ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility

The Role of N6-Methyladenosine (m6A) RNA Modification in the Pathogenesis of Parkinson's Disease

Parkinson's disease (PD) is a neurodegenerative disease with a high prevalence among the middle-aged and elderly population. The pathogenesis of PD is closely linked to the misfolding and aggregation of α-synuclein, which contributes to the formation of Lewy bodies. These processes are associated with the degeneration of dopaminergic neurons, a key neuropathological change that underlies the motor symptoms of PD. In addition, genetic susceptibility, mitochondrial dysfunction, oxidative stress and neuroinflammation are involved in the progress of the disease. Previous studies indicated that the dysregulation of epigenetic modifications, including DNA methylation and histone acetylation, may be the key pathophysiological factors in PD. N6-methyladenosine (m6A) is a dynamically reversible modification in eukaryotes RNA, and could regulate mRNA degradation, stability, maturation, and translation. Recently, clinical research has shown that the global m6A level is significantly reduced in PD patients as well as the expression changes in m6A-associated proteins. Moreover, the dysregulation of m6A modification was shown to impact dopamine metabolism and damage dopaminergic neurons, indicating that m6A RNA modification may play a critical role in the pathogenesis of PD. In this review, we summarize recent clinical studies on m6A RNA modification in PD patients and discuss the regulatory role of m6A modification in dopamine metabolism and dopaminergic neurons death. Furthermore, based on the different m6A modification databases and prediction websites, we analyzed the potential m6A modification sites on the mRNA of key PD pathogenic genes (SNCA, PRKN, PINK1, and LRRK2) for the first time, aiming to offer new gene targets and perspectives understanding the pathogenesis of PD.

Regulatory mechanisms of m6A RNA methylation in esophageal cancer: a comprehensive review

Esophageal cancer is an aggressively malignant neoplasm characterized by a high mortality rate. Frequently diagnosed at an advanced stage, it presents challenges for optimal therapeutic intervention due to its non-specific symptoms, resulting in lost opportunities for effective treatment, such as surgery, radiotherapy, chemotherapy and target therapy. The N6-methyladenosine (m6A) modification represents the most critical post-transcriptional modification of eukaryotic messenger RNA (mRNA). The reversible m6A modification is mediated by three regulatory factors: m6A methyltransferases, demethylating enzymes, and m6A recognition proteins. These components identify and bind to specific RNA methylation sites, thereby modulating essential biological functions such as RNA processing, nuclear export, stability, translation and degradation, which significantly influence tumorigenesis, invasion, and metastasis. Given the importance of m6A modification, this paper offers a comprehensive examination of the regulatory mechanisms, biological functions, and future therapeutic implications of m6A RNA methylation in the context of esophageal cancer.

METTL3-mediated m6A modification in sepsis: current evidence and future perspectives

Sepsis, a severe systemic inflammatory condition triggered by infection, is associated with high morbidity and mortality worldwide. While medical diagnosis and treatment have advanced in recent years, a specific therapy remains unavailable. Recently, significant progress has been made in studying the epigenetic RNA modification N6-methyladenosine (m6A) and its core methyltransferase METTL3. The role of m6A in sepsis has also been increasingly elucidated. This review aims to explore the pathological mechanisms of sepsis and its relationship with m6A, focusing on the role of the key m6A writer, METTL3, in sepsis.

Nuclear accumulation of YTHDF1 regulates mRNA splicing in the DNA damage response

YTH domain-containing family protein 1 (YTHDF1), a reader of N6-methyladenosine (m6A), has been implicated in regulating RNA metabolism in the cytosol. Here, we report a role of YTHDF1 within the nucleus in response to genotoxic stress. Upon radiation, YTHDF1 is phosphorylated at serine-182 in an ataxia telangiectasia and Rad3-related-dependent manner. This phosphorylation inhibits exportin 1-mediated nuclear export of YTHDF1, resulting in its accumulation within the nucleus. Nuclear YTHDF1 enhances the binding capacity of serine- and arginine-rich splicing factor 2 to a group of m6A-modified exons, leading to increased exon inclusion. Specifically, YTHDF1 promotes splicing and expression of DNA repair genes, such as BRCA1 and TP53BP1, thereby mitigating excessive DNA damage. Depletion of YTHDF1 sensitizes cancer cells to radiation treatment. Together, our study reveals a crucial role of YTHDF1 in m6A-mediated messenger RNA splicing in the DNA damage response, proposing it as a potential target for radiation therapy.

Positioning of sperm tail longitudinal columns depends on NSUN7, an RNA-binding protein destabilizing elongated spermatid transcripts

Spermatozoid's flagella assemble in transcriptionally silent spermatids and thus depend on posttranscriptional regulation of gene expression. Mutations in Nsun7 gene are known to cause male infertility in human and mice. We identified m5C-specific NSUN7 RNA methyltransferase as a protein present in elongated spermatids and interacting with RNAs specific for this type of spermatozoid's precursor cells. Inactivation of the Nsun7 gene in mice leads to upregulation of its RNA interactors, thus indicating that NSUN7 downregulates a set of RNAs in the elongated spermatids. A physiologic consequence of Nsun7 gene knockout is male infertility, which is mechanistically explained by the observed mispositioning of longitudinal columns relative to the axonemal microtubular doublets leading to a motility defect.

Methionine in embryonic development: metabolism, redox homeostasis, epigenetic modification and signaling pathway

Methionine, an essential sulfur-containing amino acid, plays a critical role in methyl metabolism, folate metabolism, polyamine synthesis, redox homeostasis maintenance, epigenetic modification and signaling pathway regulation, particularly during embryonic development. Animal and human studies have increasingly documented that methionine deficiency or excess can negatively impact metabolic processes, translation, epigenetics, and signaling pathways, with ultimate detrimental effects on pregnancy outcomes. However, the underlying mechanisms by which methionine precisely regulates epigenetic modifications and affects signaling pathways remain to be elucidated. In this review, we discuss methionine and the metabolism of its metabolites, the influence of folate-mediated carbon metabolism, redox reactions, DNA and RNA methylation, and histone modifications, as well as the mammalian rapamycin complex and silent information regulator 1-MYC signaling pathway. This review also summarizes our present understanding of the contribution of methionine to these processes, and current nutritional and pharmaceutical strategies for the prevention and treatment of developmental defects in embryos.

The N6-methyladenosine demethylase ALKBH5 is a novel epigenetic regulator of aortic valve calcification

AIMS

Calcific aortic valve disease (CAVD) is a common heart valve disease with significant clinical consequences. The mechanisms that drive the pathogenesis of CAVD remain to be fully elucidated. N6-methyladenosine (m6A), the most prevalent RNA epigenetic regulator, has recently been implicated in cardiovascular disease, but its role in CAVD has yet to be investigated. In this study, we investigated the potential function of m6A modification in CAVD.

METHODS AND RESULTS

Using clinical samples from CAVD patients in combination with human valve interstitial cell (hVIC) calcification model, we screened the expression of m6A modulators and discovered that alkB homolog 5, RNA demethylase (ALKBH5), a key m6A demethylase, was significantly down-regulated in calcified hVICs and human aortic valves. Consistently, increased m6A levels were seen in calcified hVICs, and treatment with 3-deazaadenosine (DAA), an inhibitor of m6A modification, significantly reduced hVIC osteogenic differentiation and calcification. In addition, we showed that silencing of ALKBH5 expression increased global m6A levels and accelerated hVIC osteogenic differentiation and calcification, whereas overexpression of ALKBH5 resulted in the opposite effect. We demonstrated that ALKBH5 directly modulate m6A levels of TGFBR2 and its mRNA stability, leading to altered TGFBR2 expression and SMAD2 signalling in hVICs. We further showed that inhibition of TGFBR2 or knockdown of SMAD2 attenuated ALKBH5 knockdown-induced hVIC osteogenic differentiation and calcification. The expression of the m6A reader protein YTH N6-methyladenosine RNA binding protein F1 (YTHDF1) was up-regulated during the process of hVIC calcification. Intriguingly, we revealed that the ALKBH5 silencing-induced increased hVIC osteogenic differentiation and calcification were abolished after knockdown of YTHDF1. These data suggest a potential role YTHDF1 in aortic valve calcification.

