Histone Post‐Translational Modifications Regulating Ferroptosis: The Molecular Mechanisms and Disease Associations

ABSTRACT

Ferroptosis is a form of programmed cell death characterized by iron‐dependent phospholipid peroxidation and is implicated in a wide range of human diseases. Emerging evidence highlights the critical role of epigenetic regulation in this process. Dysregulation of histone post‐translational modifications (HPTMs) is increasingly recognized as a pivotal mechanism linking metabolic reprogramming to various pathological conditions. HPTMs constitute one of the key epigenetic regulatory mechanisms and mediate ferroptosis by modulating the transcription of core ferroptosis‐related genes. This review systematically summarizes site‐specific HPTMs, including histone methylation, acetylation, ubiquitination, phosphorylation, lactylation, and β‐hydroxybutyrylation. Furthermore, we elucidate how infectious diseases, tumors, and chronic non‐infectious conditions drive disease progression via HPTMs‐dependent regulation of ferroptosis. A comprehensive dissection of these epigenetic regulatory networks may facilitate the development of combinatorial therapeutic strategies targeting HPTMs and ferroptosis inducers, thereby providing new insights into the treatment of ferroptosis‐associated disorders.

Summary

Ferroptosis, an iron‐dependent programmed cell death, is tightly implicated in the pathogenesis of cancers, infectious diseases, and chronic inflammatory disorders. Histone post‐translational modifications (HPTMs) act as central epigenetic switches that dynamically shape chromatin accessibility and govern the transcription of core ferroptosis regulators such as GPX4, SLC7A11, ACSL4, and iron‐metabolic genes. This review systematically delineates the site‐specific regulatory roles of major HPTMs—methylation, acetylation, ubiquitination, phosphorylation, lactylation, and β‐hydroxybutyrylation—in ferroptosis, and clarifies their crosstalk and context‐dependent functions in disease progression. By dissecting the epigenetic networks linking HPTMs to ferroptotic cell death, this work unveils novel mechanistic insights into disease development and identifies actionable epigenetic targets for therapeutic intervention. The comprehensive summary of HPTM‐mediated ferroptosis regulation provides a theoretical foundation for developing combinatorial strategies using histone‐modifying enzyme inhibitors and ferroptosis inducers, offering promising new avenues for the treatment of ferroptosis‐associated human diseases.

1. Introduction

The precise regulation of gene expression is a fundamental biological process for maintaining cellular homeostasis and determining cell fate. Epigenetics refers to heritable changes in gene expression that do not involve alterations in the DNA sequence itself. Epigenetic regulatory mechanisms encompass DNA methylation, non‐coding RNA‐mediated regulation, chromatin remodeling, and post‐translational modifications (PTMs) of both histone and non‐histone proteins [1]. The nucleosome, the fundamental structural unit of chromatin, consists of a histone octamer (comprising two copies each of H2A, H2B, H3, and H4) wrapped by approximately 147 base pairs of DNA, and is stabilized by linker histone H1 and non‐histone proteins [2]. Histone post‐translational modifications (HPTMs) predominantly occur on the N‐terminal tails of histone proteins, with lysine (K), arginine (R), and serine (S) residues serving as the primary modification sites. Common types of modifications include methylation, acetylation, lactylation, ubiquitination, phosphorylation, SUMOylation, and ADP‐ribosylation [3]. HPTMs are dynamically deposited by writers (modifying enzymes) and erased by erasers (demodifying enzymes), while being recognized by readers (modification‐binding proteins), forming a reversible epigenetic code that rapidly responds to metabolic cues to regulate chromatin accessibility without altering the DNA sequence [4]. Disruption of this epigenetic balance has been implicated in various pathological processes, including regulated cell death.

Ferroptosis, a novel form of iron‐dependent cell death distinct from apoptosis, was first proposed by Brent Stockwell's laboratory at Columbia University in 2012 [5]. Cells undergoing ferroptosis are morphologically characterized by shrunken mitochondria, increased mitochondrial membrane density, and reduced or absent mitochondrial cristae. The primary mechanisms underlying ferroptosis encompass iron metabolism imbalance, lipid peroxidation accumulation, and antioxidant system dysfunction. Mammalian cells maintain a dynamic balance in iron uptake, storage, and export. Disruption of this balance leads to an increase in intracellular labile ferrous iron (Fe²⁺), which serves as the core initiating event in ferroptosis. Fe²⁺ promotes oxidative stress by catalyzing the Fenton reaction to generate reactive oxygen species (ROS) and serving as a cofactor for lipoxygenases to drive lipid peroxide accumulation [6]. Lipid peroxidation is a critical factor in ferroptosis, primarily involving the peroxidation of polyunsaturated fatty acid‐phospholipids (PUFA‐PLs) catalyzed by lipid metabolic enzymes. The resulting lipid peroxides can propagate through chain reactions, leading to the disruption of cellular membrane structure. Furthermore, certain lipid peroxidation products, particularly high concentrations of 4‐hydroxynonenal (4‐HNE), can directly promote ferroptosis through a positive feedback mechanism that enhances lipid peroxidation. The primary antioxidant system against ferroptosis includes the cystine/glutamate antiporter system (System Xc⁻)—glutathione peroxidase 4 (GPX4)—glutathione (GSH) axis and the ubiquinone (CoQ) system. Classical ferroptosis inducers, such as Erastin and RAS‐selective lethal compound 3 (RSL3), trigger ferroptosis by inhibiting the System Xc⁻‐GPX4‐GSH antioxidant system. Consequently, ferroptosis has been implicated in pathological conditions, including cancer progression and therapy resistance, pathogen infections, and ischemia‐reperfusion injury in the heart, brain, and kidney.

In addition to classical signaling pathways, the expression of ferroptosis‐related genes is governed by epigenetic mechanisms, particularly HPTMs. These histone modifications function as reversible molecular switches that dynamically control key regulators such as GPX4, SLC7A11, and Acyl‐CoA synthetase long‐chain family member 4 (ACSL4). Targeting histone‐modifying enzymes sensitizes tumor cells to ferroptosis inducers, thereby overcoming drug resistance in cancer cells [7]. A recent review by Wang et al. surveyed epigenetic and post‐translational modifications related to ferroptosis [8]. By contrast, the present review focuses specifically on HPTMs and their crosstalk, providing a deeper dissection of site‐specific modifications and disease‐specific regulatory mechanisms aimed at informing future therapeutic strategies.

2. The Role of HPTMs in Ferroptosis

HPTMs regulate ferroptosis through two primary mechanisms: direct modulation of the expression of key ferroptosis‐related genes via chromatin remodeling, and indirect regulation through histone modification crosstalk or hierarchical signal transduction, thereby constituting an integrated epigenetic network that orchestrates ferroptotic cell fate.

2.1. Histone Lysine Methylation Mediates Ferroptosis

Histone methylation primarily occurs on the lysine and arginine side chains of histones. It is a dynamic and reversible post‐translational modification coordinately regulated by histone methyltransferases (HMTs) and histone demethylases (HDMTs). N‐ε‐lysine methylation is one of the most abundant histone marks in eukaryotic chromatin. Histone lysine methylation at specific sites differentially regulates ferroptosis, wherein H3K9me and H3K27me3 regulate ferroptosis through transcriptional repression of antioxidant genes, whereas H3K4me3 bidirectionally regulates ferroptosis depending on cell type and context.

2.1.1. H3K9 Methylation Bidirectionally Regulates Ferroptosis via Distinct Methylation States

Histone H3 lysine 9 methylation (H3K9me) exists in three states: monomethylation (H3K9me1), dimethylation (H3K9me2), and trimethylation (H3K9me3). H3K9me1 is associated with gene activation, whereas H3K9me2/3 drive transcriptional repression via heterochromatin formation. The H3K9me1/2 marks are mainly catalyzed by the methyltransferases G9a (EHMT2) and GLP (EHMT1), and can be removed by the demethylase KDM3B (lysine demethylase 3B). In contrast, H3K9me3 is primarily deposited by SUV39H1/2 (suppressor of variegation 3‐9 homolog 1/2) and erased by members of the KDM4 family [9].

The upregulation of H3K9me2 mediated by G9a is one of the most extensively studied epigenetic mechanisms, which promotes ferroptosis by inhibiting the transcription of antioxidant genes. In neurodegenerative diseases (e.g., multiple sclerosis) and vascular diseases (e.g., aortic dissection), G9a silences GPX4 through H3K9me2, directly impairing the cell's ability to clear lipid peroxides [10, 11]. In kidney diseases (e.g., renal fibrosis, CKD‐Vascular Calcification), H3K9me2 targets SLC7A11, blocking cystine uptake and glutathione synthesis [12, 13]. The use of G9a‐specific inhibitors UNC0642 or BRD4770 can rescue normal cells from ferroptosis by inhibiting the G9a/H3K9me2 axis. In addition to H3K9me2, H3K9me3 also promotes ferroptosis in specific scenarios, mediated by the methyltransferase SET domain bifurcated histone lysine methyltransferase 1 (SETDB1). In pulmonary fibrosis models, SETDB1 inhibits snail family transcriptional repressor 1 (SNAI1) transcription by catalyzing H3K9me3 modification at the SNAI1 promoter, blocking epithelial–mesenchymal transition (EMT), and promoting ferroptosis in EMT‐primed epithelial cells to suppress fibrosis [14].

