Nuclear m 6 A Reader YTHDC1 Regulates mRNA Splicing

SARS-CoV-2 and HCoV-OC43 regulate host m6A modification via activation of the mTORC1 signalling pathway to facilitate viral replication

N6-methyladenosine (m6A) is the most prevalent post-transcriptional modification in eukaryotic RNA and is also present in various viral RNAs, where it plays a crucial role in regulating the viral life cycle. However, the molecular mechanisms through which viruses regulate host RNA m6A methylation are not fully understood. In this study, we reveal that SARS-CoV-2 and HCoV-OC43 infection enhance host m6A modification by activating the mTORC1 signalling pathway. Specifically, the viral non-structural protein nsp14 upregulates the expression of S-adenosylmethionine synthase MAT2A in an mTORC1-dependent manner. This mTORC1-MAT2A axis subsequently stimulates the synthesis of S-adenosylmethionine (SAM). The increase of SAM then enhances the m6A methylation of host RNA and facilitates viral replication. Our findings uncover a molecular mechanism by which viruses regulate host m6A methylation and provide insights into how SARS-CoV-2 hijacks host cellular epitranscriptomic modifications to promote its replication.

Coupling mechanisms coordinating mRNA translation with stages of the mRNA lifecycle

Gene expression involves a series of consequential processes, beginning with mRNA synthesis and culminating in translation. Traditionally studied as a linear sequence of events, recent findings challenge this perspective, revealing coupling mechanisms that coordinate key steps of gene expression, even when spatially and temporally distant. In this review, we focus on translation, the final stage of gene expression, and examine its coupling with key stages of mRNA metabolism: synthesis, processing, export, and decay. For each of these processes, we provide an overview of known instances of coupling with translation. Furthermore, we discuss the role of high-throughput technologies in uncovering these intricate interactions on a genome-wide scale. Finally, we highlight key challenges and propose future directions to advance our understanding of how coupling mechanisms orchestrate robust and adaptable gene expression programs.

Interplay of m6A RNA methylation and gut microbiota in modulating gut injury

The gut microbiota undergoes continuous variations among individuals and across their lifespan, shaped by diverse factors encompassing diet, age, lifestyle choices, medication intake, and disease states. These microbial inhabitants play a pivotal role in orchestrating physiological metabolic pathways through the production of metabolites like bile acids, choline, short-chain fatty acids, and neurotransmitters, thereby establishing a dynamic "gut-organ axis" with the host. The intricate interplay between the gut microbiota and the host is indispensable for gut health, and RNA N6-methyladenosine modification, a pivotal epigenetic mark on RNA, emerges as a key player in this process. M6A modification, the most prevalent internal modification of eukaryotic RNA, has garnered significant attention in the realm of RNA epigenetics. Recent findings underscore its potential to influence gut microbiota diversity and intestinal barrier function by modulating host gene expression patterns. Conversely, the gut microbiota, through its impact on the epigenetic landscape of host cells, may indirectly regulate the recruitment and activity of RNA m6A-modifying enzymes. This review endeavors to delve into the biological functions of m6A modification and its consequences on intestinal injury and disease pathogenesis, elucidating the partial possible mechanisms by which the gut microbiota and its metabolites maintain host intestinal health and homeostasis. Furthermore, it also explores the intricate crosstalk between them in intestinal injury, offering a novel perspective that deepens our understanding of the mechanisms underlying intestinal diseases.

The role of m6A methylation in abdominal aortic aneurysms: Mechanisms, progress and future perspectives (Review)

Abdominal aortic aneurysm (AAA) is a type of cardiovascular disease. Sudden aortic rupture and subsequent bleeding are the main causes of mortality due to AAA. N6‑methyladenosine (m6A) methylation, the most common epitranscriptomic modification in eukaryotic mRNAs, has a key role in the regulation of gene expression. m6A methylation markedly influences the development and progression of AAA. The present review highlights the mechanism of m6A methylation in AAA, including current research progress and future prospects. From a mechanistic perspective, m6A methylation exerts its influence on AAA‑related genes by modulating the post‑transcriptional levels of RNA, thereby impacting the pathological process of AAA. In terms of clinical applications, the mechanisms by which m6A methylation regulators influence their development and progression in AAA involve multiple target genes and signaling pathways. These regulatory factors affect inflammatory immunomodulation, cell proliferation, apoptosis and endogenous processes by modulating the m6A modification status of target genes and the activity of immune‑related signaling pathways. Therefore, for the prevention and treatment of AAA, current therapeutic strategies should comprehensively consider the interactions and synergistic regulation among m6A methylation regulators to reveal the integrated effects of the entire regulatory network in AAA development. Consequently, a more comprehensive understanding of the precise mechanisms of m6A methylation in AAA should be attained, which will support the development of innovative therapeutic strategies aimed at m6A methylation and establish a basis for the early diagnosis and treatment of AAA.

RNA methylation: A new promising biomaker in cancer liquid biopsy

RNA methylation is a vital epigenetic modification that regulates gene expression by influencing RNA processes such as transcription, degradation, translation, and transport. Aberrant methylation, including modifications like m6A, m5C, m1A, m7G, and m3C, is closely linked to tumorigenesis and progression. Liquid biopsy, a non-invasive technique analyzing tumor markers in body fluids, offers significant potential for early diagnosis and dynamic monitoring. In this context, RNA methylation, due to its tumor-specific properties, is emerging as a valuable marker. However, significant challenges remain in its clinical application. This review explores the roles of RNA methylation in cancer, recent advances in detection technologies, and its potential as a liquid biopsy marker in tumor management. It highlights its promising applications in cancer diagnosis, prognosis, and personalized treatment in the era of precision oncology.

Decoding intricate interactions between m6A modification with mRNAs and non-coding RNAs in cervical cancer: Molecular mechanisms and clinical implications

N6-methyladenosine (m6A) methylation is the most prevalent RNA modification that is regulated by three regulatory factors: "writers", "erasers" and "readers". m6A modification regulates RNA stability and other mechanisms, including translation, cleavage, and degradation. Current research has demonstrated that m6A methylation is involved in the regulation of occurrence and development of cancers by controlling the expression of cancer-related genes. This review summarizes the role of m6A modification on messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs) in cervical cancer (CC). We highlight the dual role of m6A regulatory factors, which act as oncogenes or tumor suppressors depending on the cellular context and downstream targets. Additionally, we examine how ncRNAs reciprocally regulate m6A modification in two ways: by guiding the deposition or removal of m6A modifications on RNA targets, and by modulating the expression of m6A regulatory factors. These interactions further contribute to tumor progression. Furthermore, the therapeutic potential of targeting m6A modification has been emphasized in CC. Moreover, recent advances in small-molecule inhibitors targeting m6A regulators and RNA-based therapies which may offer new treatment strategies have been summarized. Finally, we discuss the current challenges in m6A modification research and provide suggestions for future research directions. This review aims to deepen the understanding of m6A modification in CC and contribute to the development of targeted and personalized treatment strategies.

