The first discovery of LncRNA dates back to 1984, when LncRNA-H19 was identified in mammals by Pachnis et al. LncRNAs were initially considered as “noise” of genome transcription or by-products RNA of polymerase II transcription without a biological function. However, in 1991, Borsani et al. demonstrated the involvement of Xist in the regulation of X chromosome inactivation (Borsani et al., 1991). It was not until 1994, when the enod40 gene was found to likely play a role in plant development, acting as a “ribosome regulator” (Crespi et al., 1994). In 2003, Ji et al. predicted metastasis and survival in early non-small cell lung cancers using MALAT1 and thymic β4 (Ji et al., 2003). In 2007, Rinn et al. discovered the 2.2 kb-long HOTAIR in the human HOXC locus, which officially kicked off LncRNA research (Rinn et al., 2007) (Figure 1).

Over 100,000 human LncRNAs have been recorded to date (Uszczynska-Ratajczak et al., 2018), and LncRNA research has become an important area of research in biological sciences over the last decade. Namely, there have been over 50,000 publications with the keyword “Long noncoding RNA” and over 2,000 publications reporting validated LncRNA functions (Statello et al., 2021).

LncRNAs covered a large number of highly heteromerized transcripts that differed in biogenesis from their genomic origin (Chen and Kim, 2024). The main LncRNAs were transcribed by RNA polymerase II (Pol II), and could undergo splicing similar to that of mRNAs characterised by the addition of a cap [7- methylguanosine (m7G)] at the 5′ end and a polyadenylation at the 3′ end (polyA) (Statello et al., 2021). The vast majority of LncRNAs were derived from the nuclear genome (Statello et al., 2021). Based on the relative position of genomic LncRNA to neighbouring protein-coding genes, it could be divided into five categories: (1) Positive-sense LncRNA, overlapping with one or more exons of the encoding gene; (2) Antisense transcript product, partly or completely complementary to the transcript on the opposite strand; (3) Intron LncRNA, produced by introns of the gene; (4) The bidirectional transcription product, sharing the same promoters with protein-coding genes, but transcribed in the opposite direction; (5) Intergenic LncRNAs (LincRNA), transcribed independently by sequences located between protein-coding genes (Mercer et al., 2009; Rinn et al., 2012; Wang and Chang, 2011; Guttman and Rinn, 2012; Chodurska and Kunej, 2025).

Based on the location of LncRNAs and specific interactions with DNA, RNA, and protein, LncRNA could have the following functions: (1) It could regulate chromatin function, change the stability and translation of cytoplasmic mRNA, and interfered with signal transduction pathways (Statello et al., 2021); (2) It could act as a transcriptional regulator in the form of a cis or trans-acting element (trans), regulating gene expression (cis function) near its transcription site through various mechanisms, and targeting distant transcriptional activators or repressors or affecting gene transcription localization in cells (trans function) (Rinn et al., 2012; Ponting et al., 2009); (3) It could regulate organelles, with many LncRNA localized in specific organelles, such as exosomes and mitochondria (Ro et al., 2013; Kim et al., 2017). As exosomes were regularly released into the extracellular environment, exosome-localized LncRNAs could be secreted, and eventually entered recipient cells. In recipient cells, these LncRNAs could be involved in epigenetic inheritance, cell type reprogramming, and regulation of genome instability. Mitochondria-localized LncRNA could be encoded by nuclear and mitochondrial DNA, and was often associated with mitochondrial metabolism, apoptosis, mitochondria and the nucleus crosstalking (Statello et al., 2021; Zhang et al., 2024b).

EVs are a variety of membranous structures secreted by cells that contain biologically active substances including proteins, lipids, and genetic substances (such as LncRNA) (Kim et al., 2017; Simeone et al., 2020). The study of EVs dates back to the mid-1940s, and although they were once considered the “trash bin” of our bodies, they are now regarded as the connecting bridge between cells (Chao et al., 2023). EVs travel through bodily fluids and transmit their molecular information in autocrine, paracrine, and endocrine manners (Krylova and Feng, 2023). EVs are also increasingly recognized as having a direct role in cancer and neuro-degenerative disease pathology. Therefore, the use of EVs as biomarkers of disease diagnosis and prognosis has gathered research interest (Kim et al., 2017; Urabe et al., 2020; Hill, 2019).

