In eukaryotic cells, the genome exists in the form of chromatin, whose basic structural unit is the nucleosome. In 1997, Luger et al. elucidated in detail the crystal structure of the nucleosome core particle, revealing for the first time at the atomic level that approximately 147 bp of DNA wraps around the outer surface of a histone octamer composed of four core histones―H2A, H2B, H3, and H4, with two copies of each―in 1.65 turns of a left-handed superhelix [8]. These four histones all possess flexible amino-terminal tails protruding outward from the nucleosome. These histone tails are enriched with enzymatically modifiable residues, such as lysine, arginine, and serine, and serve as the principal platform for the writing and reading of epigenetic information [8] [9].

To date, more than 20 chemical types of histone modifications have been identified, involving hundreds of specific modification sites [9]. As key epigenetic mechanisms regulating chromatin structure and gene expression, histone modifications mainly include acetylation, methylation, phosphorylation, ubiquitination, and emerging acylation modifications. Each type of modification has its own regulatory system and functional tendency. Acetylation is “written” by histone acetyltransferases (HATs) and “erased” by histone deacetylases (HDACs), with its core function being to relax chromatin by neutralizing the positive charge of histones, thereby promoting transcriptional activation. The “writing” and “erasing” of methylation are mediated by histone methyltransferases (HMTs) and histone demethylases (KDMs), respectively; its effect on transcription may be activating or repressive, depending on the modification site and the degree of methylation. Phosphorylation is “written” by kinases and “erased” by phosphatases, mainly participating in mitotic regulation and DNA damage responses. Ubiquitination is “written” by E3 ubiquitin ligases and “erased” by deubiquitinases (DUBs), with its core functions focused on transcriptional regulation and DNA repair. Emerging acylation modifications are “written” by metabolic enzymes or acyltransferases, and their central role is to sense cellular metabolic states and directly couple epigenetic regulation with cellular energy balance. These various modifications act cooperatively to form a precise and complex regulatory network of histone modifications [9]. Among them, lactylation is a novel histone modification reported by Zhang et al. in Nature in 2019. It is derived from the metabolic product lactate and can directly activate the transcription of target genes on chromatin, making it particularly important in the context of hypoxia and metabolic reprogramming [10].

Histone modifications are dynamically regulated by three classes of functional proteins, forming the “writer-reader-eraser” regulatory mode [9]. Writers catalyze the covalent addition of modification groups, such as acetyltransferases (HATs) and lysine methyltransferases (KMTs). Readers recognize and bind specific modifications through specialized domains, such as bromodomains, which recognize acetylated lysine, and chromodomains, which recognize methylated lysine, thereby recruiting effector complexes to alter chromatin states. Erasers remove modifications, such as histone deacetylases (HDACs) and lysine demethylases (KDMs). This reversible and adjustable dynamic system enables cells to mount rapid transcriptional responses to stress signals and constitutes the molecular basis for gene expression remodeling in MIRI.

Histone acetylation is one of the core mechanisms of epigenetic regulation. It is mediated by histone acetyltransferases (HATs), which catalyze the addition of acetyl groups, and histone deacetylases (HDACs), which catalyze the removal of acetyl groups. The dynamic balance between these two enzyme classes determines the degree of chromatin openness and the activity of gene transcription [9] [11]. Granger et al. [6] first demonstrated that myocardial ischemia can significantly induce an increase in HDAC enzymatic activity, resulting in global deacetylation of histones H3 and H4, whereas HAT activity does not undergo a corresponding change. This indicates that the decline in acetylation levels during ischemia is mainly caused by abnormal activation of HDAC activity. This finding reveals that ischemia-reperfusion is not only a metabolic and oxidative stress event, but also a profound process of epigenetic reprogramming.

Eighteen HDACs have been identified in mammalian cells and are classified into four groups according to structural and functional characteristics. Class I HDACs, including HDAC1, HDAC2, HDAC3, and HDAC8, are mainly localized in the nucleus and regulate gene transcription. Class II HDACs, including HDAC4, HDAC5, HDAC7, and HDAC9, can shuttle between the nucleus and cytoplasm, sensing stress signals and transmitting them to the chromatin level. Class III HDACs are the Sirtuin family, including SIRT1-7, which are NAD⁺-dependent deacetylases that tightly couple cellular metabolic status with epigenetic regulation. Class IV contains only HDAC11 [12]. In the myocardium, all of these HDAC classes are expressed, but their roles in MIRI differ substantially.