Harnessing engineered exosomes as METTL3 carriers: Enhancing osteogenesis and suppressing lipogenesis in bone marrow mesenchymal stem cells for postmenopausal osteoporosis treatment

Postmenopausal osteoporosis (PMOP), a prevalent skeletal disorder among women post-menopause, has emerged as a pressing global public health concern. Exosomes derived from serum have exhibited encouraging therapeutic potential in addressing PMOP, albeit with underlying mechanisms requiring deeper exploration. To elucidate these mechanisms, we devised a mouse model by surgically inducing ovariectomy and isolated exosomes from serum samples. Subsequently, we employed qRT-PCR, Western blotting, and immunofluorescence analysis to quantify relevant gene and protein expression patterns. To assess the biological effects on treated cells and tissues, we utilized ARS staining, oil red O staining, and micro-CT analysis. Additionally, we examined the METTL3/FOXO1 m6A site interaction and the FOXO1/YTHDF1 complex using dual-luciferase reporter assays and RIP assays. The m6A modification levels of FOXO1 were quantified via MeRIP-PCR. Furthermore, we engineered bone marrow mesenchymal stem cell exosomes by loading abundant METTL3 mRNA and decorating their surfaces with bone-targeting peptides. The successful synthesis and bone-targeting capabilities of these modified exosomes were validated through electron microscopy, in vivo imaging, and immunofluorescence staining. Our findings reveal that METTL3, in collaboration with YTHDF1 within serum-derived exosomes, enhances FOXO1 gene transcription by fostering m6A modification of FOXO1. This, in turn, promotes osteogenic differentiation of bone marrow mesenchymal stem cells while inhibiting lipogenic differentiation. Notably, our engineered exosomes, BT-oe-METTL3-EXO, not only harbor high levels of METTL3 but also demonstrate exceptional bone-targeting efficiency. In vitro studies demonstrated that BT-oe-METTL3-EXO significantly mitigated bone mass loss induced by ovariectomy in mice, bolstered osteogenic differentiation of mouse bone marrow mesenchymal stem cells, and inhibited lipogenic differentiation. Collectively, our research underscores the pivotal regulatory function of serum-derived exosomes in human bone marrow stem cells (hBMSCs) and underscores the promising therapeutic potential of BT-oe-METTL3-EXO for combating postmenopausal osteoporosis.

Alternative Splicing Regulation in Metabolic Disorders

Alternative splicing (AS) is a fundamental mechanism for enhancing transcriptome diversity and regulating gene expression, crucial for various cellular processes and the development of complex traits. This review examines the role of AS in metabolic disorders, including obesity, weight loss, dyslipidemias, and metabolic syndrome. We explore the molecular mechanisms underlying AS regulation, focusing on the interplay between cis-acting elements and trans-acting factors, and the influence of RNA-binding proteins (RBPs). Advances in high-throughput sequencing and bioinformatics have unveiled the extensive landscape of AS events across different tissues and conditions, highlighting the importance of tissue-specific splicing in metabolic regulation. We discuss the impact of genetic variants on AS, with a particular emphasis on splicing quantitative trait loci (sQTLs) and their association with cardiometabolic traits. The review also covers the regulation of spliceosome components by phosphorylation, the role of m6A modification in AS, and the interaction between transcription and splicing. Additionally, we address the clinical relevance of AS, illustrating how splicing misregulation contributes to metabolic diseases and the potential for therapeutic interventions targeting splicing mechanisms. This comprehensive overview underscores the significance of AS in metabolic health and disease, advocating for further research to harness its therapeutic potential.

YTHDC1 orchestrates oncogenic splicing via the CLK1-SRSF1 splicing machinery to regulate castration-resistant prostate cancer progression

Androgen receptor variant 7 (AR-V7) plays a critical role in castration-resistant prostate cancer (CRPC) progression even under androgen-deprivation conditions. Clinical and experimental studies have established that AR-V7 expression is a critical driver of CRPC progression and resistance to first-line anti-androgen therapy including enzalutamide. Understanding the mechanisms regulating AR-V7 generation and its contribution to drug resistance is critical for developing newer approaches to target CRPC. In this study, we have investigated the role of the RNA-binding protein YTHDC1, a m6A reader, in regulating AR-V7 splicing. Our findings reveal that YTHDC1 is overexpressed in CRPC and modulating its expression directly affects AR-V7 levels, rendering the cells sensitive to enzalutamide treatment. Mechanistically, we demonstrate that YTHDC1 binds to the AR-V7 pre-mRNA and facilitates the recruitment of phosphorylated SRSF1, a splice factor that promotes AR-V7 splicing. Additionally, we also demonstrate that it modulates the levels of CLK1, a known SRSF1 kinase supporting its role in regulating AR-V7 splicing. Furthermore, our experiments also reveal that YTHDC1 regulates the expression of other oncogenic transcripts, including Bcl-2, Cyclin D1, Nova1, and VEGF-A, highlighting its broader role in cancer progression. Overall, our study supports that targeting YTHDC1 could be a novel therapeutic approach to overcome AR-V7-mediated treatment resistance in CRPC patients.

Arg-Gly-Asp engineered mesenchymal stem cells as targeted nanotherapeutics against kidney fibrosis by modulating m6A

Background The recent surge in research on extracellular vesicles has generated considerable interest in their clinical applications. Extracellular vesicles derived from mesenchymal stem cells (MSC-EV) have emerged as a promising cell-free therapy for chronic kidney disease (CKD), offering an alternative to traditional Mesenchymal stem/stromal cells (MSCs) in extracellular vesicle-based nanotherapeutics. However, challenges such as in vivo off-target effects and limited bioavailability have impeded the wider adoption of MSC-EV in clinical settings. Methods Arginyl-glycyl-aspartic acid peptide-modified MSC-EV (RGD-MSC-EV) were developed using a donor cell-assisted membrane modification strategy. The targeting capability and therapeutic efficacy of RGD-MSC-EV were thoroughly evaluated both in vitro and in vivo. Additionally, the mechanisms of RNA N6-methyladenosine (m6A) methylation-mediated angiogenesis were extensively investigated to elucidate how RGD-MSC-EV mitigates renal fibrosis. Results RGD-MSC-EV demonstrated exceptional targeted delivery efficiency, exhibiting optimal biodistribution and retention within the target tissue. This breakthrough positions them as significantly enhanced anti-fibrotic therapeutics. Notably, RGD-MSC-EV sustains the viability of renal peritubular capillary (PTCs) endothelial cells by transporting microRNA-126-5p (miR-126-5p) and modulating alkB homolog 5 (ALKBH5)-mediated m6A modification of SIRT1(Sirtuin 1), a crucial regulator in angiogenesis. By revitalizing endothelial cells and promoting microcirculation, this approach restored oxygen metabolism homeostasis, ultimately delaying fibrogenesis associated with CKD. Conclusions RGD-MSC-EV offers a feasible and effective strategy to alleviate renal interstitial fibrosis by restoring m6A and mitigating the loss of renal PTCs. STATEMENT OF SIGNIFICANCE: Chronic kidney disease (CKD) often leads to renal fibrosis, which worsens disease progression. This study introduces a novel strategy using engineered extracellular vesicles (EVs) derived from mesenchymal stem cells (MSC-EV). By modifying these EVs with RGD peptides, we significantly enhance their targeting ability to hypoxic kidney tissues. The research reveals how these EVs deliver microRNA (miR-126-5p) to restore key molecular mechanisms, stabilizing SIRT1 expression through m6A RNA modifications. This approach promotes blood vessel health and delays fibrosis. Compared to current treatments, RGD-MSC-EV offers a safe, effective, and cell-free therapeutic alternative. These findings advance the understanding of EV-based therapies and their clinical potential, bridging basic research and real-world CKD treatment applications.