In recent years, large amounts of LncRNAs have been found in peripheral blood, emulsions, urine, gastric fluid, and other bodily fluids (Yuan et al., 2020; Arantes et al., 2018). They have also been regarded as diagnostic cancer biomarkers (Zheng et al., 2021). These LncRNAs travel outside their cells of origin, and are selectively packaged into EVs. Subsequently, LncRNAs are transferred to proximal and distal recipient cells, inducing profound phenotypic changes (Li et al., 2020). EVs can be internalized by recipient cells via membrane fusion, receptor-dependent endocytosis, microcellular drinking, or phagocytosis (Hu et al., 2020).The structure and content of the EV is shown in Figure 2.These mechanisms determine the uptake of EVs with relative targeting and specificity. Cargo LncRNAs that are transported to recipient cells play their corresponding function, and participate in the occurrence and progression of disease, including the pathogenesis of CFS.

The immune system is composed of immune organs, immune cells, and immune active substances, which have several functions including immune surveillance, defence, and regulation. Attree et al. showed that although the pathogenesis of CFS is unclear, it is associated with abnormalities in the immune system (Arroll et al., 2014; Vu et al., 2024). Since 1987, there has been substantial evidence of impaired natural killer cell function (reduced cytotoxicity) in CFS patients, which is the most consistent immune finding in CFS (Caligiuri et al., 1987; Baraniuk et al., 2024a; Eaton-Fitch et al., 2019; Zhang et al., 2024c). When researchers measured Th1 and Th2 cell levels in CFS patients, they found that the Th1/Th2 cell ratio decreased, suggesting that a diminished Th1 cell-driven immune response may be an intrinsic immune abnormality associated with CFS (Capelli et al., 2010). In addition, plasma levels of TNF-α were higher in CFS patients compared with healthy controls (Kerr et al., 2001). Increased IL-10 levels were associated with somatic symptom severity (Bested and Marshall, 2015). It has also been reported that the levels of IL-8 and IL-13 are increased (Broderick et al., 2012). Other studies have shown that the HPA axis is decreased in patients with CFS (Rusin et al., 2022). Hormonal downregulation and hypometabolic states play an important role in fatigue, which may be related to cytokines (IL-1, IL-6). However, this mechanism is not clear and will not be reviewed here.

LncRNA Erythrocyte differentiation regulator 1 (Erdr1) has been shown to act as a key immune-modulator, playing an important role in various immune cells, including T cells (Kim et al., 2020), NK cells, and macrophages, etc. Erdr1 induces T-cell apoptosis, but enhances NK-cell toxicity (Shu et al., 2025). However, the specific mechanisms involved are still unclear and deserve further investigation. Linc-MAF-4 is a LncRNA with fine-specific expression in Th1 cells. Its main function is to inhibit the expression of MAF. Knockdown of linc-MAF-4 in human peripheral blood mononuclear cells (PBMCs) induced a shift in the differentiation of CD4⁺ T cells to Th2 cells. Over-expression of linc-MAF-4 on human naive CD4⁺ T cells promoted Th1 cell differentiation and inhibited Th2 cell differentiation. The above studies showed that linc-MAF-4 is an important molecule that promotes Th1 cell differentiation (Zhang et al., 2017). LncRNA GATA3-AS1 is an antisense LncRNA located on the antisense strand of the GATA 3 gene. Specifically expressed in Th2 cells, GATA 3A S1 can modulate the expression of GATA 3 and Th2-related effector cytokines IL-5 and IL-13 (Gibbons et al., 2018), thus affecting the differentiation of Th2 cells. In addition, in TOLL-like receptor (TLR)1/2-stimulated THP 1-derived human macrophages, LncRNA THRIL trans-regulates TNF-α expression by forming a complex with ribonucleoprotein (RNP) hnRNPL which acts on the TNF-α promoter (Li et al., 2014). NEAT 1 is another antisense LncRNA that stimulates IL-8 expression in Hela cells by binding to the splicing gene SFPQ, thereby inducing SFPQ translocation from the IL-8 promoter (Imamura et al., 2014).

CFS patients often present with an underlying energy deficit. Studies had shown that mitochondrial dysfunction might be an important cause of such deficit (Cortes Rivera et al., 2019; Syed et al., 2025). Some researchers had found that mitochondrial dysfunction (reduced ATP production) caused fatigue and post-exertional malaise. Moreover, it can cause overall metabolic abnormalities (Morris and Maes, 2014). Booth et al. studied the ATP profile of 138 CFS patients and 53 healthy controls, and showed that the majority of CFS patients had mitochondrial dysfunction, proposing that the ATP profile was associated with disease severity (Booth et al., 2012). The pathogenesis of CFS involves mitochondrial dysfunction, immune dysregulation, oxidative stress and abnormal energy metabolism (Wang et al., 2023; Bjørklund et al., 2020; Holden et al., 2020). In recent years, a large number of studies have demonstrated that LncRNAs play an important role in regulating mitochondrial function, which involves various aspects such as mitochondrial energy metabolism, oxidative stress, mitochondrial dynamics (fusion and fission), mitochondrial autophagy (mitophagy), and mitochondrial DNA (mtDNA) stability (Zhu et al., 2022; Chen et al., 2021; Niu et al., 2024). Therefore, LncRNAs may play an important role in the pathogenesis of CFS by regulating mitochondrial function.