In contrast, H3K9me3 modifications mediated by SUV39H1 can inhibit ferroptosis. In intracerebral hemorrhage (ICH) models, SUV39H1‐induced H3K9me3 enrichment at the transferrin receptor (Tfr1) promoter inhibits its transcription and subsequent iron uptake, thereby protecting neurons from ferroptosis [15]. In clear cell renal cell carcinoma (ccRCC), SUV39H1‐catalyzed H3K9me3 at the dipeptidyl peptidase 4 (DPP4) promoter suppresses its expression, which indirectly inhibits NADPH oxidase 1 (NOX1) activity and lipid peroxidation, thus inhibiting ferroptosis in tumor cells [16].

Beyond writers and erasers, H3K9me3 silencing signals are decoded by heterochromatin protein 1 (HP1) readers, namely CBX5 (HP1α), CBX1 (HP1β), and CBX3 (HP1γ), which bind H3K9me3 via chromodomains to compact chromatin and repress transcription. CBX3 suppresses ferroptosis by sustaining glutathione peroxidase 2 (GPX2) expression in colorectal cancer and GPX4 expression in lung adenocarcinoma [17, 18]. By contrast, CBX5 loss drives ferroptosis resistance in mantle cell lymphoma [19], whereas HP1 promotes ferroptosis in diabetic nephropathy by inhibiting the NRF2 pathway [20]. Consequently, HP1 readers represent additional therapeutic targets for ferroptosis‐related diseases.

Taken together, H3K9me2 promotes ferroptosis in various pathological models by repressing the transcription of negative regulators of ferroptosis. H3K9me3 bidirectionally regulates ferroptosis, depending on cell specificity and the target genes. Currently, the G9a inhibitor UNC0642 and BRD4770 can effectively inhibit ferroptosis by targeting the transcriptional repression of H3K9me2. Due to the critical role of H3K9me3 in the genomic stability of normal cells, there are no specific clinical targeting inhibitors available for H3K9me3.

2.1.2. H3K27me3 Bidirectionally Regulates Ferroptosis Through PRC2 and PRC1 Complexes

Histone H3 lysine 27 trimethylation (H3K27me3) mediates gene silencing by recruiting repressive complexes. Enhancer of zeste homolog 1 (EZH1) and enhancer of zeste homolog 2 (EZH2) are polycomb repressive complex 2 (PRC2) subtypes. EZH2 is the primary H3K27 methyltransferase, and it executes its methyltransferase function through the SET domain. EZH1 and EZH2 regulate ferroptosis in a context‐dependent manner through H3K27me3‐mediated transcriptional repression.

EZH1 exacerbates hepatocyte ferroptosis in sepsis‐related acute liver injury (SALI) through H3K27me3‐mediated silencing of nuclear factor erythroid 2‐related factor 2 (Nrf2), which disables the SLC7A11/GPX4 antioxidant axis by blocking both transcription and nuclear translocation [21]. EZH2 similarly promotes ferroptosis in other acute injuries, albeit through distinct target specificity. In HBV‐associated acute liver failure, the viral HBx protein recruits EZH2 to silence SLC7A11, thereby blocking cystine uptake [22], whereas SOX4‐dependent EZH2 recruitment suppresses the same anti‐ferroptotic gene in calcium oxalate‐induced kidney injury, sensitizing renal tubular epithelial cells to crystal deposition [23]. In sepsis‐induced acute lung injury (ALI), EZH2 promotes transcriptional silencing of the ubiquitin‐specific peptidase 10 (Usp10) promoter region by catalyzing H3K27me3 modification, indirectly enhancing the ubiquitin‐mediated degradation of GPX4, thus driving ferroptosis in alveolar epithelial cells [24]. Conversely, in hepatocellular carcinoma, EZH2 suppresses ferroptosis by inhibiting pro‐ferroptotic genes such as acyl‐CoA synthetase long chain family member 1 (ACSL1) (conferring resistance to lenvatinib) [25] and transferrin receptor 2 (TFR2) (conferring resistance to sorafenib) [26], thereby enhancing tumor cell resistance by inhibiting ferroptosis.

EZH1 and EZH2 mediate bidirectional regulation of ferroptosis in a context‐dependent manner through H3K27me3‐mediated epigenetic modifications. In acute tissue injuries, EZH1/EZH2 promote ferroptosis in normal cells by silencing anti‐ferroptotic genes (e.g., Nrf2, SLC7A11, Usp10). Conversely, in hepatocellular carcinoma, EZH1/EZH2 suppress pro‐ferroptosis genes (e.g., ACSL1, TFR2) to block lipid peroxidation, thereby enhancing the drug resistance of tumor cells.

The H3K27me3 mark is recognized by the CBX subunits (CBX2/4/6/7/8) within Polycomb Repressive Complex 1 (PRC1), thereby recruiting the complex to chromatin. This sequential recognition links PRC2‐mediated methylation to gene silencing. PRC2 acts as the writer and PRC1/CBX as the reader; both are necessary for the stable repression of ferroptosis‐related genes such as SLC7A11 in cancer cells [27, 28].

2.1.3. H3K4 Methylation Bidirectionally Regulates Ferroptosis in Different Cell Types via Specific Methyltransferases

Histone H3 lysine 4 methylation (H3K4me) is associated with transcriptional activation, primarily catalyzed by SET domain methyltransferases, including SETD1A, SETD1B, SETD7, and KMT2 family proteins. Recent studies have indicated that dysregulation of H3K4 methylation status is linked to ferroptosis resistance in malignant tumors, such as non‐small cell lung cancer (NSCLC) and esophageal squamous cell carcinoma (ESCC), as well as to neuronal damage mediated by ferroptosis in ischemic stroke. H3K4 methylation includes different forms such as monomethylation (H3K4me1) and trimethylation (H3K4me3), which exert distinct regulatory effects on ferroptosis, either promoting or inhibiting this process, depending on the cell type and specific molecular mechanism.

H3K4me3 can promote ferroptosis in normal cells under certain pathological conditions, such as myocardial ischemia‐reperfusion injury and ischemic stroke. H3K4me3 is catalyzed by methyltransferases such as lysine methyltransferase 2B (KMT2B), SET domain‐containing 1A (SETD1A), and SET domain‐containing 1B (SETD1B). In normal cells, the histone methyltransferase KMT2B catalyzes H3K4me3 modification at the promoter region of the riboflavin kinase (RFK) gene, promoting RFK transcription and mediating the TNF‐α/NOX2 axis, thereby exacerbating ferroptosis in myocardial ischemia‐reperfusion injury [29]. In the ischemic stroke model, the enrichment of H3K4me3 driven by SETD1B in the transferrin receptor (Tfrc) promoter region promotes neuronal ferroptosis [30].

Both H3K4me1 and H3K4me3 can inhibit ferroptosis in cancer cells, contributing to ferroptosis resistance and tumor progression, and in some cases, mediating resistance to radiotherapy and chemotherapy. H3K4me1 is primarily catalyzed by SETD7 and KMT2D, which mark transcription enhancers to activate genes that are involved in ferroptosis resistance. In ESCC, SETD7 deposits the H3K4me1 mark in the promoter region of aldehyde dehydrogenase 1A3 (ALDH1A3), directly activating the transcriptional expression of ALDH1A3, which facilitates the metabolic clearance of lipid peroxidation end products such as 4‐HNE, thereby inhibiting ferroptosis and mediating resistance to radiotherapy/chemotherapy [31]. In cutaneous squamous cell carcinoma (cSCC), tumor‐associated M2 macrophages deliver circ_0088494 to cancer cells via exosomes, recruiting KMT2D to the promoter region of Six‐transmembrane epithelial antigen of prostate 3 (STEAP3) and promoting H3K4me1 modification. This process maintains iron metabolic homeostasis and ultimately inhibits erastin‐induced ferroptosis [32]. In non‐small cell lung cancer (NSCLC), high expression of SETD1A mediates H3K4me3 modification at the WT1‐associated protein pseudogene 1 (WTAPP1) promoter region, suppressing lung cancer cell ferroptosis through the WTAPP1/WTAP axis [33].

In summary, targeting the H3K4 histone methyltransferases SETD7 or SETD1A can overcome tumor cell ferroptosis resistance. In contrast, selective inhibition of the histone methyltransferases SETD1B or KMT2B can protect normal cells from ferroptosis in neurodegenerative and ischemic diseases.

2.2. Histone Arginine Methylation in Ferroptosis

Histone arginine methylation occurs on both histone and non‐histone proteins and participates in various cellular functions, including RNA processing, DNA repair, and transcription. The methylation status of individual arginine residues exerts distinct transcriptional effects on adjacent chromatin regions. The sites and mechanisms of ferroptosis regulation by histone methylation are summarized in Table 1.

Table 1.

Histone methylation in ferroptosis.

