N 6-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription

Interplay of transposable elements and ageing: epigenetic regulation and potential epitranscriptomic influence

Transposable elements (TEs) are mobile elements, which have been crucial for mammalian genome evolution and function. Their activity, which influences genomic stability, gene expression and chromatin state, is tightly regulated by complex mechanisms. This review examines recent findings on TE regulation and the dynamics and connection during the ageing process. Here, we explore the interplay between chromatin state, DNA, RNA, and histone modifications in controlling TE activity, with a special emphasis in elucidating the emerging role of epitranscriptomic modifications in TE regulation. Additionally, we analyse the connection between TE activation and ageing, with the perspective for future research that could reveal novel targets for alleviating physiological and pathological ageing and age-related diseases.

N6-methyladenosine RNA modification in stomach carcinoma: Novel insights into mechanisms and implications for diagnosis and treatment

N6-methyladenosine (m6A) RNA methylation is crucially involved in the genesis and advancement of gastric cancer (GC) by controlling various pathobiological aspects including gene expression, signal transduction, metabolism, cell death, epithelial-mesenchymal transition, angiogenesis, and exosome function. Despite its importance, the exact mechanisms by which m6A modification influences GC biology remain inadequately explored. This review consolidates the latest advances in uncovering the mechanisms and diverse roles of m6A in GC and proposes new research and translational directions. Key regulators (writers, readers, and erasers) of m6A, such as METTL3/14/16 and WTAP, significantly affect cancer progression, anticancer immune response, and treatment outcomes. m6A modification also impacts immune cell infiltration and the tumor microenvironment, highlighting its potential as a diagnostic and prognostic marker. Interactions between m6A methylation and non-coding RNAs offer further novel insights into GC development and therapeutic targets. Targeting m6A regulators could enhance immunotherapy response, overcome treatment resistance, and improve oncological and clinical outcomes. Models based on m6A can precisely predict treatment response and prognosis in GC. Additional investigation is needed to fully understand the mechanisms of m6A methylation and its potential clinical applications and relevance (e.g., as precise markers for early detection, prediction of outcome, and response to therapy and as therapeutic targets) in GC. Future research should focus on in vivo studies, potential clinical trials, and the examination of m6A modification in other types of cancers.

METTL14 promotes intimal hyperplasia through m6A-mediated control of vascular smooth muscle dedifferentiation genes

Vascular smooth muscle cells (VSMCs) possess significant phenotypic plasticity, shifting between a contractile phenotype and a synthetic state for vascular repair/remodeling. Dysregulated VSMC transformation, marked by excessive proliferation and migration, primarily drives intimal hyperplasia. N6-methyladenosine (m6A), the most prevalent RNA modification in eukaryotes, plays a critical role in gene expression regulation; however, its impact on VSMC plasticity is not fully understood. We investigated the changes in m6A modification and its regulatory factors during VSMC phenotypic shifts and their influence on intimal hyperplasia. We demonstrate that METTL14, crucial for m6A deposition, significantly promoted VSMC dedifferentiation. METTL14 expression, initially negligible, was elevated in synthetic VSMC cultures, postinjury neointimal VSMCs, and human restenotic arteries. Reducing Mettl14 levels in mouse primary VSMCs decreased prosynthetic genes, suppressing their proliferation and migration. m6A-RIP-seq profiling showed key VSMC gene networks undergo altered m6A regulation in Mettl14-deficient cells. Mettl14 enhanced Klf4 and Serpine1 expression through increased m6A deposition. Local Mettl14 knockdown significantly curbed neointimal formation after arterial injury, and reducing Mettl14 in hyperplastic arteries halted further neointimal development. We show that Mettl14 is a pivotal regulator of VSMC dedifferentiation, influencing Klf4- and Serpine1-mediated phenotypic conversion. Inhibiting METTL14 is a viable strategy for preventing restenosis and halting restenotic occlusions.

The landscape of N 6-methyladenosine RNA methylation in skin diseases

Skin diseases encompass a diverse range of conditions with significant psychological and physiological impacts. N6-methyladenosine (m6A) RNA methylation is a key epitranscriptomic modification that regulates gene expression by influencing RNA stability, splicing, translation, export and degradation. Recent studies have highlighted the crucial role of m6A modification in the pathogenesis and progression of various skin diseases. m6A modification affects critical biologic processes of the skin, such as inflammation, immune response and cellular ageing. This review systematically explores the landscape of m6A modification in nontumour skin diseases, elucidating its regulatory roles and therapeutic implications, including wound healing, scar and keloid, skin ageing, psoriasis, systemic lupus erythematosus, acne vulgaris, rosacea, chronic actinic dermatitis and scleroderma. The intricate mechanisms of m6A modification can lead to the development of novel diagnostic biomarkers and therapeutic strategies, ultimately improving patient outcomes.

Advances in understanding LINE-1 regulation and function in the human genome

LINE-1 (long interspersed nuclear element 1, L1) retrotransposons constitute ~17% of human DNA (~0.5 million genomic L1 copies) and exhibit context-dependent expression in different cell lines. Recent studies reveal that L1 is under multilayered control by diverse factors that either collaborate or compete with each other to ensure precise L1 activity. Remarkably, L1s have been co-opted as various transcription-dependent regulatory elements, such as promoters, enhancers, and topologically associating domain (TAD) boundaries, that regulate gene expression in zygotic genome activation, aging, cancer, and other disorders. This review highlights the regulation of L1 and its regulatory functions that influence disease and development.

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.

