Epigenetic Regulation of Aging and its Rejuvenation

DNA methylation is one of the most well‐known epigenetic modifications. DNA methylation is catalyzed by DNA methyltransferases (DNMTs) using S‐adenosyl‐methionine (SAM) as the methyl donor, which transfers a methyl group (–CH₃) to specific bases in defined genomic regions. In mammals, the three principal methyltransferases are DNMT3A, DNMT3B, and DNMT1. According to the methylation pattern they establish, these enzymes are classified as either de novo or maintenance methyltransferases. DNMT3A and DNMT3B are de novo methyltransferases responsible for establishing methylation on previously unmethylated DNA. This de novo methylation—that is, the creation of new methylation marks on unmethylated cytosines—occurs predominantly during embryonic stem‐cell development and sets up novel methylation patterns. DNMT1 is a maintenance methyltransferase that preserves existing methylation patterns. After DNA replication, DNMT1, as an integral component of the replication complex, recognizes hemimethylated CpG sites on the nascent strand. Through a nucleophilic attack, it catalyzes methylation of these hemimethylated positions, thereby copying the methylation pattern from the parental strand to the daughter strand and ensuring faithful propagation of the methylation landscape originally established by the de novo methyltransferases [9, 10]. This modification is crucial for regulating gene expression, maintaining genomic stability, and facilitating cellular differentiation.

Histones are small, basic proteins rich in amino acids such as lysine and arginine, and they are the major structural proteins of eukaryotic chromatin [53]. They bind to DNA to form nucleosomes, which are the fundamental repeating units of chromatin. There are four core histones: H2A, H2B, H3, and H4, each composed of two molecules to form an octamer, around which DNA is wound to form the nucleosome [54]. H1 is the linker histone [55], located at the linker DNA regions between nucleosomes, helping to compact higher‐order chromatin structures. The amino acid sequences of histones are highly conserved through evolution, especially H3 and H4, indicating the importance of their functions [56].

Histone modification refers to the process by which specific amino acid residues (especially at the N‐terminal tails) on histones undergo covalent chemical modifications. By adding or removing small chemical groups (such as methyl, acetyl, or phosphate groups), histone modifications dynamically regulate chromatin structure and gene expression [22, 57]. These modifications do not alter the DNA sequence but are heritable and influence cellular functions, making them one of the core mechanisms of epigenetic regulation. This process is dynamic and reversible, with "writers" (such as histone acetyltransferases [HATs] and HMTs) adding modifications and "erasers" (such as histone deacetylases [HDACs] and KDMs) removing them [58, 59]. Histone modifications include various types, with common ones being methylation, acetylation, phosphorylation, and ubiquitination. On one hand, these posttranslational modifications can activate or repress gene expression by regulating chromatin structure. On the other hand, different combinations of modifications can form a "histone code" [60, 61], which is recognized by effector proteins (such as proteins containing Bromo/Chromo domains) and recruits the transcriptional machinery to initiate distinct gene expression programs. Histone modifications play multiple biological roles in eukaryotic cells, participating in the regulation of chromatin structure, gene expression, DNA damage and repair, and the cell cycle [60, 61]. These functions are realized through complex interaction networks, and different modifications may have synergistic or antagonistic effects [62, 63]. Abnormal histone modifications are closely associated with various diseases, such as tumors [64], neurodegenerative diseases [65], and aging [66, 67, 68], and are potential therapeutic targets.

Recent studies have shown that aging is accompanied by significant chromatin structural remodeling, including the loss of heterochromatin, disintegration of the 3D genome, and activation of transposons, which are epigenetic changes [157, 158, 159, 160]. The downregulation of nuclear lamina protein Lamin B1 in aging cells leads to nuclear membrane wrinkling and the redistribution of LADs, with LADs dissociating in aged tissues, resulting in the abnormal expression of previously silenced genes [161]. This change is closely associated with the SASP, LAD dissociation releases ERVs, driving chronic inflammation by activating the cGAS–STING pathway [162].

At the level of heterochromatin, several studies have reported aging‐related histone modification abnormalities. SUV39H1 catalyzes the trimethylation of histone H3 at lysine 9 (H3K9me3), which is specifically recognized and bound by the chromodomain of HP1 proteins. HP1 then homodimerizes and recruits additional SUV39H1, driving the formation of liquid‐like heterochromatin droplets and leading to heterochromatin relaxation [163, 164, 165, 166]. During stem cell aging, SUV39H1‐mediated H3K9me3 significantly decreased, leading to the derepression of satellite DNA repeats [167, 168, 169]. In 2023, research indicated that loss of H3K27me3 reactivates LINE‐1 transposons, promoting genomic instability [170]. 3D genome analysis revealed that in aging cells, the transition between A/B compartments increases, TAD boundary integrity weakens (especially at tumor suppressor gene loci such as p53), and enhancer–promoter interactions decrease, all of which collectively lead to disrupted gene expression networks [171, 172].