Site	Enzyme	Target (s)	Effect	Mechanism	Ref
Lysine methylation
H3K9me2	G9a (writer)	GPX4, CBS, GCLC	Promote	Represses antioxidant gene expression, reduces GSH levels, promotes ferroptosis in neuronal cells	[10]
H3K9me2	G9a (writer)	SLC7A11	Promote	G9a cooperates with Bach1 to silence SLC7A11, promoting renal fibrosis	[12]
H3K9me2	G9a (writer)	SLC7A11	Promote	G9a‐mediated H3K9me2 suppresses SLC7A11 transcription, exacerbating vascular calcification	[13]
H3K9me3	SETDB1 (writer)	SNAI1	Promote	SETDB1‐catalyzed H3K9me3 represses SNAI1, blocking EMT and promoting ferroptosis in pulmonary fibrosis	[14]
H3K9me3	SUV39H1 (writer)	Tfr1	Inhibit	SUV39H1 deposits H3K9me3 to repress Tfr1, reducing iron uptake and ferroptosis in neurons	[15]
H3K9me3	SUV39H1 (writer)	DPP4	Inhibit	H3K9me3‐mediated DPP4 suppression reduces NOX1 activity and lipid peroxidation in ccRCC	[16]
H3K9me3	CBX3 (reader, HP1γ)	GPX2	Inhibit	CBX3 binds CUL3 promoter to prevent NRF2 degradation, sustaining GPX2 and suppressing ferroptosis in CRC	[17]
H3K9me3	CBX3 (reader, HP1γ)	GPX4	Inhibit	CBX3 cooperates with EP300 to upregulate GPX4, conferring ferroptosis resistance in CTCs during metastasis	[18]
H3K9me3	CBX5 (reader, HP1α)	—	Promote	CBX5 loss drives PI3Kδ inhibitor resistance; CAPE restores CBX5 expression to induce ferroptosis in MCL	[19]
H3K9me3	HP1 (reader)	NRF2	Promote	HP1 suppresses NRF2 pathway, inducing ferroptosis in renal tubular epithelial cells in diabetic nephropathy	[20]
H3K27me3	EZH1 (writer)	Nrf2	Promote	EZH1 silences Nrf2 via H3K27me3, impairing antioxidant defense and promoting hepatocyte ferroptosis	[21]
H3K27me3	EZH2 (writer)	SLC7A11	Promote	HBV HBx recruits EZH2 to silence SLC7A11, inducing ferroptosis in acute liver failure	[22]
H3K27me3	EZH2 (writer)	SLC7A11	Promote	SOX4‐dependent EZH2 recruitment suppresses SLC7A11, promoting ferroptosis in kidney injury	[23]
H3K27me3	EZH2 (writer)	USP10	Promote	EZH2‐mediated H3K27me3 silences USP10, promoting GPX4 degradation and ferroptosis in ALI	[24]
H3K27me3	EZH2 (writer)	ACSL1	Inhibit	EZH2 suppresses ACSL1 expression, conferring lenvatinib resistance in HCC	[25]
H3K27me3	EZH2 (writer)	TFR2	Inhibit	EZH2 represses TFR2 via H3K27me3, reducing ferroptosis sensitivity in HCC	[26]
H3K27me3	PRC1/CBX (reader)	SLC7A11	Promote	CBX subunits recognize H3K27me3, anchor PRC1, and deposit H2AK119ub1 to repress SLC7A11, enhancing ferroptosis sensitivity	[28]
H3K4me3	KMT2B (writer)	RFK	Promote	KMT2B promotes cardiomyocyte ferroptosis by catalyzing H3K4me3 at the RFK promoter and mediating the TNF‐α/NOX2 axis.	[29]
H3K4me3	SETD1B (writer)	Tfrc	Promote	SETD1B promotes H3K4me3 at Tfrc promoter, driving neuronal ferroptosis in ischemic stroke	[30]
H3K4me1	SETD7 (writer)	ALDH1A3	Inhibit	SETD7 deposits H3K4me1 to activate ALDH1A3, clearing lipid peroxidation products in ESCC	[31]
H3K4me1	KMT2D (writer)	STEAP3	Inhibit	M2 macrophage exosomes recruit KMT2D to deposit H3K4me1, activating STEAP3 and inhibiting ferroptosis in cSCC	[32]
H3K4me3	SETD1A (writer)	WTAPP1	Inhibit	SETD1A‐mediated H3K4me3 activates WTAPP1/WTAP axis, suppressing ferroptosis in NSCLC	[33]
Arginine methylation
H4R3me2a	PRMT1 (writer)	SLC7A11	Inhibit	PRMT1 deposits H4R3me2a to activate SLC7A11, conferring ferroptosis resistance in colorectal cancer	[34]
H4R3me2s	PRMT5 (writer)	ALKBH5	Inhibit	PRMT5‐mediated H4R3me2s silences ALKBH5, stabilizing SLC7A11 mRNA and suppressing ferroptosis	[35]
H4R3me2s	PRMT5 (writer)	SLC7A11	Inhibit	STC2 activates PRMT5 to deposit H4R3me2s, upregulating SLC7A11 and inducing radioresistance in ESCC	[36]
H4R3me2a	PRMT1 (writer); JMJD6 (eraser)	METTL14	Promote	JMJD6 removes H4R3me2a to suppress METTL14, activating METTL14/SLC3A2 axis and promoting ferroptosis in lung cancer	[37]
H3R2me2s	PRMT5 (writer)	GPX4, FTH1, Nrf2, SLC7A11	Inhibit	PRMT5 deposits H3R2me2s to maintain expression of anti‐ferroptosis genes, suppressing ferroptosis in HCC	[38]
H3R2me1	PRMT7 (writer)	RAP1A	Promote	PRMT7‐catalyzed H3R2me1 activates RAP1A, promoting monocyte infiltration and ACSL4‐driven ferroptosis in COPD	[39]

Abbreviations: Enzymes: ALKBH5, alkB homolog 5; CBX3, chromobox 3; CBX5, chromobox 5; EZH1, enhancer of zeste 1 PRC2 subunit; EZH2, enhancer of zeste 2 PRC2 subunit; G9a, euchromatic histone lysine methyltransferase 2 (EHMT2); HP1, heterochromatin protein 1; JMJD6, jumonji domain containing 6; KMT2B, lysine methyltransferase 2B; KMT2D, lysine methyltransferase 2D; METTL14, methyltransferase like 14; PRC1, polycomb repressive complex 1; PRMT1, protein arginine methyltransferase 1; PRMT5, protein arginine methyltransferase 5; PRMT7, protein arginine methyltransferase 7; RFK, riboflavin kinase; SETD1A, SET domain containing 1 A; SETD1B, SET domain containing 1B; SETD7, SET domain containing 7; SETDB1, SET domain bifurcated 1; SUV39H1, suppressor of variegation 3‐9 homolog 1. Genes: ACSL1, acyl‐CoA synthetase long chain family member 1; ALDH1A3, aldehyde dehydrogenase 1 family member A3; CBS, cystathionine beta‐synthase;CUL3, cullin 3;DPP4, dipeptidyl peptidase 4; FTH1, ferritin heavy chain 1; GCLC, glutamate‐cysteine ligase catalytic subunit;GPX2, glutathione peroxidase 2; GPX4, glutathione peroxidase 4; NOX1, NADPH oxidase 1; NRF2, nuclear factor erythroid 2‐related factor 2; PI3Kδ, phosphoinositide 3‐kinase δ;RAP1A, RAP1A member of RAS oncogene family; SLC3A2, solute carrier family 3 member 2; SLC7A11, solute carrier family 7 member 11;SNAI1, snail family transcriptional repressor 1; STEAP3, STEAP3 metalloreductase; TFR1, transferrin receptor 1; TFR2, transferrin receptor 2; USP10, ubiquitin specific peptidase 10; WTAPP1, WT1 associated protein pseudogene 1. Diseases: ALI, acute lung injury; ccRCC, clear cell renal cell carcinoma; COPD, chronic obstructive pulmonary disease; CRC, colorectal cancer; cSCC, cutaneous squamous cell carcinoma; CTC, circulating tumor cell; EMT, epithelial‐mesenchymal transition; ESCC, esophageal squamous cell carcinoma; HCC, hepatocellular carcinoma; MCL, mantle cell lymphoma; NSCLC, non‐small cell lung cancer. Other: CAPE, caffeic acid phenethyl ester.

2.2.1. H4R3me2 Inhibits Ferroptosis by Regulating the Transcription of Antioxidant Genes

Histone H4 arginine 3 dimethylation (H4R3me2) exists in two distinct forms: asymmetric dimethylation (H4R3me2a) is primarily catalyzed by protein arginine methyltransferase 1 (PRMT1), which mediates gene transcription activation, while symmetric dimethylation (H4R3me2s) is mainly catalyzed by protein arginine methyltransferase 5 (PRMT5), which mediates gene transcription repression. Jumonji domain‐containing protein 6 (JMJD6) can simultaneously remove both H3R2me2 and H4R3me2 modifications [40].

In colorectal cancer, PRMT1 is enriched in the promoter region of the SLC7A11 gene and catalyzes H4R3me2a, recruiting the transcription machinery to drive the high expression of SLC7A11, which endows colorectal cancer cells with resistance to ferroptosis [34]. PRMT5 directly inhibits transcription of the m⁶A demethylase ALKBH5 by inducing H4R3me2s modification, thereby enhancing SLC7A11 mRNA stability and expression. This promotes colorectal cancer progression by suppressing ferroptosis [35]. In esophageal squamous cell carcinoma (ESCC) cells, H4R3me2s is catalyzed by PRMT5, which alters the chromatin state and upregulates SLC7A11, thereby indirectly endowing the cells with the ability to resist ferroptosis [36]. In lung cancer, jumonji domain‐containing 6 (JMJD6) suppresses the transcription of methyltransferase‐like 14 (METTL14) by removing the H4R3me2a modification in the promoter region of METTL14. This, in turn, inhibits the METTL14‐SLC3A2 ferroptosis axis, thereby promoting ferroptosis in lung cancer cells and ultimately suppressing the progression of lung cancer [37].