Given the detrimental effect of ischemia-induced global deacetylation on the myocardium, the cardioprotective potential of HDAC inhibitors (HDACi) has attracted extensive attention. In a mouse I/R model, Granger et al. [6] found that trichostatin A (TSA), even when administered 1 hour after ischemia, could still reduce infarct size by approximately 50%. Xie et al. [13] further confirmed in a rabbit I/R model that SAHA, also known as vorinostat, among HDAC inhibitors, significantly reduced infarct size when administered at the time of reperfusion. The underlying mechanism involved the induction of cardiomyocyte autophagy to remove damaged proteins and mitochondria. In addition, Zhang et al. [14], by generating cardiomyocyte-specific HDAC4-overexpressing transgenic mice, directly demonstrated that sustained activation of HDAC4 aggravates ventricular dysfunction and infarct expansion after I/R, thereby validating the rationale for HDAC inhibition. Selective inhibition of class I HDACs has also been shown to produce cardioprotective effects [12], suggesting that different HDAC subclasses contribute unequally to I/R injury. Therefore, future precise intervention strategies targeting specific HDAC isoforms may have important translational value.

As class III HDACs, the Sirtuin family directly links cellular energy metabolism with deacetylation regulation through its NAD⁺ dependence. Several family members play key cardioprotective roles in myocardial ischemia-reperfusion (I/R) injury. SIRT1 is the most extensively studied cardioprotective Sirtuin. Using SIRT1 knockout mice and transgenic models, Hsu et al. [15] demonstrated that SIRT1 can directly protect the myocardium from I/R injury through deacetylation. Mechanistically, SIRT1 activates the FOXO3a transcription factor through deacetylation, thereby upregulating the expression of antioxidant enzymes such as manganese superoxide dismutase (MnSOD) and catalase, ultimately reducing oxidative damage and apoptosis [16] [17]. SIRT3 is the major mitochondrial deacetylase, and its role in I/R injury has received increasing attention. Parodi-Rullán et al. [18] found that SIRT3 knockout mice exhibited significantly poorer cardiac functional recovery after I/R compared with wild-type mice, accompanied by increased mitochondrial ROS production and reduced SOD2 activity. Mechanistically, SIRT3 activates SOD2 through deacetylation, enhancing the clearance of superoxide anions within mitochondria [19]. In addition, Hafner et al. [20] revealed that SIRT3 deacetylates cyclophilin D (CypD) at lysine 166, thereby inhibiting abnormal opening of the mitochondrial permeability transition pore (mPTP) and maintaining mitochondrial membrane potential stability. Functional synergy also exists between SIRT1 and SIRT3. The study by Liao et al. [21] showed that abnormalities in the SIRT1-SIRT3 axis can induce ferroptosis by silencing the PINK1/Parkin signaling pathway, thereby aggravating myocardial ischemia-reperfusion injury (MIRI). As a nuclear Sirtuin member, SIRT6 exerts multiple protective functions in myocardial I/R injury. Wang et al. [22] demonstrated using SIRT6 heterozygous knockout mice that SIRT6 deficiency aggravates myocardial injury and oxidative stress after I/R, whereas restoration of SIRT6 expression upregulates MnSOD and catalase expression by activating the AMPK-FOXO3α axis. In addition, SIRT6 regulates glycolytic gene expression through deacetylation and participates in DNA damage repair, thereby maintaining genomic stability [23]. In terms of agonists, the natural polyphenolic compound resveratrol is a classic SIRT1 activator and has been shown to alleviate myocardial I/R injury by activating the Sirt1/Sirt3-FoxO pathway, restoring the balance between mitochondrial fusion and fission, recovering autophagic flux, and promoting mitochondrial biogenesis [24].

Corresponding to HDACs, the role of HATs in MIRI should also not be overlooked. p300/CBP-associated factor (PCAF) is an important member of the GCN5-related N-terminal acetyltransferase family and possesses histone acetyltransferase activity. Qiu et al. [25] found that MIRI significantly upregulates PCAF expression in the myocardium, whereas downregulation of PCAF can inhibit excessive autophagy by activating the PI3K/Akt/mTOR signaling pathway, thereby reducing myocardial infarct size in rats. Further studies showed that PCAF downregulation can also alleviate cardiomyocyte apoptosis, inflammatory responses, and oxidative stress by suppressing the NF-κB signaling pathway [26]. As a large acetyltransferase, p300 is closely associated with cardiac development and pathological remodeling. Under ischemic stress, p300 can be activated and acetylate cardiac transcription factors such as GATA4, participating in myocardial hypertrophy and remodeling [27]. These findings indicate that the imbalance between HATs and HDACs jointly drives epigenetic disorders in MIRI, and HATs may also serve as potential intervention targets.