CONCLUSION

This study showed that ALKBH5 attenuated aortic valve calcification through the TGFBR2/SMAD2 signalling pathway via direct m6A modification of TGFBR2.

Role and mechanisms of m6A demethylases in digestive system tumors

Digestive system tumors are common malignancies in humans, often accompanied by high mortality and poor prognosis. Therefore, intensive research on the pathogenesis of digestive system tumors is imperative. N6-methyladenosine (m6A) is the most common RNA modification in eukaryotes and exerts regulatory effects on RNA expression and metabolism, including splicing, translation, stability, decay, and transport. m6A demethylases belong to the AlkB family of dioxygenases that can catalyze m6A demethylation. Accumulating evidence in recent years has shown that abnormal m6A levels caused by m6A demethylases play crucial roles in different aspects of human cancer development. In this review, we comprehensively summarize the recent findings on the functions and underlying molecular mechanisms of m6A demethylases in cell proliferation, apoptosis, migration, invasion, metastasis, angiogenesis, resistance to chemo- and radiotherapy, and the tumor immune microenvironment (TIME) of digestive system tumors. Furthermore, we discuss the therapeutic potential of targeting these m6A demethylases for treatment.

Methylations in dilated cardiomyopathy and heart failure

Dilated cardiomyopathy (DCM) is characterized by impaired expansion or contraction of the left or both ventricles in the absence of abnormal load conditions (such as primary valve disease) or severe coronary artery disease that can lead to ventricular remodeling. Genetic mutations, infections, inflammation, autoimmune diseases, exposure to toxins, and endocrine or neuromuscular factors have all been implicated in the causation of DCM. Cardiomyopathy, particularly DCM, often has genetic underpinnings, with established or suspected genetic origins. Up to 40% of DCM cases involve probable or confirmed genetic variations. The significance of RNA modification in the pathogenesis of hypertension, cardiac hypertrophy, and atherosclerosis is well-established. Of late, RNA methylation has garnered attention for its involvement in DCM. This review examines the biological mechanisms and effects of RNA methylation in DCM and heart failure.

The Role of N6-Methyladenosine in Mitochondrial Dysfunction and Pathology

Mitochondria are indispensable in cells and play crucial roles in maintaining cellular homeostasis, energy production, and regulating cell death. Mitochondrial dysfunction has various manifestations, causing different diseases by affecting the diverse functions of mitochondria in the body. Previous studies have mainly focused on mitochondrial-related diseases caused by nuclear gene mutations or mitochondrial gene mutations, or mitochondrial dysfunction resulting from epigenetic regulation, such as DNA and histone modification. In recent years, as a popular research area, m6A has been involved in a variety of important processes under physiological and pathological conditions. However, there are few summaries on how RNA methylation, especially m6A RNA methylation, affects mitochondrial function. Additionally, the role of m6A in pathology through influencing mitochondrial function may provide us with a new perspective on disease treatment. In this review, we summarize several manifestations of mitochondrial dysfunction and compile examples from recent years of how m6A affects mitochondrial function and its role in some diseases.

Poly-(ADP-ribose) serves as a scaffold for the methyltransferase METTL3/14 complex in the DNA damage response

PARP1, a crucial DNA break sensor, synthesizes poly-(ADP-ribose) (PAR), a nucleic acid that promotes the recruitment of DNA repair proteins. Emerging evidence highlights a role of RNA and RNA-binding proteins in DNA repair. Notably, the RNA-m6A methyltransferase complex METTL3/14 is implicated in repairing ultraviolet-induced DNA lesions. Here, we dissected the interplay between the two nucleic acids PAR and RNA and how METTL3/14 recruitment and m6A accumulation at laser-induced DNA lesions responds to PAR dynamics. In vitro, METTL3/14 recognized both PAR and RNA, yet PAR presence did not inhibit the methyltransferase complex's catalytic activity. Acute knock-out of METTL3 rendered cells sensitive to transcription-blocking DNA damage and resulted in defects in transcription recovery and transcription-coupled DNA repair. Furthermore, combining METTL3 and PARP inhibitors led to an enhanced antiproliferative effect on cancer cells. Future therapeutic avenues may thus leverage the interplay between the nucleic acids PAR and RNA.

A comprehensive review of m6 A methylation in coronary heart disease

The morbidity and mortality rates of coronary heart disease (CHD) are high worldwide. The primary pathological changes in CHD involve stenosis and ischemia caused by coronary atherosclerosis (AS). Extensive research on the pathogenesis of AS has revealed chronic immunoinflammatory processes and cell proliferation in all layers of coronary vessels, including endothelial cells (ECs), vascular smooth muscle cells, and macrophages. m6 A methylation is a common posttranscriptional modification of RNA that is coordinated by a variety of regulators (writers, readers, erasers) to maintain the functional stability of modified mRNAs and ncRNAs. In recent years, there has been increasing focus on the involvement of m6 A methylation in the incidence and progression of CHD, which starts with atherosclerotic plaque formation, leads to myocardial ischemia, and ultimately results in the occurrence of myocardial infarction (MI). m6 A regulators modulate relevant signaling pathways to participate in the inflammatory response, programmed death of cardiomyocytes, and fibrosis. Therefore, diagnostic models based on m6 A profiling are helpful for the early detection of CHD, and m6 A methylation shows promise as a sensitive target for new drugs to treat CHD in the future.

Environmental Exposure, Epitranscriptomic Perturbations, and Human Diseases

Epitranscriptomics is a rapidly evolving field, and it examines how chemical modifications on RNA regulate gene expression. Increasing lines of evidence support that exposure to various environmental agents can change substantially chemical modifications on RNA, thereby perturbing gene expression and contributing to disease development in humans. However, the molecular mechanisms through which environmental exposure impairs RNA modification-associated proteins ("reader", "writer", and "eraser" or RWE proteins) and alters the landscape of RNA modifications remain poorly understood. Here, we provide our perspectives on the current knowledge about how environmental exposure alters the epitranscriptome, where we focus on dynamic changes in RNA modifications and their regulatory proteins elicited by exposure to environmental agents. We discuss how these epitranscriptomic alterations may contribute to the development of human diseases, especially neurodegeneration and cancer. We also discuss the potential and technical challenges of harnessing RNA modifications as biomarkers for monitoring environmental exposure. Finally, we emphasize the need to integrate multiomics approaches to decipher the complex interplay between environmental exposure and the epitranscriptome and offer a forward-looking viewpoint on future research priorities that may inform public health interventions and environmental regulations.

METTL3, an Independent Adverse Prognostic Factor for AML, Promotes the Development of AML by Modulating the PGC-1α-MAPK Pathway and PGC-1α-Antioxidant System Axis

BACKGROUND

m6A represents a prevalent epigenetic modification of mammalian mRNAs. Studies have demonstrated that m6A RNA methylation-modifying enzymes play crucial roles in the onset and progression of AML. However, their clinical relevance remains undefined, and the mechanisms underlying their modulation of AML have yet to be elucidated.

RESULTS

The expression levels of the m6A RNA-modifying enzymes METTL3, METTL14, WTAP, FTO and ALKBH5 were elevated in AML patients. METTL3-positive AML is often accompanied by DNMT3A mutations and is also an independent poor prognostic factor for AML patients. Following METTL3 knockdown, we observed a decrease in the m6A level of the mitochondrial oxidative stress gene PGC-1α in K562 and MV4-11 cells. We analyzed the expression levels of PGC-1α and METTL3 mRNA in 105 patients with primary AML. The expression levels of PGC-1α and METTL3 mRNA were positively correlated. Similar to METTL3 knockdown, PGC-1α gene knockdown resulted in increased phosphorylation of the key signaling molecules P38, c-Jun and ERK1/2 in the MAPK signaling pathway, and decreased mRNA levels of SOD1, GPX1, catalase and UCP2 in the antioxidant system of K562 cells. Analysis of the TCGA and GSE13159 datasets, along with samples from West China Hospital, revealed that patients exhibiting high PGC-1α expression had a poor prognosis.