At the molecular level, chromatin remodeling involves abnormalities in multiple layers of regulation. Dysregulation of histone‐modifying enzymes is manifested by decreased HDAC activity, causing an increase in H4K16ac [173], decreased DNMT expression leading to global hypomethylation [174, 175], and NSD2 upregulation drives the aberrant accumulation of H3K36me2 [176]. This increase renders chromatin more open, facilitating the binding of transcription factors and other proteins to DNA and thereby enhancing gene transcription. Concurrently, the elevated H3K36me2 level mediated by NSD2 antagonizes EZH2‐catalyzed H3K27me3 deposition. Because H3K27me3 is a repressive mark, its reduction weakens chromatin‐mediated repression [177, 178, 179]. The function of chromatin remodeling complexes is also significantly impaired, SWI/SNF engages nucleosomes, transiently disrupts their DNA contacts, and generates short DNA loops that allow the nucleosome to slide to new positions, thereby promoting either transcriptional activation or repression. Concurrently, SWI/SNF forms a dynamic balance with Polycomb complexes (PRC1 and PRC2) during developmental gene regulation. SWI/SNF opens chromatin by dismantling PRC2‐mediated H3K27me3 domains, whereas PRC1 recondenses heterochromatin through deposition of H2AK119ub1. Disruption of this equilibrium is frequently associated with disease [180, 181, 182, 183], These changes drive Brg1 (SMARCA4) to bind the promoter of Klf2a, activating the Klf2a–NO pathway and thereby disrupting stem cell function [184]. Deficiency in the NuRD complex reduces DNA repair efficiency [185, 186, 187]. The regulatory role of ncRNAs is increasingly recognized, with the accumulation of aging‐related long ncRNAs (lncRNAs) like TERRA causing telomere heterochromatin disintegration [188, 189], and the circRNA affecting chromatin accessibility by influencing HMGB1 [190].

These chromatin changes are closely linked to various aging‐related diseases. In neurodegenerative diseases, AD patients' neurons show an abnormal increase in H3K27ac, promoting tau overexpression [191, 192], while Parkinson's disease (PD) is associated with increased chromatin accessibility at the SNCA gene locus [193, 194]. Research in cancer shows that aging‐related disruption of TAD boundaries in leukemia activates proto‐oncogenes [195]. Metabolic diseases like diabetes are related to a decrease in enhancer–promoter interactions at the PDX1 locus in pancreatic β‐cells [196], while atherosclerosis involves inflammation triggered by the loss of H3K9me3 in endothelial cells [197].

In response to these findings, researchers have developed various intervention strategies. In epigenetic reprogramming, OSKM induction can partially restore chromatin structure in aging cells [198, 199], and HDACis can improve cognitive function in aging mice [200]. Attempts to target chromatin remodeling include inhibiting NSD2 to delay stem cell aging [201] and activating SIRT6 to enhance heterochromatin stability [202, 203]. In gene therapy, CRISPR–dead Cas9 (dCas9)‐mediated epigenetic editing has achieved precise regulation of disease‐associated loci [204, 205]. Despite the progress, the field still faces challenges such as unclear tissue‐specific regulations and the limitations of 3D genome dynamic monitoring technologies. Future work will need to develop single‐cell multiomics technologies and strengthen clinical translation research.

ncRNAs are critical regulators of gene expression and play significant roles in the aging process. This diverse class of RNA molecules, including microRNAs (miRNAs), lncRNAs, and circular RNAs, contributes to various cellular functions and the pathogenesis of age‐related diseases [206].

miRNAs are small RNA molecules that posttranscriptionally regulate gene expression by targeting complementary mRNA sequences for degradation or translational repression. Recent studies have highlighted the importance of specific miRNAs in aging, for example. The most applicable age predictor miRNAs include miR‐9, miR‐21, miR‐34a, miR‐96, miR‐132, miR‐212, and miR‐145 [207]. Moreover, the dysregulation of specific miRNAs has been linked to the pathogenesis of age‐related diseases, including neurodegenerative disorders and cardiovascular diseases [208, 209]. The dysregulation of miRNAs, such as the downregulation of miR‐29, has been implicated in age‐related diseases, suggesting their potential as biomarkers and therapeutic targets [210].

The proven mechanism of miRNAs in aging regulation mainly involves targeting and binding to the mRNA sequences of aging‐related genes to induce degradation or inhibit translation. Here are some specific ways: (1) Affecting cell aging by regulating the p53 and p21 signaling pathways. For instance, the downregulation of miR‐15, 17, 19b, 20a, 302b, 106a, and b can boost p21 expression and promote aging. miR‐34a and miR‐217 can accelerate aging by targeting and suppressing SIRT1, which in turn increases p53 expression [211, 212]. (2) Influencing aging via oxidative stress regulation. For example, miR‐34a and miR‐335 are upregulated in aging cells. MiR‐34a targets mitochondrial antioxidant enzyme TXNRD2, and miR‐335 targets SOD2. These actions raise ROS levels and speed up cell aging [213]. (3) Impacting aging by regulating inflammation. miR‐146a and b can target and suppress the expression of IL6 and IL8, thereby slowing down aging [214].

Studies have shown that lncRNAs such as ANRIL, MALAT1, and H19 are abnormally expressed during aging, accelerating aging by affecting telomere maintenance, DNA damage repair, and cell cycle regulation [215, 216, 217, 218]. For example, ANRIL regulates the CDKN2A/B loci by binding to the PRC2, influencing cell senescence [219, 220]. H19 promotes the IGF1R/mTOR signaling pathway by inhibiting let‐7 miRNA activity, exacerbating aging‐related metabolic dysfunction [221, 222].