Epitranscriptome-epigenome interactions in development and disease mechanisms

Crosstalk between epitranscriptomic modifications to RNA and epigenomic modifications to DNA and histones plays fundamental roles in development and disease. Here, we summarize two major regulatory modes of the crosstalk between the epigenome and epitranscriptome. In the 'cis mode', the crosstalk occurs co-transcriptionally, with direct interactions observed between epigenetic modifications mediated by their regulators. In the 'trans mode', the modification of an epigenetic layer regulates the expression of another epigenetic layer's writers/erasers and subsequently induces downstream epigenetic alteration. Additionally, we focus on the functional roles of the crosstalk mechanism in physiological and pathological contexts, including development, differentiation, cancer, and complex genetic diseases. Lastly, we discuss the potential future directions for a systematic understanding of epigenetic crosstalk in development and disease.

YTHDC1 promotes postnatal brown adipose tissue development and thermogenesis by stabilizing PPARγ

Brown adipose tissue (BAT) plays a vital role in non-shivering thermogenesis and energy metabolism and is influenced by factors like environmental temperature, ageing, and obesity. However, the molecular mechanisms behind BAT development and thermogenesis are not fully understood. Our study identifies the m6A reader protein YTHDC1 as a crucial regulator of postnatal interscapular BAT development and energy metabolism in mice. YTHDC1 directly interacts with PPARγ through its intrinsically disordered region (IDR), thus protecting PPARγ from binding the E3 ubiquitin ligase ARIH2, and preventing its ubiquitin-mediated proteasomal degradation. Specifically, the ARIH2 RING2 domain is essential for PPARγ degradation, while PPARγ's A/B domain is necessary for their interaction. Deletion of Ythdc1 in BAT increases PPARγ degradation, impairing interscapular BAT development, thermogenesis, and overall energy expenditure. These findings reveal a novel mechanism by which YTHDC1 regulates BAT development and energy homeostasis independently of its m6A recognition function.

Targeting PSMD14 combined with arachidonic acid induces synthetic lethality via FADS1 m6A modification in triple-negative breast cancer

Dysregulation of deubiquitination is essential for cancer growth. However, the role of 26S proteasome non-ATPase regulatory subunit 14 (PSMD14) in the progression of triple-negative breast cancer (TNBC) remains to be determined. Gain- and loss-of-function experiments showed that silencing PSMD14 notably attenuated the growth, invasion, and metastasis of TNBC cells in vitro and in vivo. Overexpression of PSMD14 produced the opposite results. Mechanistically, PSMD14 decreased K63-linked ubiquitination on SF3B4 protein to de-ubiquitin and stabilize SF3B4 protein. Then, SF3B4/HNRNPC complex bound to FADS1 mRNA and promoted exon inclusion in the target mRNA through m6A site on FADS1 mRNA recognized by HNRNPC, thereby up-regulating the expression of FADS1 and activating Akt/mTOR signaling. Exogenous arachidonic acid supplementation combined with PSMD14 knockdown induced synthetic lethality, which was further confirmed in TNBC organoid (PDO) and TNBC patient-derived xenograft (PDX) mouse models. Overall, our findings reveal an oncogenic role of PSMD14 in TNBC progression, which indicates a potential biomarker and ferroptosis-mediated therapeutic strategy for TNBC.

Immunomodulatory role of RNA modifications in sex hormone-dependent cancers

Recent studies have identified that RNA epigenetic modifications, including m6A, m1A, m5C, etc, play pivotal roles in tumor progression. These modifications influence mRNA stability, RNA processing, translational efficiency, and decoding precision. However, comprehensive reviews detailing the connection between m6A RNA modifications and hormone-dependent cancers in both male and female populations remain scarce(breast cancer, ovarian cancer, and endometrial cancer, prostate cancer). In this article, we explore the cellular and molecular roles of various RNA modifications alongside the key elements of the tumor microenvironment. We examine how these RNA modifications influence the development of hormone-dependent cancers through their impact on immune mechanisms. By enhancing our understanding of the function of RNA modifications within the immune systems of four specific tumors, we offer fresh insights for their potential applications in diagnosis and treatment.

From bone marrow mesenchymal stem cells to diseases: the crucial role of m6A methylation in orthopedics

Elucidating the molecular mechanisms underlying orthopedic diseases is crucial for guiding therapeutic strategies and developing innovative interventions. N6-methyladenosine (m6A)-an epitranscriptomic modification-has emerged as a key regulator of cellular fate and tissue homeostasis. Specifically, m6A plays a pivotal role in several RNA biological processes such as precursor RNA splicing, 3'-end processing, nuclear export, translation, and stability. Recent advancements indicate that m6A methylation regulates stem cell proliferation and osteogenic differentiation by modulating various signaling pathways. Extensive research has shown that abnormalities in m6A methylation contribute significantly to the onset and progression of various orthopedic diseases such as osteoporosis (OP), osteoarthritis (OA), rheumatoid arthritis (RA), and bone tumors. This review aims to summarize the key proteases involved in m6A methylation and their functions. The detailed mechanisms by which m6A methylation regulates osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) through direct and indirect ways are also discussed, with a focus on specific molecular pathways. Finally, this review analyzes the roles and mechanisms of m6A modification in the development and progression of multiple orthopedic diseases, offering a comprehensive understanding of the pathophysiology of these conditions and proposing new directions and molecular targets for innovative treatment strategies.

Transcriptomic analysis reveals the function of m6A regulators in aged cochlea

OBJECTIVE

Presbycusis is a prevalent health issue among the elderly. Previous studies have shown mechanisms related to this condition, but the underlying mechanisms of presbycusis remain elusive. N6-methyladenosine (m6A) modification in regulating gene expression and cellular functions has been implicated in the development of various diseases. Nevertheless, the potential role of m6A regulators in presbycusis is still unclear. In this study, we aim to determine the expression of m6A regulators in the cochleae of young and old mice, and to investigate their potential role in aging.

METHODS

We sequenced the transcriptome from the cochleae of six young (2-mo) and six old mice (24-mo) bioinformatics analysis. Differential expression analysis and downstream functional analysis was performed to identify m6A regulators. Association of m6A regulators with protein-protein interaction and transcription factor-miRNA networks were constructed to explore their regulatory mechanisms.