Mechanistic insights into stem cell fate regulation via RNA methylation

Stem cells possess an extraordinary ability for self-renewal and differentiation, making them essential for tissue repair, regeneration, and anti-aging. RNA methylation is crucial in regulating stem cell fate by modulating gene expression. This review synthesizes current research on RNA methylation modifications, such as m6A, m7G, m5C, and m1A, and their impact on adult stem cell fate. It provides a comprehensive overview of the molecular machinery involved in RNA methylation, emphasizes the critical roles of these modifications in stem cell biology, reviews the latest advancements in sequencing technologies, and discusses potential crosstalk between RNA methylation and epigenetic mechanisms.

Constraints on the optimization of gene product diversity

RNA and proteins can have diverse isoforms due to post-transcriptional and post-translational modifications. A fundamental question is whether these isoforms are mostly beneficial or the result of noisy molecular processes. To assess the plausibility of these explanations, we developed mathematical models depicting different regulatory architectures and investigated isoform evolution under multiple population genetic regimes. We found that factors beyond selection, such as effective population size and the number of cis-acting loci, significantly influence evolutionary outcomes. We found that sub-optimal phenotypes are more likely to evolve when populations are small and/or when the number of cis-loci is large. We also discovered that opposing selection on cis- and trans-acting loci can constrain adaptation, leading to a non-monotonic relationship between effective population size and optimization. More generally, our models provide a quantitative framework for developing statistical tests to analyze empirical data; as a demonstration of this, we analyzed A-to-I RNA editing levels in coleoids and found these to be largely consistent with non-adaptive explanations.

The importance of physiological and disease contexts in capturing mRNA modifications

The variety of modifications decorating various RNA species has prompted researchers to study messenger RNA (mRNA) modifications that are likely to have, like N6-methyladenosine (m6A), important biological functions. Yet tackling these modifications has proved more complicated than anticipated. In this Perspective, we discuss two major obstacles to progress in epitranscriptomic research: the low abundance of most mRNA modification and the nonspecificity of many mRNA modifiers. We then shift our focus to the removal of mRNA modifications and their upstream regulation, emphasizing the context-dependent nature of epitranscriptomic regulation. We illustrate how specific modifications, such as N1-methyladenosine (m1A) and pseudouridine, are enriched in distinct environments, most notably within mitochondria and in certain physiopathological conditions. By focusing on biological settings in which non-m6A modifications are more abundant, we could deepen our understanding of their precise roles in gene regulation.

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.

m6A modification profiles of the CHO cells with differential recombinant protein expression using MeRIP-seq/RNA-seq

Chinese hamster ovary (CHO) cells remain the primary host system for recombinant therapeutic protein production. Enhancing transgene expression efficiency while maintaining stable production persists as a key challenge in CHO cell engineering. While N6-methyladenosine (m6A) modification - the most abundant RNA methylation - regulates RNA stability and translational efficiency, its role in modulating recombinant protein expression remains underexplored. In this study, through m6A-specific methylated RNA immunoprecipitation sequencing (MeRIP-seq) of high- (ADM-H) and low- (ADM-L) recombinant adalimumab (ADM)-producing CHO cell lines, we identified 668 differentially methylated peaks. Notably, m6A methylation patterns showed positive correlation with heavy chain (HC)/light chain (LC) expression levels between ADM-H and ADM-L cell lines. Differential expression of factors, such as Igf2bp2, Gli2, and Met correlated with PI3K-Akt and Hippo signaling pathways, suggesting m6A-mediated regulatory functions of recombinant protein expression in CHO cells. Furthermore, pharmacological inhibition of Gli2 or Met in cell culture effectively enhanced ADM production while suppressing target gene expression. These findings elucidate m6A's functional role in recombinant protein production and provide actionable strategies for CHO cell line optimization.

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.

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.

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.

Acetylation of METTL3: A negative regulator of m6A deposition on chromatin-associated regulatory RNAs

In this issue, Huang et al.1 report the acetylation of METTL3 as a negative regulator of m6A deposition of chromatin-associated regulatory RNAs from enhancers and promoters. This acetylation is mediated by p300 and positively regulated by PAK2.

Deletion of Tfap2a in hepatocytes and macrophages promotes the progression of hepatocellular carcinoma by regulating SREBP1/FASN/ACC pathway and anti-inflammatory effect of IL10

The transcription factor AP-2α plays a crucial role in the control of tumor development and progression, and suppresses the proliferation and migration of hepatocellular carcinoma (HCC). However, the detailed function and mechanisms of AP-2α in the pathogenesis of HCC are still elusive. In the current study, we investigated the role of AP-2α regulation in liver injury-mediated HCC development. Downregulation of Tfap2a expression was found in the livers of DEN/CCl4-induced fibrosis and HCC mouse model. Hepatocyte (Alb-Cre), hepatic stellate cell (HSC) (Lrat-Cre) and macrophage (LysM-Cre) specific Tfap2a knockout mice were generated, respectively. Conditional knockout of Tfap2a was able to promote hepatic steatosis in Tfap2aΔHep and Tfap2aΔMΦ mice, but not in Tfap2aΔHSC mice fed with normal chow. Tfap2aΔHep and Tfap2aΔMΦ mice treated with DEN/CCl4 for 6 months increased tumor burden compared to Tfap2a flox controls. Tfap2a-deleted macrophages or hepatocytes could enhance lipid droplet (LD) accumulation in hepatocytes. Mechanistically, AP-2α binds to the promoter regions of SREBP1/ACC/FASN and inhibits hepatic lipid de novo synthesis. Deletion of Tfap2a in macrophages enhances polarization of M1 macrophages with increased iNOS expression but decreased CD206 expression, which resulted in increased pro-inflammatory cytokines and decreased anti-inflammatory factors, especially the hepatoprotective factor IL-10. The m6A modification writer WTAP could reduce the mRNA stability of AP-2α in a reader YTHDC1-dependent manner, whereas knockdown of WTAP or YTHDC1 enhances AP-2α expression and decreases lipid accumulation in HCC cells. Clinically, AP-2α expression negatively correlates with the expression of FASN, WTAP, YTHDC1 and the development of liver disease. Taken together, hepatocyte- or macrophage-specific deletion of Tfap2a promotes hepatic steatosis, fibrosis, and the development of HCC. These results suggest that AP-2α has been identified as a novel therapeutic target in fibrosis and inflammation-related HCC, exerting anti-lipogenesis, anti-inflammatory, and anti-tumor multi-roles.