Overall, H4R3me exerts a predominant anti‐ferroptotic effect in most tumor models. It mediates tumor cell resistance to ferroptosis through the direct or indirect modulation of genes involved in the antioxidant system, thereby promoting tumor pathology progression.

2.2.2. H3R2me Bidirectionally Regulates Ferroptosis via PRMT5 and PRMT7

Symmetric dimethylation of histone H3 at arginine 2 (H3R2me2s) is catalyzed by protein arginine methyltransferase 5 (PRMT5), whereas monomethylation of histone H3 at the same position (H3R2me1) is primarily catalyzed by protein arginine methyltransferase 7 (PRMT7). Both modifications play a crucial role in mediating gene transcription activation.

PRMT5‐mediated H3R2me2s functions to inhibit ferroptosis by upregulating key antioxidant and iron storage genes. In hepatocellular carcinoma (HCC), PRMT5‐mediated H3R2me2s is enriched in the promoter regions of GPX4, ferritin heavy chain 1 (FTH1), Nrf2, and SLC7A11, maintaining the high expression of genes that inhibit ferroptosis, thereby enabling cells to acquire resistance to ferroptosis. Following the use of the PRMT5‐specific inhibitor GSK3326595 in vitro, H3R2me2s levels decreased, and HCC cells became sensitive to ferroptosis inducers [38].

PRMT7‐mediated H3R2me1 acts to promote ferroptosis by driving pro‐ferroptotic signaling cascades in inflammatory lung disease. In chronic obstructive pulmonary disease (COPD), upregulation of the NF‐κB/RelA signaling pathway in macrophages induces the expression of PRMT7, which subsequently catalyzes H3R2me1 modification at regulatory elements of the RAP1A gene, thereby promoting RAP1A transcription. Elevated RAP1A expression accelerates monocyte adhesion and migration, leading to abnormal accumulation of macrophages in lung tissue. These accumulated macrophages upregulate ALOX5 and its metabolite leukotriene B4 (LTB4), activating ACSL4 and driving lipid peroxidation and ferroptosis, ultimately exacerbating tissue damage in COPD [39].

PRMT5 and PRMT7 bidirectionally regulate ferroptosis by mediating different methylation states of H3R2. In cancer therapy, inhibiting PRMT5 can break the resistance of tumors to ferroptosis; in inflammatory diseases, inhibiting PRMT7 can block tissue‐damaging ferroptosis.

2.3. Histone Acetylation Bidirectionally Regulates Ferroptosis

Histone acetylation promotes gene transcription via charge neutralization of lysine residues on histone tails, which weakens histone‐DNA interactions and relaxes chromatin structure. Histone acetyltransferases (HATs) and histone deacetylases (HDACs) jointly maintain the dynamic balance of acetylation levels. HATs primarily comprise three families: GCN5‐related N‐acetyltransferase (GNAT), MYST, and p300/CBP, whereas HDACs are classified into four classes based on sequence homology, catalytic mechanism, and subcellular localization.

2.3.1. H3K9ac Bidirectionally Regulates Ferroptosis by Distinct Enzymatic Identities

Histone H3 lysine 9 acetylation (H3K9ac), a promoter‐enriched transcriptional activation mark, bidirectionally regulates ferroptosis through activating ferroptosis‐related gene transcription, and this regulation is mediated by different types of epigenetic enzymes.

H3K9ac promotes ferroptosis mainly through the mediation of histone acetyltransferase Lysine acetyltransferase 2 A (KAT2A), a prototypical member of the GNAT family. In diabetic cardiomyopathy, KAT2A promotes enrichment of H3K9ac and H3K27ac at the promoter regions of Tfrc and heme oxygenase‐1 (HMOX1), thereby upregulating their expression and promoting ferroptosis [41].

H3K9ac inhibits ferroptosis through two main pathways mediated by Lysine acetyltransferase 6 A (KAT6A) and Histone deacetylase Sirtuin 6 (Sirt6), respectively. KAT6A, a MYST family histone acetyltransferase, preferentially catalyzes histone H3 lysine 9 (H3K9) acetylation [42]. KAT6A‐catalyzed H3K9 acetylation is one of the factors contributing to tumor cell resistance to ferroptosis. In colorectal cancer, KAT6A specifically enriches H3K9ac in the promoter region of GPX4 through its HAT domain, directly activating GPX4 transcription, inhibiting ferroptosis, and promoting malignant progression of tumors [43]. In pancreatic cancer, the circ_0005397/KAT6A axis regulates the enrichment of H3K9ac at the promoter of poly(rC) binding protein 2 (PCBP2), thereby activating the expression of PCBP2 and indirectly inhibiting ferroptosis [44]. Sirt6, a member of class III HDAC and the sirtuin family, can directly deacetylate H3K9ac, thereby inhibiting gene transcription. Liu et al. employed a multifunctional nanoenzyme drug delivery technology to load the Sirt6 allosteric activator MDL‐800, which specifically activates Sirt6‐mediated H3K9ac deacetylation. This activation subsequently initiates the downstream System Xc⁻‐GPX4‐GSH antioxidant pathway, ultimately achieving the inhibition of ferroptosis. This provides a novel targeted strategy for the treatment of early brain injury following subarachnoid hemorrhage [45].

In summary, histone acetyltransferase KAT2A mediates H3K9ac to promote ferroptosis by activating Tfrc/HMOX1, while KAT6A mediates H3K9ac to inhibit ferroptosis by activating GPX4/PCBP2. Additionally, histone deacetylase Sirt6 mediates H3K9 deacetylation to inhibit ferroptosis through activation of the System Xc⁻‐GPX4‐GSH antioxidant pathway. These studies indicate that ferroptosis is not determined by the H3K9ac mark itself, but rather by the identity of the epigenetic enzymes that write or erase this mark.

2.3.2. H3K27ac Bidirectionally Regulates Ferroptosis via Cell Context‐Dependent Pathways

Histone H3 lysine 27 acetylation (H3K27ac) promotes gene transcription by altering chromatin structure and recruiting transcriptional regulators, which exerts a bidirectional regulatory effect on ferroptosis.

Studies have shown that in various cancer cells, H3K27ac suppresses ferroptosis and promotes tumor cell proliferation and migration. Bromodomain‐containing protein 4 (BRD4) serves as a reader of H3K27ac by recognizing it through its bromodomain, and it also possesses histone acetyltransferase (HAT) activity. The bromodomain and extraterminal domain (BET) protein inhibitor (+)‐JQ1 reduces H3K27ac levels by inhibiting BRD4, leading to downregulation of the expression of anti‐ferroptotic genes GPX4, SLC7A11, and SLC3A2 and subsequent induction of ferroptosis in tumor cells [46]. Similarly, in breast cancer cells, the acetyltransferase KAT5 inhibitor ketamine promotes ferroptosis by reducing H3K27ac levels at the GPX4 promoter and thereby suppressing GPX4 transcription [47]. In NSCLC, the YEATS family histone reader GAS41 recognizes H3K27ac and interacts with Nrf2, leading to Nrf2 recruitment to the SLC7A11 promoter and subsequent suppression of ferroptosis [48].

Under specific conditions, however, H3K27ac can promote ferroptosis. For example, ferroptosis suppressor protein 1 (FSP1) is one of the main regulatory molecules of ferroptosis. FSP1 functions through the FSP1‐coenzyme Q10 (CoQ10)‐NAD(P)H axis and the vitamin K redox cycle. In colorectal cancer cells, histone deacetylase inhibitors (HDACi) such as vorinostat (SAHA) enhance ferroptosis sensitivity by targeting HDAC1 to promote H3K27ac enrichment at the FTO and ALKBH5 promoters. Activated FTO and ALKBH5 remove N6‐methyladenosine (m⁶A) modifications from FSP1 mRNA, reducing its stability and suppressing FSP1 expression, thereby sensitizing colorectal cancer cells to ferroptosis [49].

In summary, H3K27ac demonstrates a context‐dependent dual role in ferroptosis regulation. It can either activate anti‐ferroptotic genes (GPX4, SLC7A11) to inhibit ferroptosis in most tumors, or promote ferroptosis through the FTO/ALKBH5 pathway under conditions treated with HDAC inhibitors (such as vorinostat/SAHA).

2.4. Histone Ubiquitination Promotes Ferroptosis

Histone ubiquitination is a common epigenetic modification that serves as a core component of DNA damage repair and participates in the regulation of gene transcription. Ubiquitin, a 76‐amino acid protein, is covalently conjugated to specific lysine residues on core histones (H2A, H2B, H3, and H4) through enzymatic reactions. H2AK119ub1 is catalyzed by the polycomb repressive complex (PRC) and plays a central role in PRC‐mediated gene silencing, whereas H2BK120ub1 is associated with promoting gene transcription and constitutes an important component of the RNA polymerase II transcriptional elongation machinery [50].