RESULTS

ALKBH5 and YTHDC1 were found upregulated in the aged cochleae. They were strongly correlated with immune-related pathways, immune molecular subtypes, and immune infiltration levels in old mice, suggesting their potential involvement in immune-related mechanisms of presbycusis. Receiver Operating Characteristic (ROC) curve analysis demonstrated the high diagnostic potential molecules of AlkB Homolog 5 (ALKBH5) and YTHDC1.

CONCLUSION

This study has established a molecular foundation and introduce a novel perspective on the role of m6A regulators in presbycusis, emphasizing ALKBH5 and YTHDC1 as potential markers.

LEVEL OF EVIDENCE

Acknowledging methodological similarities with Level 3 (non-randomized controlled cohort or case-control studies) in clinical research, we reference Level 3 as a comparative framework, while recognizing the distinct differences between clinical and animal research settings.

m6A-mRNA Reader YTHDF2 Identified as a Potential Risk Gene in Autism With Disproportionate Megalencephaly

Among autistic individuals, a subphenotype of disproportionate megalencephaly (ASD-DM) seen at three years of age is associated with co-occurring intellectual disability and poorer prognoses later in life. However, many of the genes contributing to ASD-DM have yet to be delineated. In this study, we identified additional ASD-DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD-DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection, totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD-DM genes harboring de novo protein-impacting variants. Our findings include 14 high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM, including CHD8 and PTEN. By performing functional network analysis, we expanded to additional candidate genes, including one previously implicated in ASD-DM (PIK3CA) as well as 184 additional genes connected with ASD or DM alone. Using zebrafish, we modeled a de novo tandem duplication impacting YTHDF2, encoding an N6-methyladenosine (m6A)-mRNA reader, in an ASD-DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size, while overexpressing YTHDF2 resulted in increased head/brain size matching that of the proband. Single-cell transcriptomes of YTHDF2 gain-of-function larvae point to reduced expression of Fragile-X-syndrome-associated FMRP-target genes globally and in the developing brain, providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader, YTHDC1, in our ASD-DM cohort. Though we highlight only two cases to date, our study provides support for the m6A-RNA modification pathway as potentially contributing to this severe form of autism.

Hepatitis B Virus Promotes Angiogenesis in Hepatocellular Carcinoma by Increasing m6A Modification of VEGFA mRNA via IGF2BP3

Angiogenesis plays a crucial role in the development of HBV-related hepatocellular carcinoma (HCC). VEGFA is a key angiogenic factor, and while its transcriptional regulation by HBV has been extensively studied, its posttranscriptional regulation by HBV remains poorly understood. Building on our previous findings that delineated an RBM15/YTHDF2/IGF2BP3 regulatory axis in m6A-mediated RNA metabolism in HCC, this study further explores the posttranscriptional regulation of VEGFA by HBV. By MeRIP-qPCR and integrating MeRIP-seq data, we discovered that HBV enhances m6A methylation of VEGFA mRNA. Comprehensive cellular and molecular biology experiments demonstrated that HBV induces the upregulation of IGF2BP3, which serves as a key "reader" that recognizes and stabilizes VEGFA mRNA in an m6A methylation-dependent manner. This stabilization leads to elevated VEGFA expression, promoting enhanced cellular functions such as HUVEC migration and tube formation. Furthermore, in an HBV-associated HCC xenograft model, IGF2BP3 knockdown resulted in decreased VEGFA expression and inhibited tumor growth. This study expands our understanding of HBV-driven angiogenesis and identifies the IGF2BP3-VEGFA axis as a potential therapeutic target for antiangiogenic strategies in HBV-related HCC.

METTL16 and YTHDC1 Regulate Spermatogonial Differentiation via m6A

Spermatogenesis is a highly unique and intricate process, finely regulated at multiple levels, including post-transcriptional regulation. N6-methyladenosine (m6A), the most prevalent internal modification in eukaryotic mRNA, plays a significant role in transcriptional regulation during spermatogenesis. Previous research indicated extensive m6A modification at each stage of spermatogenesis, but depletion of Mettl3 and/or Mettl14 in spermatogenic cells with Stra8-Cre did not reveal any detectable abnormalities up to the stage of elongating spermatids. This suggests the involvement of other methyltransferases in the regulation of m6A modification during spermatogonial differentiation and meiosis. As a METTL3/14-independent m6A methyltransferase, METTL16 remains insufficiently studied in its roles during spermatogenesis. We report that male mice with Mettl16vasa-cre exhibited significantly smaller testes, accompanied by a progressive loss of spermatogonia after birth. Additionally, the deletion of Mettl16 in A1 spermatogonia using Stra8-Cre results in a blockade in spermatogonial differentiation. Given YTHDC1's specific recognition for METTL16 target genes, we further investigated the role of YTHDC1 using Ythdc1-sKO mouse model. Our results indicate that Ythdc1Stra8-cre also impairs spermatogonial differentiation, similar to the effects observed in Mettl16Stra8-cre mice. RNA-seq and m6A-seq analyses revealed that deletion of either Mettl6 or Ythdc1 disrupted the gene expression related to chromosome organisation and segregation, ultimately leading to male infertility. Collectively, this study underscores the essential roles of the m6A writer METTL16 and its reader YTHDC1 in the differentiation of spermatogonia.

The regulatory role of m6A in cancer metastasis

Metastasis remains a primary cause of cancer-related mortality, with its intricate mechanisms continuing to be uncovered through advancing research. Among the various regulatory processes involved, RNA modification has emerged as a critical epitranscriptomic mechanism influencing cancer metastasis. N6-methyladenosine (m6A), recognized as one of the most prevalent and functionally significant RNA modifications, plays a central role in the regulation of RNA metabolism. In this review, we explore the multifaceted role of m6A in the different stages of cancer metastasis, including epithelial-mesenchymal transition, invasion, migration, and colonization. In addition to summarizing the current state of our understanding, we offer insights into how m6A modifications modulate key oncogenic pathways, highlighting the implications of recent discoveries for therapeutic interventions. Furthermore, we critically assess the limitations of previous studies and propose areas for future research, including the potential for targeting m6A as a novel approach in anti-metastatic therapies. Our analysis provides a comprehensive understanding of the regulatory landscape of m6A in metastasis, offering directions for continued exploration in this rapidly evolving field.

Research progress on m6A and drug resistance in gastrointestinal tumors

Gastrointestinal (GI) tumors represent a significant global health burden and are among the leading causes of cancer-related mortality worldwide. their drug resistance is one of the major challenges in cancer therapy. In recent years, epigenetic modifications, especially N6-methyladenosine (m6A) RNA modifications, have become a hot research topic. m6A modification plays an important role in gene expression and cancer progression by regulating RNA splicing, translation, stability, and degradation, which are regulated by "writers," "erasers" and "readers." In GI tumors, resistance to chemotherapy, targeted therapy, and immunotherapy is closely associated with m6A RNA modification. Therefore, the molecular mechanism of m6A modification and its targeted drug development provide new therapeutic strategies for overcoming drug resistance and therapeutic efficacy in GI tumors. In this review, the biological functions of m6A were explored, the specific resistance mechanisms of m6A in different types of GI tumors were explored, new ideas and targets for future treatment resistance were identified, and the limitations of this field were highlighted.

