lymphocytes are the core component of the adaptive immune system, essential for various functions including infection resistance, anti-tumor immunity, and immune regulation (1). Recent years, an increasing number of studies have focused on a distinct lineage of memory T cells which was defined as tissue-resident memory T cells (TRM) (2). Distinct from central memory T cells (TCM) and effector memory T cells (TEM) which engage in the recirculation through the blood and lymphoid organs, TRM are primarily localized to specific organs such as skin, lung, liver, and small intestine (3). This residency property mainly ascribes to low expression of C-C chemokine receptor type 7, sphingosine-1-phosphate receptor 1 (S1PR1) (4) and CD62L, which are critical for the egress of TCM and TEM from peripheral tissues. Notably, TRM are not a single entity. Despite considerable overlap, CD4⁺and CD8⁺TRM exhibit lineage-specific features and regulatory differences that are influenced by both the tissue niche and the disease setting (5). There is substantial phenotypic heterogeneity, but TRM commonly express specific cell surface markers such as C-type lectin CD69 and integrin α E (CD103), which facilitate their maintenance in tissues and play a role in modulating their functional responses (2). Due to this specificity, TRM play a first-line role in the body’s resistance to foreign pathogen invasion and anti-tumor immunity (6). However, recent studies have highlighted that dysregulation or excessive activation of TRM can contribute to autoimmune diseases (7–9). Thus, TRM are considered as a potential target of several chronic recurrent inflammatory diseases, most notably inflammatory bowel disease, psoriasis and rheumatoid arthritis. Due to the importance of TRM in disease onset and relapse, it is necessary to explore the detailed mechanism of TRM regulation in order to find a viable way to cure diseases.

Regulation mechanisms of TRM encompass various aspects of cellular life cycle including formation, maintenance, and function in the previous studies (2). Thus far, substances like transcription factors, cytokines, tissue-specific cell adhesion molecules and anatomic compartments are well-established influencing factors in the regulation processes of TRM (10). Recent study have demonstrated that TRM display a unique epigenetic landscape amidst memory T cell subsets (11). However, the epigenetic characteristics behind all these influencing factors have not received as much attention. Understanding these epigenetic characteristics could provide deeper insights into how TRM are regulated and may reveal novel avenues for therapeutic intervention. Emerging evidence indicates that the tissue microenvironment plays a pivotal role in shaping the epigenetic landscape of TRM. Local cues such as cytokines, metabolites, and stromal cell-derived signals can influence chromatin accessibility, DNA methylation, and histone modifications in TRM and their precursors, thereby guiding their differentiation and maintenance within specific tissues (12). These microenvironmental signals integrate with intrinsic transcriptional programs to generate distinct, tissue-adapted epigenetic profiles, underpinning the functional heterogeneity of TRM across different organs.

The central dogma of molecular biology posits that DNA undergoes self-replication, transcription into RNA, and subsequent translation into proteins (13). Each of these processes is regulated by various factors, which can modulate the expression levels of specific proteins. This regulatory mechanism which enables cells with identical DNA sequences to undergo differential development and differentiation is referred to as epigenetic modification (14). Divergent from genetic changes, epigenetic modifications regulate gene expression and cellular phenotypes dynamically without altering the DNA sequence itself. These modifications can influence gene activity and can be inherited across generations, thereby impacting cellular functions and traits (15). The most recognized epigenetic regulations are DNA methylation, histone modifications, non-coding RNA-mediated regulation, among others (16). Together, these alterations dynamically regulate chromatin structure and accessibility, ultimately fine-tuning gene expression. This process shape the unique gene expression profile of TRM, enabling them to adapt to the specific tissue microenvironment and exert corresponding functions (17). Moreover, emerging evidences indicate that the molecular mechanisms associated with the epigenetics of TRM could present novel targets for cancer immunotherapy and the treatment of autoimmune diseases. This review aims to summarize recent advances in how distinct epigenetic mechanisms—including chromatin accessibility, DNA methylation, histone modifications, and non-coding RNAs—individually contribute to the differentiation, maintenance, and functional regulation of TRM. Each section is structured to follow this biological sequence, discussing relevant epigenetic mechanisms accordingly.