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.

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.

SRSF4-Associated ca-circFOXP1 Regulates Hypoxia-Induced PASMC Proliferation by the Formation of R Loop With Host Gene

BACKGROUND

Pulmonary hypertension (PH) is a rare and fatal disease, the pathological changes of which include pulmonary arterial smooth muscle cell (PASMC) proliferation, which is the pathological basis of pulmonary vascular remodeling. Studies have demonstrated that chromatin-associated circRNA can regulate a variety of biological processes. However, the role of chromatin-associated circRNA in the proliferation of PH remains largely unexplored. In this study, we aimed to identify the function and mechanism of chromatin-associated circRNA in PASMC proliferation in PH.

METHODS

The role of chromatin-associated circFOXP1 (ca-circFOXP1) was investigated in hypoxic mouse PASMCs and SuHX (Sugen5416+hypoxia) model mice through the use of antisense oligonucleotide knockdown and adeno-associated virus-mediated knockdown. Through bioinformatic sequence alignment, chromatin isolation by RNA purification, Cell Counting Kit 8, 5-ethynyl-2-deoxyuridine, Western blot, and other experiments, the function and mechanism of ca-circFOXP1 were verified.

RESULTS

The expression of ca-circFOXP1 was found to be significantly increased in SuHX model mice and hypoxic mouse PASMCs. Moreover, ca-circFOXP1 was found to regulate the level of the host protein FOXP1 (forkhead box protein 1) through the R loop, thereby influencing the phosphorylation activity of SMAD2 (SMAD family member 2) and, consequently, the proliferation of mouse PASMCs. It is noteworthy that the m6A modification was found to promote the formation of the R loop between ca-circFOXP1 and the host gene FOXP1, thereby regulating the expression of the host protein. Furthermore, we have identified that the splicing factor SRSF4 (serine/arginine rich splicing factor 4) can upregulate the expression of ca-circFOXP1 by splicing exons 6 and 9 of FOXP1 pre-mRNA.

CONCLUSIONS

The results demonstrated that the splicing factor SRSF4 upregulated the expression of ca-circFOXP1, and m6A methylation promoted R-loop formation between ca-circFOXP1 and host genes, regulated the level of host protein FOXP1, and then affected the phosphorylation activity of SMAD2, mediating PASMC proliferation, leading to pulmonary vascular remodeling. These results provide a theoretical basis for further study of the pathological mechanisms of hypoxic PH and may provide certain insights.

PCIF1 drives oesophageal squamous cell carcinoma progression via m6Am-mediated suppression of MTF2 translation

Oesophageal squamous cell carcinoma (OSCC) represents a highly aggressive malignancy with limited therapeutic options and poor prognosis. This study uncovers PCIF1 as a critical driver of OSCC progression via m6Am RNA modification, leading to translational repression of the tumour suppressor MTF2. Our results demonstrate that PCIF1 selectively suppresses MTF2 translation, activating oncogenic pathways that promote OSCC growth. In vitro and in vivo models confirm that PCIF1 knockdown reduces OSCC progression, whereas MTF2 knockdown counteracts this effect, highlighting the importance of the PCIF1-MTF2 axis. Clinical analyses further reveal that high PCIF1 expression and low MTF2 expression correlate with advanced tumour stage, poor treatment response and decreased overall survival. Furthermore, in a preclinical mouse model, PCIF1 knockout enhanced the efficacy of anti-PD1 immunotherapy, reducing tumour burden and improving histological outcomes. Notably, flow cytometry analysis indicated that PCIF1 primarily exerts its effects through tumour-intrinsic mechanisms rather than direct modulation of the immune microenvironment, distinguishing its mode of action from PD1 blockade. These findings establish PCIF1 and MTF2 as promising prognostic markers and therapeutic targets for OSCC, offering new avenues for treatment strategies and patient stratification. KEY POINTS: PCIF1 promotes OSCC progression via m6Am methylation at the MTF2 mRNA 5' cap. m6Am methylation suppresses MTF2 translation, enhancing tumour cell proliferation and invasion. Targeting PCIF1 holds therapeutic potential for OSCC treatment.

Rewired m6A methylation of promoter antisense RNAs in Alzheimer's disease regulates global gene transcription in the 3D nucleome

N6-methyladenosine (m6A) is the most prevalent internal RNA modification that can impact mRNA expression post-transcriptionally. Recent progress indicates that m6A also acts on nuclear or chromatin-associated RNAs to impact transcriptional and epigenetic processes. However, the landscapes and functional roles of m6A in human brains and neurodegenerative diseases, including Alzheimer's disease (AD), have been under-explored. Here, we examined RNA m6A methylome using total RNA-seq and meRIP-seq in middle frontal cortex tissues of post-mortem human brains from individuals with AD and age-matched counterparts. Our results revealed AD-associated alteration of m6A methylation on both mRNAs and various noncoding RNAs. Notably, a series of promoter antisense RNAs (paRNAs) displayed cell-type-specific expression and changes in AD, including one produced adjacent to the MAPT locus that encodes the Tau protein. We found that MAPT-paRNA is enriched in neurons, and m6A positively controls its expression. In iPSC-derived human excitatory neurons, MAPT-paRNA promotes expression of hundreds of genes related to neuronal and synaptic functions, including a key AD resilience gene MEF2C, and plays a neuroprotective role against excitotoxicity. By examining RNA-DNA interactome in the three-dimensional (3D) nuclei of human brains, we demonstrated that brain paRNAs can interact with both cis- and trans-chromosomal target genes to impact their transcription. These data together reveal previously unexplored landscapes and functions of noncoding RNAs and m6A methylome in brain gene regulation, neuronal survival and AD pathogenesis.