CONCLUSION

The m6A methylation-modifying enzyme METTL3 is an independent prognostic factor for poor prognosis in AML patients. PGC-1α is a downstream signaling molecule of METTL3, and METTL3 affects its expression by regulating the m6A level of PGC-1α. PGC-1α acts as an oncogene in AML by affecting the MAPK pathway and antioxidant system.

The dynamics of N6-methyladenine RNA modification in resistant and susceptible rice varieties responding to rice stem borer damage

N6-methyladenosine (m6A) is the most prevalent modification in cellular RNA which orchestrates diverse physiological and pathological processes during stress response. However, the differential m6A modifications that cope with herbivore stress in resistant and susceptible crop varieties remain unclear. Here, we found that rice stem borer (RSB) larvae grew better on indica rice (e.g., MH63, IR64, Nanjing 11) than on japonica rice varieties (e.g., Nipponbare, Zhonghua 11, Xiushui 11). Then, transcriptome-wide m6A profiling of representative resistant (Nipponbare) and susceptible (MH63) rice varieties were performed using a nanopore direct RNA sequencing approach, to reveal variety-specific m6A modifications against RSB. Upon RSB infestation, m6A methylation occurred in actively expressed genes in Nipponbare and MH63, but the number of methylation sites decreased across rice chromosomes. Integrative analysis showed that m6A methylation levels were closely associated with transcriptional regulation. Genes involved in herbivorous resistance related to mitogen-activated protein kinase, jasmonic acid (JA), and terpenoid biosynthesis pathways, as well as JA-mediated trypsin protease inhibitors, were heavily methylated by m6A, and their expression was more pronounced in RSB-infested Nipponbare than in RSB-infested MH63, which may have contributed to RSB resistance in Nipponbare. Therefore, dynamics of m6A modifications act as the main regulatory strategy for expression of genes involved in plant-insect interactions, which is attributed to differential responses of resistant and susceptible rice varieties to RSB infestation. These findings could contribute to developing molecular breeding strategies for controlling herbivorous pests.

Decoding N6-methyladenosine's dynamic role in stem cell fate and early embryo development: insights into RNA-chromatin interactions

N6-methyladenosine (m6A), a reversible and dynamic RNA modification, plays pivotal roles in regulating stem cell pluripotency and early embryogenesis. Disruptions in m6A homeostasis lead to profound developmental defects, impairing processes such as stem cell self-renewal, lineage specification, oocyte maturation, zygotic genome activation, and maternal RNA degradation after fertilization. Beyond its well-recognized roles in mRNA transport, stability, and translation, recent studies have highlighted m6A's critical role in transcriptional regulation through intricate RNA-chromatin interactions, notably involving chromatin-associated regulatory RNAs (carRNAs) and retrotransposon RNAs. This review delves into the dynamic regulatory landscape of m6A, highlighting its critical interplay with chromatin modifications, and explores its broader implications in stem cell biology and early embryonic development.

m6A eraser ALKBH5/treRNA1/DDX46 axis regulates BCR expression

Epitranscriptomic modifications, particularly N6-methyladenosine (m6A), have emerged as critical regulators of RNA stability, localization, and translation, shaping immune responses and tumor progression. In B-cell biology, m6A modifications influence germinal center formation and antigen-driven differentiation, underscoring their importance in immune regulation. Among m6A regulators, ALKBH5 (RNA demethylase) is pivotal in removing methylation marks and modulating gene expression in diverse cellular contexts. Despite advancements in understanding m6A dynamics, the mechanistic interplay between m6A demethylation and B-cell receptor (BCR) signaling pathways still needs to be explored. This study reveals a novel regulatory axis involving ALKBH5, treRNA1 (Translation Regulatory Long Non-Coding RNA 1), and DDX46 (RNA helicase). Upon activation signals, ALKBH5 and treRNA1 translocate to the nucleus, forming a functional complex with DDX46 to orchestrate the removal of m6A modifications on key transcripts, including those involved in BCR signaling. This demethylation enhances transcript stability and facilitates cytoplasmic export through interaction with the RNA-binding protein HuR, promoting efficient translation. Disruption of this axis, via loss of ALKBH5, DDX46, or treRNA1, led to impaired transcript processing and diminished BCR-related gene expression, highlighting the critical role of m6A demethylation in maintaining RNA dynamics. These findings uncover a previously unrecognized epitranscriptomic mechanism driven by the ALKBH5-treRNA1-DDX46 complex, with significant implications for B-cell functionality, immune regulation, and oncogenic pathways. Targeting this axis offers a promising avenue for developing therapeutic strategies in cancer and immune-related disorders where m6A dysregulation plays a central role.

RNA m6A modification meets plant hormones

Plant hormones are essential signalling molecules that control and coordinate diverse physiological processes in plant development and adaptation to ever-fluctuating environments. This hormonal regulation of plant development and environmental responses has recently been shown to extensively involve the most widespread RNA modification, N6-methyladenosine (m6A). Here we discuss the current understanding of the crosstalk between m6A and plant hormones, focusing on their reciprocal regulation, where hormonal signals induce m6A reprogramming and m6A affects hormone biosynthesis and signalling cascades. We also highlight new insights into how m6A contributes to the hormonal control of plant development and stress responses. Furthermore, we discuss future prospects for unveiling the regulatory networks that orchestrate epitranscriptome-hormone interactions and harnessing the related knowledge accrued to enhance crop productivity and resilience in changing environments.

WTAP-mediated m6A modification of Hmgb2 contributes to spermatogenic damage induced by PM2.5 exposure

N6-methyladenosine (m6A) is extensively involved in complex spermatogenesis while being extremely sensitive to environmental exposure. Numerous studies have revealed the toxicity of fine particulate matter (PM2.5) to the male reproductive system, but the specific epigenetic mechanisms involved have been underexplored. Here, we investigated the effect of m6A modification on PM2.5-induced male reproductive impairment by establishing a real-time PM2.5-exposed mouse model and a GC-2spd cell model. PM2.5 exposure resulted in damage to the spermatogenic epithelium and mitochondrial abnormalities in spermatocytes and significantly reduced sperm motility in mice. Gene enrichment analyses of testicular tissue differential m6A modified genes were significantly enriched to spermatogenesis in the PM2.5-treated mice compared with the control group, and the expression of the methylase WTAP was markedly decreased after PM2.5 exposure. Moreover, PM2.5 exposure resulted in a significant reduction in the expression of the spermatogenesis-related gene Hmgb2, as well as in the level of the Hmgb2 m6A modification. Transcriptome sequencing and verification experiments suggested that Hmgb2 may regulate spermatocyte ATP levels. In addition, we demonstrated that the m6A methylase WTAP affects Hmgb2 mRNA stability via m6A modification. Our study provides new insights into PM2.5-induced damage to spermatogenesis and reduced sperm motility.

N6-methyladenosine modification of the subgroup J avian leukosis viral RNAs attenuates host innate immunity via MDA5 signaling

Subgroup J avian leukosis virus (ALV-J), a retrovirus, elicits immunosuppression and persistent infections in chickens. Although it is widely acknowledged that ALV-J can evade the host's innate immune defenses, the mechanisms behind this immune evasion remain elusive. N6-methyladenosine (m6A), the most prevalent internal RNA modification, plays a role in innate immune evasion. Our research identified ALV-J as an inefficient stimulator of innate immunity in vitro and in vivo, with its genomic RNA featuring m6A modifications predominantly in the envelope protein (Env) region and 3' untranslated region (3'UTR). To elucidate the functional consequences of m6A modification, we subsequently generated m6A-deficient ALV-J through its culturing in the DF-1 overexpressing fat mass and obesity-associated protein (FTO) cells. The m6A-deficient ALV-J virus, or its RNAs significantly enhanced IFN-β production compared to the wild-type (wt) ALV-J, suggesting a pivotal regulatory function of m6A modifications in modulating innate immune response. Mechanistically, the m6A modification of the ALV-J genomic RNA directly impacted its recognition by MDA5, weakening its binding and ubiquitination and attenuating IFN-β activation. Moreover, m6A-deficient ALV-J, created by inducing mutations in m6A sites within Env and 3'UTR, exhibited reduced replication capacity and elevated IFN-β expression in host cells. Importantly, this phenomenon was abolished in MDA5-knockout DF-1 cells, further demonstrating the core role of MDA5. These data demonstrate that m6A modification of ALV-J genomic RNA dampens the host's innate immune response through MDA5 signaling pathway.