Chromatin accessibility refers to the degree to which chromatin, the complex of DNA and proteins in the nucleus, is open and accessible for transcriptional machinery, regulatory proteins, and other factors involved in gene expression. This accessibility is often regulated by epigenetic mechanisms, including DNA methylation, histone modifications, and non-coding RNAs. Recent studies indicate that chromatin accessibility is a crucial determinant of TRM identity and functionality, influencing their response to local microenvironments. First, the chromatin accessibility landscape of TRM diverge from those of circulating T cells (18, 19). Current studies predominantly focus on CD8⁺T cells, with limited attention given to their CD4⁺counterparts. The assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis on day 7 post-infection revealed that CD8⁺T cells in non-lymphoid tissues, such as intraepithelial lymphocytes (IEL) TRM precursors, exhibit distinct chromatin profiles compared to splenic effector cells. Regions near TRM-associated genes, such as Cd69and Nr4a1, were accessible, while regions near recirculation-associated genes, such as Klf2and S1pr1, were less accessible (18). A recent study establishing a multiomic single cell atlas of antigen-specific CD8⁺T cell states across infection and cancer reveals the unique transcriptional and epigenetic features of TRM. In this study, tumor-infiltrating lymphocytes and TRM shared unique changes in the expression of 293 genes and accessibility patterns of 796 regions compared with other antigen-specific T cells, suggesting significant alterations in chromatin accessibility in tissue-resident T cells. Further analysis demonstrated that the transcription factor KLF2 likely repressed accessibility and expression of residency-related genes, while BATF likely enhanced accessibility at loci associated with TRM characteristics (19). Second, TRM exhibit distinct chromatin accessibility profiles depending on their tissue environment. In one study, 7,150 differentially accessible regions (DARs) were identified when comparing splenic circulating P14 cells to TRM from the IEL, kidney, salivary glands (SG), fat, and liver following lymphocytic choriomeningitis virus (LCMV) infection. Clusters of accessible genomic regions were classified into tissue-specific, tissue-shared, broadly circulating, and broadly resident profiles. For example, the TRM marker Itgaeshowed increased accessibility at its transcription start site (TSS) in IEL and SG TRM, while the circulation-associated gene Sellwas more accessible in splenic T cells. A uniquely accessible TSS region of Ccr9was identified specifically in IEL TRM (17). Furthermore, chromatin accessibility also distinguishes TRM subsets within the same tissue. A study revealed that intestinal CD8⁺TRM clustered distinctly based on differential chromatin accessibility. Four different parts of intestinal tissue were analyzed using cellular indexing of transcriptomes and epitopes. Uniform manifold approximation and projection (UMAP) analyses revealed that TRM from each intestinal tissue compartment formed distinct clusters; however, small intestine intraepithelial and lamina propria TRM clustered more closely with each other, as did colon intraepithelial and lamina propria TRM. Additional heterogeneity within and among TRM populations from each intestinal compartment was also observed (20). In addition, Chromatin accessibility profiles also distinguish different skin CD8⁺TRM subsets (21). To investigate epigenetic differences among CD8⁺TRM subsets in human skin, ATAC-seq was performed on four major populations defined by CD103 and CD49a expression, identifying over 100,000 chromatin-accessible regions, most of which were located in enhancer regions. Principal component analysis showed clear separation between dermal and epidermal TRM, with dermal cells displaying the most distinct chromatin features. Epidermal CD103⁺CD49a⁺TRM had unique accessible regions near genes linked to cytotoxicity (e.g., GZMB, PRF1, and IFNG) and TCR/NK signaling (21).

While chromatin accessibility profiling reveals the static epigenetic landscapes that define TRM across tissues and subsets, recent studies have also begun to uncover the upstream mechanisms that dynamically shape these accessible regions. Notably, extrinsic signals from the tissue microenvironment, such as those derived from fibroblastic reticular cells (FRCs) and IL-6, have been shown to actively remodel chromatin accessibility during the early stages of CD8⁺T cell activation, thereby influencing TRM differentiation. FRCs along with IL-6 can enhance cytokine production of IL-2 and Tumor Necrosis Factor-α (TNF-α) and remodel chromatin accessibility lead to the upregulation of 778 genes through driving greater accessibility at 402 chromatin-accessible regions in newly activated CD8⁺T cells. Signals from FRCs have been shown to enhance the accessibility of transcription factor binding motifs such as MYC, HIF-1α, and HIF-1β, which are associated with the activation of metabolic pathways following T cell activation. Additionally, FRC-derived factors promote the enrichment of motifs for key transcription factors involved in CD8⁺T cell survival and memory differentiation, including BATF, ETS1, and BACH2. That would induce profound metabolic reprogramming in CD8⁺T cells, including enhanced glycolysis, increased oxidative phosphorylation, and upregulation of lipid synthesis and storage pathways. These metabolic features closely resemble the energy profiles observed in memory CD8⁺T cells and TRM, leading to epigenetic changes that facilitate their differentiation into TRM Chromatin-accessible regions induced by both FRCs and IL-6 conditioning were significantly enriched for memory precursor-specific epigenetic modifications, suggesting a priming effect on the transcriptional landscape of CD8⁺T cells. Consistently, FRC-educated CD8⁺T cells exhibited markedly improved persistence at both early (day 8) and later (day 37) stages following influenza infection, and preferentially differentiated into TRM by day 143. This result indicates that FRC-derived signals could drive metabolism-associated epigenetic changes that support CD8⁺T cell survival and memory differentiation in tissues (22).