DRLiPS: a novel method for prediction of druggable RNA-small molecule binding pockets using machine learning

Ribonucleic Acid (RNA) is the central conduit for information transfer in the cell. Identifying potential RNA targets in disease conditions is a challenging task, given the vast repertoire of functional non-coding RNAs in a human cell. A potential druggable target must satisfy several criteria, including disease association, cellular accessibility, binding pockets for drug-like molecules, and minimal cross-reactivity. While several methods exist for prediction of druggable proteins, they cannot be repurposed for RNAs due to fundamental differences in their binding modality. Taking all these constraints into account, a new structure-based model, Druggable RNA-Ligand binding Pocket Selector (DRLiPS), is developed here to predict binding site-level druggability of any given RNA target. A novel strategy for sampling negative binding sites in RNA structures using three parallel approaches is demonstrated here to improve model specificity: backbone motif search, exhaustive pocket prediction, and blind docking. An external blind test dataset has also been curated to showcase the model's generalizability to both experimental and modelled apo state RNA structures. DRLiPS has achieved an F1-score of 0.70, precision of 0.61, specificity of 0.89, and recall of 0.73 on this external test dataset, outperforming two existing methods, DrugPred_RNA and RNACavityMiner. Further analysis indicates that the features selected for model-building generalize well to both apo and holo states with a backbone RMSD tolerance of 3 Å. It can also predict the effect of binding site single point mutations on druggability, which can aid in optimizing synthetic RNA aptamers for small molecule recognition. The DRLiPS model is freely accessible at https://web.iitm.ac.in/bioinfo2/DRLiPS/.

The nuclear exosome co-factor MTR4 shapes the transcriptome for meiotic initiation

Nuclear RNA decay has emerged as a mechanism for post-transcriptional gene regulation in cultured cells. However, whether this process occurs in animals and holds biological relevance remains largely unexplored. Here, we demonstrate that MTR4, the central cofactor of the nuclear RNA exosome, is essential for embryogenesis and spermatogenesis. Embryonic development of Mtr4 knockout mice arrests at 6.5 day. Germ cell-specific knockout of Mtr4 results in male infertility with a specific and severe defect in meiotic initiation. During the pre-meiotic stage, MTR4/exosome represses meiotic genes, which are typically shorter in size and possess fewer introns, through RNA degradation. Concurrently, it ensures the expression of mitotic genes generally exhibiting the opposite features. Consistent with these regulation rules, mature replication-dependent histone mRNAs and polyadenylated retrotransposon RNAs were identified as MTR4/exosome targets in germ cells. In addition, MTR4 regulates alternative splicing of many meiotic genes. Together, our work underscores the importance of nuclear RNA degradation in regulating germline transcriptome, ensuring the appropriate gene expression program for the transition from mitosis to meiosis during spermatogenesis.

Short-term and long-term high-fat diet promote metabolic disorder through reprogramming mRNA m6A in white adipose tissue by gut microbiota

BACKGROUND

Although short-term high-fat diet (S-HFD) and long-term high-fat diet (L-HFD) induce metabolic disorder, the underlying epigenetic mechanism is still unclear.

RESULTS

Here, we found that both 4 days of S-HFD and 10 weeks of L-HFD increased mRNA m6A level in epididymal white adipose tissue (eWAT) and impaired metabolic health. Interestingly, S-HFD activated transposable elements (TEs), especially endogenous retroviruses (ERVs) in eWAT, while L-HFD activated long interspersed elements (LINEs). Subsequently, we demonstrated that both S-HFD and L-HFD increased m6A level of Ehmt2 and decreased EHMT2 protein expression and H3K9me2 level, accounting for activation of ERVs and LINEs. Overexpression of EHMT2 in eWAT or inhibition of ERVs and LINEs by antiviral therapy improved metabolic health under HFD feeding. Notably, we found that both short-term and long-term HFD feeding increased Fimicutes/Bacteroidota ratio and decreased the gut microbiome health index. Fecal microbiota transplantation (FMT) experiments demonstrated that gut microbiota from S-HFD and L-HFD was responsible for increased m6A level in eWAT, resulting in glucose intolerance and insulin insensitivity. Furthermore, we identified that both S-HFD and L-HFD increased the abundance of the gut microbial metabolite homogentisic acid (HGA), and HGA level was positively correlated with unclassified_f__Lachnospiraceae which was both increased in S-HFD and L-HFD feeding mice. Administration of HGA increased the m6A level of Ehmt2 and decreased the EHMT2 protein expression and H3K9me2 level in eWAT, leading to metabolic disorder in mice.

CONCLUSIONS

Together, this study reveals a novel mechanism that S-HFD and L-HFD induce metabolism disorder through gut microbiota-HGA-m6A-Ehmt2-ERV/LINE signaling. These findings may provide a novel insight for prevention and treatment of metabolism disorder upon short-term or long-term dietary fat intake. Video Abstract.

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.

Investigating the efficacy of immune checkpoint inhibitors in clear cell renal cell carcinoma based on methylation cross talk scoring

Methylation processes in different molecular contexts (DNA, RNA, and histones) are controlled by different regulatory factors and serve as critical determinants in cancer development. However, the mechanistic links between these epigenetic modifications during malignant transformation, metastasis, disease relapse, and therapeutic resistance remain incompletely understood. In this research, we investigated the transcriptional and genetic alterations of regulators associated with 3 major types of methylation modifications in clear cell renal cell carcinoma. Utilizing ChIP/MeRIP-seq and 450K methylation array data, we identified genes regulated by multiple methylation modifications and constructed a scoring model to quantify the methylation patterns for each patient. Our findings indicate that patients with a low score may be more likely to respond to immunotherapy, whereas patients with a high score may be more sensitive to targeted therapy, such as RITA, Pazopanib, Irlotinib, SU-11274, BRD-K16762525, and FCCP. In conclusion, the score model can serve as a valuable biomarker to guide clinical selection of immunotherapy and targeted drugs and help to improve personalized clear cell renal cell carcinoma treatment.