CircRNAs form through back‐splicing of precursor mRNA, resulting in a covalently closed circular structure with no 5′ cap or 3′ poly‐A tail, making them highly stable in cells [190]. Studies have found that circRNAs increase linearly during aging, suggesting their accumulation is primarily due to their high stability rather than increased synthesis rates [223, 224]. CircRNAs such as circHIPK3, circCDKN2B, and circFoxo3 regulate aging by adsorbing miRNAs or binding to RNA‐binding proteins [225, 226, 227, 228, 229]. CircHIPK3 acts as a sponge for miR‐124‐3p, upregulating the STAT3 signaling pathway and promoting cellular senescence [230]. CircCDKN2B inhibits cell cycle progression by binding to p21 protein [231]. CircFoxo3 exacerbates aging‐related muscle atrophy by stabilizing p21 and p27 mRNA [232].

Recent research has focused on elucidating the specific roles of ncRNAs in aging. For instance, manipulating levels of specific miRNAs has been shown to influence lifespan in model organisms, suggesting that miRNA‐based therapies could be developed for age‐related diseases [211, 233]. Additionally, lncRNAs that modulate cellular responses to stress and inflammation have gained attention for their potential implications in aging [234]. Findings indicate that specific circular RNAs can regulate SASP factors, further linking ncRNAs to aging and inflammation [235]. This highlights the intricate role of ncRNAs in the aging process and suggests that they may serve as potential therapeutic targets for age‐related interventions.

As research progresses, the development of therapies that target specific ncRNAs may provide innovative strategies for mitigating age‐related decline and promoting healthy longevity. For instance, the use of small RNA molecules to modulate miRNA expression levels could help restore normal cellular function in aging tissues, offering promising avenues for future therapeutic interventions.

In addition to epigenetic changes in individuals caused by various factors (Figure 3), specific epigenetic modifications can be inherited, leading to phenotypic changes in offspring, which is known as the inheritance and transgenerational effects of epigenetics. For instance, exposure to environmental stressors, such as toxins or dietary changes, can induce epigenetic alterations that persist across multiple generations [236, 237, 238, 239]. Parental exposure to a high‐fat diet can alter the DNA methylation patterns of offspring, making them more susceptible to metabolic disorders [240, 241]. Moreover, epigenetic changes can affect not only the phenotype of individuals but also their reproductive fitness, potentially leading to evolutionary implications. For example, if adverse environmental conditions trigger heritable epigenetic changes that confer a survival advantage, these modifications may become prevalent in the population over time [242, 243]. These findings emphasize the importance of understanding how parental environmental exposures affect offspring's epigenetic landscape. They may explain the intergenerational transmission of age‐related diseases and raise important questions about how lifestyle choices impact the long‐term health of future generations.

The progressive accumulation of genomic instability and decline in DNA repair capacity constitute fundamental drivers of the aging process, creating a vicious cycle that accelerates cellular and organismal decline [247, 248]. As organisms age, their genomes become increasingly susceptible to various forms of damage [249], with DSBs representing particularly deleterious lesions that accumulate in multiple tissues including brain, liver, and hematopoietic systems [54]. This damage accrual stems from both increased genotoxic stress and diminished repair capacity—endogenous sources like ROS and replication stress combine with exogenous factors such as UV radiation to overwhelm protective mechanisms [250, 251]. Crucially, the efficiency of DNA repair pathways including nonhomologous end joining and homologous recombination declines with age due to epigenetic silencing of repair genes like BRCA1 [252] and ATM [253], reduced expression of critical proteins such as Ku70/80 and RAD51 [254], and NAD+ depletion impairing SIRT1/SIRT6 function [255, 256]. The consequences of this repair‐deficit are severe: unrepaired DSBs lead to chromosomal translocations, telomere dysfunction, and permanent cell cycle arrest, while misrepaired breaks generate mutagenic outcomes that further destabilize the genome [257].

Epigenetic dysregulation plays a central role in this process, both as a cause and consequence of genomic instability. Age‐related loss of heterochromatin marks like H3K9me3 and H3K27me3 permits activation of transposable elements (TEs) and repetitive sequences [258], creating new sites of genomic vulnerability. Simultaneously, epigenetic changes disrupt the precise coordination of DDR pathways—aberrant histone modifications alter the recruitment of repair factors to damage sites, while DNA methylation changes silence critical repair genes [63, 259]. This epigenetic deterioration creates a self‐reinforcing cycle where DNA damage induces epigenetic changes that in turn impair damage repair, leading to further genomic instability [260]. The functional consequences manifest across multiple biological levels: at the cellular level, persistent DNA damage triggers senescence or apoptosis; in stem cell populations, accumulated mutations impair regenerative capacity [261]; and at the tissue level, these changes contribute to age‐related pathologies including neurodegeneration, metabolic dysfunction, and increased cancer risk [262, 263].