2.4.1. H2AK119ub1 Promotes Ferroptosis via BAP1 Mediation

Monoubiquitination of histone H2A at lysine 119 (H2AK119ub1) is a key epigenetic mark through which the deubiquitinating enzyme BRCA1‐associated protein 1 (BAP1) regulates gene expression and ferroptosis. Integrative multi‐omics analysis has identified ACSL4 as a novel target gene of BAP1. By removing H2AK119ub1, BAP1 upregulates ACSL4 expression, thereby promoting lipid synthesis and increasing cellular sensitivity to ferroptosis [51]. Furthermore, BAP1 cooperates with the E3 ubiquitin ligase Polycomb Repressive Complex 1 (PRC1) to dynamically regulate H2AK119ub1 levels at the SLC7A11 promoter, leading to suppression of SLC7A11 expression and enhanced ferroptosis sensitivity in cancer cells [27].

2.4.2. H2BK120ub1 Promotes Ferroptosis via p53/USP7 Mediation

Monoubiquitination of histone H2B at lysine 120 (H2BK120ub1) is an epigenetic mark associated with transcriptional activation. The tumor suppressor p53 negatively regulates H2BK120ub1 levels at the SLC7A11 promoter by promoting nuclear translocation of the deubiquitinating enzyme ubiquitin‐specific peptidase 7 (USP7). Consequently, the ferroptosis inducer erastin enhances cellular sensitivity to ferroptosis through activation of the p53/USP7/H2BK120ub1 axis. Additionally, direct loss of H2BK120ub1 promotes ferroptosis by increasing intracellular labile iron concentrations via modulation of iron metabolism‐related gene expression [52].

2.5. Histone Phosphorylation (p‐H3S10) Promotes Ferroptosis by Activating Ferritinophagy

Histone phosphorylation is a dynamic modification occurring on serine, threonine, or tyrosine residues, coordinately regulated by kinases and phosphatases. Recent studies have shown that anisomycin induces phosphorylation of histone H3 serine 10 (p‐H3S10) by activating the p38 MAPK signaling pathway. This modification is primarily enriched at the promoter region of the nuclear receptor coactivator 4 (NCOA4) gene, upregulating NCOA4 expression and subsequently promoting ferritinophagy. This process enhances lipid peroxidation through the Fenton reaction, thereby inducing ferroptosis in hepatocellular carcinoma cells [53].

2.6. Histone Lactylation (H3K18la) Bidirectionally Regulates Ferroptosis via the Warburg Effect

Histone lactylation, a novel metabolic⁻epigenetic post‐translational modification, primarily occurs on lysine residues within the N‐terminal tail of histone H3. Under pathological conditions characterized by the Warburg effect, the resultant accumulation of lactate serves as a precursor for lactyl‐coenzyme A (lactyl‐CoA) synthesis. This process is enzymatically driven by "writers" such as the acyltransferase p300/CBP, whereas its removal is catalyzed by "erasers" including class I (HDAC1–3) and class III (SIRT1–3) histone deacetylases [54]. Studies on ACSS2 (acetyl‐CoA synthetase 2) and nuclear GTPSCS (GTP‐specific succinyl‐CoA synthetase) revealed how lactate signals are transmitted to chromatin. Upon EGFR‐ERK–mediated phosphorylation at S267, ACSS2 enters the nucleus, where it binds KAT2A and converts lactate into lactyl‐CoA—the donor for KAT2A‐driven histone lactylation [55]. Similarly, nuclear GTPSCS generates lactyl‐CoA to induce p300‐dependent histone lactylation [56]. Notably, H3K18la modulates ferroptosis in a context‐dependent manner to drive various pathologies.

In degenerative and inflammatory settings, H3K18la typically functions as a pro‐ferroptotic mediator. For instance, in intervertebral disc degeneration, H3K18la enrichment at the ACSL4 promoter upregulates its transcription and exacerbates ferroptosis in nucleus pulposus cells through enhanced phospholipid peroxidation [57]. Similarly, H3K18la promotes ferroptosis in acute pancreatitis and septic lung injury by activating NCOA4 and ACSL4 to facilitate ferritinophagy and lipid peroxide accumulation [58, 59].

Conversely, in the malignant microenvironment, H3K18la often functions as an anti‐ferroptotic mechanism to promote tumor survival. In ectopic endometrial stromal cells, H3K18la‐mediated activation of the methyltransferase‐like protein 3 (METTL3) promoter enhances hypoxia inducible factor 1 subunit alpha (HIF1A) mRNA stability and upregulates HMOX1 to confer ferroptosis resistance [60]. Furthermore, p300‐mediated H3K18la in colorectal cancer activates insulin‐like growth factor 2 mRNA binding protein 2 (IGF2BP2) transcription to stabilize Nrf2 mRNA and bolster antioxidant defenses [61]. This regulatory axis also extends to ovarian cancer, where H3K18la modulates STIL‐L (long isoform) gene splicing to favor the STIL‐L isoform and suppress ferroptosis, ultimately inducing cisplatin resistance [62]. How H3K18la is deposited at specific chromatin sites remains unclear. ACSS2‐KAT2A and GTPSCS‐p300 complexes are likely recruited to specific genomic regions through transcription factor‐mediated recruitment, with YEATS‐domain readers subsequently stabilizing the modification [63]. Nonetheless, H3K18la already serves as a key epigenetic node through which metabolic cues influence ferroptosis‐related gene expression in inflammatory and oncogenic contexts.

2.7. Histone β‐Hydroxybutyrylation (H3K9bhb) Inhibits Ferroptosis by Regulating Antioxidant Defense Genes

Lysine β‐hydroxybutyrylation (Kbhb) is a novel lysine acylation modification that utilizes β‐HB as its primary acyl donor. This modification is enzymatically installed on histone lysine residues by acyltransferases such as p300/CBP and can be removed by erasers including HDAC1‐3 and SIRT1‐3 [64]. ACSS2 also functions as a BHB‐CoA synthetase. Elevated β‐hydroxybutyrate promotes ACSS2 nuclear translocation, where it binds Lysine Acetyltransferase 7 (KAT7) and converts BHB into BHB‐CoA, fueling KAT7‐catalyzed H3K9bhb [65]. Downstream, this modification is recognized by ENL (eleven‐nineteen leukemia), the first identified reader for this modification [66].

Unlike the context‐dependent bidirectional regulation observed with H3K18la, histone H3 lysine 9 β‐hydroxybutyrylation (H3K9bhb) primarily exerts a protective role by inhibiting ferroptosis through increased chromatin accessibility and the subsequent transcriptional activation of suppressor genes such as GPX4, acyl‐CoA synthetase long chain family member 3 (ACSL3), and SLC7A11. For instance, in acute liver failure, the reduction of β‐hydroxybutyrate (BHB) production leads to diminished H3K9bhb levels in pancreatic tissue, which downregulates ferroptosis suppressors and exacerbates cellular damage [67]. In line with this, exogenous supplementation of BHB has emerged as a promising therapeutic strategy to selectively elevate H3K9bhb levels. In idiopathic pulmonary fibrosis, BHB‐induced H3K9bhb enrichment at the promoters of glutamate‐cysteine ligase catalytic subunit (GCLC) and GPX4 enhances glutathione synthesis and suppresses lipid peroxidation [68]. Similarly, BHB effectively attenuates ferroptosis in Parkinson's disease by upregulating the RNA‐binding protein ZFP36 and inhibiting ACSL4 expression [69]. Furthermore, BHB administration demonstrates renoprotective effects in acute kidney injury by restoring H3K9bhb levels to upregulate the SLC7A11/GPX4 axis [70]. Why H3K9bhb marks some genes but not others is unresolved. Collectively, H3K9bhb serves as a critical epigenetic defense mechanism that protects various tissues from oxidative stress and ferroptotic cell death. The regulation of ferroptosis by diverse histone modifications is summarized in Table 2.

Table 2.

Histone acetylation, ubiquitination, phosphorylation, lactylation and β‐hydroxybutyrylation in ferroptosis regulation.