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.

METTL3-Mediated m6A Modification Regulates the Polycomb Repressive Complex 1 Components BMI1 and RNF2 in Hepatocellular Carcinoma Cells

Methyltransferase-like 3 (METTL3) is a primary RNA methyltransferase that catalyzes N6-methyladenosine (m6A) modification. The current study aims to further delineate the effect and mechanism of METTL3 in hepatocellular carcinoma (HCC). By using a murine model of hepatocellular cancer development induced via hydrodynamic tail vein injection, we showed that METTL3 enhanced HCC development. In cultured human HCC cell lines (Huh7 and PLC/PRF/5), we observed that stable knockdown of METTL3 by short hairpin RNA significantly decreased tumor cell proliferation, colony formation, and invasion, in vitro. When Huh7 and PLC/PRF/5 cells with short hairpin RNA knockdown of METTL3 were inoculated into the livers of SCID mice, we found that METTL3 knockdown significantly inhibited the growth of HCC xenograft tumors. These findings establish METTL3 as an important oncogene in HCC. Through m6A sequencing, RNA sequencing, and subsequent validation studies, we identified BMI1 and RNF2, two key components of the polycomb repressive complex 1, as direct downstream targets of METTL3-mediated m6A modification in HCC cells. Our data indicated that METTL3 catalyzed m6A modification of BMI1 and RNF2 mRNAs which led to increased mRNA stability via the m6A reader proteins IGF2BP1/2/3. Furthermore, we showed that the METTL3 inhibitor, STM2457, significantly inhibited HCC cell growth in vitro and in mice. Collectively, this study provides novel evidence that METTL3 promotes HCC development and progression through m6A modification of BMI1 and RNF2. Our findings suggest that the METTL3-m6A-BMI1/RNF2 signaling axis may represent a new therapeutic target for the treatment of HCC. Implications: The METTL3-m6A-BMI1/RNF2 signaling axis promotes HCC development and progression.

NERD-dependent m6A modification of the nascent FLC transcript regulates flowering time in Arabidopsis

N6-methyladenosine (m6A) is the most prevalent internal modification on messenger RNA. Although recent studies have shown m6A effects on determining the fate of mRNA through modulating various aspects of plant mRNA metabolism, whether and how m6A affects gene transcription in plants remains elusive. Here we show that NEEDED FOR RDR2-INDEPENDENT DNA METHYLATION (NERD), a plant-specific protein, is an essential component of the m6A methyltransferase complex required for regulating the transcription of a central floral repressor FLOWERING LOCUS C (FLC) in Arabidopsis. NERD interacts with and stabilizes the two core methyltransferases, mRNA adenosine methylases A and B, to promote m6A modification of nascent RNA, conferring an overall negative effect on gene transcription. At the FLC locus, NERD-mediated m6A modification on the nascent transcript negatively affects H3K36me3 deposition and FLC transcription through NERD interaction with the H3K36me3 methyltransferase SET DOMAIN GROUP 8. Collectively, our findings reveal that NERD mediates the crosstalk between epitranscriptomic and epigenetic regulation of FLC to modulate flowering in Arabidopsis.

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.

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.

Fine-tuning of gene expression through the Mettl3-Mettl14-Dnmt1 axis controls ESC differentiation

The marking of DNA, histones, and RNA is central to gene expression regulation in development and disease. Recent evidence links N6-methyladenosine (m6A), installed on RNA by the METTL3-METTL14 methyltransferase complex, to histone modifications, but the link between m6A and DNA methylation remains scarcely explored. This study shows that METTL3-METTL14 recruits the DNA methyltransferase DNMT1 to chromatin for gene-body methylation. We identify a set of genes whose expression is fine-tuned by both gene-body 5mC, which promotes transcription, and m6A, which destabilizes transcripts. We demonstrate that METTL3-METTL14-dependent 5mC and m6A are both essential for the differentiation of embryonic stem cells into embryoid bodies and that the upregulation of key differentiation genes during early differentiation depends on the dynamic balance between increased 5mC and decreased m6A. Our findings add a surprising dimension to our understanding of how epigenetics and epitranscriptomics combine to regulate gene expression and impact development and likely other biological processes.

Tuning up gene transcription via direct crosstalk of DNA and RNA methylation

In a recent Cell study,1 Quarto et al. uncovered a mechanism by which the METTL3-METTL14-DNMT1 axis fine-tunes gene expression during embryonic stem cell (ESC) differentiation. This work highlights the interplay between epigenetics and epitranscriptomics, shedding light on how methylation of DNA and RNA coordinately regulates a subset of differentiation genes.

N 6-methyladenosine reader YTHDF2 in cell state transition and antitumor immunity

Recent studies have revealed that the YTHDF family proteins bind preferentially to the N 6-methyladenosine (m6A)-modified mRNA and regulate the functions of these RNAs in different cell types. YTHDF2, the first identified m6A reader in mammals, has garnered significant attention because of its profound effect to regulate the m6A epitranscriptome in multiple biological processes. Here, we review current knowledge on the mechanisms by which YTHDF2 exerts its functions and discuss recent advances that underscore the multifaceted role of YTHDF2 in development, stem cell expansion, and immune evasion. We also highlight potential therapeutic interventions targeting the m6A/YTHDF2 axis to improve the response to current antitumor therapies.