DNA methylation, which plays a pivotal role in the epigenetic mechanism of the mammalian genome, involves the modifications of cytosine by add a methyl group to the fifth carbon to form 5-methylcytosine (5mC) (23). It participates in various biological processes, including genomic imprinting, X-chromosome inactivation, and repression of transposable elements and germline-specific genes, by which it influences the courses of gene expression, cell differentiation, and development (24). Despite its capability to activate transcription in certain cases, DNA methylation is more commonly regarded as repressor of gene expression through different mechanisms (23). One of the most established mechanisms involves the methylation of CpG islands within gene promoters. Although not fully understood, this process can interfere with the binding of transcription factors, ultimately impacting cellular function and development through gene silencing (25). Some research has indicated that this mechanism exerts influence in the modulation of TRM.

Previous studies have shown that both CD4⁺and CD8⁺T cells exhibit distinct DNA methylation patterns in key genes that determine their cell fate (26). During acute LCMV infection, memory precursor cells undergo dynamic methylation changes: effector-associated genes such as Ifng, Prf1, and Gzmbbecome demethylated and expressed, while naïve-associated genes are initially methylated. Interestingly, a subset of these repressed naïve genes is later demethylated and re-expressed in memory T cells, reflecting epigenetic flexibility (27). In addition, DNA methylation of the Gzmbgene serves as a useful marker to distinguish memory CD4⁺Th1 cells from T follicular helper (Tfh) cells (27). Deletion of Dnmt3a, a de novoDNA methyltransferase, accelerates memory formation by preventing the stable silencing of memory-favoring genes (28). Conversely, deficiency of TET2, a DNA demethylase, also enhances memory generation, but through increased methylation of transcription factors (e.g., Tbx21, Prdm1, Runx3) that drive effector differentiation, indirectly skewing the fate toward memory (29). The transcription factor FOXP1, which regulates memory T cell differentiation, is subject to DNA methylation control, with a progressive loss of methylation observed during the transition to memory cells. Furthermore, the expression of Foxp3in memory regulatory T cells (Tregs) is regulated by DNA methylation at the Treg-specific demethylated region (30). As a subtype of memory T cells, TRM also exhibit different DNA methylation landscape. In the differentiation of CD4⁺memory T cells, a bone-marrow resident T cell population was observed to diverge early from the main pathway (naïve T cells-TCM-TEM-terminally differentiated TEM), exhibiting a distinct epigenomic profile, as revealed by comprehensive transcriptome analyses, primarily including genome-wide DNA methylation profiles. These findings suggest that acquisition of a resident phenotype is linked to extensive DNA methylation reprogramming (31).

