Throughout the human lifespan, several factors such as diet, physical activity, aging, illness, infections, pollutants, and other environmental inputs can disrupt redox homeostasis, thus affecting hormesis and triggering metabolic adaptations along with epigenetic modifications. Redox signaling through reactive oxygen species (ROS) is crucial in redox homeostasis, where low oxidative stress levels trigger adaptive responses that enhance cellular resilience. At physiological concentrations, ROS act as signaling molecules, activating Nuclear factor-erythroid 2-related factor 2 (NRF2) and NF-κB transcription factors to induce the expression of antioxidant defenses and other protective responses. Among others, NRF2 [1] and NF-κB mediated responses [2] are regulated by epigenetic mechanisms as well as redox control [3]. This process helps cells withstand future stress, highlighting the dual role of ROS as both a beneficial signal and a potential source of damage when upregulated. It is noteworthy that adaptive responses mediated through transcription factors are typically transitory rather than long-lasting [4]. In contrast, epigenetic regulation can have prolonged effects, as it is maintained not only as a cellular response but also through DNA replication [5].

Epigenetics, often seen as a leitmotif in the regulation of cellular function and adaptation, encompasses the study of mechanisms that govern gene expression through modifications independently of the DNA sequence itself [[6], [7], [8], [9]].

Key metabolic intermediates from central metabolic pathways like glycolysis (aerobic and anaerobic), the tricarboxylic acid (TCA) cycle, and mitochondrial oxidative phosphorylation (OXPHOS), and the methionine cycle are known to link cellular metabolism—through specific metabolites, intermediates, and co-factors—with gene expression regulation via epigenetic mechanisms. Importantly, energy metabolism is both a source and a target of oxidant species [10], which can directly produce epigenetic changes.

Epigenetic mechanisms lead to alterations in gene expression and chromatin structure and are orchestrated by three primary mechanisms: DNA methylation at cytosine residues, transcriptional regulation by non-coding RNAs (including microRNAs, long non-coding RNAs, and circular RNAs), and chemical modifications on histone tails, such as acetylation, methylation, and phosphorylation, which are post-translational modifications in histones (PTMs). Together, these epigenetic mechanisms form the basis of the "histone code," which serves as a versatile platform for controlling gene activity and cellular identity [[6], [7], [8], [9]]. In addition, recent findings point to a role for epigenetics, not only in transcription, but also in translation [11], through epitranscriptomic regulation mechanisms.

DNA methylation is one of the most thoroughly studied and well-characterized epigenetic mechanisms, primarily involving the addition of a methyl group to the 5′ carbon of cytosine bases within CpG dinucleotides. This process is facilitated by DNA methyltransferases (DNMTs), specifically DNMT1, DNMT3A, and DNMT3B, which transfer a methyl group from the methyl donor S-adenosylmethionine (SAM) to the target cytosine [9,12]. DNA methylation is essential for cellular function and gene silencing, playing a critical role in processes such as pluripotency, embryonic development, X-chromosome inactivation, cell proliferation, and maintaining genomic stability.

Aside from DNA methylation, chromatin compaction is another key regulator of gene expression, influenced by both histone variants and PTMs of histone proteins. Chromatin is organized into repeating nucleosome units, each consisting of an octamer of histones around which 147 base pairs of DNA are wrapped. This histone core comprises two copies of each histone—H2A, H2B, H3, and H4. Protruding from these histones are the histone tails, which are chains of amino acids accessible to various chromatin-modifying enzymes [6,9]. These enzymes catalyze PTMs (e.g., acetylation, methylation, phosphorylation, and ubiquitination, among others) and modify chromatin structure, influencing gene accessibility. Such modifications either relax or compact chromatin, thereby controlling transcriptional activity across nucleosome domains.

Current research is highlighting the importance of epigenetics in regulating the gene expression changes that underlie metabolic adaptation. However, the precise mechanisms by which metabolic alterations influence epigenetic control, particularly during oxidative stress, remain incompletely understood. In addition, redox post-translational modifications (oxPTMs) may contribute to cellular responses by dynamically regulating chromatin accessibility and transcriptional activity in response to oxidative cues. Understanding how oxidative stress and oxPTMs impact epigenetic mechanisms is crucial for elucidating the pathways involved in metabolic plasticity, which plays a significant role in metabolic adaptation and is instrumental for both health and disease.