Mettl3/Eed/Ythdc1 regulatory axis controls endometrial receptivity and function

The regulatory mechanism between N6-methyladenosine (m6A) RNA methylation and histone modification in endometrial receptivity remains poorly understood. In this study, we depict that RIF induced m6A and Mettl3 level restrain, affecting H3K27me3 modification and chromatin accessibility. We show that Mettl3 deletion in the endometrium alters mRNA m6A methylation via Eed interaction. This reduces m6A recognized by Ythdc1, which recruits Eed to suppress H3K27me3 modification co-transcriptionally. The reduction of H3K27me3 disrupts chromatin accessibility and impairs transcription of genes critical for endometrial receptivity. Collectively, these results shed light on a Mettl3-Eed-m6A-Ythdc1 axis that links m6A and histone modification in regulating local chromatin state and gene expression, advancing our understanding of the epigenetic crosstalk between RNA and DNA modification in infertility disease.

Exploring the methyl-verse: Dynamic interplay of epigenome and m6A epitranscriptome

The orchestration of dynamic epigenetic and epitranscriptomic modifications is pivotal for the fine-tuning of gene expression. However, these modifications are traditionally examined independently. Recent compelling studies have disclosed an interesting communication and interplay between m6A RNA methylation (m6A epitranscriptome) and epigenetic modifications, enabling the formation of feedback circuits and cooperative networks. Intriguingly, the interaction between m6A and DNA methylation machinery, coupled with the crosstalk between m6A RNA and histone modifications shape the transcriptional profile and translational efficiency. Moreover, m6A modifications interact also with non-coding RNAs, modulating their stability, abundance, and regulatory functions. In the light of these findings, m6A imprinting acts as a versatile checkpoint, linking epigenetic and epitranscriptomic layers toward a multilayer and time-dependent control of gene expression and cellular homeostasis. The scope of the present review is to decipher the m6A-coordinated circuits with DNA imprinting, chromatin architecture, and non-coding RNAs networks in normal physiology and carcinogenesis. Ultimately, we summarize the development of innovative CRISPR-dCas engineering platforms fused with m6A catalytic components (m6A writers or erasers) to achieve transcript-specific editing of m6A epitranscriptomes that can create new insights in modern RNA therapeutics.

WTAP Regulates SOX1 Expression to Affect the Tumorigenicity of Colorectal Cancer via an m6A-YTHDF2-Dependent Manner

BACKGROUND

Wilms tumor 1-associated protein (WTAP) plays a critical role in various cancers, including colorectal cancer (CRC). However, the biological function and molecular mechanisms of WTAP in CRC remain to be elucidated.

METHODS

We determined the expression of WTAP and its correlation with unfavorable prognosis of CRC using RNA-seq and the UALCAN dataset. And we investigated the effects of WTAP on CRC cells using cell proliferation assay, colony formation, cell migration and invasion, and subcutaneous xenograft experiments. We then knockdown of WTAP to identify candidate targets of WTAP. Moreover, the mRNA stability of SRY-box transcription factor 1 (SOX1) was assessed by overexpressing YTHDF2. Finally, we investigated the regulatory mechanism of WTAP in CRC by MeRIP assay, RNA pulldown, dual-luciferase reporter assay, and RIP assay.

RESULTS

We demonstrated that CRC patients with a high expression of WTAP have a risk prognosis. Additionally, WTAP expression can serve as a predictor of survival in CRC. WTAP promoted the proliferation and tumor growth of CRC cells. Moreover, WTAP has been recognized as the upstream regulator of SOX1. WTAP regulated the m6A modification, resulting in the post-transcriptional inhibition of SOX1. YTHDF2 plays a role in promoting mRNA degradation. Then, SOX1 can hinder the progression of CRC. Furthermore, WTAP can regulate the proliferation, migration, and invasion of CRC cells by SOX1 via an m6A-YTHDF2-dependent manner.

CONCLUSION

Our findings demonstrate that WTAP-mediated m6A modification facilitated the progression of CRC through the YTHDF2-SOX1 axis and could serve as a potential therapeutic targeting for CRC.

From the genome's perspective: Bearing somatic retrotransposition to leverage the regulatory potential of L1 RNAs

Transposable elements (TEs) are mobile genomic elements constituting a big fraction of eukaryotic genomes. They ignite an evolutionary arms race with host genomes, which in turn evolve strategies to restrict their activity. Despite being tightly repressed, TEs display precisely regulated expression patterns during specific stages of mammalian development, suggesting potential benefits for the host. Among TEs, the long interspersed nuclear element (LINE-1 or L1) has been found to be active in neurons. This activity prompted extensive research into its possible role in cognition. So far, no specific cause-effect relationship between L1 retrotransposition and brain functions has been conclusively identified. Nevertheless, accumulating evidence suggests that interactions between L1 RNAs and RNA/DNA binding proteins encode specific messages that cells utilize to activate or repress entire transcriptional programs. We summarize recent findings highlighting the activity of L1 RNAs at the non-coding level during early embryonic and brain development. We propose a hypothesis suggesting a mutualistic relationship between L1 mRNAs and the host cell. In this scenario, cells tolerate a certain rate of retrotransposition to leverage the regulatory effects of L1s as non-coding RNAs on potentiating their mitotic potential. In turn, L1s benefit from the cell's proliferative state to increase their chance to mobilize.