DNA methylation patterns are also altered in key functional genes of memory T cells. Lung CD8⁺TRM play a paramount role in viral reinfection (32). A study has demonstrated that the expression of the transmembrane protein Interferon-induced transmembrane protein 3(IFITM3), which facilitates survival and resistance to viral infection during subsequent exposures in CD8⁺TRM, is regulated by DNA methylation. As one of main methods to identify DNA methylation, Bisulfite sequencing was applied to detect the CpG island in the Ifitm3promoter in genomic DNA extracted from CD8⁺and CD4⁺TRM from mice recovered after influenza virus infection (33). The results showed that constitutive expression of IFITM3 in CD8⁺rather than CD4⁺TRM correlates with hypomethylation of the IFITM3 promoter 20 days after infection with influenza virus (33). However, IFITM3 expression was found to be upregulated in lung TRM as early as 10 days post-influenza infection and remained elevated for at least 60 days, indicating a long-term hypomethylated state of the IFITM3promoter. Upregulation of IFITM3 was not found in effector T cells, suggesting that demethylation of IFITM3 plausibly occurs during the effector-to-memory transition. Notably, IFITM3 upregulation was induced either by recognition of the cognate antigen or by exposure to interferon-α (IFN-α). Nevertheless, these stimuli are not responsible for maintaining sustained IFITM3 expression, as IFN-α was undetectable in the lungs after the resolution of acute infection at 10 days post-influenza virus clearance. The expression of IFITM3is essential for the functional integrity and long-term survival of lung TRM, which not only mediate protection against the primary pathogen that induced their formation but also confer resistance to other cytopathic viruses encountered in peripheral tissues. Meanwhile, IFITM3expression may not be a phenomenon restricted to the lung. Elevated IFITM3expression is also a characteristic feature of brain TRM generated during vesicular stomatitis virus (VSV) infection, although it remains unclear whether this is a consequence of hypomethylation at the IFITM3promoter (34). Similarly, this kind of demethylation has also been observed in tumors. TRM demonstrate ascendant cytotoxic capability in human urinary bladder cancer (UBC) when compared to other types of T cells, such as TCM (35). This phenomenon occurs due to the less methylated locus in the Perforin1(PRF1) reporter CpG site (–1053), identified in the enhancer region of PRF1in CD8⁺TRM (35). The hypomethylation at this locus leads to elevated expression of perforin, a protein that perforates the target cell membrane, facilitating the entry of granzyme and promoting apoptosis of tumor cells (35). However, no significant difference in DNA methylation at the PRF1 locus was observed between patients with non-muscle-invasive (stage I) and those with muscle-invasive (stage ≥II) tumors, suggesting that PRF1remains transcriptionally active across both early and advanced tumor stages. In another research, during Simian Immunodeficiency Virus (SIV) infection, promoter-wide and CpG-site specific methylation increased at Ifngand Il2promoters but decreased at the Tnfpromoter in intestinal tissue-derived CD8⁺T cells, although CD8⁺TRM were not tested directly (36). Taken together, DNA methylation plays a crucial role in enhancing cytotoxicity against infected or cancer cells by influencing the expression of key genes that regulate the function of TRM. However, further research is needed to understand how alterations in DNA methylation at key gene loci impact TRM commitment and function. Besides, the role of other DNA methylation modifiers, such as DNMT1 and TET1/3, in TRM remains undefined. DNMT1 maintains DNA methylation essential for T cell survival, lineage fidelity, and controlled cytokine expression. Its loss disrupts TCRαβ development, induces aberrant CD8⁺TCRγδ⁺cells, and enhances cytokine gene activation via demethylation (37). TET1 and TET3 regulate epigenetic programs critical for CD8⁺T cell maintenance by mediating DNA demethylation at survival- and metabolism-related genes. Their deletion results in increased apoptosis, impaired IL-7 signaling, and reduced peripheral CD8⁺T cells (38). Therefore, elucidating their regulatory function in TRM is of great importance.

Chromatin refers to the intricate combination of DNA and histone proteins present within the nucleus of eukaryotic cells, serving as the structural foundation for the organization of the entire genome. The fundamental building block of chromatin is the nucleosome, comprising 147 base pairs of DNA intricately wound around a histone octamer composed of two instances each of histones H2A, H2B, H3, and H4 (39). Although histone modifications can occur at the core residues of histone proteins, the majority of modifications, such as acetylation, methylation, phosphorylation, ubiquitination, sumoylation, adenosine diphosphate ribosylation, and deamination, primarily take place on the more flexible and exposed histone tails. The histone tails extend from the nucleosome core and are more accessible to the enzymes responsible for adding or removing these chemical groups. After these alterations, chromatin compaction and accessibility can be influenced which ultimately changes the state of transcription (40). Although there exist several kind of modifications, histone acetylation and histone methylation are the most extensively studied (41).