Modification	Enzyme	Target (s)	Effect	Mechanism	Ref
Histone acetylation
H3K9ac	KAT2A (writer)	Tfrc, HMOX1	Promote	KAT2A deposits H3K9ac at Tfrc and HMOX1 promoters, upregulating iron uptake and heme oxygenase‐1, promoting ferroptosis in diabetic cardiomyopathy	[41]
H3K9ac	KAT6A (writer)	GPX4	Inhibit	KAT6A deposits H3K9ac at GPX4 promoter to inhibit ferroptosis	[43]
H3K9ac	KAT6A (writer)	PCBP2	Inhibit	KAT6A deposits H3K9ac at PCBP2 promoter to inhibit ferroptosis	[44]
H3K9ac	SIRT6 (eraser)	SLC7A11, GPX4	Inhibit	SIRT6 deacetylates H3K9ac, suppressing SLC7A11 and GPX4 transcription; allosteric activator MDL‐800 activates System Xc‐‐GPX4‐GSH axis to inhibit ferroptosis in subarachnoid hemorrhage	[45]
H3K27ac	BRD4 (reader)	GPX4, SLC7A11, SLC3A2	Inhibit	BRD4 recognizes H3K27ac to maintain anti‐ferroptotic gene expression; BET inhibitor (+)‐JQ1 blocks this axis, inducing ferroptosis	[46]
H3K27ac	KAT5 (writer)	GPX4	Inhibit	KAT5 catalyzes H3K27ac at GPX4 promoter, upregulating GPX4 and inhibiting ferroptosis in breast cancer; ketamine reduces KAT5 recruitment	[47]
H3K27ac	GAS41 (reader)	SLC7A11	Inhibit	GAS41 recognizes H3K27ac and anchors NRF2 to SLC7A11 promoter, maintaining SLC7A11 expression and suppressing ferroptosis in lung cancer	[48]
H3K27ac	HDAC1 (eraser)	FTO, ALKBH5	Promote	HDAC1 inhibition (SAHA) increases H3K27ac at FTO and ALKBH5 promoters, reducing FSP1 expression via m6A demethylation and enhancing ferroptosis sensitivity in colorectal cancer	[49]
Histone ubiquitination
H2AK119ub1	BAP1 (eraser)	ACSL4	Promote	BAP1 removes H2AK119ub1, increasing chromatin accessibility and ACSL4 expression, promoting PUFA esterification and ferroptosis sensitivity	[51]
H2AK119ub1	BAP1 (eraser); PRC1 (writer)	SLC7A11	Promote	BAP1 and PRC1 dynamically regulate H2A ubiquitination at SLC7A11 promoter, suppressing its expression and enhancing ferroptosis sensitivity in cancer cells	[27]
H2BK120ub1	USP7 (eraser)	SLC7A11	Promote	Erastin induces p53‐USP7 binding and USP7 nuclear translocation, removing H2BK120ub1 from SLC7A11 gene, suppressing its expression and promoting ferroptosis	[52]
Histone phosphorylation
p‐H3S10	p38 MAPK (kinase)	NCOA4	Promote	Anisomycin activates p38 MAPK, phosphorylating H3S10 at NCOA4 promoter, upregulating NCOA4 to promote ferritinophagy and ferroptosis in HCC	[53]
Histone lactylation
H3K18la	p300 (writer); HDAC1‐3, SIRT1‐3 (erasers)	ACSL4	Promote	Lactate upregulates ACSL4 via H3K18la and downregulates SIRT3 through microRNA‐708‐5p, inducing ferroptosis in nucleus pulposus cells	[57]
H3K18la	—	ACSL4, NCOA4	Promote	H3K18la activates NCOA4 and ACSL4, promoting ferritinophagy and lipid peroxidation in acute pancreatitis and septic lung injury	[58, 59]
H3K18la	—	METTL3	Inhibit	Lactate upregulates METTL3 via H3K18la; METTL3 activates HIF1A/HMOX1 axis via m6A, suppressing ACSL4 and inducing SLC7A11/GPX4 expression, conferring ferroptosis resistance in endometriosis	[60]
H3K18la	p300 (writer)	IGF2BP2	Inhibit	p300 mediates H3K18la at IGF2BP2 promoter, activating its transcription; IGF2BP2 stabilizes NRF2 mRNA, suppressing ferroptosis in colorectal cancer	[61]
H3K18la	—	STIL	Inhibit	H3K18la promotes TRA2A‐mediated alternative splicing of STIL to produce long isoform STIL‐L, which inhibits ferroptosis and confers cisplatin resistance in ovarian cancer	[62]
Histone Lysine β‐hydroxybutyrylation
H3K9bhb	p300 (writer); HDAC1/2, SIRT3 (erasers)	GPX4, ACSL3, SLC7A11	Inhibit	β‐HB deficiency reduces H3K9bhb, impairing chromatin accessibility and expression of ferroptosis suppressor genes, leading to pancreatic ferroptosis in acute liver failure	[67]
H3K9bhb	—	GPX4, GCLC, FSP1	Inhibit	Promoting the transcription of antioxidant genes GPX4, GCLC, and FSP1 reduces lipid peroxidation and inhibits ferroptosis.	[68]

Abbreviations: Enzymes: BAP1, BRCA1 associated protein 1; BRD4, bromodomain containing 4; FTO, FTO alpha‐ketoglutarate dependent dioxygenase; GAS41, glioma amplified sequence 41; HDAC1, histone deacetylase 1; HDAC3, histone deacetylase 3; KAT2A, lysine acetyltransferase 2 A; KAT5, lysine acetyltransferase 5; KAT6A, lysine acetyltransferase 6 A; METTL3, methyltransferase like 3; p300, E1A binding protein p300; p38 MAPK, p38 mitogen‐activated protein kinase; SIRT1, sirtuin 1; SIRT3, sirtuin 3; SIRT6, sirtuin 6; USP7, ubiquitin specific peptidase 7. Genes: ACSL3, acyl‐CoA synthetase long chain family member 3; ACSL4, acyl‐CoA synthetase long chain family member 4; FSP1, ferroptosis suppressor protein 1; HIF1A, hypoxia inducible factor 1 subunit alpha; HMOX1, heme oxygenase 1; IGF2BP2, insulin like growth factor 2 mRNA binding protein 2; NCOA4, nuclear receptor coactivator 4; PCBP2, poly(rC) binding protein 2; STIL, STIL centriolar assembly protein; TRA2A, transformer 2 alpha homolog. Other: BET, bromodomain and extraterminal domain; CoQ10, coenzyme Q10; GSH, glutathione; HDACi, histone deacetylase inhibitor; m⁶A, N6‐methyladenosine; NADPH, nicotinamide adenine dinucleotide phosphate; PUFA, polyunsaturated fatty acid; SAHA, vorinostat.

3. Crosstalk of HPTMs Mediates Ferroptosis

The transcriptional regulation of ferroptosis genes depends not only on individual histone modifications but also on a dynamic crosstalk network. This network operates through competitive and cooperative mechanisms among various types of histone modifications, collectively orchestrating the expression of ferroptosis genes (Figure 1).

Figure 1.

Histone post‐translational modifications crosstalk in ferroptosis. (A) Intra‐nucleosome crosstalk. Modifications on the same nucleosome interact through competition between H3K27ac and H3K27me3, and cross‐tail cooperation (H2BK120ub1 and H3K4me3; H3K9ac and H3K4me3). (B) Inter‐nucleosome propagation. Repressive marks (H3K9me2 and H3K27me3) spread through read‐write feedback loops (G9a‐GLP and PRC2/EZH2), while activating domains are maintained by BRD4 recognizing H3K27ac on multiple nucleosomes through cooperative assembly. PRC2, polycomb repressive complex 2; TFR2, transferrin receptor 2; TFRC, transferrin receptor 1; G9a‐GLP, G9a and G9a‐like protein; PRC/EZH2, polycomb repressive complex/enhancer of zeste homolog 2; BRD4, bromodomain‐containing protein 4; GPX4, glutathione peroxidase 4; SLC7A11, solute carrier family 7 member 11; SLC3A2, solute carrier family 3 member 2. This image was authorized to be drawn by Figdraw with authorization ID: OATTYd033b.

3.1. Crosstalk of HPTMs Within Individual Nucleosomes

Multiple histone modifications that co‐occur on the same nucleosome engage in crosstalk through two fundamental modes: competitive antagonism at shared residues and synergistic recruitment across sites.

3.1.1. Competitive Modifications at Shared Residues Determine Ferroptosis Gene Transcription

The antagonistic balance between H3K27me3 and H3K27ac regulates the transcription of iron metabolism genes, thereby dictating ferroptosis outcomes in a tumor type‐dependent manner. In HCC, EZH2, the catalytic subunit of PRC2, deposits H3K27me3 at the TFR2 promoter to antagonize H3K27ac, thereby reducing RNA polymerase II occupancy, silencing TFR2 transcription, suppressing ferroptosis, and conferring sorafenib resistance [26]. In diffuse large B‐cell lymphoma (DLBCL), EZH2 inhibitors reduce H3K27me3 and enrich H3K27ac at the TFRC promoter, driving iron influx. However, concurrent stabilization of GPX4 via Heat Shock Protein Family A Member 5 (HSPA5) upregulation offsets this pro‐ferroptotic effect. Co‐treatment with erastin restores ferroptosis sensitivity [71].

3.1.2. Cooperative Cross‐Tail Modifications Orchestrate Ferroptosis‐Related Genes Expression

Within individual nucleosomes, sequential recruitment of epigenetic enzymes to different histone tails forms a signaling cascade. The microsporidian effector EnP1 translocates to the host nucleus, binds with H2B, and disrupts H2BK120ub1. This reduces H3K4me3, downregulates p53, and derepresses SLC7A11, thereby inhibiting host cell ferroptosis and promoting parasite proliferation [72]. H3K9ac and H3K4me3 are well‑established histone marks linked to transcriptional activation. In A549 cells, five activating histone modifications, including H3K9ac, H3K4me3, H3K4me2, H3K4me1, and H3K27ac, co‑occupy the promoter region of phosphogluconate dehydrogenase (PGD), a key ferroptosis‑related gene in lung adenocarcinoma [73]. In sickle cell erythroblasts, dimethyl fumarate enhances both H3K9ac and H3K4me3 at the cystathionine beta‐synthase (CBS) gene, activating the transsulfuration pathway to protect against ferroptosis [74]. The enzymatic regulators governing cross‑tail crosstalk among distinct histone modifications during ferroptosis remain poorly characterized and require further mechanistic investigation.