Epitranscriptomic Role of m6A in Obesity-Associated Disorders and Cancer Metabolic Reprogramming

The global rise in obesity and its associated metabolic disorders underscores the need for a deeper investigation into their underlying molecular mechanisms. While genetic factors are well-established contributors, recent research has increasingly focused on epigenetic regulators, particularly N6-methyladenosine (m6A)-the most prevalent internal RNA modification in eukaryotes. This post-transcriptional modification plays a crucial role in RNA metabolism by regulating mRNA stability, splicing, nuclear export, and translation efficiency. Notably, emerging evidence implicates m6A in both adipogenesis and metabolic dysregulation. In this review, we systematically examine three key dimensions: (1) the molecular mechanisms of m6A modification, including writers, erasers, and readers, in obesity; (2) dysregulated m6A patterns in obesity-related pathologies, such as type 2 diabetes (T2D), insulin resistance, metabolic dysfunction-associated steatotic liver disease (MASLD), and the glycolysis in cancer cells; and (3) the therapeutic potential of targeting m6A and the regulators. By critically assessing recent advancements, we highlight m6A's dual role as both a metabolic sensor and a disease modulator, offering novel insights into potential strategies for combating obesity-related metabolic syndromes.

Trametinib ameliorated Adriamycin-induced podocyte injury by inhibiting METTL3 modified m6A RCAN1 RNA methylation

N6-methyladenosine (m6A) plays a crucial role in kidney diseases. Methyltransferase-like 3 (METTL3) as a key m6A writer can be regulated by trametinib. However, the epigenetic regulation of trametinib in focal segmental glomerulosclerosis (FSGS) remains unclear. We investigated whether trametinib protects podocytes by modulating METTL3-methylated target RNAs. Regulator of calcineurin 1 (RCAN1) was predicted as a target binding RNA of METTL3 by THEW database. Immunostaining of METTL3 and RCAN1 with podocyte marker Wilm's tumor-1 (WT-1) confirmed their localization within podocytes in renal biopsy from FSGS patients. Transfection METTL3 to human podocytes reduced WT-1, synaptopodin (SYNPO), and RCAN1 protein levels. Total m6A, m6A methylated RNA of RCAN1 increased and total RCAN1 mRNA decreased. Inhibition of METTL3 using siRNA or trametinib reversed these changes and attenuated the ADR-induced downregulation of WT-1 and SYNPO in vitro. In ADR-induced FSGS mice, trametinib ameliorated proteinuria, hypoalbuminemia, renal dysfunction, glomerulosclerosis and podocyte foot process effacement. Additionally, trametinib preserved podocyte function assessed by WT-1 and SYNPO as well as delayed renal fibrosis assessed by α-smooth muscle actin and fibronectin. Consistent with results in vitro, trametinib also decreased the ADR-induced upregulation of METTL3 and reversed the changed levels of total m6A, m6A methylated Rcan1 and total Rcan1 in FSGS mice. In conclusion, trametinib may serve as a renal protective agent for FSGS by regulating METTL3-dependent RCAN1 methylation levels.

Insight into mechanism of ALKBH5-mediated N6-methyladenosine (m6A) regulating porcine epidemic diarrhea virus infection in IPEC-J2 cells

Porcine epidemic diarrhea (PED), induced by porcine epidemic diarrhea virus (PEDV) infection, represents a highly contagious swine disease that causes substantial economic losses in the global pig industry. As the most prevalent RNA modification, N6-methyladenosine (m6A) has emerged as a crucial epitranscriptomic regulator of host-pathogen interactions, although its functional significance in PEDV-infected porcine intestinal epithelial cells (IPEC-J2) remains to be fully elucidated. This study drew m6A maps before and after ALKBH5 interfering with IPEC-J2 cells, revealing the mechanism by which ALKBH5 mediated m6A regulates PEDV infection in IPEC-J2 cells. This study employs an in vitro model of PEDV-induced IPEC-J2 cell damage to investigate the regulatory mechanisms of m6A methylation in host antiviral responses. Utilizing a comprehensive multi-omics approach, including MeRIP-seq, RNA-seq, qPCR, Western blot, MeRIP-qPCR, and RIP-qPCR, we systematically uncovered the critical role of m6A methylation in antiviral defense. Our findings reveal that ALKBH5, a key demethylase during PEDV infection, plays a pivotal role in modulating m6A modification levels. Specifically, gene silencing of ALKBH5 significantly upregulates m6A modification but downregulates expression of the antiviral effector genes IFIT3 and HERC5. Mechanistically, we demonstrate that the YTHDC2 protein selectively recognizes m6A modification sites within IFIT3 and HERC5 transcripts, thereby mediating ALKBH5-dependent regulation of mRNA stability and protein expression. Functional analyses further reveal that IFIT3 activates the IRF3/TBK1 signaling axis, while HERC5 enhances antiviral responses by modulating the key effector molecule ISG15. Together, these findings establish a synergistic antiviral mechanism in IPEC-J2 cells. This study is the first to elucidate the novel ALKBH5-YTHDC2-m6A molecular axis, which orchestrates host antiviral immunity through a dual-pathway regulatory mode. These findings provide a theoretical foundation for understanding the role of RNA epigenetic modifications in enterovirus infections and offer a molecular basis for developing m6A-targeted strategies to prevent and control porcine infectious gastroenteritis.

m6A deficiency impairs uterine spiral artery remodeling to induce preeclampsia-like symptoms via FGF2

Failures in uterine spiral artery remodeling can lead to placental defects and subsequent preeclampsia, a leading cause of fetal and maternal mortality during pregnancy. N6-methyladenosine (m6A), the most abundant mRNA modification, is dysregulated in samples with preeclampsia. However, whether and how m6A regulates uterine spiral artery remodeling and leads to subsequent preeclampsia in vivo remains unexplored. In this study, we generated two m6A deficiency mouse models: one with a trophoblast-specific knockout of the m6A methyltransferase gene Mettl3, and another with a methyltransferase enzyme mutation. Using these models, we demonstrated that m6A deficiency impaired extravillous trophoblasts (EVTs) infiltration into the uterine spiral arteries, and the remodeling of the spiral arteries in vivo. We further showed that m6A inhibition induced preeclampsia-like symptoms. Mechanistically, we revealed that the m6A modification of FGF2 mRNA, which encodes a secreted peptide implicated in preeclampsia, facilitated its expression. Notably, administration of the FGF2 peptide largely restored EVTs invasion and uterine spiral artery remodeling in m6A-deficient mice. Our findings underscore the importance of m6A in facilitating uterine spiral artery remodeling and prove the pathological mechanisms in vivo, suggesting a new therapeutic approach for preeclampsia caused by m6A deficiency.