TRM differentiation can be regulated by histone modifications in the context of inflammatory diseases and foodborne pathogen infection. Inflammatory Bowel Diseases (IBD) are characterized by chronic inflammation of the gastrointestinal tract. TRM play a central role in the pathogenesis of IBD (42). Recent studies have demonstrated that the insulin receptor of intestinal mucosal T-cells can promote intestinal CD4⁺TRM differentiation via Enhancer of zeste homolog 2 (EZH2) (43). EZH2 is a key catalytic subunit of the Polycomb repressive complex 2, which functions by catalyzing the trimethylation of Lys-27 on histone 3, leading to the alteration of gene expression (44). Barrier disruption and pathogen invasion trigger the expansion of effector T cells in the gut. Insulin signaling enhances EZH2 expression, which facilitates these effector T cells differentiation into TRM through H3K27 trimethylation. This epigenetic regulation is thought to involve genomic regions controlling core transcription factors such as Hobit and Blimp1, although the precise targets remain to be fully elucidated (43). Another study on intestinal CD8⁺TRM reveals that histone modifications regulated by key transcription factors are crucial for their tissue residency and functional capacity in a Listeria monocytogenesinfection model. The transcription factor B cell leukemia/lymphoma 11B (Bcl11b), which acts both as a transcription repressor and as a transcription activator, plays a crucial role not only in thymocyte development but also in the differentiation and function of mature T cells (45). It has been considered as a frontrunner in CD8⁺TRM programs. Bcl11b effectively maintains the expression of multipotent/multifunctional (MP/MF)-related genes in TRM while suppressing the expression of effector program genes, suggesting its role in preserving the developmental and functional potential of TRM (46). By conducting Bcl11b Chromatin Immunoprecipitation Sequencing (ChIP-seq), H3K27ac ChIP-seq and H3K4me3 Cleavage Under Targets and Release Using Nuclease on TRM-like cells, Bcl11b was found to regulate the epigenetic landscape and directly controlling expression of essential genes of the MP/MF program. Bcl11b enhances H3K27ac, H3K4me3, and chromatin accessibility at the promoter regions of various MP/MF-related genes, such as Transcription Factor 7(Tcf7), Inhibitor of DNA binding 3(Id3).Recent study found that small intestine CD8⁺TRM expressing Tcf7and high levels of Id3represent a subset with enhanced memory potential (47, 48). This suggests that Bcl11b is necessary for maintaining H3K27ac, H3K4me3, and chromatin accessibility at the promoter regions of these genes, thereby sustaining their expression and preserving the memory potential of CD8⁺TRM. Additionally, Bcl11b can suppress the expression of effector program genes, including Prdm1and Ahr, restricting CD8⁺TRM differentiation (46). Further research focusing on histone modifications regulated by key transcription factors is needed to advance therapies targeting TRM through these mechanisms.

In muscle-invasive bladder cancer, RNA-seq data show that tumors with high infiltration of CD103⁺CD8⁺TRM exhibit significantly more frequent alterations in the gene lysine methyltransferase 2A(KMT2A) compared to tumors with low TRM infiltration (49). Conversely, mutations in the gene lysine demethylase 6A(KDM6A) are more prevalent in the low TRM infiltration subgroup (49). The proteins products of these two genes respectively function as the methyltransferase and demethylases towards histone tails, particularly the histone H3 tail. Both enzymes are crucial for chromatin dynamics, which influence the accessibility of genes for transcription (50, 51). KMT2A has not been functionally defined in T cell biology. KDM6A, a sex chromosome, is enriched in Th17 cells from female patients with ankylosing spondylitis and is associated with a pro-inflammatory transcriptional profile (52). Although these findings suggest a correlation between histone modification gene mutations and TRM abundance, direct mechanistic evidence linking KMT2A or KDM6A to TRM differentiation, migration, or retention in tumors is currently lacking. To further establish causality, future studies could employ Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-mediated knockout or pharmacological inhibition of KMT2A/KDM6A in tumor-infiltrating CD8⁺T cells, followed by assessment of TRM phenotype and localization in vivo. Additionally, tumor organoid models co-cultured with TRM precursors or adoptive TRM transfer systems into genetically engineered mouse models could provide tractable platforms to explore how these epigenetic regulators shape TRM residency and function. Given that KDM6A is X-linked and escapes X inactivation, it may exhibit sex-specific regulatory effects on T cells, contributing to differential TRM responses (53). Future studies using sex-matched T cells or four-core genotype mouse models will be valuable to dissect its dosage- and context-dependent immunological roles. This finding raise the possibility that changes of histone modification may influence the infiltration of TRM in the tumor tissue thus make an impact to the prognosis of muscle-invasive bladder cancer (49).