N4-acetylcytidine and other RNA modifications in epitranscriptome: insight into DNA repair and cancer development

N4-acetylcytidine (ac4C) is a post-transcriptional RNA modification that plays a crucial role in the epitranscriptome, influencing gene expression and cellular function. This modification occurs at the cytosine base, where an acetyl group is installed to the nitrogen at the 4th position (N4). This co-transcription modification affects RNA stability, RNA structure, and translation efficiency. Recent studies have uncovered a potential link between RNA modifications and DNA repair mechanisms, suggesting that ac4C-modified or methylated RNAs may interact with factors involved in DNA repair pathways; thus, influencing the cellular response to DNA damage. Dysregulation of modified RNAs, including ac4C RNA, has been implicated in cancer development, where aberrant levels of these RNAs may contribute to oncogenic transformation by altering genome stability and the expression of key genes regulating cell proliferation, cell cycle progression, and apoptosis. Understanding the dynamics of modified RNAs offers promising insights into the role of epitranscriptome in DNA repair processes and cancer treatment.

An epitranscriptomic program maintains skeletal stem cell quiescence via a METTL3-FEM1B-GLI1 axis

Skeletal stem cells (SSCs) maintain the skeletal system via pluripotency and differentiation capacity. However, it remains largely unknown how these cells precisely regulate their function to maintain skeletal organization. Here, we delineate the RNA m6A modification landscape across skeletal cell populations in the mouse epiphysis. Our findings show that m6A modifications are prevalent in skeletal stem cell and progenitor populations and play critical roles in cell fate determination. Genetic deletion of Mettl3, the core catalytic subunit of the m6A-methyltransferase complex, in murine skeletal stem and progenitors impaired bone development, leading to shortened limbs, disrupted growth plate zonation, and decreased bone mass. Moreover, Mettl3 deficiency induced quiescence exit in SSCs, together with compromised self-renewal capacity and differentiation potential. Mechanistically, Mettl3-mediated m6A modification reduced mRNA stability of the Cul2-RING E3 ligase complex subunit Fem1b, which subsequently stabilizes Gli1 protein, a key transcription factor of Hedgehog pathway for maintaining SSC identity and function. Thus, we present a comprehensive RNA m6A modification landscape of skeletal cell hierarchy and uncover the essential function of epitranscriptomically-regulated proteostasis in maintaining SSCs quiescence and potency.

hnRNPC Functions with HuR to Regulate Alternative Splicing in an m6A-Dependent Manner and is Essential for Meiosis

N6-methyladenosine (m6A) and its reader proteins are involved in pre-mRNA processing and play a variety of roles in numerous biological processes. However, much remains to be understood about the regulation of m6A and the function of its specific readers during meiotic processes. Here, this study shows that the potential m6A reader protein hnRNPC is essential for both male and female meiosis in mice. Germ cell-specific knockout of Hnrnpc causes meiotic arrest at pachynema in male mice. Specifically, hnRNPC-deficient males show abnormal meiosis initiation and defective meiotic progression, ultimately leading to meiotic arrest at the pachytene stage. Interestingly, hnRNPC-null females show similar meiotic defects to males. Mechanistically, this study discovers that in male germ cells, hnRNPC works with HuR to directly bind and modulate alternative splicing of meiotic-related genes (e.g., Sycp1, Brca1, and Smc5) in an m6A-dependent manner during spermatogenesis. Collectively, these findings reveal hnRNPC as a critical factor for meiosis and contribute to a mechanistic understanding of the hnRNPC-HuR interaction in alternative splicing of mRNAs during germ cell development.

Unlocking the potential of circular RNA vaccines: a bioinformatics and computational biology perspective

Bioinformatics has significantly advanced RNA-based therapeutics, particularly circular RNAs (circRNAs), which outperform mRNA vaccines, by offering superior stability, sustained expression, and enhanced immunogenicity due to their covalently closed structure. This review highlights how bioinformatics and computational biology optimise circRNA vaccine design, elucidates internal ribosome entry sites (IRES) selection, open reading frame (ORF) optimisation, codon usage, RNA secondary structure prediction, and delivery system development. While circRNA vaccines may not always surpass traditional vaccines in stability, their production efficiency and therapeutic efficacy can be enhanced through computational strategies. The discussion also addresses challenges and future prospects, emphasizing the need for innovative solutions to overcome current limitations and advance circRNA vaccine applications.

Wolbachia elevates host methyltransferase expression and alters the m6A methylation landscape in Aedes aegypti mosquito cells

Wolbachia pipientis is an intracellular endosymbiotic bacterium that blocks the replication of several arboviruses in transinfected Aedes aegypti mosquitoes, yet its antiviral mechanism remains unknown. For the first time, we employed Nanopore direct RNA sequencing technology to investigate the impact of wAlbB strain of Wolbachia on the host's N6-methyladenosine (m6A) machinery and post-transcriptional modification landscape. Our study revealed that Wolbachia infection elevates the expression of genes involved in the mosquito's m6A methyltransferase complex. However, knocking down these m6A-related genes did not affect Wolbachia density. Nanopore sequencing identified 1,392 differentially modified m6A DRACH motifs on mosquito transcripts, with 776 showing increased and 616 showing decreased m6A levels due to Wolbachia. These m6A sites were predominantly enriched in coding sequences and 3'-untranslated regions. Gene Ontology analysis revealed that genes with reduced m6A levels were over-represented in functional GO terms associated with purine nucleotide binding functions critical in the post-transcriptional modification process of m6A. Differential gene expression analysis of the Nanopore data uncovered that a total of 643 protein-coding genes were significantly differentially expressed, 427 were downregulated, and 216 were upregulated. Several classical and non-classical immune-related genes were amongst the downregulated DEGs. Notably, it revealed a critical host factor, transmembrane protein 41B (TMEM41B), which is required for flavivirus infection, was upregulated and methylated in the presence of Wolbachia. Indeed, there is a strong correlation between gene expression being upregulated in genes with both increased and decreased levels of m6A modification, respectively. Our findings underscore Wolbachia's ability to modulate many intracellular aspects of its mosquito host by influencing post-transcriptional m6A modifications and gene expression, and it unveils a potential link behind its antiviral properties.

FTO suppresses DNA repair by inhibiting PARP1

Maintaining genomic integrity and faithful transmission of genetic information is essential for the survival and proliferation of cells and organisms. DNA damage, which threatens the integrity of the genome, is rapidly sensed and repaired by mechanisms collectively known as the DNA damage response. The RNA demethylase FTO has been implicated in this process; however, the underlying mechanism by which FTO regulates DNA repair remains unclear. Here, we use an unbiased quantitative proteomic approach to identify the proximal interactome of endogenous FTO protein. Our results demonstrate a direct interaction with the DNA damage sensor protein PARP1, which dissociates upon ultraviolet stimulation. FTO inhibits PARP1 catalytic activity and controls its clustering in the nucleolus. Loss of FTO enhances PARP1 enzymatic activity and the rate of PARP1 recruitment to DNA damage sites, accelerating DNA repair and promoting cell survival. Interestingly, FTO regulates PARP1 function and DNA damage response independent of its catalytic activity. We conclude that FTO is an endogenous negative regulator of PARP1 and the DNA damage response in cells beyond its role as an RNA demethylase.

The Role of M6A LncRNA Modification in Papillary Thyroid Cancer

Thyroid Cancer (TC) is the most common endocrine cancer, of which papillary thyroid cancer (PTC), a well-differentiated type of TC, accounts for 80-90%. Long non-coding RNAs (lncRNAs), which comprise non-protein-coding segments of the genome, have been found to play a crucial role in various biological processes, including cancer development. The activity of lncRNAs is modified through epigenetic modifications, with N6-Methyladenosine (m6A) modifications implicated in the progression of several malignancies. The activity of m6A is further regulated by modifying enzymes classified as "readers", writers", and "erasers", of which specific enzymes have been found to play a role in various aspects of PTC. Recent research has highlighted the significance of m6A modification in regulating the expression and function of lncRNAs associated with PTC pathogenesis. Dysregulation of this process implicates tumor proliferation, invasion, and metastasis, with subsequent impact on prognosis. Therefore, understanding the interplay between m6A modification and lncRNAs provides valuable insights into the molecular mechanisms underlying PTC progression. This narrative review aims to explore the established role of several prominent m6A modifying enzymes and lncRNAs on cancer pathogenesis and seeks to clarify the function of these enzymes in PTC pathogenesis.

