101/2023.08.21.554165 (2023). ↩︎
52. Bell, C. G. et al. DNA methylation aging clocks: challenges and recommendations. Genome Biol. 20, 1–24 (2019). ↩︎