Recently, emerging evidence has highlighted the regulatory role of histone modifications in modulating the functional activities of TRM, particularly in the contexts of tumor immunity and inflammatory diseases. Basic helix-loop-helix transcription factor 40 (Bhlhe40) is a stress-responsive transcription factor that is important for numerous cell physiological responses. Bhlhe40 functions to promote mitochondrial gene transcription in TRM. Mitochondria play key roles in the biosynthesis and epigenetic regulation of gene expression. The deficiency of Bhlhe40leads to reduction in metabolites in the tricarbox ylic acid (TCA) cycle, butanoate metabolism, amino acid (aa) metabolism. These metabolites involved in acetyl coenzyme A synthesis, which is a critical substrate of histone acetylated modification in CD8⁺T cells including TRM (54). Conversely, enforced expression of Bhlhe40modestly enhanced the expression of mitochondrial respiratory chain genes and promoted histone H3 acetylation, suggesting that Bhlhe40 may regulate histone acetylation at functional gene loci in CD8⁺T cells. In accordance, Bhlhe40 deficiency attenuates the function of the CD8⁺TRM by decreasing the acetylation in H3K9 and H3K27 in the Ifnglocus in an acute influenza virus infection model (54). Subsequently, addition of the downstream products of Bhlhe40, especially tubastatin A and acetate, could restore the interferon (IFN) -γ production by CD8⁺T cells that lack Bhlhe40, as well as increase CD69 and CD103 expression through increasing histone H3 acetylation, thus promoting the TRM residency and function of resistance to tumors (54). This study suggests that gene deficiency can also lead to epigenetic changes, although in most cases, it is the epigenetic alterations that regulate the expression of critical genes, thereby influencing the residency and function of TRM. In addition, epigenetic modification sometimes correlates with metabolism in TRM. Appropriate combinations of epigenetic modulators and specific metabolites may represent promising strategies to optimally reinvigorate the antiviral or antitumor functions of tissue- or tumor-resident CD8⁺T cells.

Similar to DNA methylation modifiers, several key histone-modifying enzymes remain poorly studied in the context of TRM. HDAC1 plays distinct, context-dependent roles in T cell development and lineage stability. It is essential for thymocyte maturation, peripheral T cell homeostasis, and antiviral CD8⁺T cell responses. Deletion of HDAC1 impairs the transition from immature CD8⁺CD4^-thymocytes to the double-positive stage and reduces the expansion of virus-specific CD8⁺T cells, despite enhanced IFN-γ production by effector cells (55). Recent evidence also implicates HDAC1 in regulating exhausted CD8⁺T cell fate during chronic viral infection (56). In parallel, HDAC1 together with HDAC2 maintains CD4⁺T cell lineage integrity by repressing CD8-lineage genes such as Cd8aand Cd8b1. Loss of HDAC1/2 in CD4⁺T cells leads to aberrant activation of a CD8⁺effector-like program via Runx–CBFβ complexes, particularly in Th0 and Th1 subsets (57). Moreover, HDAC1 could promote CD4⁺T cell hyperactivation in systemic lupus erythematosus by repressing microRNA-124(miR-124) expression through promoter binding. Reduced miR-124 results in the upregulation of interferon regulatory factor 1, thereby enhancing T cell immunoactivity (58). These findings highlight HDAC1 as a critical epigenetic regulator with diverse functions in T cell biology, including development, lineage fidelity, and immune dysregulation in autoimmunity. HDAC3 acts as a transcriptional repressor of chemokines such as CXCL10 in KRAS-mutant lung cancer cells, limiting T cell recruitment to the tumor microenvironment. Its inhibition enhances chemokine expression via an NF-κB/p65-dependent pathway and promotes T cell infiltration into lung tumors in vivo ( 59). HDAC4 appears to play a limited role in T cell immunity under steady-state conditions. Although it is expressed in multiple T cell lineages, T cell-specific HDAC4 deficiency does not alter the frequencies or cytokine production of conventional T cells, iNKT cells, or regulatory T cells (60). Given their established roles in regulating T cell activation, lineage differentiation, and tissue-specific transcriptional programs, HDACs—particularly HDAC1—may also participate in the formation, maintenance, or functional adaptation of TRM. Whether these enzymes modulate TRM epigenetic identity or residency-related gene expression remains to be determined, warranting further investigation.