Review of the role and potential clinical value of m6A methylation modifications in the biological process of osteosarcoma

Osteosarcoma (OS), an aggressive bone tumor, is a substantial threat to the quality of life and survival of affected individuals. Despite recent improvements in OS therapies, the considerable variability and chemotherapy resistance of this cancer necessitate continuous research to discover new treatment targets and biomarkers. Recent epigenetic advances highlight the crucial role of N6-methyladenosine (m6A) methylation in cancer. In OS, m6A methylation has been demonstrated to be a pivotal component in the pathogenesis. This review introduces new findings regarding the association between m6A methylation regulators and OS, and summarizes the potential clinical applications of OS and m6A methylation regulators, including the role of m6A methylation in OS proliferation, growth, apoptosis, and cell migration, invasion, and metastasis; relationship between m6A methylation and OS chemotherapy resistance; and relationship between m6A methylation and OS prognosis. Our review had certain limitations. The interaction between m6A methylation regulators and other oncogenic factors, such as lncRNAs and ncRNAs, is not fully understood. We hope that these potential methods will be translated into clinical applications and effective treatment.

Characterization of the m6A Regulatory Gene Family in Phaseolus vulgaris L. and Functional Analysis of PvMTA in Response to BCMV Infection

Common bean (Phaseolus vulgaris L.) is known for its high protein, dietary fiber, and various trace element contents, making it a widely grown leguminous crop globally. The bean common mosaic virus (BCMV) poses a significant threat to leguminous crop production, causing substantial yield reductions when common beans are infected. Widely occurring in mRNA, the m6A modification is vital for maintaining mRNA stability, facilitating splicing, enabling nuclear export, supporting polyadenylation, and initiating translation. Recent studies have identified the m6A regulatory gene family in various plant species, and its ability to regulate plant virus infection has been confirmed. There is currently insufficient information regarding the m6A regulatory gene family in beans and how it responds to BCMV infection. Consequently, we carried out a genome-wide characterization of the m6A regulatory gene family in common bean, which led to the identification of 31 potential regulatory gene members associated with m6A. According to evolutionary analysis, the increase in the bean m6A regulatory gene family appears to be linked to either whole-genome duplication or segmental duplication events. Subsequent investigations into the expression levels of these genes throughout different phases of BCMV infection showed that all candidate genes responded to the infection with various changes in expression. Moreover, we characterized the methyltransferase activity of PvMTA and validated the interactive relationship between mRNA adenosine methyltransferase A (MTA) and mRNA adenosine methyltransferase B (MTB) in common beans. Through overexpressing and silencing PvMTA, we further ascertained that this particular gene has a detrimental impact on the regulation of BCMV infection. This research provides fresh perspectives on the molecular processes that govern the interaction between the common bean and BCMV and aids progress in molecular bean breeding.

Genome-wide identification and characterization of ALKB homolog gene family in wheat (Triticum aestivum L.)

Introduction

N6-methyladenosine (m6A) is the most prevalent posttranscriptional modification in eukaryotic mRNAs. AlkB homologs (ALKBHs) are involved in plant responses to stress by modulating m6A methylation. However, homologous genes in wheat remain largely uncharacterized.

Methods and results

In this study, 30 ALKBH genes were identified in wheat, and analyzed their physicochemical properties. The phylogenetic analysis allowed the classification of these genes into seven distinct subfamilies. Additionally, their conserved domains, motif compositions, gene structures, chromosomal localization, and synteny, and the predicted cis-acting elements within their promoters were examined. Expression analysis revealed that TaALKBH9B-5 exhibited the highest expression and its demethylase activity was investigated. Furthermore, TaALKBH9B-5 was significantly upregulated in response to abscisic acid treatment and cold stress, indicating a positive regulatory trend.

Discussion

In conclusion, this study provides a comprehensive genomic assessment of the TaALKBH gene family and offers a theoretical framework for understanding the role of TaALKBH9B in the response to abiotic stress in wheat.

Epitranscriptomic regulation of HIF-1: bidirectional regulatory pathways

BACKGROUND

Epitranscriptomics, the study of RNA modifications such as N6-methyladenosine (m6A), provides a novel layer of gene expression regulation with implications for numerous biological processes, including cellular adaptation to hypoxia. Hypoxia-inducible factor-1 (HIF-1), a master regulator of the cellular response to low oxygen, plays a critical role in adaptive and pathological processes, including cancer, ischemic heart disease, and metabolic disorders. Recent discoveries accent the dynamic interplay between m6A modifications and HIF-1 signaling, revealing a complex bidirectional regulatory network. While the roles of other RNA modifications in HIF-1 regulation remain largely unexplored, emerging evidence suggests their potential significance.

MAIN BODY

This review examines the reciprocal regulation between HIF-1 and epitranscriptomic machinery, including m6A writers, readers, and erasers. HIF-1 modulates the expression of key m6A components, while its own mRNA is regulated by m6A modifications, positioning HIF-1 as both a regulator and a target in this system. This interaction enhances our understanding of cellular hypoxic responses and opens avenues for clinical applications in treating conditions like cancer and ischemic heart disease. Promising progress has been made in developing selective inhibitors targeting the m6A-HIF-1 regulatory axis. However, challenges such as off-target effects and the complexity of RNA modification dynamics remain significant barriers to clinical translation.

CONCLUSION

The intricate interplay between m6A and HIF-1 highlights the critical role of epitranscriptomics in hypoxia-driven processes. Further research into these regulatory networks could drive therapeutic innovation in cancer, ischemic heart disease, and other hypoxia-related conditions. Overcoming challenges in specificity and off-target effects will be essential for realizing the potential of these emerging therapies.

YTHDF1 and YTHDC1 m6A reader proteins regulate HTLV-1 tax and hbz activity

Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus responsible for adult T-cell leukemia/lymphoma (ATLL) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), a progressive neurodegenerative disease. Regulation of viral gene expression plays a key role in viral persistence and pathogenesis. However, the molecular mechanisms underlying this fine-tuned regulation remain poorly understood. Little is known regarding RNA chemical modifications of HTLV-1 RNA and how these affect viral biology and disease development. Post-transcriptional chemical modification of RNA is common in eukaryotes, with N6-methyladenosine (m6A) being the most prevalent. In this study, we investigated the role of m6A RNA modifications on HTLV-1 gene expression. Using MeRIP-Seq, we mapped the sites of m6A modification to the 3' end of the viral genome. We found HTLV-1 RNA, as well as viral oncogene transcripts tax and hbz, contained m6A modifications. m6A-depletion in HTLV-1-transformed cells decreased sense-derived viral genes (Tax, Gag, and Env) and increased antisense-derived Hbz expression. Tax and hbz transcripts were bound by reader proteins YTHDF1 and YTHDC1 in a panel of HTLV-1 T-cell lines. Using expression vectors and shRNA-mediated knockdown, we found that YTHDF1 had opposing effects on viral gene expression, decreasing sense-derived viral genes and increasing antisense-derived Hbz. Upon further study, the YTHDF1 effects on tax abundance were dependent on tax m6A deposition. The nuclear m6A reader protein YTHDC1 affected the abundance of both sense- and antisense-derived viral transcripts and specifically enhanced the nuclear export of tax transcript. Collectively, our results demonstrate global m6A levels and m6A reader proteins YTHDF1 and YTHDC1 regulate HTLV-1 gene expression.IMPORTANCEHuman T-cell leukemia virus type 1 (HTLV-1) persistence and pathogenesis are controlled through tight regulation of viral gene expression. The fate of RNA can be controlled by epigenetic modifications that impact gene expression without altering the DNA sequence. Our study details the impact of N6-methyladenosine (m6A) RNA chemical modifications on HTLV-1 gene expression. We found that reductions in global m6A levels affected viral gene expression, decreasing Tax and other sense-derived viral genes, whereas increasing the antisense-derived Hbz. Our results suggest the oncogenic viral transcripts, tax and hbz, are m6A-modified in cells. We found that these viral RNA modifications are interpreted by reader proteins YTHDF1 and YTHDC1, which dictate the fate of the viral RNA. Understanding HTLV-1 RNA chemical modifications offers potential insights into novel therapeutic strategies for HTLV-1-associated diseases.