N-6-methyladenosine (m6A) promotes the nuclear retention of mRNAs with intact 5' splice site motifs

In humans, misprocessed mRNAs containing intact 5' Splice Site (5'SS) motifs are nuclear retained and targeted for decay by ZFC3H1, a component of the Poly(A) Exosome Targeting complex, and U1-70K, a component of the U1 snRNP. In S. pombe, the ZFC3H1 homolog, Red1, binds to the YTH domain-containing protein Mmi1 and targets certain RNA transcripts to nuclear foci for nuclear retention and decay. Here we show that YTHDC1 and YTHDC2, two YTH domain-containing proteins that bind to N-6-methyladenosine (m6A) modified RNAs, interact with ZFC3H1 and U1-70K, and are required for the nuclear retention of mRNAs with intact 5'SS motifs. Disruption of m6A deposition inhibits both the nuclear retention of these transcripts and their accumulation in YTHDC1-enriched foci that are adjacent to nuclear speckles. Endogenous RNAs with intact 5'SS motifs, such as intronic poly-adenylated transcripts, tend to be m6A-modified at low levels. Thus, the m6A modification acts on a conserved quality control mechanism that targets misprocessed mRNAs for nuclear retention and decay.

Lactylation-driven ALKBH5 diminishes macrophage NLRP3 inflammasome activation in patients with G6PT deficiency

BACKGROUND

Neutropenia represents an important clinical problem in patients with glycogen storage disease type Ib, characterized by genetic deficiency in glucose-6-phosphate translocase (G6PT/SLC37A4). However, the role of G6PT in macrophages has not been elucidated.

OBJECTIVE

We sought to investigate the function of G6PT in macrophage inflammation.

METHODS

Functional assays (including immunoblotting, real-time quantitative PCR, flow cytometry, immunofluorescence staining, and enzyme-linked immunosorbent assay) and RNA sequencing were performed.

RESULTS

We find that macrophages from patients deficient in G6PT exhibited diminished NLRP3 inflammasome activation. Mechanistically, deficiency of G6PT promotes glycolysis and lactate production in macrophages. Lactate accumulation potently induces ALKBH5 upregulation via H3K18 lactylation. ALKBH5 decreases m6A modification on NLRP3 messenger RNA, attenuating its transcript stability and thus inhibiting inflammasome activation. Further, treating G6PT-deficient macrophages with an inhibitor of the lactate dehydrogenase to lower their lactate levels restores NLRP3 inflammasome activation and rescues bacterial handling defect.

CONCLUSION

These findings reveal a previously unknown pathogenic mechanism of lactylation-driven defective NLRP3 inflammasome signaling and subsequent impaired antimicrobial activity as driving factors in these inflammatory disorders, indicating that glycolysis/lactate/histone lactylation cascade may be a potential therapeutic target for glycogen storage disease type Ib.

Acute exercise promotes WAT browning by remodeling mRNA m6A methylation

AIMS

Regular exercise promotes the beiging and metabolic adaptations of white adipose tissue (WAT) through the cumulative transcriptional responses that occur after each exercise session. However, the effects of a single bout of acute exercise and the role of N6-methyladenosine (m6A) in these adaptations remain unclear. We aim to investigate this further.

MATERIALS AND METHODS

We constructed mouse models for chronic (8 weeks of running) and acute (single 1-hour run) exercise to study the effects on white adipose tissue (WAT) metabolism and beiging through metabolic phenotyping and transcriptome sequencing. Additionally, we explored the impact of acute exercise on WAT m6A modification and target genes, combining m6A regulators with cell models to elucidate the role of m6A in WAT exercise adaptation.

KEY FINDINGS

Here, we reveal that upregulated m6A modification after acute exercise induces the formation of glycolytic beige fat (g-beige fat) in WAT. Mechanistically, the metabolite β-hydroxybutyrate (BHBA) secreted after acute exercise upregulates m6A modification in WAT. This enhances m6A-dependent translation of the histone acetyltransferase CREBBP, promoting the transcription of key beiging genes by increasing chromatin accessibility. Pharmacologically elevating circulating BHBA mimics the metabolic response induced by acute exercise, upregulating m6A modification and its downstream signals. Additionally, BHBA exhibits long-term effects, improving metabolic homeostasis in obesity by promoting thermogenesis in WAT.

SIGNIFICANCE

Our results reveal the role of metabolites in WAT metabolic adaptation through m6A-mediated chromatin accessibility after acute exercise, providing a novel therapeutic target for regulating WAT metabolism from a nutritional epigenetics perspective.

N6-methyladenosine RNA modification regulates the transcription of SLC7A11 through KDM6B and GATA3 to modulate ferroptosis

BACKGROUND

Recent studies indicate that N6-methyladenosine (m6A) RNA modification may regulate ferroptosis in cancer cells, while its molecular mechanisms require further investigation.

METHODS

Liquid Chromatography-Tandem Mass Spectrometry (HPLC/MS/MS) was used to detect changes in m6A levels in cells. Transmission electron microscopy and flow cytometry were used to detect mitochondrial reactive oxygen species (ROS). RNA sequencing (RNA-seq) was employed to analyze the factors regulating ferroptosis. Chromatin immunoprecipitation (ChIP) was used to assess the binding of regulatory factors to the SLC7A11 promoter, and a Dual-Luciferase reporter assay measured promoter activity of SLC7A11. The dm6ACRISPR system was utilized for the demethylation of specific transcripts. The Cancer Genome Atlas Program (TCGA) database and immunohistochemistry validated the role of the METTL3/SLC7A11 axis in cancer progression.

RESULTS

The m6A methyltransferase METTL3 was upregulated during cancer cell ferroptosis and facilitated erastin-induced ferroptosis by enhancing mitochondrial ROS. Mechanistic studies showed that METTL3 negatively regulated the transcription and promoter activity of SLC7A11. Specifically, METTL3 induced H3K27 trimethylation of the SLC7A11 promoter by suppressing the mRNA stability of H3K27 demethylases KDM6B. Furthermore, METTL3 suppressed the expression of GATA3, which regulated SLC7A11 transcription by binding to the putative site at - 597 to - 590 of the SLC7A11 promoter. METTL3 decreased the precursor mRNA stability of GATA3 through m6A/YTHDF2-dependent recruitment of the 3'-5' exoribonuclease Dis3L2. Targeted demethylation of KDM6B and GATA3 m6A using the dm6ACRISPR system significantly increased the expression of SLC7A11. Moreover, the transcription factor YY1 was responsible for erastin-induced upregulation of METTL3 by binding to its promoter-proximal site. In vivo and clinical data supported the positive roles of the METTL3/SLC7A11 axis in tumor growth and progression.