Pathological α-synuclein dysregulates epitranscriptomic writer METTL3 to drive neuroinflammation in microglia

Recent reports suggest dysregulation of the N6-methyladenosine (m6A) RNA modification may contribute to the pathology of neurodegenerative diseases. Herein, we show the m6A methyltransferase complex including METTL3-the catalytic component of the nuclear-localized complex-is robustly upregulated in human microglia and astrocytes exposed to αSynf and Mn. Subcellular localization studies reveal METTL3 was predominantly cytoplasmic following Mn insult but remained nuclear following αSynf stimulation in activated microglia. Functional analysis revealed METTL3 and downstream m6A readers, including YTHDF2 and IGF2BP1-3, may regulate the proinflammatory secretome of activated microglia. Notably, methyltransferase activity and m6A abundance were significantly increased following Mn and αSynf treatment. METTL3 in Mn and αSynfin vivo models of neuroinflammation, along with human postmortem tissues from Alzheimer's disease (AD), Parkinson's disease (PD), and dementia with Lewy bodies (DLB) patients, was significantly upregulated. This was further confirmed by single-cell RNA sequencing (scRNA-seq) analysis. Overall, we demonstrate the m6A writer METTL3 may function as a major regulator of chronic neuroinflammation in synucleinopathies.

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-dependent m6A RNA methylation regulates transposable elements and represses human naïve pluripotency through transposable element-derived enhancers

N 6-methyladenosine (m6A) is the most prevalent messenger RNA modification with diverse regulatory roles in mammalian cells. While its functions are well-documented in mouse embryonic stem cells (mESCs), its role in human pluripotent stem cells (hPSCs) remains to be fully explored. METTL3 is the main enzyme responsible for m6A deposition. Here, using a METTL3 inducible knockout (iKO) system, we uncovered that, unlike in mESCs, METTL3 was indispensable for hPSC maintenance. Importantly, loss of METTL3 caused significant upregulation of pluripotency factors including naïve pluripotency genes and failure to exit pluripotency, thus impairing stem cell differentiation towards both embryonic and extraembryonic cell lineages. Mechanistically, METTL3 iKO in hPSCs promoted expression and enhancer activities of two primate-specific transposable elements (TEs), SVA_D and HERVK/LTR5_Hs. At SVA_D elements, loss of METTL3 leads to reduced H3K9me3 deposition. On the other hand, the activation of LTR5_Hs in the METTL3 iKO cells is accompanied by increased chromatin accessibility and binding pluripotency factors. The activated SVA_D and LTR5_Hs elements can act as enhancers and promote nearby naïve gene expression by directly interacting with their promoters. Together these findings reveal that METTL3-dependent m6A RNA methylation plays critical roles in suppressing TE expression and in regulating the human pluripotency network.

High-glucose-associated YTHDC1 lactylation reduces the sensitivity of bladder cancer to enfortumab vedotin therapy

Hyperglycemia is a recognized risk factor for bladder cancer (BC). Enfortumab vedotin (EV), the first NECTIN4-targeting antibody-drug conjugate, demonstrates promising clinical efficacy in patients with advanced BC. In this study, we show that EV treatment is less effective in BC patients with diabetes than in those with normoglycemia. The subsequent in vitro and in vivo experiments indicate that high glucose decreases the sensitivity of BC cells to EV. Mechanistically, lactate overproduction associated with high glucose promotes AARS1-mediated YTHDC1 lactylation and enhances RNF183-mediated YTHDC1 ubiquitination. Downregulated YTHDC1 reduces JUND mRNA stability in an m6A-dependent manner, subsequently decreasing NECTIN4 expression and EV responsiveness. Our study identifies a high-glucose-associated lactate-AARS1-YTHDC1-JUND-NECTIN4 axis that affects EV sensitivity in BC. Targeting this axis with JUND activators or β-alanine may offer therapeutic strategies to enhance the sensitivity of BC cells to EV.

Combined Transcriptomic and Epitranscriptomic Profiling Identifies THBS1 as A Regulator of Enzalutamide Resistance in Prostate Cancer

Cancer drug resistance arises not only from selection of resistant clones, but also through rapid activation of adaptive transcriptional programs. One mechanism of transcriptional regulation involves N6-methyladenosine (m6A) RNA modification, which dynamically regulates mRNA processing and alternative splicing, ultimately impacting cell fate and differentiation. In prostate cancer (PC), resistance to systemic therapies such as the androgen receptor pathway inhibitor (ARPI) enzalutamide is associated with a host of well-documented androgen receptor (AR) alterations, including amplification, mutation, and alternative splicing. Given these functions, we hypothesized that m6A modifications play a role in the transition to enzalutamide resistance in PC. To test this, we used methyl-RNA-immunoprecipitation followed by sequencing (MeRIP-seq) in parallel with RNA-seq to identify gene transcripts that were both differentially methylated and differentially expressed between enzalutamide-sensitive and enzalutamide-resistant PC cells. We filtered and prioritized these genes using clinical and functional database tools, including Gene Ontology (GO) enrichment analysis and Gene Set Enrichment Analysis (GSEA), The Cancer Genome Atlas (TCGA), and the Oncology Research Information Network (ORIEN) avatar. Using this approach, we identified 487 transcripts that were both differentially methylated and differentially expressed and validated six of the top 12 candidates via targeted qPCR and MeRIP-PCR. One of these, THBS1, was found to have increased m6A level associated with decreased transcript levels in enzalutamide-resistant cells, a finding recapitulated in publicly available preclinical and clinical data. Moreover, in enzalutamide-sensitive cells, depletion of THBS1 by siRNA-knockdown induced resistance to enzalutamide. While THBS1 has previously been implicated in aggressive PC phenotypes, we now show that THBS1 downregulation directly contributes to a rapid transition to enzalutamide resistance, suggesting a novel role for this gene in PC hormonal therapy resistance. These results constitute the first comprehensive epitranscriptomic profiling of ARPI resistance and identify THBS1 as a potential driver of acute resistance in prostate 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.

METTL3 orchestrates cancer progression by m6A-dependent modulation of oncogenic lncRNAs

RNA modifications, particularly N6-methyladenosine (m6A), play crucial roles in gene expression regulation. While extensively studied in the context of mRNA, the impact of m6A on long non-coding RNAs (lncRNAs) remains elusive. This research aimed to reveal the regulatory landscape of m6A in lncRNA expression. In a comprehensive analysis across 6219 samples spanning 12 cancer types, we unveiled METTL3 as the most potent regulator of lncRNA expression among the examined 19 m6A regulators. A total of 397 METTL3-mediated m6A-modified lncRNAs (mmlncRs) were unveiled across 12 cancer types, indicating a consistent mechanism of METTL3-mediated lncRNA regulation. Functional assays demonstrated that METTL3 knockout significantly impeded lung cancer cell proliferation and progression. Leveraging RNA-seq and MeRIP-seq, we identified C1RL-AS1 as a bona fide m6A target of METTL3 in lung cancer, revealing its oncogenic role. Mechanistically, METTL3 depletion disrupts m6A modification on C1RL-AS1, leading to its downregulated expression. YTHDF2 binds to C1RL-AS1, maintaining its stability in a m6A-dependent manner. This study provides a valuable resource for the exploration of mmlncRs as promising therapeutic targets in cancers, shedding light on the intricate regulatory networks orchestrated by METTL3.