The term oxidative stress was first introduced by Helmut Sies to describe an imbalance between oxidants and antioxidants which can arise due to various factors, typically involving an increase in oxidants, a decrease in antioxidants, or both [13,14]. Maintaining redox balance is a continuous challenge which Sies referred to as oxidative eustress [15]. This term denotes oxidative stress within a physiological range that supports biological functions, through mechanisms that involve the role of reactive oxygen species (ROS) and reactive nitrogen species (RNS) as physiological signaling molecules. In contrast, prolonged or unresolved stress, known as oxidative distress, can negatively affect biological processes [16], among which energetic metabolism is directly affected. This impacts the production of substrates needed for epigenetic control, such as DNA methylation and PTMs [[17], [18], [19], [20]], ultimately influencing transcriptional programs which may alter cell function.

Oxidative stress and inflammation are widely recognized as key contributors to disease progression. However, oxidative stress is also a factor in physiological adaptation, influencing cellular processes not only through direct oxidation of biomolecules and enzymes but also via alterations in redox signaling pathways [21]. Central metabolic pathways, including glycolysis, TCA cycle, methionine cycle, and OXPHOS, are intimately involved in cellular responses to oxidative stress and have significant implications for epigenetic and transcriptional regulation.

During glycolysis, glucose is metabolized to pyruvate, which under aerobic conditions enters the mitochondria and is converted to acetyl-CoA by the pyruvate dehydrogenase complex (PDHC), serving as an essential substrate for the TCA cycle. Acetyl-CoA plays a critical role in epigenetic control by donating acetyl groups for histone acetylation, a modification linked to transcriptional activation. However, glycolysis and acetyl-CoA production can be significantly impacted by oxidative stress. ROS, produced during oxidative stress, can inhibit key glycolytic enzymes such as glyceraldehyde-3-phosphate dehydrogenase (GAPDH), as the cysteine residue in the active site of this enzyme is oxidized by hydrogen peroxide (H2O2) and peroxynitrite (NOO·) [[22], [23], [24]], as well as pyruvate kinase [25], therefore reducing glycolytic flux and the availability of acetyl-CoA (Fig. 1). Furthermore, oxidative stress can impair not only GAPDH, but also mitochondrial function, controlling pyruvate entry into the mitochondria and further affecting acetyl-CoA production. For example, the PDHC regulator pyruvate dehydrogenase kinase 2 (PDHK2) can be inactivated by oxidation of Cys, thus decreasing PDHC phosphorylation and increasing PDHC activity, in turn intensifying acetyl-CoA formation [26]. Meanwhile, oxidative stress may also impair acetyl-CoA formation from pyruvate and β-oxidation [10,27].

The TCA cycle's main function is to generate high-energy electron carriers (NADH and FADH2) through the oxidation of acetyl-CoA derived from carbohydrates, fats, and proteins, and fuels electron transport in OXPHOS, subsequently impacting ROS production and redox balance [28,29] (Fig. 1). Moreover TCA cycle is crucial for generating intermediates essential for the epigenetic enzymes; including α-ketoglutarate (α-KG, 2-oxoglutarate), succinate, fumarate, and NAD+/NADH play important roles in DNA and histone methylation, histone acetylation, and histone poly(ADP-ribosyl)ation (PARsylation) [30] (Fig. 1).

Importantly, the TCA cycle is redox-sensitive [28], so the TCA cycle flux is disrupted under oxidative stress as aconitase becomes inactivated (Fig. 1). However, α-KG dehydrogenase (α-KGDH) remains functional, allowing the cycle to persist temporarily through glutamate-derived α-KG until ROS levels inhibit α-KGDH [28].