Telomere shortening is a key biomarker for aging and age‐related tissue degeneration, as well as a driving factor for aging [264]. It triggers DDRs at the ends of chromosomes, promoting cellular aging and tissue dysfunction [265]. This process is tightly linked to epigenetic regulation—telomere attrition correlates with DNA hypomethylation [266, 267], while RNA methylation (e.g., m5C on TERC and m6A on TERRA) modulates telomerase activity and heterochromatin stability [268, 269, 270]. Key histone modifications, including H3K9me3 and H4K20me3, maintain telomeric integrity, with their age‐related loss exacerbating genomic instability. Additionally, alternative nucleic acid structures like G‐quadruplexes and R‐loops, which interact with epigenetic regulators, further contribute to replication stress and DNA damage accumulation in aging cells [271]. Together, telomere erosion and its associated epigenetic dysregulation create a self‐reinforcing cycle that accelerates functional decline.

Premature aging syndrome demonstrates the systematic nature of genomic instability, such as premature aging, Werner syndrome, Bloom syndrome, Cochrane syndrome, Seckel syndrome, and hair sulfur malnutrition [272]. Among them, genetic defects in the DNA repair pathway reproduced the phenotype of accelerated aging [273]. While these syndromes demonstrate the catastrophic consequences of repair deficiency, they also reveal that simple enhancement of DNA repair may not suffice to extend lifespan, highlighting the complexity of aging as a system‐wide phenomenon.

The aging process is fundamentally linked to progressive transcriptional dysregulation mediated through multiple epigenetic mechanisms [274, 275]. A central feature is the activation of TEs [276], which constitute 30–80% of eukaryotic genomes [277]. Normally silenced by heterochromatin marks like H3K9me3 [278], TEs become derepressed during aging due to heterochromatin loss and decreased SIRT6‐mediated repression [279]. This TE activation creates genomic instability through insertional mutagenesis and disrupts normal gene expression patterns [280]. The consequences are particularly evident in neurodegenerative diseases and cellular senescence, where increased chromatin accessibility at retrotransposon sites drives further transcriptional dysregulation [281, 282].

Transcriptional precision deteriorates significantly with age through both chromatin‐based and epitranscriptomic mechanisms. Key histone modifications like H3K36me3, which normally suppress cryptic intragenic transcription, decline with age, leading to spurious transcript production. This loss of transcriptional fidelity is conserved from yeast to mammals and correlates with reduced lifespan [283]. Concurrently, age‐related changes in RNA modifications (the "epitranscriptome") further disrupt gene expression regulation [284]. rRNA methyltransferases like NSUN5 influence lifespan through translational control, while mRNA m6A modifications affect neuronal function and stress resistance [285, 286]. These multilayered regulatory failures create increasing transcriptional noise, particularly in postmitotic cells like cardiomyocytes, though the effects appear cell‐type specific with HSCs showing different patterns of age‐related transcriptional change [287].

The cumulative effect of age‐related transcriptional dysregulation is profound loss of cellular identity and function. Upregulation of repeat elements and ribosomal protein genes, coupled with suppression of DNA repair pathways, creates a maladaptive cellular state [288]. In stem cells like HSCs, this leads to impaired regenerative capacity and skewed differentiation potential [289]. The inflammatory tone from SASP and other age‐related transcriptional changes contributes to chronic low‐grade inflammation ("inflammaging"), while stochastic expression noise reduces cellular fitness [290]. Importantly, these transcriptional alterations appear mechanistically linked through chromatin state changes, suggesting that interventions targeting epigenetic regulators could potentially restore more youthful transcriptional patterns and ameliorate age‐related functional decline [289].

The functional decline of stem and progenitor cells during aging manifests through two key mechanisms: depletion of dedicated stem cell pools and loss of injury‐induced cellular plasticity. Tissue‐specific stem cells, such as muscle satellite cells and HSCs, exhibit reduced self‐renewal capacity and biased differentiation with age. For example, aged HSCs show myeloid skewing that compromises adaptive immunity, while muscle stem cells lose regenerative potential, contributing to sarcopenia [291]. Epigenetic alterations, including aberrant DNA methylation (e.g., DNMT3a/3b dysregulation) and histone modifications, underlie this dysfunction by silencing stemness genes (OCT4, NANOG) while activating senescence pathways (p16INK4a) [292, 293]. The stem cell niche further exacerbates this decline through chronic inflammation ("inflammaging") and extracellular matrix remodeling, creating a hostile microenvironment that impairs stem cell maintenance and activation. These changes collectively reduce tissue homeostasis and predispose to age‐related pathologies like anemia, immune senescence, and muscle wasting [291].

The loss of cellular plasticity represents an equally critical aspect of regenerative decline. While most organs maintain some basal renewal capacity, injury repair often depends on facultative reprogramming of differentiated cells—a process that becomes severely impaired with age. In young organisms, tissues like liver, lung, and intestine can activate latent regenerative programs through dedifferentiation (e.g., hepatocytes re‐entering cell cycle) or transdifferentiation (e.g., alveolar type II cells repairing lung epithelium) [3]. This plasticity requires precise epigenetic regulation, including DNA demethylation (mediated by TET enzymes) and chromatin remodeling at embryonic gene loci [294]. However, aging introduces epigenetic barriers—such as hypermethylation of plasticity genes and accumulation of repressive histone marks—that lock cells in differentiated states [22]. The resulting failure to mount adequate repair responses leads to prolonged recovery after injury and increased fibrosis, particularly in organs with low baseline turnover like heart and brain. Notably, this plasticity loss often precedes overt stem cell depletion, suggesting it may be the primary driver of age‐related regenerative failure [295].