3.2. Crosstalk of HPTMs Across Nucleosomes

Histone modifications propagate beyond individual nucleosomes through read‐write feedback, remodeling chromatin domains that determine ferroptosis gene expression.

3.2.1. Repressive Modification Spreading Across Nucleosomes Dictates Ferroptosis Gene Expression Programs

Repressive histone modifications spread across nucleosomes to expand silencing domains and inhibit target genes. The G9a‐GLP complex mediates nucleosomal H3K9me2 propagation, predominantly silencing antioxidant genes. In multiple sclerosis, the expanding H3K9me2 domain silences GPX4, CBS, and GCLC simultaneously, impairing glutathione synthesis and lipid peroxide clearance [10]. Likewise, PRC2 spreads H3K27me3 through a read‐write loop in which the EED subunit recognizes existing H3K27me3 and allosterically activates EZH2 to methylate H3K27 on adjacent nucleosomes [28]. Its defining feature is that multiple ferroptosis genes are silenced in a coordinated manner. EZH2 simultaneously silences GPX4 and SLC7A11 in rheumatoid arthritis and polycystic kidney disease [75, 76], and silences ACSL1 and TFR2 in hepatocellular carcinoma [25, 26].

3.2.2. Activating Modification Propagation Across Nucleosomes Determines Ferroptosis Sensitivity

Activating domains form when a reader recognizes identical modifications on adjacent nucleosomes and recruits writers to reinforce the signal. BRD4‑anchored super‑enhancers exemplify this mechanism, wherein BRD4 binds H3K27ac over broad genomic intervals via its tandem bromodomains to nucleate transcriptional condensates for sustaining target‑gene expression. In ferroptosis, GPX4, SLC7A11, and SLC3A2 reside within BRD4‐bound super‐enhancers in multiple cancers. The BET inhibitor JQ1 displaces BRD4 from these domains, downregulating all three genes and sensitizing tumor cells to ferroptosis [46]. Whether other readers build similar activating domains at different ferroptosis gene clusters is not known.

Taken together, intranucleosomal crosstalk governs the local expression status of individual ferroptosis genes, whereas internucleosomal propagation translates such regulatory signals into coordinated gene network outputs across chromatin domains.

4. HPTMs Mediate Ferroptosis in Clinical Diseases

Ferroptosis, as an important form of programmed cell death, is subject to epigenetic regulatory mechanisms that play critical roles in various disease processes. HPTMs are closely linked to tissue damage, immune responses, and therapeutic outcomes through the dynamic regulation of ferroptosis‐related gene expression. The following sections will elaborate on the specific mechanisms and pathological implications of HPTMs‐mediated ferroptosis regulation in infectious diseases, tumors, and noninfectious chronic diseases, respectively.

4.1. Pathogens Infections Mediate HPTMs and Ferroptosis

HPTMs are involved in the pathogenic processes of pathogens by modulating ferroptosis‐related genes. For instance, certain viruses, bacteria, and parasites can induce histone post‐translational modifications by encoding effector proteins, thereby targeting the ferroptosis pathway to create favorable conditions for their survival and immune evasion, as illustrated in Figure 2.

Figure 2.

Molecular mechanisms of pathogens‐mediated HPTMs in regulating host cell ferroptosis. Schematic illustration of how viral (Hepatitis B virus [HBV], Human papillomavirus [HPV]), bacterial (Mycobacterium tuberculosis [M. tuberculosis]), and parasitic (Encephalitozoon hellem [E. hellem]) pathogens manipulate host histone modifications to modulate ferroptosis‐related gene expression, thereby promoting pathogen survival or tissue damage. EZH2, enhancer of zeste homolog 2; ESCO1, establishment of sister chromatid cohesion N‐acetyltransferase 1; PRMT6, protein arginine methyltransferase 6; RNF20, ring finger protein 20; TUBORF, TUBA3FP open reading frame; p53, tumor protein p53. This image was authorized to be drawn by Figdraw with authorization ID: ATTOO8aa97.

4.1.1. Virus Infections Mediate HPTMs and Ferroptosis

Hepatitis B virus (HBV)‐encoded X protein (HBx) is a key factor in its pathogenesis. Liu et al. demonstrated that HBx recruits EZH2 to catalyze H3K27me3 at the SLC7A11 promoter, downregulating its expression and promoting hepatocyte ferroptosis, thereby exacerbating acute liver injury [22].

In human papillomavirus (HPV)‐associated cervical cancer, the viral oncoproteins E6 and E7 recruit the acetyltransferase establishment of cohesion 1 homolog 1 (ESCO1) to induce H3K27ac modification at the enhancer region of TUBORF, a peptide encoded by the host long non‐coding RNA TUBA3FP. This modification promotes the degradation of the immunity‐related GTPase Q (IRGQ) protein and suppresses ferroptosis by modulating the expression of key ferroptosis‐related proteins such as SLC7A11 and GPX4. Targeting TUBORF or ESCO1 enhances the anti‐tumor efficacy of paclitaxel, offering a potential therapeutic target for cervical cancer treatment [77].

4.1.2. Bacterial Infections Mediate HPTMs and Ferroptosis

The effector protein PtpA secreted by Mycobacterium tuberculosis (M. tuberculosis) targets the host protein arginine methyltransferase PRMT6 to catalyze H3R2me2a modification. This modification is enriched at the GPX4 promoter and represses its transcription, leading to accumulation of lipid peroxides and subsequent induction of ferroptosis and tissue necrosis, thereby enhancing Mtb pathogenicity and dissemination [78].

4.1.3. Parasite Infections Mediate HPTMs and Ferroptosis

Encephalitozoon hellem (E. hellem) secretes the nuclear‐localized effector protein EnP1, which directly binds to host histone H2B and downregulates the positive ferroptosis regulator p53. This specifically interferes with H2B monoubiquitination (H2BK120ub1), a modification that suppresses p53 gene expression and subsequently downregulates SLC7A11. By inhibiting ferroptosis in host cells, this mechanism creates a favorable environment for intracellular pathogen survival and replication [72].

4.2. HPTMs Mediate Ferroptosis in Cancer

Ferroptosis, widely studied in tumors and closely related to tumor cell proliferation, survival, and metastasis, is only partially summarized herein. Targeting key histone‐modifying enzymes, such as HDACs, PRMTs, G9a, and KMT2D, can alter the sensitivity of tumor cells to ferroptosis, thereby influencing tumor initiation and progression. Therefore, combining histone‐modifying enzyme inhibitors with ferroptosis inducers represents a promising therapeutic strategy for cancer. The specific mechanisms of HPTMs regulating ferroptosis in malignant tumors are illustrated in Figure 3.

Figure 3.

HPTMs‐mediated ferroptosis sensitivity and resistance in tumors. Overview of epigenetic mechanisms in colorectal cancer (CRC), cutaneous squamous cell carcinoma (cSCC), hepatocellular carcinoma (HCC), and breast cancer (BC). Drugs or exogenous factors (SAHA, M2 exosomes, ketamine) modulate histone‐modifying enzymes, altering ferroptosis sensitivity. HDAC1, histone deacetylase 1; PRMT5, protein arginine methyltransferase 5; KMT2D, lysine methyltransferase 2D; HMGCL, 3‐hydroxy‐3‐methylglutaryl‐CoA lyase; KAT5, lysine acetyltransferase 5; ALKBH5, alkB homolog 5; STEAP3, six‐transmembrane epithelial antigen of prostate 3 metalloreductase; DPP4, dipeptidyl peptidase 4. This image was authorized to be drawn by Figdraw with authorization ID: AUTAIb4e4a.

4.2.1. Colorectal Cancer (CRC)

CRC exhibits a certain degree of resistance to ferroptosis, a characteristic that limits the application of related therapeutic strategies. Studies have shown that the HDAC1 inhibitor SAHA targets HDAC1 to activate the H3K27ac‐FTO/ALKBH5‐FSP1 axis, thereby enhancing the sensitivity of colorectal cancer cells to ferroptosis. Combined treatment with an HDAC1 inhibitor and the ferroptosis inducer RSL3 significantly increases cancer cell death [49]. Notably, the net effect of HDAC inhibitors is dependent on the tumor microenvironment and the corresponding cellular state. Further research by Wei et al. revealed that in 3D soft fibrin gel‐cultured CRCs, SAHA induces histone H3 acetylation, activating the WNT/β‐catenin signaling pathway. This activation triggers a mixed epithelial‐mesenchymal transition phenotype and upregulates GPX4 and ferritin expression, increasing resistance to RSL3 in colorectal cancer by two to threefold [79]. In addition to targeting histone deacetylases, PRMT5 also serves as a potential therapeutic target in colorectal cancer. PRMT5 suppresses ferroptosis and consequently promotes colorectal cancer progression by activating the PRMT5/ALKBH5/SLC7A11 axis [35].

4.2.2. cSCC

cSCC is a common type of skin cancer worldwide. Yin et al. demonstrated that M2 macrophage‐derived exosomes (circ_0088494) recruit the histone methyltransferase KMT2D to induce H3K4me1 at the six‐transmembrane epithelial antigen of the prostate 3 (STEAP3) promoter, thereby suppressing ferroptosis and driving tumor progression [32]. This suggests that KMT2D inhibitors may block this epigenetic regulatory pathway, thereby inducing ferroptosis in cSCC.