Single-cell sequencing analysis reveals the essential role of the m 6A reader YTHDF1 in retinal visual function by regulating TULP1 and DHX38 translation

N6-methyladenosine (m 6A) modification of mRNA is a critical post-transcriptional regulatory mechanism that modulates mRNA metabolism and neuronal function. The m 6A reader YTHDF1 has been shown to enhance the translational efficiency of m 6A-modified mRNAs in the brain and is essential for learning and memory. However, its role in the mature retina remains unclear. Herein, we report a novel role of Ythdf1 in the maintenance of retinal function using a genetic knockout model. Loss of Ythdf1 resulted in impaired scotopic electroretinogram (ERG) responses and progressive retinal degeneration. Detailed analyses of rod photoreceptors confirmed substantial degenerative changes in the absence of ciliary defects. Single-cell RNA sequencing revealed comprehensive molecular alterations across all retinal cell types in Ythdf1-deficient retinas. Integrative analysis of methylated RNA immunoprecipitation (MeRIP) sequencing and RIP sequencing identified Tulp1 and Dhx38, two inheritable retinal degeneration disease-associated gene homologs, as direct targets of YTHDF1 in the retina. Specifically, YTHDF1 recognized and bound m 6A-modified Tulp1 and Dhx38 mRNA at the coding sequence (CDS), enhancing their translational efficiency without altering mRNA levels. Collectively, these findings highlight the essential role of YTHDF1 in preserving visual function and reveal a novel regulatory mechanism of m 6A reader proteins in retinal degeneration, identifying potential therapeutic targets for severe retinopathies.

Global analysis by LC-MS/MS of N6-methyladenosine and inosine in mRNA reveal complex incidence

The precise and unambiguous detection and quantification of internal RNA modifications represents a critical step for understanding their physiological functions. The methods of direct RNA sequencing are quickly developing allowing for the precise location of internal RNA marks. This detection is, however, not quantitative and still presents detection limits. One of the biggest remaining challenges in the field is still the detection and quantification of m6A, m6Am, inosine, and m1A modifications of adenosine. The second intriguing and timely question remaining to be addressed is the extent to which individual marks are coregulated or potentially can affect each other. Here, we present a methodological approach to detect and quantify several key mRNA modifications in human total RNA and in mRNA, which is difficult to purify away from contaminating tRNA. We show that the adenosine demethylase FTO primarily targets m6Am marks in noncoding RNAs in HEK293T cells. Surprisingly, we observe little effect of FTO or ALKBH5 depletion on the m6A mRNA levels. Interestingly, the upregulation of ALKBH5 is accompanied by an increase in inosine level in overall mRNA.

The Role of M6A Modification in Autoimmunity: Emerging Mechanisms and Therapeutic Implications

N6-methyladenosine (m6A), a prevalent and essential RNA modification, serves a key function in driving autoimmune disease pathogenesis. By modulating immune cell development, activation, migration, and polarization, as well as inflammatory pathways, m6A is crucial in forming innate defenses and adaptive immunity. This article provides a comprehensive overview of m6A modification features and reveals how its dysregulation affects the intensity and persistence of immune responses, disrupts immune tolerance, exacerbates tissue damage, and promotes the development of autoimmunity. Specific examples include its contributions to systemic autoimmune disorders like lupus and rheumatoid arthritis, as well as conditions that targeting specific organs like multiple sclerosis and type 1 diabetes. Furthermore, this review explores the therapeutic promise of target m6A-related enzymes ("writers," "erasers," and "readers") and summarizes recent advances in intervention strategies. By focusing on the mechanistic and therapeutic implications of m6A modification, this review sheds light on its role as a promising tool for both diagnosis and treatment in autoimmune disorders, laying the foundation for advancements in customized medicine.

mRNA m6A regulates gene expression via H3K4me3 shift in 5' UTR

BACKGROUND

N6-methyladenosine (m6A) is a prevalent and conserved RNA modification in eukaryotes. While its roles in the 3' untranslated regions (3' UTR) are well-studied, its role in the 5' UTR and its relationship with histone modifications remain underexplored.

RESULTS

We demonstrate that m6A methylation in the 5' UTR of mRNA triggers a downstream shift in H3K4me3 modification. This regulatory mechanism is conserved in Arabidopsis, rice, and chrysanthemum. The observed shift in H3K4me3 is genetically controlled by m6A modifiers and influences gene expression. MTA, the m6A methylase, preferentially binds to phosphorylated serine 5 (Ser5P)-CTD of RNA Pol II during transcription, leading to the displacement of ATX1, the H3K4me3 methylase. This dynamic binding of MTA and ATX1 to RNA Pol II ultimately results in the shift of H3K4me3 modification. Genetic evidence demonstrates that m6A in the 5' UTR controls H3K4me3 shift, thereby affecting SEDOHEPTULOSE-BISPHOSPHATASE expression and leaf senescence.

CONCLUSIONS

Our study provides new insights into the roles of m6A modification and its crosstalk with histone modification in 5' UTRs, shedding light on the mechanism of m6A-mediated gene expression regulation.

Targeting m6A RNA Modification in Tumor Therapeutics

The prevalent eukaryotic RNA modification N6-methyladenosine (m6A), which is distributed in more than 50% of cases, has demonstrated significant implications in both normal development and disease progression, particularly in the context of cancer. This review aims to discuss the potential efficacy of targeting tumor cells through modulation of m6A RNA levels. Specifically, we discuss how the upregulation or downregulation of integral or specific targets is effective in treating different tumor types and patients. Additionally, we will cover the factors influencing the efficacy of m6A RNA targeting in tumor treatment. Our review will focus on the impact of targeting m6A mRNA on genes and cells and assess its potential as a therapeutic strategy for tumors. Despite the challenges involved, further research on m6A RNA in tumors and its integration with existing tumor therapy approaches is warranted.

IMPlications of IMP2 in RNA Biology and Disease

Insulin-like growth factor 2 mRNA-binding protein 2 (IMP2) is an RNA-binding protein that positively regulates m6A-modified RNAs involved in critical cellular processes such as metabolism, oncogenesis, and immune function. Here, we elucidate facets of IMP2 biology, including several mechanisms of action on RNA, factors that regulate IMP2 expression, its relevant biological target RNAs, its role in normal development and disease, and its potential as a therapeutic target. IMP2 is a multi-level regulator of metabolism, influencing pathways linked to diabetes, obesity, and adipose function. Through genomic amplification and transcriptional overexpression in cancer cells, IMP2 can drive the initiation and progression of multiple cancer types, and high expression is associated with decreased overall survival of patients with cancer. IMP2 influences normal immune function, inflammation, macrophage polarization, and tumor immune evasion. IMP2 has emerged as a promising therapeutic target, particularly for cancers and metabolic diseases.

m6A modified pre-miR-503-5p contributes to myogenic differentiation through the activation of mTOR pathway

The post-transcriptional regulation of epigenetic modification is a hot topic in skeletal muscle development research. Both m6A modifications and miRNAs have been well-established as crucial regulators in skeletal muscle development. However, the interacting regulatory mechanisms between m6A modifications and miRNAs in skeletal muscle development remain unclear. In this study, miRNA sequencing analysis of goat primary myoblasts (GPMs) pre- and post-differentiation revealed that miR-503-5p was upregulated during myogenic differentiation, and its precursor was identified to contain m6A modification sites. Combined analysis of RIP, qRT-PCR and mRNA stability assay showed that Ythdf2 could recognize and bind the m6A site on pre-miR-503-5p, thereby facilitating the maturation of pre-miR-503-5p in an m6A-dependent manner. Moreover, the overexpression of miR-503-5p significantly inhibits the proliferation of GPMs, promotes myogenic differentiation, and enhances mitochondrial biogenesis while activating the mTOR pathway. However, the suppression of mTOR activity can effectively counteract the accelerated myogenic differentiation induced by miR-503-5p overexpression. Collectively, our results indicate that Ythdf2-dependent m6A modification facilitates the maturation of pre-miR-503-5p, thereby promoting skeletal muscle differentiation through the activation of the mTOR pathway. These insights lay a valuable foundation for further investigation into the complexities of skeletal muscle development and the potential implications of epigenetic regulation in this process.