Histone methylation has a unique “positional code” characteristic: different degrees of methylation on the same lysine residue, including mono-, di-, or trimethylation, can produce markedly different functional consequences. For example, H3K4me3 usually marks active gene promoters, whereas H3K27me3 and H3K9me3 are closely associated with gene silencing [28]. This precise regulation, which couples modification sites with methylation degree, makes the role of histone methylation in MIRI highly complex. By integrating transcriptomic data with histone modification epigenomic data, Ni et al. [5] first mapped the genome-wide histone modification landscape after myocardial I/R injury. They found that within 24 and 48 hours after I/R, disease-specific changes in histone marks were mainly concentrated in regions marked by H3K27me3, H3K27ac, and H3K4me1. The differentially modified genes involved were associated with key processes such as immune responses, cardiac conduction and contraction, cytoskeletal organization, and angiogenesis.

H3K4me3 is a hallmark histone modification associated with transcriptional activation. The KMT2 family, also known as the MLL family, is the major methyltransferase family responsible for catalyzing H3K4 trimethylation. Cao et al. [29] found that KMT2B was significantly upregulated in the peripheral blood of patients with acute myocardial infarction and in I/R myocardial tissues. KMT2B promotes the transcription of the riboflavin kinase (RFK) gene by catalyzing H3K4me3 modification, thereby activating the TNF-α/NOX2 inflammatory signaling pathway, aggravating oxidative stress and ferroptosis, and expanding myocardial infarct size. Knockdown of KMT2B can significantly alleviate these injuries. This finding suggests that H3K4me3 does not always play a protective role in MIRI. Instead, its ultimate biological effect depends on the spectrum of target genes whose transcription it promotes. When H3K4me3 is enriched at the promoters of pro-inflammatory and pro-death genes, it can instead aggravate injury.

H3K27me3 is catalyzed by polycomb repressive complex 2 (PRC2), in which EZH2 serves as the core catalytic subunit. Ni et al. [5] showed that H3K27me3 levels and PRC2 expression are significantly upregulated in myocardial tissue after I/R, whereas selective inhibition of EZH2 improves cardiac function, promotes angiogenesis, and reduces fibrosis. The mechanism involves relieving the repressive H3K27me3 modification at the promoters of multiple pro-angiogenic genes. However, EZH2 does not play a purely detrimental role in myocardial injury. Peng et al. [30] found that mesenchymal stem cell-derived exosomes reduce EZH2 and H3K27me3 levels in cardiomyocytes by delivering miR-25-3p, thereby derepressing the expression of protective genes such as eNOS and SOCS3 and alleviating post-infarction apoptosis and inflammation. Another study showed that lncRNA JPX can reduce H3K27me3 modification in the SERCA2a promoter region by binding to EZH2, restoring SERCA2a expression to alleviate calcium overload and thereby attenuating I/R injury [31]. Therefore, the role of EZH2 in MIRI is clearly target gene-dependent and dual-sided. In addition, H3K9me2/3 is also an important mark of heterochromatin formation and gene silencing. Using cardiac-specific G9a knockout mice combined with genome-wide ChIP-seq analysis, Papait et al. [32] revealed that the histone methyltransferase G9a maintains transcriptional homeostasis in adult cardiomyocytes by preserving H3K9me2 modifications at key gene regions in cardiomyocytes. Loss of G9a causes abnormal reactivation of the fetal gene program and induces myocardial hypertrophy. Thienpont et al. [33] further confirmed that H3K9me2 serves as a key repressive epigenetic modification regulating cardiomyocyte differentiation homeostasis. In a heart failure model, Yan et al. [34] also found that G9a is highly expressed in heart failure and can silence BDNF expression by mediating repressive H3K9me2 modification in the BDNF promoter region, thereby blocking the downstream TrkB signaling pathway and further aggravating cardiomyocyte apoptotic injury and heart failure progression.