trithorax is an essential regulator of cardiac Hox gene expression and anterior-posterior patterning of the Drosophila embryonic heart tube

The precise regulation of transcription required for embryonic development is partially controlled by the actions of the Trithorax group (TrxG) and Polycomb group (PcG) proteins. The genes trithorax (trx), trithorax-related (trr), and SET domain containing 1 (Set1) encode COMPASS-like histone methyltransferases, a subgroup of TrxG proteins that impart H3K4 methylation modifications onto chromatin in order to activate and maintain transcription. In this study, we identify the role of these genes in the development of the embryonic heart of the fruit fly Drosophila melanogaster. trx, trr, and Set1 independently ensure proper cardiac cell divisions. Additionally, trx regulation of collinear Hox expression is necessary for the anterior-posterior cardiac patterning of the linear heart tube. trx inactivation in Drosophila results in a remarkable homeotic transformation of the posterior heart-proper segment into an aorta-like fate due to the loss of posterior abdominal A expression. Furthermore, cardiac expression of Antennapedia, Ultrabithorax, and Abdominal B is also deregulated in trx mutants. Together, these data suggest that the COMPASS-like histone methyltransferases are essential developmental regulators of cardiogenesis, being necessary for both cardiac cell divisions and heart patterning.

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.

Spatial control of m6A deposition on enhancer and promoter RNAs through co-acetylation of METTL3 and H3K27 on chromatin

Interaction between the N6-methyladenosine (m6A) methyltransferase METTL3 and METTL14 is critical for METTL3 to deposit m6A on various types of RNAs. It remains to be uncovered whether there is spatial control of m6A deposition on different types of RNAs. Here, through genome-wide CRISPR-Cas9 screening in the A549 cell line, we find that H3K27ac acetylase p300-mediated METTL3 acetylation suppresses the binding of METTL3 on H3K27ac-marked chromatin by inhibiting its interaction with METTL14. Consistently, p300 catalyzing the acetylation of METTL3 specifically occurs on H3K27ac-marked chromatin. Disruptive mutations on METTL3 acetylation sites selectively promote the m6A of chromatin-associated RNAs from p300-bound enhancers and promoters marked by H3K27ac, resulting in transcription inhibition of ferroptosis-inhibition-related genes. In addition, PAK2 promotes METTL3 acetylation by phosphorylating METTL3. Inhibition of PAK2 promotes ferroptosis in a manner that depends on the acetylation of METTL3. Our study reveals a spatial-selective way to specifically regulate the deposition of m6A on enhancer and promoter RNAs.

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.

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.

Regulation and application of m6A modification in tumor immunity

The m6A modification is an RNA modification that impacts various processes of RNA molecules, including transcription, splicing, stability, and translation. Recently, researchers have discovered that the presence of m6A modification can influence the interaction between tumor cells and immune cells and also play a role in regulating the expression of immune response-related genes. Additionally, m6A modification is intricately involved in the regulation of tumor immune evasion and drug resistance. Specifically, certain tumor cells can manipulate the gene expression through m6A modification to evade immune system attacks. Therefore, it might be possible to enhance tumor immune surveillance and improve the effectiveness of immune-based therapies by manipulating m6A modification. This review systematically discusses the role of m6A modification in tumor immunity, specifically highlighting its regulation of immune cells and immune-related genes in tumor cells. Furthermore, we explore the potential of m6A modification inhibitors as anti-cancer therapies and the significance of m6A regulatory factors in predicting the efficacy of tumor immune therapy.

Global Co-regulatory Cross Talk Between m6A and m5C RNA Methylation Systems Coordinate Cellular Responses and Brain Disease Pathways

N6 adenosine and C5 cytosine modification of mRNAs, tRNAs and rRNAs are regulated by the behaviour of distinct sets of writer, reader and eraser effector proteins which are conventionally considered to function independently. Here, we provide evidence of global cross-regulatory and functional interaction between the m6A and m5C RNA methylation systems. We first show that m6A and m5C effector protein transcripts are subject to reciprocal base modification supporting the existence of co-regulatory post-transcriptional feedback loops. Using global mass spectrometry proteomic data generated after biological perturbation to identify proteins which change in abundance with effector proteins, we found novel co-regulatory cellular response relationships between m6A and m5C proteins such as between the m6A eraser, ALKBH5, and the m5C writer, NSUN4. Gene ontology analysis of co-regulated proteins indicated that m6A and m5C RNA cross-system control varies across cellular processes, e.g. proteasome and mitochondrial mechanisms, and post-translational modification processes such as SUMOylation and phosphorylation. We also uncovered novel relationships between effector protein networks including contributing to intellectual disability pathways. Finally, we provided in vitro confirmation of colocalisation between m6A-RNAs and the m5C reader protein, ALYREF, after synaptic NMDA activation. These findings have important implications for understanding control of RNA metabolism, cellular proteomic responses, and brain disease mechanisms.

XIAP promotes metastasis of bladder cancer cells by ubiquitylating YTHDC1

X-linked inhibitor of apoptosis protein (XIAP), a member of the IAP family, is overexpressed in a variety of tumors and plays an important role in tumor progression. Increasing evidence suggests that XIAP promotes metastasis of bladder cancer but the underlying mechanism is not very clear. The RNA N6-methyladenosine (m6A) reader YTHDC1 regulates RNA splicing, nuclear transport, and mRNA stability and is a potential tumor target; however, its ubiquitin E3 ligase has not been described. In this study, screening of proteins that specifically interact with XIAP identified YTHDC1 as its degradation substrate. Ectopic overexpression of XIAP promoted degradation of YTHDC1, and knockout of XIAP upregulated YTHDC1, which inhibited metastasis of bladder cancer. Furthermore, YTHDC1 reduced the expression of matrix metalloproteinase-2 (MMP-2) by destabilizing its mRNA. These experiments revealed that XIAP promotes ubiquitination of YTHDC1, positively regulating expression of the MMP-2 and promoting metastasis of bladder cancer. Collectively, these findings demonstrate that XIAP is a critical regulator of YTHDC1 and pinpoint the XIAP/YTHDC1/MMP-2 axis as a promising target for the treatment of bladder cancer.

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.