Age‐related epigenetic alterations also drive the onset of mitochondrial dysfunction. Existing studies have shown that intragenic hypomethylation of the SNCA gene (encoding α‐synuclein [SNCA]) promotes abnormal SNCA aggregation, which—in synergy with oxidative stress and mitochondrial dysfunction—accelerates PD pathology. Likewise, hypomethylation of the PARK2 gene disrupts parkin expression, leading to decreased mitochondrial membrane potential, reduced ATP levels, and mitochondrial fragmentation [296]. HDACis induce hyper‐acetylation of histones H2, H3, H4, and the p300 promoter region associated with SNCA, thereby diminishing sirtuin 1/2 activity, impairing mitochondrial biogenesis, and fostering SNCA aggregation [297]. Multiple miRNAs (e.g., miR‐485, miR‐366a) downregulate PGC‐1α, curtailing the expression of mitochondrial biogenesis‐related genes (e.g., Nrf1/2, SIRT‐3) and exacerbating mitochondrial dysfunction [298]. At the same time, oxidative stress triggers epigenetic modifications (such as DNA methylation and ncRNA regulation) that alter the expression of relevant genes, further impairing mitochondrial function and elevating oxidative stress levels.

Mitochondrial dysfunction emerges as a central driver of aging, manifesting through progressive bioenergetic failure and disruptive signaling cascades. As the cell's powerhouses, mitochondria in aged tissues accumulate debilitating mutations in mtDNA while exhibiting impaired proteostasis and diminished quality control through reduced mitophagy [299]. These defects lead to a vicious cycle of metabolic insufficiency—respiratory chain complexes destabilize, membrane potentials decline, and ROS production escalates [300]. The consequences are particularly severe in high‐energy tissues: neuronal mitochondria show reduced axonal transport capacity, cardiac mitochondria demonstrate impaired calcium handling, and muscle mitochondria lose oxidative phosphorylation efficiency [301, 302]. Beyond energy deficits, damaged mitochondria become pathological signaling hubs, releasing proinflammatory mitochondrial DNA that activates cytosolic sensors like cGAS–STING and leaking intermembrane proteins that trigger apoptotic and pyroptotic cell death pathways [303, 304]. This mitochondrial distress propagates cellular senescence while creating an inflammatory microenvironment that further disrupts tissue homeostasis. The metabolic inflexibility of aged cells is compounded by declining NAD⁺ levels, which impair sirtuin activity and disrupt critical processes including DNA repair and stress resistance [305, 306].

The systemic repercussions of mitochondrial decline manifest through interconnected metabolic disturbances. Age‐related shifts in nutrient sensing pathways (e.g., mTOR, AMPK) alter substrate utilization, promoting insulin resistance and lipid accumulation even in nonadipose tissues. Hepatic mitochondria lose fatty acid oxidation capacity, contributing to age‐related steatosis, while pancreatic β‐cell mitochondria fail to adequately couple glucose metabolism to insulin secretion [307, 308, 309]. Neurons become particularly vulnerable as mitochondrial trafficking defects impair synaptic maintenance and antioxidant defenses weaken. These tissue‐specific manifestations share common roots in deteriorating mitochondrial membrane integrity, redox imbalance, and failing quality control mechanisms [310]. Notably, the accumulation of oxidized macromolecules and lipofuscin in lysosomes further compromises cellular clearance capacity, creating a self‐reinforcing cycle of metabolic dysfunction [311]. The resulting bioenergetic crisis not only limits tissue repair but also alters systemic metabolism, predisposing to characteristic aging phenotypes including sarcopenia, cognitive decline, and cardiovascular disease [312]. These pathological changes are exacerbated by the age‐related decline in mitochondrial‐encoded microproteins like humanin and MOTS‐c, which normally serve as systemic regulators of metabolic homeostasis and stress resistance [313].

Epigenetic alterations play a pivotal role in cancer development by disrupting normal gene expression patterns that regulate cell proliferation, apoptosis, and DNA repair [314]. Age‐related DNA hypomethylation can lead to genomic instability and activation of oncogenes, while hypermethylation of tumor suppressor gene promoters (e.g., p16INK4a, BRCA1) silences their expression, facilitating uncontrolled cell growth [315, 316]. Histone modifications, such as loss of H4K16 acetylation and H3K27 trimethylation, contribute to chromatin compaction and transcriptional repression of critical anticancer genes [317, 318, 319]. Additionally, dysregulation of ncRNAs (e.g., miR‐21, miR‐155) promotes tumorigenesis by modulating oncogenic signaling pathways (e.g., PI3K/AKT, Wnt/β‐catenin) [320, 321]. The SASP in aged cells further exacerbates chronic inflammation, creating a tumor‐permissive microenvironment [322]. Epigenetic therapies, such as DNMT inhibitors (DNMTis) (e.g., 5‐azacytidine) and HDACis (e.g., vorinostat), are being explored to reverse these aberrations and restore normal gene function in cancer cells [323].

In AD, epigenetic dysregulation contributes to amyloid‐β (Aβ) accumulation and tau hyperphosphorylation. Age‐related DNA methylation changes in genes like BACE1 and APP enhance Aβ production [324], while histone deacetylation (e.g., reduced SIRT1 activity) impairs synaptic plasticity and memory formation [325]. Hypomethylation of the MAPT gene increases tau expression, promoting neurofibrillary tangle formation [326]. Additionally, oxidative stress‐induced DNA damage in neurons accelerates epigenetic drift, exacerbating neurodegeneration [327].