Corresponding to methyltransferases, histone demethylases (KDMs) also play certain roles in MIRI. He et al. [35] found that the histone demethylase KDM1A/LSD1 can suppress SOX9 transcription by reducing H3K4me3 modification in the SOX9 promoter region, thereby inhibiting hypoxia/reoxygenation-induced cardiomyocyte apoptosis. However, under myocardial ischemia-reperfusion injury conditions, downregulation of KDM1A relieves this inhibitory effect and aggravates cardiomyocyte apoptosis. Zhang et al. [36] reported that KDM3A, an H3K9me2-specific demethylase, is upregulated in the myocardium after pressure overload and promotes myocardial hypertrophy and fibrosis by activating Timp1 transcription; the pan-KDM inhibitor JIB-04 can effectively suppress this process. These studies indicate that the dynamic balance between the “writing” and “erasing” enzymes of methylation modifications is critical for maintaining myocardial homeostasis, and disruption of this balance can aggravate pathological remodeling after MIRI.

Phosphorylation of the histone variant H2AX at serine 139, known as γH2AX, is a classic marker of DNA double-strand breaks (DSBs) and plays an important role in MIRI. Corbucci et al. [37] demonstrated in patients undergoing cardiac valve surgery that ischemia can induce extensive γH2AX formation in the human left ventricular myocardium. As a specific substrate of ATM kinase and a core marker of myocardial DNA double-strand breaks, γH2AX phosphorylation is significantly increased during myocardial ischemia. It represents a key node in ischemia-induced DNA damage response activation and can drive downstream activation of the p53/p21 pathway. After reperfusion, TUNEL staining is reduced, but ATM activation persists, indicating that reperfusion provides a time window for DNA repair, and the outcome of this repair directly determines cardiomyocyte survival [37].

Phosphorylation of histone H3 at serine 10 (H3S10) and serine 28 (H3S28) is a key epigenetic mark that rapidly transmits extracellular stress signals to the chromatin level [38]. MSK-mediated phosphorylation of histone H3S28 is a core epigenetic regulatory event in macrophages under inflammatory stimulation and can directly activate p300/CBP-dependent transcription of inflammatory genes. MSK1/2 can amplify inflammatory transcriptional programs at the chromatin level through this histone phosphorylation modification and can also drive pathological transcriptional upregulation of the mast cell growth factor SCF under inflammatory conditions by phosphorylating NF-κB p65 at Ser276. Thus, MSK1/2 acts as a central hub linking epigenetic regulation by histone phosphorylation with the NF-κB inflammatory pathway [39] [40]. In the cardiac field, Robinson et al. [41] showed that MAPK pathway-activated MSK-mediated H3S28 phosphorylation is required for the induction of immediate early genes (IEGs) during myocardial hypertrophy. pH3S28 initiates gene expression programs by recruiting the BRG1 subunit of the BAF60 chromatin remodeling complex. Blocking MSK activity and IEG induction can suppress the hypertrophic response. Considering the key role of p38 MAPK in reperfusion injury, the MSK1/2-H3S10/S28 phosphorylation axis is likely to play an important role in inflammatory responses and gene reprogramming in MIRI [42].

Pyruvate kinase M2 (PKM2) is a rate-limiting enzyme in glycolysis, but its non-canonical function―as a protein kinase that catalyzes phosphorylation of histone H3 at threonine 11 (H3T11)―has attracted widespread attention in recent years [43]. In myocardial ischemic injury, the metabolic reprogramming function of PKM2 has been shown to be of great importance. PKM2 tetramers protect the myocardium from ischemic injury by promoting pyruvate oxidation and ATP production, whereas PKM2 dimers promote the entry of glycolytic intermediates into the pentose phosphate pathway to support cardiomyocyte proliferation and regeneration [44]. Magadum et al. [45] demonstrated in a mouse myocardial infarction model that cardiomyocyte-specific expression of PKM2 promotes myocardial regeneration and cardiac functional recovery. Recent research has also found that MTX2 regulates cardiac glucose metabolic flux by promoting PKM2 tetramerization; loss of MTX2 aggravates I/R injury, whereas the PKM2 activator TEPP-46 can reverse this metabolic defect [46]. These findings suggest that PKM2-mediated H3T11 phosphorylation and glucose metabolic reprogramming may constitute an important epigenetic-metabolic coupling mechanism in the adaptive response of ischemic myocardium.