N4-acetylcytidine coordinates with NP1 and CPSF5 to facilitate alternative RNA processing during the replication of minute virus of canines

RNA modifications play crucial roles in RNA metabolism, structure, and functions. N4-acetylcytidine (ac4C) modifications have been shown to enhance stability and translation efficiency of messenger RNAs and viral RNAs. However, the relationship between ac4C and alternative RNA processing remains unexplored. Here, N-acetyltransferase 10 (NAT10) and its catalyzed ac4C modifications on minute virus of canines (MVC) were shown to regulate viral DNA replication and RNA processing, including both the alternative RNA splicing and polyadenylation. Through acRIP-seq and RedaC:T-seq, functional ac4C-modified residue 3311 was identified and characterized, which affected MVC RNA processing rather than altered the viral RNA stability. Ac4C modification at nt 3311 was revealed to participate in NP1-mediated viral RNA processing without influencing RNA affinity of NP1. Meanwhile, CPSF5 was identified to interact with NP1 and mediate viral RNA processing in an ac4C-dependent manner. Further in vitro assays showed that NP1 recruited CPSF5 to MVC RNAs, and the ac4C modification promoted specific binding of CPSF5 to the target region, which ensured precise alternative MVC RNA processing. This study not only reveals the functions of NAT10 and ac4C but also elucidates the mechanisms by which RNA modifications orchestrate MVC proteins and host factors for efficient viral replication and alternative RNA processing.

Single-molecule m6A detection empowered by endogenous labeling unveils complexities across RNA isoforms

The landscape of N6-methyadenosine (m6A) on different RNA isoforms is still incompletely understood. Here, in HEK293T cells, we endogenously label the methylated m6A sites on single Oxford Nanopore Technology (ONT) direct RNA sequencing (DRS) reads by APOBEC1-YTH-induced C-to-U mutations 10-100 nt away, obtaining 1,020,237 5-mer single-read m6A signals. We then trained m6Aiso, a deep residual neural network model that accurately identifies and quantifies m6A at single-read resolution. Analyzing m6Aiso-determined m6A on single reads and isoforms uncovers distance-dependent linkages of m6A sites along single molecules. It also uncovers specific methylation of identical m6A sites on intron-retained isoforms, partly due to their differential distances to exon junctions and isoform-specific binding of TARBP2. Moreover, we find that transcription factor SMAD3 promotes m6A deposition on its transcribed RNA isoforms during epithelial-mesenchymal transition, resulting in isoform-specific regulation of m6A on isoforms with alternative promoters. Our study underscores the effectiveness of m6Aiso in elucidating the intricate dynamics and complexities of m6A across RNA isoforms.

YTHDC1 cooperates with the THO complex to prevent RNA-damage-induced DNA breaks

Certain environmental toxins and chemotherapeutics are nucleic acid-damaging agents, causing adducts in DNA and RNA. While most of these adducts occur in RNA, the consequences of RNA damage are largely unexplored. Here, we demonstrate that nuclear RNA damage can result in loss of genome integrity in human cells. Specifically, we show that YTHDC1 regulates alkylation damage responses with the THO complex (THOC). In addition to its established binding to N6-methyladenosine (m6A), YTHDC1 binds to chemically induced N1-methyladenosine (m1A). Without YTHDC1, cells have greater alkylation damage sensitivity and increased DNA breaks, which are rescued by an RNA-specific dealkylase. These RNA-damage-induced DNA breaks (RDIBs) depend on R-loop formation, which is converted to DNA breaks by the XPG nuclease. Strikingly, in the absence of YTHDC1 or THOC, a nuclear RNA m1A methyltransferase is sufficient to induce DNA breaks. Our results provide mechanistic insight into how damaged RNAs can impact genomic integrity.

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.

m6A RNA methylation dynamics during in vitro maturation of cumulus-oocyte complexes derived from adult or prepubertal sheep

PURPOSE

N6-methyladenosine (m6A) is the most prevalent base epigenetic modification within eukaryotic mRNAs. It participates in post-transcriptional regulation, including maternal RNA maintenance and decay in mouse oocytes and during maternal-to-zygotic transition. The landscape in other mammalian species remains largely unexplored. The present work analyzed m6A dynamics in sheep cumulus oocyte complexes (COCs), during in vitro maturation. To explore potential relationships with oocyte developmental competence, a previously established model consisting of oocytes derived from adult and prepubertal sheep was adopted.

METHODS

m6a dynamics were analyzed in terms of m6A RNA methylation abundance in cumulus cells (CCs) by colorimetric assay and expression of key m6A methylation-related proteins (METTL3, METTL14, METTL16, VIRMA, YTHDC1, YTHDC2, YTHDF2, YTHDF3, ALKBH5, and FTO) in both cumulus cells and oocytes by real-time PCR.

RESULTS

We report the dynamics of m6A in sheep COCs, and reveal alterations in both oocytes and cumulus cells derived from prepubertal donors. These changes were observed in terms of m6A RNA methylation levels and transcript dynamics of several m6A methylation-related proteins. Notably, our study shows that dysregulations occur after IVM.

CONCLUSION

Overall, this work describes for the first time the dynamics of m6A in sheep COCs and uncovers the involvement of m6A RNA methylation in oocyte developmental potential.

YTHDC1 negatively regulates UBE3A to influence RAD51 ubiquitination and inhibit apoptosis in colorectal cancer cells

YTHDC1, a key protein in the m6A-related regulatory network within cells, is involved in multiple cellular processes such as chromatin-related regulation, RNA splicing, and nuclear export. Understanding its role in colorectal cancer (CRC) development and DNA damage repair is critical for the advancement of treatment strategies. Our study found that YTHDC1 was highly expressed in high-malignancy CRC tissues compared with low-malignancy ones. Upon silencing YTHDC1, we observed a pronounced suppression of the proliferation of CRC cell lines, accompanied by a substantial increase in cell apoptosis. Furthermore, we identified RAD51 as a crucial downstream target of YTHDC1. Knocking down YTHDC1 led to a notable decrease in RAD51 protein levels, and silencing RAD51 also inhibited cancer cell proliferation. Interestingly, RNA-sequencing data indicated that the YTHDC1 deletion did not affect RAD51 transcription. However, Western blot revealed that this deletion increased the ubiquitination of RAD51, likely due to the upregulated E3 ligase UBE3A. Ubiquitination experiments subsequently confirmed that RAD51 is indeed one of the substrates of UBE3A. In summary, our study provides novel insights into how YTHDC1 modulates the expression of RAD51 through post-translational modifications. These findings offer valuable information that may potentially contribute to the development of more effective therapeutic strategies for CRC.

Tumor-promoting effect and tumor immunity of SRSFs

Serine/arginine-rich splicing factors (SRSFs) are a family of 12 RNA-binding proteins crucial for the precursor messenger RNA (pre-mRNA) splicing. SRSFs are involved in RNA metabolism events such as transcription, translation, and nonsense decay during the shuttle between the nucleus and cytoplasm, which are important components of genome diversity and cell viability. SRs recognize splicing elements on pre-mRNA and recruit the spliceosome to regulate splicing. In tumors, aberrant expression of SRSFs leads to aberrant splicing of RNA, affecting the proliferation, migration, and anti-apoptotic ability of tumor cells, highlighting the therapeutic potential of targeted SRSFs for the treatment of diseases. The body's immune system is closely related to the occurrence and development of tumor, and SRSFs can affect the function of immune cells in the tumor microenvironment by regulating the alternative splicing of tumor immune-related genes. We review the important role of SRSFs-induced aberrant gene expression in a variety of tumors and the immune system, and prospect the application of SRSFs in tumor. We hope that this review will inform future treatment of the disease.