NAD+ and NADH, essential coenzymes in the TCA cycle, are crucial for mitochondrial ATP production via OXPHOS. Their ratio regulates cellular redox balance and NAD + -dependent biosynthetic pathways, including cytosolic and nuclear NAD + salvage processes, ensuring NAD + recycling [31]. NAD + also plays a key role in epigenetic regulation by supporting PARPs, which catalyze histone PARsylation in response to oxidative stress and single breaks damage, facilitating DNA repair [32,33]. In addition, high levels of ADP-ribose within the nucleus may produce reactions ultimately leading to the carbonylation of proteins [34], including histones. In fact, protein carbonylation can also occur through reaction with reducing sugars or their oxidation products (glycation) [30,[35], [36], [37], [38]].

The TCA cycle facilitates the integration of several pathways, playing a critical role in supplying intermediates and cofactors for the biosynthesis of amino acids, fatty acids, and glucose (i.e. gluconeogenesis), but beyond this, the TCA cycle is also required for epigenetic machinery, including α-KG, succinate, and fumarate. These metabolites regulate the activity of α-KG-dependent dioxygenases, such as ten-eleven translocase (TET) proteins and Jumonji C (jmjC) histone demethylases, which are essential for DNA and histone demethylation [18,[39], [40], [41], [42], [43], [44], [45]] (Fig. 1).

Specifically, α-KG and Fe(II)-dependent dioxygenases, TETs and jmjCs, can be inhibited by succinate, fumarate, citrate and hydroxyglutarate [[46], [47], [48], [49], [50]].

Meanwhile, OXPHOS, occurring in the mitochondria, serves as a primary source of ATP through the electron transport chain (ETC), which is directly linked to superoxide (O2∙−) generation, by Complex I and Complex III, as a byproduct [51]. It is noteworthy that redox inhibition of aconitase activity could inhibit the TCA cycle, leading to the accumulation of upstream metabolites, decreased ETC, and lower O2∙− production by the ETC (Fig. 1) [52].

The one-carbon metabolism, TCA cycle, and transsulfuration pathway are interconnected through key metabolites that regulate biosynthesis, redox balance, and energy metabolism. Homocysteine links one-carbon metabolism to transsulfuration by serving as a precursor for cystathionine and ultimately glutathione (GSH) synthesis [53,54]. Additionally, serine and glycine, derived from glycolysis, contribute carbon units to the tetrahydrofolate (THF) cycle and cystathionine synthesis, supporting GSH production. The methionine pathway is central to redox homeostasis, metabolic regulation, and methylation reactions (Fig. 2), transferring methyl groups to DNA and histones, with alterations impacting transcriptional regulation [55], redox homeostasis and metabolic regulation.

The transsulfuration pathway connects methylation processes with redox homeostasis by regulating homocysteine metabolism. SAM is converted into S-adenosylhomocysteine (SAH), which is further broken down by SAH hydrolase (SAHH) into adenosine and homocysteine. Homocysteine then enters the transsulfuration pathway, where cystathionine β-synthase (CBS) and cystathionine γ-lyase (CGL) convert it into cysteine, a key precursor for GSH synthesis (Fig. 2). This regulation is critical, as SAHH activity connects the production of GSH, a major antioxidant, with the methylation of DNA and histones. Notably, SAHH downregulation has been shown to induce DNA hypomethylation by disrupting this balance. Alternatively, homocysteine can be recycled back to methionine through the action of methionine synthase (MS), which requires THF and vitamin B12, which is also regulated by oxidative stress [56].

Alterations in redox balance affect the levels of the methyl donor SAM due to the presence of redox-sensitive cysteine residues (including Cys121 and Cys243) [51] in the catalytic site of methionine adenosyltransferase (MAT), the enzyme responsible for SAM synthesis. As a result, reduced MAT activity leads to a decrease in SAM availability, ultimately lowering the substrate required for DNA methylation [57]. Interestingly, these cysteine residues are often oxidized in response to oxidative stress, and NO and hydroxyl radicals can oxidize C121, the cysteine located at the active site loop of MAT I/III in some of these in vivo models, leading to enzyme inactivation [[58], [59], [60]]. Moreover, DNA hypomethylation can arise from oxidative stress, which depletes SAM—the primary methyl donor for methyltransferase reactions—and decreases GSH levels. GSH depletion triggers regeneration in the form of extensive methionine catabolism via the cystathionine pathway, resulting in methylation impairment [61]. Moreover, GSH depletion also causes methionine depletion via the GSH-depleting agent bromobenzene, which leads to an increase in unmethylated CpG sites in genomic DNA [62]. This occurs because GSH depletion disrupts the metabolism of cysteine and methionine, further diminishing the cellular SAM pool. Reduced SAM availability disrupts essential methyltransferase reactions, leading to altered DNA and histone methylation patterns. Persistent SAM depletion results in a widespread loss of histone H3 di- and tri-methylation marks, while H3K9me1 remains preserved to prevent heterochromatin instability and the de-repression of silenced DNA elements [63].