HOXA11os is an LncRNA specifically expressed in the distal colon, and decreased levels of HOXA11os in colonic myeloid cells lead to complex I deficiency, oxidative phosphorylation dysfunction (OXPHOS), and the production of mitochondrial reactive oxygen species (mtROS) (Shmuel-Galia et al., 2023), which may contribute to intestinal dysfunction and inflammation in patients with CFS, if they have defective HOXA11os, and inflammation in the intestinal tract. Mitochondrial dysfunction leads to an increase in the production of ROS in the cell (LeFort et al., 2024), which induces oxidative stress and exacerbates mitochondrial damage (Veluthakal et al., 2024; Mo et al., 2024), whereas a study by Vicky et al. confirmed the role of the LncRNA ROSALIND as a novel ROS buffering system that protected mitochondrial translation from oxidative stress (Katopodi et al., 2025). Many studies have shown that oxidative stress is present in CFS patients (Bjørklund et al., 2020; Shankar et al., 2024; Skare et al., 2024; Sukocheva et al., 2022), so the dysregulation of ROSALIND without protection of dysfunctional mitochondria may be an important reason why fatigue is not alleviated in CFS patients. LncMtDloop, a LncRNA encoded within the D-loop region of the mitochondrial genome, plays a critical role in maintaining mitochondrial RNA levels and function. Although its precise mechanisms remain unclear, recent research has highlighted its potential involvement in neurodegenerative diseases. A study investigating the role of LncMtDloop in Alzheimer’s disease (AD) revealed that its expression levels are significantly reduced in AD patients. Experimental enhancement of LncMtDloop in AD model mice demonstrated a marked improvement in AD-like pathological and behavioral deficits (Xiong et al., 2024). Given that neurocognitive impairment is a shared characteristic between AD and CFS patients (Arron et al., 2024; Liu et al., 2024; Ferreira et al., 2024; Baraniuk et al., 2024b), we hypothesize that the downregulation of LncMtDloop in CFS patients may contribute to their cognitive deficits. However, this hypothesis requires further validation through extensive clinical studies to establish a definitive link between LncMtDloop dysregulation and cognitive impairment in CFS.

Glycolysis influences ATP production by providing pyruvate and NADH, supporting the mitochondrial TCA cycle and oxidative phosphorylation (Chandel, 2021). Glycolysis depends on mitochondrial pyruvate carboxylation and energy supply to maintain blood glucose levels (Hernández, 2021). The balance between glycolysis and gluconeogenesis is critical for maintaining mitochondrial function and cellular energy homeostasis, and its imbalance may lead to metabolic diseases (Guasch-Ferré et al., 2020; Dalga et al., 2023). Zhu et al. first proposed that a LncRNA termed glycoLINC could serve as a scaffold to assemble glycolytic enzymes into functional metabolons, enhancing glycolytic flux and ATP production to support cell survival under nutrient-deprived conditions (Zhu et al., 2022). In a separate study, it was demonstrated that LncRNA H19 modulates mitochondrial functions, including calcium homeostasis, ATP production, and ROS levels, as well as endoplasmic reticulum (ER)-mitochondrial coupling, by regulating the expression of the mitochondrial outer membrane protein VDAC1. Suppression of H19 was shown to enhance ER-mitochondrial coupling and significantly upregulate the expression of gluconeogenesis-related genes (Nandwani et al., 2024). Based on these findings, we hypothesize that alterations in the levels of glycoLINC and H19 in patients with CFS may disrupt the balance between glycolysis and gluconeogenesis. This imbalance could subsequently impair mitochondrial function, leading to metabolic dysregulation, which may underlie the metabolism-related symptoms observed in CFS patients.Table 2 summarises the association between CFS and LncRNAs in regulating mitochondrial functions.