4.2.3. Hepatocellular Carcinoma (HCC)

HCC ranks as the third leading cause of cancer‐related deaths worldwide. Studies have shown that downregulation of 3‐hydroxy‐3‐methylglutaryl‐CoA lyase (HMGCL) is a characteristic feature of HCC proliferation and metastasis. HMGCL increases β‐HB levels and promotes H3K9 acetylation, driving DPP4 transcription. DPP4, a key regulator of iron accumulation and lipid peroxidation, mediates ferroptosis via the HMGCL‐DPP4 axis, thereby overcoming resistance to sorafenib and erastin in HCC [80].

4.2.4. Breast Cancer (BC)

BC is a prevalent malignancy among women worldwide. Ketamine, a commonly used clinical anesthetic, exhibits potential anti‐tumor activity beyond its anesthetic effects. Li et al. demonstrated that ketamine suppresses KAT5 recruitment to the GPX4 promoter, decreasing H3K27ac and subsequently downregulating GPX4 [47].

4.3. HPTMs Mediate Ferroptosis in Noninfectious Chronic Diseases

Beyond pathogen infection and tumor progression, HPTMs also drive chronic disease progression via epigenetic regulation of ferroptosis. These include COPD, renal fibrosis, and multiple sclerosis. Studies have shown that inhibiting enzymes such as PRMT7 and G9a can restore antioxidant defenses and block ferroptosis in animal models, underscoring the potential of targeting the “epigenetics–ferroptosis” axis in chronic disease intervention. The specific mechanisms of HPTMs regulating ferroptosis in various chronic diseases are illustrated in Figure 4.

Figure 4.

Schematic diagram of HPTMs‐mediated ferroptosis regulation in chronic diseases. Disease‐specific mechanisms in COPD, renal fibrosis, and multiple sclerosis (MS). Environmental triggers (smoking) or pathological conditions upregulate methyltransferases (PRMT7, G9a), leading to repressive histone marks that suppress antioxidant genes and promote ferroptosis. PRMT7, protein arginine methyltransferase 7; G9a, euchromatic histone‐lysine N‐methyltransferase 2 (EHMT2); RAP1A, RAP1A member of RAS oncogene family; ALOX5, arachidonate 5‐lipoxygenase. This image was authorized to be drawn by Figdraw with authorization ID: URSWY4c4d3.

4.3.1. COPD

COPD is a highly prevalent chronic inflammatory disease of the airways and alveoli, leading to irreversible and progressive airflow limitation. In COPD, smoking activates the NF‐κB/RelA signaling pathway in monocytes, directly upregulating PRMT7 expression. PRMT7 subsequently catalyzes H3R2me1 and H3R2me2 modifications at the RAP1A promoter, promoting monocyte migration to lung tissue and their differentiation into inflammatory macrophages. These macrophages release LTB4, which acts on alveolar type II epithelial cells (AT2) to induce ACSL4 expression and lipid peroxidation, sensitizing them to ferroptosis and ultimately driving alveolar destruction and emphysema progression [39]. These findings reveal a central role for PRMT7 in COPD pathogenesis and highlight its potential as a therapeutic target.

4.3.2. Renal Fibrosis

Renal fibrosis serves as a common pathway for the progression of multiple nephropathies to end‐stage renal disease. Notably, G9a expression is significantly elevated in renal fibrosis patients and mouse models. Mechanistically, G9a interacts with Bach1 and catalyzes H3K9me2 at the SLC7A11 promoter, suppressing its transcription and triggering ferroptosis [12].

4.3.3. Multiple Sclerosis (MS)

MS is a neuroimmune disease featuring CNS inflammatory demyelination. Pathologically, increased G9a methyltransferase activity promotes H3K9me2‐mediated repression of GPX4, triggering neuronal ferroptosis and driving neuroinflammatory injury. Notably, pharmacological inhibition of G9a with UNC0642 reinstates antioxidant function and abrogates ferroptosis, highlighting a potential therapeutic strategy [10].

5. Methodological Limitations and Challenges in Clinical Translation

5.1. Methodological Limitations

HPTM‐ferroptosis research faces methodological limitations. Most evidence comes from chromatin immunoprecipitation (ChIP)‐based assays, where antibody specificity remains a concern. Pharmacological inhibitors, another common tool, also carry inherent limitations. Shah et al. found that many commercial antibodies poorly distinguish between H3K4 methylation states (me1/me2/me3), leading to divergent biological interpretations [81]. Similarly, many histone methyltransferase inhibitors, such as UNC0379 and BRD4770, exhibit off‐target effects [82, 83]. These off‐target effects make it difficult to assign a ferroptosis phenotype to a single histone modification with confidence. Where possible, genetic strategies such as knockdown, knockout, or catalytically inactive mutants provide a more direct test of causality.

5.2. Challenges in Clinical Translation

The translation of HPTM‐ferroptosis biology into clinical application faces several challenges. Ferroptosis inducers such as Erastin and RSL3 are not tissue‐selective. Erastin is poorly water‐soluble and nephrotoxic, whereas RSL3 is metabolically unstable; newer analogs have improved pharmacokinetics, but the selectivity problem remains unsolved [84]. Additionally, epigenetic inhibitors commonly cause hematologic and gastrointestinal toxicities [85]. When combined with a ferroptosis inducer, these adverse effects would expose proliferating tissues to both epigenetic and oxidative stress. Furthermore, there are no specific biomarkers to predict the efficacy of epigenetic‐ferroptosis combination therapy in clinical translation. Measuring histone marks at specific gene promoters in clinical samples is technically demanding and not part of routine pathological practice [86]. Cancer cells possess multiple ferroptosis defense systems. It remains unclear whether these pathways mediate resistance to the combinatorial treatment or whether prolonged inhibitor exposure remodels chromatin to reactivate resistance‐related genes.

6. Conclusions and Perspectives

Since the concept of ferroptosis was proposed, its epigenetic regulatory mechanisms have become a focus of research in the life sciences. HPTMs, a core component of epigenetic regulation, form a multi‐dimensional and dynamic regulatory network. By altering chromatin structure and modulating the expression of key ferroptosis‐related genes (e.g., GPX4, SLC7A11, ACSL4), it plays a critical role in disease pathogenesis and progression. The regulatory characteristics can be summarized as follows: multiple HPTMs can coordinately regulate the same key molecule, such as the synergistic regulation of GPX4 expression by both histone methylation and acetylation in tumor cells; Ferroptosis occurrence depends not only on the level of a single HPTM but also on the dynamic balance between modification and removal, as exemplified by the precise regulation of SLC7A11 transcriptional activity through dynamic ubiquitination and deubiquitination of H2AK119ub1; furthermore, metabolism‐associated modifications such as histone lactylation and β‐hydroxybutyrylation directly link cellular metabolic states to epigenetic control, enriching the metabolic‐epigenetic crosstalk network in ferroptosis. Currently, some drugs targeting epigenetic regulators have been successfully applied in the clinical treatment of hematologic malignancies, providing new insights for the therapy of related diseases.

Although the role of HPTMs in ferroptosis regulation is increasingly being uncovered, the underlying mechanisms remain incompletely elucidated. First, the crosstalk mechanisms among different HPTMs are still unclear, and their synergistic or antagonistic patterns under specific physiological and pathological contexts require further investigation. Second, research on the association between novel histone modifications and ferroptosis is limited, and their regulatory mechanisms and biological functions remain to be elucidated. Moreover, the enzymes discussed herein also modify non‐histone substrates; for instance, CBP/p300 acetylates over 200 non‐histone proteins including transcription factors [87], and EZH2 methylates non‐histone targets such as signal transducer and activator of transcription 3 (STAT3) and GATA binding protein 4 (GATA4) [88]. While beyond the scope of this histone‐focused review, this integrated PTM network warrants future investigation. The clinical translation of HPTMs‐mediated ferroptosis regulation still faces challenges, and combination therapies involving modifying enzyme inhibitors and ferroptosis inducers require more clinical data for support. Future efforts should integrate multi‐omics and multidisciplinary approaches to elucidate the molecular mechanisms and biological functions underlying HPTMs‐mediated ferroptosis. Such endeavors will facilitate the clinical translation of targeted strategies and ultimately provide new theoretical frameworks and therapeutic avenues for ferroptosis‐related diseases.

Declaration of Generative AI and AI‐Assisted Technologies in the Writing Process

The authors declare that no Gen AI was used in the creation of this manuscript.

Author Contributions

Xiaoqian Tang: writing – review and editing, writing – original draft. Haodang Luo: writing – review and editing. Siqi Gao: writing – review and editing. Xiaocheng Liu: writing – review and editing. Qing Sun: writing – review and editing. Yanhua Zeng: Proposing the concept and general outline of this review – review and editing.

Conflicts of Interest

The authors declare no conflicts of interest.

Tang X., Luo H., Gao S., Liu X., Sun Q., and Zeng Y., “Histone Post‐Translational Modifications Regulating Ferroptosis: The Molecular Mechanisms and Disease Associations,” Cell Biochemistry and Function 44 (2026): e70300. 10.1002/cbf.70300.

Data Availability Statement

Data sharing is not applicable to this article as no datasets were generated or analyzed during the current study.