Pharmacological interventions aimed at restoring GSH homeostasis have been shown to be effective in promoting the proper functioning of the methionine cycle, which includes methionine adenosyltransferase (MAT1A) and MS, facilitating the regeneration of SAM [61]. These interventions not only enable the recovery of SAM levels but also prevent non-specific methylation reactions by reducing the activity of methionine sulfoxide reductase (MSR). GSH depletion is associated with alterations in DNA methylation, highlighting the relevance of glutathione homeostasis for epigenetic regulation [62]. Furthermore, the decrease in methyl metabolites triggers adaptive responses that favor heterochromatin stability and epigenetic persistence, suggesting that cellular adaptations to the lack of methyl donors are crucial for maintaining epigenetic integrity in the face of biochemical disturbances [63].

Furthermore, oxidative stress directly regulates the activity of MS, which produces methionine [64]. This amino acid serves as a substrate for MAT1A—an enzyme also controlled by the GSH/glutathione disulfide (GSSG) ratio—to generate SAM [65,66]. SAM, in turn, not only acts as a substrate for DNMTs and histone methyltransferases (HMTs) but also serves as a precursor for the transsulfuration pathway [36,66]. The transsulfuration pathway ultimately generates cysteine, a critical substrate for GSH synthesis (Fig. 2), thus creating a feedback loop that connects methylation, redox balance, and epigenetic regulation.

When there is a correct balance between oxidants (ROS and RNS) and antioxidants (both enzymatic and non-enzymatic), cells and organisms can maintain normal physiological functions [67]. At moderate levels, ROS serve as signaling molecules that influence the activity of epigenetic enzymes, such as histone deacetylases (HDACs) and DNMTs [68]. This regulated ROS signaling creates a functional link between mitochondrial activity and gene expression, allowing cells to adapt their genetic expression in response to metabolic changes and stress signals [68]. However, when ROS levels exceed physiological thresholds, the regulated ROS signaling transitions to dysregulated responses, disrupting the activity of epigenetic enzymes and altering the metabolite levels required for their proper function [37]. This interaction between ROS, epigenetic regulation and metabolism not only impacts chromatin remodeling and gene expression but also contributes to the pathogenesis of various diseases, including cancer, cardiovascular disorders, and neurodegenerative diseases.

Inflammation, as a response to cellular injury, shares an intricate and highly interdependent relationship with oxidative stress [69,70]. This intricate interaction intensifies under conditions of high oxidative stress. As previously described, high ROS and RNS levels impact negatively on cell metabolism by oxidizing key biological molecules such as proteins, lipids, and nucleic acids [21]. When inflammation becomes chronic, it can perpetuate oxidative damage to DNA, proteins, and lipids, leading to further transcriptional dysregulation and cellular dysfunction [71]. Therefore, maintaining a balanced interplay between oxidative and inflammatory responses is critical for cellular homeostasis, including the epigenetic control, and may hold therapeutic potential in managing diseases linked to chronic inflammation and oxidative stress.

Oxidative stress is significantly affected by inflammatory processes and vice versa, contributing to the progression of chronic inflammation and various diseases [69,70]. Similarly, epigenetics can impact genes needed for cellular adaptation to metabolic changes [72,73], as well as genes involved in both inflammatory and anti-inflammatory responses [74]. Importantly, epigenetics acts as a regulatory switch that controls the expression of many of these genes [[75], [76], [77]], influencing cellular behavior in response to metabolic, oxidative and inflammatory signals.