Studies had suggested that CFS might be associated with genetic susceptibility. Van et al. compared dozens of adolescent CFS patients with healthy controls and their parents, and showed that children of women with CFS had similar mental illness conditions. The opposite was true for fathers (van de Putte et al., 2006). CFS is associated with several genetic pathways, including immune regulation and neurotransmission, inflammation and oxidative stress, and catecholamine pathways (Wang et al., 2017). These included changes in related genes such as TNF- α, IL-1, IL-4, IL-6, HLA, IFN-γ, and 5-HT (Wang et al., 2017). In addition, some CFS patients developed autoimmunity, which might be related to genetic backgrounds and disorders that promote B cell cloning, which in turn responded to self-antigens (Blomberg et al., 2018). Moreover, there were also methylation differences in the PRF 1 gene and at multiple CpG sites in T cells from CFS patients when compared with healthy controls (Herrera et al., 2018).

The effects of EV-LncRNAs on the immune system and the regulation of inflammatory factors had been described above. In addition to affecting immunological functions, EV-LncRNAs could also affect the genomic regulation of children from CFS patients. LncRNAs interacted with proteins and nucleic acids that regulated gene expression, facilitating solid, flexible and specific transcriptional and post-transcriptional control in the nucleus and cytoplasm (Herman et al., 2022). LncRNAs may have very important genetic and epigenic roles, indicating involvement in the regulation of altered genetic information in CFS patients. Nonetheless, there is a paucity of studies on the genetic aspects of LncRNA and CFS, and a large number of studies are needed to confirm the genetic association between them.

As early as 1985, Jones et al. reported for the first time the association between CFS (then called “chronic EBV infection syndrome”) and EBV infection. The study found that some CFS patients showed elevated EBV antibody titres, suggesting that EBV infection may be associated with the development of CFS (Winston et al., 1985). It has been demonstrated that human herpesvirus (HHV)-7, parvovirus B19, Borna disease virus (BDV), enterovirus, and coxsackie group B virus infections are risk factors for the development of CFS, with BDV being the most strongly associated (Hwang et al., 2023; Ariza, 2021). During the COVID-19 pandemic, many studies had shown that in the months following a SARS-CoV-2 infection, patients experienced immune, inflammatory, cardiovascular, intestinal, metabolic, and neurological changes which had some overlapping symptoms with CFS (Sukocheva et al., 2022; Vojdani et al., 2023), which suggested that there might be a potential correlation between the occurrence and progression of CFS and COVID-19.

LncRNAs have recently been described as key regulators of viral infections, with involvement in antiviral responses and virus-host interactions (Sarfaraz et al., 2023; Vierbuchen and Fitzgerald, 2021; Chen et al., 2022), some of which may be beneficial to the virus (Liu and Ding, 2017). This was confirmed by Cao et al. who found that LncRNA-BTX is upregulated by IRF3 -type I interferon-independent pathway after viral infection to help the virus evade clearance by the immune system, and also regulates the intracellular localisation of DHX9 and ILF3 by enhancing the interactions of RNA-binding proteins (RBPs) DHX9 and ILF3 with their partner proteins (JMJD6 and ILF2). Intracellular localisation of DHX9 and ILF3: facilitates viral replication by promoting the return of DHX9 to the cytoplasm while retaining ILF3 in the nucleus (Cao et al., 2023). IFN is a glycoprotein produced by viruses or other interferon inducers that has antiviral properties (Samuel, 2001), LncRNA-ISIR deficiency in vivo can lead to reduced IFN production, uncontrolled viral replication, and increased mortality (Xu et al., 2021). CHROMR, an LncRNA induced to be expressed in influenza A virus and SARS-CoV-2 infections, enhances the antiviral immune response by sequestering the interferon regulatory factor (IRF)-2-dependent transcriptional co-repressor, IRF2BP2, and promoting the expression of interferon stimulated genes (ISGs) (van Solingen et al., 2022). LncRNA-MALAT1 may contribute to antiviral responses through interactions with IRF 1, IRF 4, STAT 1, STAT 3, and STAT5A (Kesheh et al., 2022). Alternatively, Yang et al. showed that LncRNA modulates RIG -1 signalling, including the regulation of biological processes involved in COVID-19 and subsequent disease states (Yang et al., 2021). B cells infected by viruses can act on Th cells through the release of exosomes containing LncRNA. These can alter Th1 and Th2 cell differentiation, preventing cellular and humoral immunity from occurring normally. In addition, LncRNA may directly affect Th1 cell secretion of IFN-γ to activated other cells, such as epithelial cells, endothelial cells, fibroblastic, and glial cells. The latter express MHC-Ⅱ molecules and become non-professional antigen-presenting cells during EBV infection (Ruiz-Pablos et al., 2021) (Figure 6). Therefore, the regulatory role of LncRNAs in viral infections and their impact on immune responses, which suggests that LncRNAs may be involved in the pathogenesis of CFS, and that viral infections may participate in the onset and progression of CFS through LncRNA-mediated mechanisms.