Post-Transcriptional Regulation of Gene Expression and the Intricate Life of Eukaryotic mRNAs

In recent years, there has been a growing appreciation for how regulatory events that occur either co- or post-transcriptionally contribute to the control of gene expression. Messenger RNAs (mRNAs) are extensively regulated throughout their metabolism in a precise spatiotemporal manner that requires sophisticated molecular mechanisms for cell-type-specific gene expression, which dictates cell function. Moreover, dysfunction at any of these steps can result in a variety of human diseases, including cancers, muscular atrophies, and neurological diseases. This review summarizes the steps of the central dogma of molecular biology, focusing on the post-transcriptional regulation of gene expression.

BRD4 regulates m6A of ESPL1 mRNA via interaction with ALKBH5 to modulate breast cancer progression

The interaction between m6A-methylated RNA and chromatin modification remains largely unknown. We found that targeted inhibition of bromodomain-containing protein 4 (BRD4) by siRNA or its inhibitor (JQ1) significantly decreases mRNA m6A levels and suppresses the malignancy of breast cancer (BC) cells via increased expression of demethylase AlkB homolog 5 (ALKBH5). Mechanistically, inhibition of BRD4 increases the mRNA stability of ALKBH5 via enhanced binding between its 3' untranslated regions (3'UTRs) with RNA-binding protein RALY. Further, BRD4 serves as a scaffold for ubiquitin enzymes tripartite motif containing-21 (TRIM21) and ALKBH5, resulting in the ubiquitination and degradation of ALKBH5 protein. JQ1-increased ALKBH5 then demethylates mRNA of extra spindle pole bodies like 1 (ESPL1) and reduces binding between ESPL1 mRNA and m6A reader insulin like growth factor 2 mRNA binding protein 3 (IGF2BP3), leading to decay of ESPL1 mRNA. Animal and clinical studies confirm a critical role of BRD4/ALKBH5/ESPL1 pathway in BC progression. Further, our study sheds light on the crosstalks between histone modification and RNA methylation.

TDP-43/ALKBH5-mediated m6A modification of CDC25A mRNA promotes glioblastoma growth by facilitating G1/S cell cycle transition

Glioblastoma (GBM) exhibits significant intratumor heterogeneity (ITH), indicating the presence of tumor cells with diverse growth rates. Here, we aimed to identify fast-growing cells in GBM and elucidate the underlying mechanisms. Precisely targeting these cells could offer an improved treatment option. Our results found that targeting ALKBH5 expression impaired GBM proliferation and tumor stemness. Nuclear but not overall expression of ALKBH5 differs between monoclonal cells derived from the same patient with different proliferation rates. Mechanistically, ALKBH5 interacted with TAR DNA-binding protein 43 (TDP-43) in fast-growing cells. Furthermore, TDP-43 facilitated the nuclear localization of ALKBH5 and its binding to cell division cycle 25A (CDC25A) pre-mRNA. The TDP-43/ALKBH5 complex regulates CDC25A mRNA splicing via N6-methyladenosine (m6A) demethylation to maintain the expression of its oncogenic isoform (CDC25A-1), ultimately promoting the G1/S phase transition and growth of GBM cells. TRAD01 selectively targeted the interaction between TDP-43 and ALKBH5, leading to significant antitumor effects both in vitro and in vivo. Our study identified a novel epigenetic mechanism by which TDP-43/ALKBH5 contributes to GBM growth via m6A modification and alternative splicing. Therefore, targeting the TDP-43/ALKBH5 axis might be a promising therapeutic strategy for GBM patients.

RNA methylation: where to from here for hematologic malignancies?

RNA methylation and the machinery that regulates or "reads" its expression has recently been implicated in the pathogenesis of acute myeloid leukemia (AML) and other hematologic malignancies. Modulation of these epigenetic marks has started to become a reality as several companies around the world seek to leverage this knowledge therapeutically in the clinic. Although the bases of observed activity in AML have been described by numerous groups, the exact context in which these therapies will ultimately be used remains to be properly determined. While context is likely to be of great importance here, a more "global" mechanism of action might allow for more widespread applicability to multiple disease subtypes. In other areas such as the myelodysplastic and other preleukemic syndromes, data remain sparse. Ongoing work is needed to determine whether therapeutic modulation of RNA modifications is a viable and biologically plausible approach in these cases. Regardless of the outcomes, this is an exciting era for "epitranscriptomics" as we navigate a pathway forward. Here, I describe the current knowledge around RNA methylation and hematologic malignancies at the end of 2024 including some of the relevant questions that are yet to be answered.

METTL3-mediated m6A modification regulates muscle development by promoting TM4SF1 mRNA degradation in P-body via YTHDF2

N6-methyladenosine (m6A), a well-known post-transcriptional modification, is implicated in diverse cellular and physiological processes. However, much remains unknown regarding the precise role and mechanism of m6A modification on muscle development. In this study, we make observation that the levels of m6A and METTL3 are markedly elevated during the differentiation phase (DM) compared to the growth phase (GM) in both C2C12 and bovine myoblasts. Notably, deletion of METTL3 decreased m6A levels, and promoted myoblast proliferation, inhibited myoblast differentiation in vitro. By performing m6A sequencing in both GM and DM myoblast, we further identified that TM4SF1 is involved in m6A -regulated muscle development. Mechanistically, METTL3 increases m6A-modified TM4SF1 transcripts, and subsequently YTHDF2 promotes TM4SF1 mRNA degradation in P-body through liquid-liquid phase separation (LLPS). Additionally, the rescue experiments in vivo showed that overexpressing METTL3 could rescue the attenuated myogenesis induced by TM4SF1 overexpression during muscle regeneration in mice. Collectively, our findings shed light on a regulatory mechanism by which m6A modulates muscle development and raise a new model for m6A-mediated mRNA degradation within P-bodies.

Exon junction complexes regulate osteoclast-induced bone resorption by influencing the NFATc1 m6A distribution through the "shield effect"

BACKGROUND

The distribution of the m6A methylation modification on the transcriptome is highly regionally selective and is mainly concentrated in abnormally long exons and stop codons. However, in-depth research on the selective mechanism of m6A methylation is still lacking.

METHODS

In this research, meRIP sequencing, mRNA sequencing, meRIP, luciferase reporter assays and CRISPR/Cas9 conditional knockout mice were used to elucidate the distribution characteristics of NFATc1 m6A.

RESULTS

METTL14 controls osteoclast-mediated bone resorption by means of the methylation (4249 A) of the NFATc1 gene during osteoclast differentiation. Exon junction complexes (EJCs) selectively protect the m6A methylation sites of the NFATc1 gene. When the methylation sites are located within short exon fragments (50-200 nt), EJCs prevent their hypermethylation and degradation through the "shield effect"; when the methylation sites are located in the 3' UTR region or long exon fragments (greater than 300 nt), the "shield effect" disappears. Downstream, YTHDF2 induced the degradation of hypermethylation NFATc1 transcripts without site restriction.

CONCLUSIONS

EJCs act as "shields" to regulate the m6A region selectivity of the NFATc1 gene, thereby determining the characteristics of m6A distribution in the gene. Importantly, EJCs can raise the level of m6A methylation of NFATc1 and degrade its mRNA, thereby inhibiting osteoclast differentiation and preserving bone mass. These results will be helpful for identifying potential molecular targets for osteoporosis treatment.