In PD, SNCA gene overexpression due to hypomethylation leads to Lewy body formation [328]. Epigenetic silencing of PARK2 (Parkin) and PINK1 disrupts mitophagy, causing mitochondrial dysfunction and dopaminergic neuron death [296]. HDACis show promise in reducing SNCA aggregation, while restoring DNA methylation patterns may slow PD progression [329].

Epigenetic mechanisms drive endothelial dysfunction, vascular inflammation, and atherosclerosis. Hypomethylation of proinflammatory genes (IL‐6, MCP‐1) and hypermethylation of endothelial nitric oxide synthase impair vasodilation and promote plaque formation [330]. HDACs contribute to VSMC senescence and arterial stiffening, while SIRT1/SIRT6 deficiency accelerates vascular aging [331]. ncRNAs (miR‐217, miR‐34a) further exacerbate oxidative stress and endothelial senescence [332, 333]. Epigenetic interventions targeting DNA methylation (e.g., folate supplementation) or HDAC inhibition may mitigate CVD progression [334].

Epigenetic changes in pancreatic β‐cells and adipose tissue contribute to insulin resistance and T2DM. Hypermethylation of PDX‐1 and GLUT4 impairs insulin secretion and glucose uptake [335], while hypomethylation of inflammatory genes (TNF‐α, IL‐1β) promotes chronic low‐grade inflammation [336]. Age‐related loss of SIRT1 and SIRT3 disrupts mitochondrial function, exacerbating oxidative stress in metabolic tissues [337]. Additionally, miRNA dysregulation (miR‐375, miR‐29) alters insulin signaling pathways. Epigenetic reprogramming via caloric restriction (CR) or NAD+ boosters (e.g., NMN) shows potential in restoring metabolic homeostasis [338].

Epigenetic modifications (DNA methylation, histone acetylation) drive hepatic lipid accumulation and fibrosis. Hypomethylation of PPARγ2 promotes steatosis [339], while hypermethylation of CPT1A reduces fatty acid oxidation [340]. SIRT1/SIRT3 downregulation impairs mitochondrial function, increasing ROS production and hepatocyte senescence [341]. Dysregulated miRNAs (miR‐34a, miR‐122) further exacerbate inflammation and fibrogenesis [342]. Epigenetic therapies targeting DNMTs or HDACs may prevent NAFLD progression to cirrhosis [341].

Epigenetic dysregulation plays a critical role in osteoporosis, a disease characterized by decreased bone mineral density and increased fracture risk in aging individuals. Key mechanisms include DNA methylation changes in osteogenic genes (e.g., RUNX2, SP7/Osteri), which impair osteoblast differentiation and bone formation [343]. Additionally, histone deacetylation (mediated by HDACs) suppresses Wnt/β‐catenin signaling, a crucial pathway for bone formation, while miRNA dysregulation (e.g., miR‐214 upregulation) inhibits osteoblast activity [344, 345]. Senescent osteocytes and mesenchymal stem cells (MSCs) contribute to bone loss via the SASP, secreting factors like RANKL that enhance osteoclastogenesis [346]. SIRT1 and SIRT6, key epigenetic regulators of bone homeostasis, decline with age, leading to impaired DNA repair and increased oxidative stress in bone tissue [347]. Therapeutic strategies targeting epigenetic modifications—such as HDACis, SIRT1 activators, and DNA methylation modulators—are being explored to restore bone remodeling balance and prevent osteoporosis progression [348, 349].

Reprogramming senescent cells and induced pluripotent stem cell (iPSC) technology have emerged as significant breakthroughs in the fields of antiaging and regenerative medicine in recent years. The core principle of these approaches is to reverse the cellular aging state and restore tissue function through epigenetic reprogramming. This strategy has shown potential in a variety of aging‐related diseases, including neurodegenerative diseases, cardiovascular diseases, osteoarthritis, and fibrotic diseases.

Studies have demonstrated that the transient expression of OSKM (Oct4, Sox2, Klf4, and c‐Myc) can initiate extensive chromatin remodeling of target regions, enabling the reprogramming of terminally differentiated somatic cells into pluripotent cells and the rejuvenation of human senescent fibroblasts [350]. Ectopic expression of OSK (without c‐Myc) can restore DNA methylation in retinal ganglion cells of mice, improving vision problems in aged mice with glaucoma. In addition, cyclic reprogramming technology, through transient expression of the NANOG gene, can significantly enhance muscle regeneration in mouse models while preserving tissue‐specific gene expression [351].

In terms of disease applications, the safety and potential efficacy of human embryonic stem cell‐derived dopaminergic neurons transplanted into patients with PD have been reported [352]. Another clinical trial involved the transplantation of allogeneic iPSC‐derived dopaminergic progenitors into the bilateral putamen of seven patients with PD. The results showed that among six patients, four had significant improvements in motor symptoms (MDS‐UPDRS scores) and a 44.7% increase in dopamine synthesis capacity. These studies provide important evidence for the use of iPSCs in the treatment of PD and may become an alternative to traditional therapies in the future [353].