Non-coding RNAs (ncRNAs) are RNA molecules that lack the genetic information necessary for protein production (61). Of the three billion base pairs in the human genome, only 2% are responsible for encoding proteins, while the remainder consists of ncRNAs (62). NcRNAs exhibit significant heterogeneity in their length, conformation, and cellular functions. Recent taxonomy distinguishes between long non-coding RNA (lncRNA) and small non-coding RNA. Within lncRNA, distinctions can be made between linear RNAs and circular RNAs. Moreover, each group can be subdivided into tens of thousands of specific ncRNAs, all of which play vital roles in various physiological and pathological processes (63).

Several studies have explored the relationship between different ncRNAs and various types of T cells, including CD4⁺T cells, CD8⁺T cells, regulatory T cells, and others (64). Among ncRNAs, miRNAs, lncRNAs and circular RNAs (circRNAs) are the most well-studied subtypes which were found to impact the differentiation (65, 66) and function (67, 68) of T cells. However, the regulation of TRM by ncRNAs was not well investigated.

MiRNAs consist of short RNA molecules, typically about 22 nucleotides in size and are produced by two Ribonuclease III proteins, Drosha and Dicer (69). They play a role in posttranscriptional silencing of target genes, with each miRNA capable of targeting a multitude of messenger RNAs. This process affects the expression of numerous genes, particularly those involved in functional interacting pathways (70). Various miRNAs are involved in the regulation of T cell function. MiR-155 plays a crucial role in T cell-mediated immunity by promoting Th1 and cytotoxic T cell responses and is essential for T cell activation, cytokine production, and immune memory (71, 72). MiR-146a acts as a negative regulator of T cell-driven inflammation by suppressing NF-κB signaling through targeting Traf6 and Irak1, and it is vital for Treg function and the control of Th1-mediated immune responses (73, 74). The miR-17~92a cluster enhances T cell activation and Th1 differentiation by promoting IFN-γ production (75). MiR-181 is critical for thymocyte development and TCR sensitivity by modulating both positive and negative selection processes (76). Although miRNAs have been extensively studied in T cells, only miR-155 and miR-181a have been directly investigated in TRM. MiR-155 is a class of miRNAs produced by lymphoid cells, myeloid cells, and bone marrow blasts, exerting its influence on immune cell proliferation and differentiation, as well as on the regulation of innate and adaptive immune responses, inflammation, and carcinogenesis (77, 78). MiR-155 has been found to closely correlate with the fate of CD4⁺T and CD8⁺T cells, partly through its posttranscriptional regulation of multiple target genes (79, 80). A recent study investigated the role of miR-155 in the development of TRM by infecting mouse brains with a lethal dose of Listeria monocytogenes. Following the infection, mice were treated with either antibiotics combined with a miR-155 inhibitor or antibiotics combined with a scramble control. It was found that the application of miR-155 inhibitor led to reduced accumulation of brain CD8⁺TRM compared to the scramble group (81). Meanwhile, numbers of brain CD8⁺TRM in infected miR-155 ^-/-mice were also significantly reduced compared to infected wild-type mice (81). These results suggest that miR-155 is critical for the maintenance of TRM. MiR-181a, initially discovered in murine thymocytes and T cells, serves as a pivotal modulator of the T cell receptor activation threshold (82). It exhibits high expression levels in double-positive thymocytes, yet undergoes a decremental trend in single-positive thymocytes and peripheral T cells (76). This distinctive expression profile is posited to expedite positive selection via autoantigen recognition while concurrently mitigating the risk of autoimmunity (83). A recent study found that mature CD8⁺T cells with miR-181 deficiency failed to acquire a tissue-resident phenotype in the liver following infection with lymphocytic choriomeningitis virus (84). Importantly, this effect was observed not only during acute infection but also persisted into later memory time points (84). Taken together, current research predominantly focuses on miRNAs, while other ncRNAs with potential regulatory roles in TRM remain underexplored. MiR-155 and miR-181a play distinct tissue-residency roles in TRM, which differ from their functions in conventional T cells. This suggests that other types of miRNAs may also possess unique properties in TRM, making this a promising area for future research.