KEY POINTS

METTL14 controls osteoclast-mediated bone resorption by means of the methylation (4249 A) of the NFATc1 gene during osteoclast differentiation. Exon junction complexes (EJCs) protect the remaining methylation sites of the NFATc1 gene (located in the inner exon fragment of 50-200 nt) from hypermethylation and degradation. The "shield effect" disappears when the exon fragment is extended to 300 nt. Downstream, YTHDF2 induced the degradation of hypermethylation NFATc1 transcripts without site restriction.

The epigenetic approach of varicocele: a focus on sperm DNA and m6A-RNA methylation

BACKGROUND

Varicocele is an abnormal dilation and torsion of the pampiniform venous plexus in the scrotum due to venous reflux, primarily affecting the left side. It affects 15% of men and is a prevalent contributor to male infertility. Varicocele is a complex disorder influenced by genetic, epigenetic, and environmental factors. Epigenetic modifications, which regulate genome activity independently of DNA or RNA sequences, may contribute to the development and severity of varicocele. These include DNA methylation, histone modifications, and RNA modifications like N6-methyladenosine (m6A). Irregularities in DNA and m6A-RNA methylation during spermatogenesis can cause gene expression abnormalities, DNA damage, and decreased fertility in varicocele patients.

OBJECTIVE AND RATIONALE

The review aims to comprehensively understand the underlying mechanisms of varicocele, a condition that can significantly impact male fertility. By exploring the role of methylation modifications, specifically DNA and m6A-RNA methylation, the review aims to synthesize evidence from basic, preclinical, and clinical research to expand the existing knowledge on this subject. The ultimate goal is to identify potential avenues for developing targeted treatments that can effectively improve varicocele and ultimately increase sperm quality in affected individuals.

SEARCH METHODS

A thorough investigation of the scientific literature was conducted through searches in PubMed, Google Scholar, and Science Direct databases until May 2024. All studies investigating the relationship between DNA and m6A-RNA methylation and male infertility, particularly varicocele were reviewed, and the most pertinent reports were included. Keywords such as varicocele, epigenetics, DNA methylation, m6A-RNA methylation, hypermethylation, hypomethylation, spermatozoa, semen parameters, spermatogenesis, and male infertility were used during the literature search, either individually or in combination.

OUTCOMES

The sperm has a specialized morphology essential for successful fertilization, and its epigenome is unique, potentially playing a key role in embryogenesis. Sperm DNA and RNA methylation, major epigenetic marks, regulate the expression of testicular genes crucial for normal spermatogenesis. This review explores the role of DNA and m6A-RNA methylation, in responding to oxidative stress and how various nutrients influence their function in varicocele condition. Evidence suggests a potential link between varicocele and aberrant DNA/m6A-RNA methylation patterns, especially hypomethylation, but the body of evidence is still limited. Further studies are needed to understand how abnormal expression of DNA/m6A-RNA methylation regulators affects testicular gene expression. Thus, analyzing sperm DNA 5mC/5hmC levels and m6A-RNA methylation regulators may reveal spermatogenesis defects and predict reproductive outcomes.

WIDER IMPLICATIONS

Nutri-epigenomics is an emerging field that could enhance the knowledge and management of diseases with unpredictable risks and consequences, even among individuals with similar lifestyles, by elucidating the influence of nutrition on DNA/m6A-RNA methylation through one-carbon metabolism. However, the importance of one-carbon metabolism to varicocele is not well-recognized. Health status and diet influence one-carbon metabolism and its associated DNA/m6A-RNA methylation modification. Future research should identify optimal methylation patterns that promote health and investigate modulating one-carbon metabolism to achieve this. Furthermore, additional studies are necessary to develop personalized dietary strategies through clinical and longitudinal research. However, a research gap exists on dietary interventions utilizing epigenetics as a therapeutic method for treating varicocele.

REGISTRATION NUMBER

Not applicable.

Liver ALKBH5 regulates glucose and lipid homeostasis independently through GCGR and mTORC1 signaling

Maintaining glucose and lipid homeostasis is crucial for health, with dysregulation leading to metabolic diseases such as type 2 diabetes mellitus (T2DM) and metabolic dysfunction-associated fatty liver disease (MAFLD). This study identifies alkylation repair homolog protein 5 (ALKBH5), an RNA N6-methyladenosine (m6A) demethylase, as a major regulator in metabolic disease. ALKBH5 is up-regulated in the liver during obesity and also phosphorylated by protein kinase A, causing its translocation to the cytosol. Hepatocyte-specific deletion of Alkbh5 reduces glucose and lipids by inhibiting the glucagon receptor (GCGR) and mammalian target of rapamycin complex 1 (mTORC1) signaling pathways. Targeted knockdown of hepatic Alkbh5 reverses T2DM and MAFLD in diabetic mice, highlighting its therapeutic potential. This study unveils a regulatory mechanism wherein ALKBH5 orchestrates glucose and lipid homeostasis by integrating the GCGR and mTORC1 pathways, providing insight into the regulation of metabolic diseases.

The epigenetic landscape of brain metastasis

Brain metastasis represents a significant challenge in oncology, driven by complex molecular and epigenetic mechanisms that distinguish it from primary tumors. While recent research has focused on identifying genomic mutation drivers with potential clinical utility, these strategies have not pinpointed specific genetic mutations responsible for site-specific metastasis to the brain. It is now clear that successful brain colonization by metastatic cancer cells requires intricate interactions with the brain tumor ecosystem and the acquisition of specialized molecular traits that facilitate their adaptation to this highly selective environment. This is best exemplified by widespread transcriptional adaptation during brain metastasis, resulting in aberrant gene programs that promote extravasation, seeding, and colonization of the brain. Increasing evidence suggests that epigenetic mechanisms play a significant role in shaping these pro-brain metastasis traits. This review explores dysregulated chromatin patterns driven by chromatin remodeling, histone modifications, DNA/RNA methylation, and other epigenetic regulators that underpin brain metastatic seeding, initiation, and outgrowth. We provide novel insights into how these epigenetic modifications arise within both the brain metastatic tumor and the surrounding brain metastatic tumor ecosystem. Finally, we discuss how the inherent plasticity and reversibility of the epigenomic landscape in brain metastases may offer new therapeutic opportunities.

Enhanced or reversible RNA N6-methyladenosine editing by red/far-red light induction

The RNA N6-methyladenosine (m6A) modification is a critical regulator of various biological processes, but precise and dynamic control of m6A remains a challenge. In this work, we present a red/far-red light-inducible m6A editing system that enables efficient and reversible modulation of m6A levels with minimal off-target effects. By engineering the CRISPR dCas13 protein and sgRNA with two pairs of light-inducible heterodimerizing proteins, ΔphyA/FHY1 and Bphp1/PspR2, we achieved targeted recruitment of m6A effectors. This system significantly enhances m6A writing efficiency and allows dynamic regulation of m6A deposition and removal on specific transcripts, such as SOX2 and ACTB. Notably, reversible m6A editing was achieved through cyclic modulation at a single target site, demonstrating the ability to influence mRNA expression and modulate the differentiation state of human embryonic stem cells. This optogenetic platform offers a precise, versatile tool for cyclic and reversible m6A regulation, with broad implications for understanding RNA biology and its potential applications in research and medicine.

Discovery of a Novel Selective and Cell-Active N6-Methyladenosine RNA Demethylase ALKBH5 Inhibitor

N6-methyladenosine (m6A), the most abundant methylation on mRNA, plays pivotal roles in regulating mRNA biological functions, which affect cell functions. ALKBH5, an m6A demethylase, was found to be an oncogene in several cancer types, including triple-negative breast cancer (TNBC). Here, we report a novel and selective ALKBH5 covalent inhibitor, W23-1006, through virtual screening and structure optimization. It covalently bonds to the ALKBH5 C200 residue with an IC50 value of 3.848 μM, representing roughly 30- and 8-fold stronger inhibitory activity than that against FTO and ALKBH3, respectively. Cellular experiments demonstrated that W23-1006 could efficiently enhance the m6A level on fibronectin 1 (FN1) mRNA, leading to strong suppression of TNBC cell proliferation and migration in vitro as well as tumor growth and metastasis in vivo. Collectively, our study developed a novel, selective, and cell-active ALKBH5 covalent inhibitor, W23-1006, which could be a potential therapeutic option for cancer, such as TNBC treatment.