However, the field still needs to address the balance between reprogramming efficiency and tumorigenicity. Future directions include the development of small molecules to replace reprogramming factors and the optimization of personalized treatment plans using organ‐on‐a‐chip models. Overall, the technology of reprogramming senescent cells is moving from proof‐of‐concept to clinical translation, but further research is needed to support its long‐term safety and in‐depth mechanistic understanding.

Epigenetic regulation, as a key driving force of aging, has in recent years become an important target for the development of antiaging drugs. Strategies based on epigenetic reprogramming, histone modification regulation, and DNA methylation intervention have shown significant therapeutic potential in a variety of aging‐related diseases. Studies have shown that suberoylanilide hydroxamic acid, a HDACi, can prevent premature skin aging associated with Cockayne syndrome [354]. The HDACi ITF2357 can inhibit diastolic dysfunction induced by aging in mice [355]. Sodium butyrate, an HDACi, can treat muscle atrophy caused by aging in mice [356]. The latest research has found that vorinostat, an HDACi and a novel hormone‐like substance, can extend the lifespan of nematodes and enhance stress resistance by activating the SKN‐1 pathway [357]. Similarly, dihydromyricetin (DHM) is an inhibitor of DNMT1. Studies have shown that DHM can act as an epigenetic inhibitor with antiaging effects and has regenerative effects on aging human skin [358].

Sirtuins are a class of proteins that regulate cellular processes such as metabolism, DNA repair, and stress response, and are key participants in the aging process. Sirtuin activators such as resveratrol and NAD⁺ precursors (e.g., nicotinamide riboside and NMN) have attracted attention for their potential to reverse aging cells. Resveratrol has been shown to activate SIRT1, an important sirtuin in regulating DNA repair and inflammation. Studies have shown that resveratrol not only extends lifespan but also restores cell function by modulating epigenetic marks, including histone acetylation and DNA methylation [1]. With increasing age, NAD⁺ levels decline, impairing mitochondrial function and DNA repair. NAD⁺ precursors, such as NMN and NR, have been shown to restore NAD⁺ levels, activate sirtuins, and improve cell function [142]. In mammals, supplementation with NR can enhance mitochondrial function and extend the lifespan of mice. Moreover, filling NAD⁺ with NMN or NR can improve meibomian gland dysfunction associated with aging in elderly mice and improve cognitive function in an AD mouse model. Clinical trials have also validated the efficacy of NAD⁺ supplements, showing that 8 weeks of NMN safely and effectively promoted NAD⁺ biosynthesis in healthy middle‐aged men and alleviated postprandial hyperinsulinemia [359]. Another clinical study showed that overweight, obese, and middle‐aged or older adults taking MIB‐626 (precursor β‐NMN) can safely increase circulating NAD⁺ levels and significantly reduce total LDL and non‐HDL cholesterol, weight, and diastolic blood pressure [360].

Metformin and rapamycin, drugs known for treating other diseases, have become potential antiaging drugs. Metformin, widely used for treating type 2 diabetes, has been shown to activate AMPK, thereby improving cell function and extending lifespan, and reducing the epigenetic age of model organisms [361]. Rapamycin, an mTOR inhibitor, has been shown to extend the lifespan of various organisms and improve cellular aging through epigenetic regulation [362, 363].

Despite the promising prospects of epigenetic drugs, their clinical application still faces challenges. Tissue‐specific delivery and dose control are key to avoiding off‐target effects, while epigenetic drugs exhibit cellular heterogeneity in response. Future development directions include: (1) developing small‐molecule modulators targeting specific epigenetic marks; (2) optimizing spatiotemporal specificity control strategies, such as optogenetic epigenetic editing systems; (3) exploring the synergistic effects of epigenetic drugs with other antiaging therapies. With the development of precise assessment tools such as the epigenetic clock, personalized antiaging treatments are gradually becoming a reality.

Epigenetic clocks are predictive algorithms based on DNA methylation patterns that estimate biological age, often reflecting physiological health better than chronological age. Early models, such as the Horvath and Hannum clocks, laid the groundwork for this field, but recent innovations have significantly enhanced their precision and utility [40, 41].

Second‐generation clocks like PhenoAge and GrimAge incorporate additional data, such as inflammatory markers and clinical measures, to predict biological aging more accurately [42, 43]. These clocks are highly correlated with healthspan, chronic disease incidence, and mortality risk. For example, GrimAge has been validated across diverse populations and has demonstrated its ability to predict outcomes such as time‐to‐death and cancer incidence with remarkable accuracy [43].

Technological advancements, such as the integration of deep learning algorithms, have further improved the resolution of epigenetic clocks. Tools like DeepAge analyze multiomics data, enabling predictions of biological age that account for complex interactions between epigenetic, transcriptomic, and proteomic changes [387]. Tissue‐specific clocks, such as those developed for brain and liver cells, provide insights into organ‐specific aging processes, which are critical for targeted therapies [388, 389, 390].