LncRNAs are a diverse and underexplored class of regulatory molecules that have emerged as key modulators of gene expression in various branches of the immune system (85, 86). A lot of studies have been conducted to investigate the regulatory role of lncRNAs in T lymphocytes. Distinct lncRNAs modulate different intracellular signal transduction pathways across specific T cell lineages, participating in key biological processes such as development, differentiation, activation, and effector functions (87). A microarray analysis of mouse naïve, memory, and effector CD8⁺T cells identified 1,106 expressed lncRNAs, with 10% showing differential expression, including 21 associated with naïve-to-memory cell differentiation. The lncRNA Morrbid, induced by lymphocytic choriomeningitis virus infection or T cell receptor stimulation in mouse CD8⁺T cells, is required for the upregulation of Bcl2l11—an apoptosis-inducing factor essential for CD8⁺T cell contraction—in both CD4⁺TCM and TEM following in vitrostimulation. These studies suggest that lncRNAs may also promote the acquisition of TRM memory characteristics, although their roles remain to be experimentally validated (88, 89). CircRNAs are stable single-stranded RNA molecules that form a covalently closed continuous loop (90). A recent study demonstrated that circular circRNAs are differentially expressed during thymocyte differentiation, which can be categorized into three main stages: early immature (ST1; CD34⁺CD2^-), intermediate (ST2; CD1A⁺), and mature (ST3; CD1A^-) thymocytes (91). Among these, hsa_circIKZF1_0001, which was previously identified as a T cell-specific circRNA in mature blood cell populations, exhibited a progressive increase in expression throughout thymocyte development (92). In contrast, hsa_circHIPK3_0001, which has been reported to modulate cell growth and proliferation in various human cell types, showed a decreasing expression pattern during differentiation (93). As we know, circRNAs regulate mRNA expression by acting as sponges for specific miRNAs. Notably, the downregulation of RAG2, a gene essential for V(D)J recombination during early T cell development, from ST1 to ST3 stages may be mediated by the reduced expression of hsa_circ_0031584 (ARHGAP5) and hsa_circ_0019079 (KIF20B), potentially through the release of hsa-miR-609. These results indicated that circRNAs get involved in T-cell differentiation in the thymus through circRNA–miRNA–mRNA networks (91). Future experimental validation is required to establish the involvement of circRNAs in regulating genes critical for T cell differentiation in the thymus, with some circRNAs potentially playing important roles in TRM cell fate determination. However, it is important to note that while these findings suggest potential regulatory roles of lncRNAs and circRNAs in T cell biology, there is a lack of direct experimental evidence demonstrating their functions specifically in tissue-resident memory T cells. To address this gap, future studies could apply targeted loss- or gain-of-function approaches, such as in vivoCRISPR interference or CRISPR activation, to modulate candidate lncRNAs or circRNAs in tissue-resident CD8⁺T cells. Such experiments would enable functional validation of these non-coding RNAs in TRM differentiation, maintenance, and effector function within their physiological tissue niches.

In this review, we summarized the current understandings of epigenetic regulation of crucial genes which play influential role in the differentiation, long-term persistence, and function of TRM. Several studies have demonstrated that three major kinds of epigenetics including DNA methylation, histone modifications and ncRNAs are all involved in the regulation of the biology of TRM (Figure 1). As a subset of T cells, CD4⁺and CD8⁺TRM retain many canonical features of their helper and cytotoxic lineages, sharing epigenetic traits with circulating T cells, yet displaying a distinct chromatin landscape. Their hallmark is tissue residency. TRM-specific loci such as Cd69, Itgae, and Prf1exhibit sustained hypomethylation and increased chromatin accessibility, facilitating tissue retention and cytotoxicity. In contrast, recirculation-associated genes like S1pr1and Klf2are epigenetically repressed. These stable epigenetic signatures underscore the non-recirculating identity of TRM (17).

Collectively, current evidence establishes that epigenetic regulation is integral to the formation, persistence, and functional specialization of tissue-resident memory T cells. Chromatin remodeling, DNA methylation, histone modifications, and non-coding RNAs converge with tissue-specific cues to define TRM identity and heterogeneity. Despite these advances, key gaps remain in understanding how dynamic epigenetic landscapes are orchestrated during TRM differentiation and recall responses. Addressing these questions will benefit from single-cell multi-omic approaches, lineage tracing, and CRISPR-based epigenome editing to resolve causal mechanisms with spatial and temporal precision. Therapeutically, selective modulation of TRM epigenetic programs represents a promising strategy to augment antitumor immunity, enhance vaccine-induced protection, and attenuate pathogenic TRM activity in autoimmunity and chronic inflammation.