Epigenetic clocks are increasingly used to evaluate the success of rejuvenation interventions by measuring reductions in biological age. For example, partial cellular reprogramming with Yamanaka factors has been shown to reduce epigenetic age markers in fibroblasts, highlighting its potential to reverse cellular aging [391, 392, 393]. Similarly, CR and intermittent fasting have demonstrated measurable reductions in biological age as indicated by PhenoAge and GrimAge [378, 394]. Clinical trials are now incorporating epigenetic clocks to monitor the impact of therapies like senolytics, NAD⁺ precursors, and CRISPR‐based gene editing. For instance, a study on NMN supplementation showed significant improvements in biological age, as reflected by reduced DNA methylation age in muscle and liver tissues [395]. The use of these clocks not only validates the efficacy of interventions but also provides feedback for refining personalized rejuvenation protocols.

Aging is a heterogeneous process, affecting different tissues and cell types in unique ways. Single‐cell epigenomics has emerged as a transformative technology for studying these cell‐specific changes. Techniques like single‐cell DNA methylation sequencing and single‐cell ATAC‐seq have enabled researchers to map the epigenetic landscape at an unprecedented resolution [396, 397]. For example, studies on HSCs have revealed distinct methylation signatures associated with age‐related declines in regenerative capacity [398, 399]. Similarly, single‐cell analyses of brain tissues have identified neuronal and glial populations with divergent aging trajectories, highlighting the vulnerability of certain cell types to age‐related diseases [400, 401]. These insights are critical for understanding the interplay between cellular heterogeneity and aging. By identifying epigenetic markers specific to vulnerable cell populations, researchers can develop targeted interventions to mitigate age‐associated decline.

The precise positioning and spatial relationships of cells also greatly impact aging. Spatial transcriptomics is a new method that can capture gene expression and epigenetic data linked to spatial information, offering the exact location of these elements within tissues. For example, in muscle aging research, this technology has revealed key mechanisms like fiber‐specific degeneration and satellite cell dysfunction. In senescent cells, heterochromatin decreases while euchromatin increases. The loss of heterochromatin near the nuclear membrane causes genomic instability and triggers aging‐related diseases. Spatial epigenomics allows for a more precise analysis of chromatin state changes in different nuclear regions. It shows how these changes affect gene expression and cell function, thus uncovering the fundamental molecular mechanisms of aging.

Antiaging therapies often have cell type‐specific effects, which can be clarified through single‐cell and spatial epigenomics. For example, partial reprogramming has been shown to rejuvenate fibroblasts more effectively than neurons, highlighting differences in epigenetic plasticity across cell types [402, 403]. Similarly, senolytics selectively clear senescent cells, preserving healthy populations and improving overall tissue function [404, 405].

Recent studies using single‐cell technologies have demonstrated that CR alters chromatin accessibility in energy‐regulating pathways in muscle cells while restoring DNA methylation patterns in neurons associated with memory and learning [406, 407]. These findings underscore the potential of tailoring rejuvenation strategies to the specific needs of different tissues. The integration of single‐cell and spatial epigenomics in clinical research is paving the way for precision medicine. By capturing the nuanced effects of therapies at the cellular level, this approach ensures that interventions are both effective and safe, minimizing off‐target effects while maximizing therapeutic benefits.

In the field of antiaging research, the development of effective and safe intervention measures is one of the core goals. To achieve this goal, it is essential to establish scientifically reliable efficacy evaluation models to accurately assess the short‐term and long‐term effects of antiaging interventions. A good efficacy evaluation model should not only consider changes in biomarkers but also integrate multiple aspects, including physiological function, healthspan, and lifespan.

With the advancement of epigenetic aging research, ethical considerations and social impacts related to epigenetic reprogramming and genome modification have become increasingly prominent. First, epigenetic research involves a large amount of highly sensitive personal health and lifestyle information. If leaked, this information could cause serious harm to individuals. Moreover, gene editing, compound treatments, individual lifestyle factors, and environmental factors can all cause epigenetic changes. For example, the same stress response pathway (such as oxidative stress) can be activated by different substances like pesticides and nicotine, and there is a lack of specific biomarkers. This complexity makes it difficult to clearly define disease liability and also makes it challenging for research participants to fully understand the implications and potential impacts. Second, the ability to modify the epigenome raises questions about the long‐term effects of these modifications on individuals and their offspring. For instance, if epigenetic changes can be transmitted to future generations, they may have transgenerational effects on aging and disease susceptibility. This could also lead to the creation of "designer babies," raising a host of complex ethical and moral issues [438]. Finally, research and interventions in epigenetics will prompt policymakers to pay more attention to the relationship between the environment and health and to strengthen measures such as environmental pollution control and public health improvement to reduce disease risks. It will also promote public awareness of the impact of lifestyle and environmental factors on health and foster interdisciplinary collaboration to address complex health problems. However, at the same time, it may also lead to a further widening of health disparities and exacerbate social inequality. Therefore, the rapid development of epigenetics and its therapies brings new hope for human health but also brings complex ethical and social issues. Issues such as privacy protection, misuse of gene editing, and social inequality need to be given sufficient attention alongside technological development. It is essential to develop reasonable policies and regulations to promote the positive role of epigenetics in human health while minimizing its potential negative impacts.

One of the most important advances in epigenetic aging research has been the development of high‐resolution mapping techniques [439]. These methods have allowed researchers to identify subtle age‐related changes in the epigenome with unprecedented accuracy. The integration of single‐cell multiomics has provided further insights into how aging affects gene expression at the cellular level, allowing for a better understanding of the molecular underpinnings of aging and related diseases [440].