CONCLUSIONS

METTL3 regulated the transcription of SLC7A11 through GATA3 and KDM6B to modulate ferroptosis in an m6A-dependent manner. This study provides a novel potential strategy and experimental support for the future treatment of cancer.

Core factor of NEXT complex, ZCCHC8, governs the silencing of LINE1 during spermatogenesis

The overactivation of transposable elements (TEs) is a significant threat to male reproduction, particularly during the delicate process of spermatogenesis. Here, we report that zinc finger protein ZCCHC8-a key component of the nuclear exosome targeting (NEXT) complex that is involved in ribonucleic acid (RNA) surveillance-is required for TE silencing during spermatogenesis. Loss of ZCCHC8 results in delayed meiotic progression and reduced production of round spermatids (RS). We observed that young long-interspersed nuclear element (LINE1, L1) subfamilies that are targeted by ZCCHC8 were upregulated in both spermatogonial stem cells (SSC) and pachytene spermatocytes (PS) of Zcchc8 null testes. Further study found that a reduced H3K9me3 modification in SSC and elevated H3 lysine 4 trimethylation in the PS of Zcchc8 KO mice occurred upon young L1, especially L1Md_A, which may have contributed to impairment of the chromatin condensation from PS to RS during spermatogenesis. This study highlights the crucial role of RNA surveillance-mediated chromatin repression by the NEXT complex during spermatogenesis.

METTL3 improves the development of somatic cell nuclear transfer embryos through AURKB and H3S10ph in goats

Developmental abnormalities are more common in somatic cell nuclear transfer (SCNT) embryos due to epigenetic barriers that occur during the maternal-to-zygotic transition (MZT). N6-methyladenosine (m6A) is an RNA epigenetic modification that plays a significant role in numerous biological processes. However, the relationship between m6A and SCNT embryonic development is largely unexplored. In the present study, we found that the low expression of m6A methyltransferase-like 3 (METTL3) was associated with developmental arrest before zygotic genome activation (ZGA) in goat SCNT embryos and that karyokinesis defects were evident during their development. Notably, we demonstrated that METTL3 overexpression rescued the karyokinesis abnormalities, enhanced embryonic development and elevated the blastocyst formation rate. Further experiments revealed that METTL3 could mitigate the defects of maternal mRNA degradation, enhance the translation of Aurora kinase B (AURKB) and increase the phosphorylation of serine 10 on histone H3 (H3S10ph) to ensure the normal karyokinesis in SCNT embryos before ZGA in goats. Overall, our study highlights the essential role of METTL3 in enhancing the development of goat SCNT embryos. These findings indicate that METTL3 is critical for optimal SCNT efficiency and advance our understanding of m6A's role in embryonic development.

When animal viruses meet N6-methyladenosine (m6A) modifications: for better or worse?

N6-methyladenosine (m6A) is a prevalent and dynamic RNA modification, critical in regulating gene expression. Recent research has shed light on its significance in the life cycle of viruses, especially animal viruses. Depending on the context, these modifications can either enhance or inhibit the replication of viruses. However, research on m6A modifications in animal virus genomes and the impact of viral infection on the host cell m6A landscape has been hindered due to the difficulty of detecting m6A sites at a single-nucleotide level. This article summarises the methods for detecting m6A in RNA. It then discusses the progress of research into m6A modification within animal viruses' infections, such as influenza A virus, porcine epidemic diarrhoea virus, porcine reproductive, and respiratory syndrome virus. Finally, the review explores how m6A modification affects the following three aspects of the replication of animal RNA viruses: the regulation of viral genomic RNA function, the alteration of the m6A landscape in cells after viral infection, and the modulation of antiviral immunity through m6A modification. Research on m6A modifications in viral RNA sheds light on virus-host interactions at a molecular level. Understanding the impact of m6A on viral replication can help identify new targets for antiviral drug development and may uncover novel regulatory pathways that could potentially enhance antiviral immune responses.

Role of N6-methyladenosine methylation in nasopharyngeal carcinoma: current insights and future prospective

Nasopharyngeal carcinoma (NPC) is a distinct type of head and neck squamous cell carcinoma prevalent in Southern China, Southeast Asia, and North Africa. Despite advances in treatment options, the prognosis for advanced NPC remains poor, underscoring the urgent need to explore its underlying mechanisms and develop novel therapeutic strategies. Epigenetic alterations have been shown to play a key role in NPC progression. Recent studies indicate that dysregulation of RNA modifications in NPC specifically affects tumor-related transcripts, influencing various oncogenic processes. This review provides a comprehensive overview of altered RNA modifications and their regulators in NPC, with a focus on m6A and its regulatory mechanisms. We discuss how m6A RNA modification influences gene expression and affects NPC initiation and progression at the molecular level, analyzing its impact on cancer-related biological functions. Understanding these modifications could reveal new biomarkers and therapeutic targets for NPC, offering promising directions for future research and precision medicine.

Interpretable deep cross networks unveiled common signatures of dysregulated epitranscriptomes across 12 cancer types

Cancer is a complex and multifaceted group of diseases characterized by uncontrolled cell growth that leads to the formation of malignant tumors. Recent studies suggest that N6-methyladenosine (m6A) RNA methylation plays pivotal roles in cancer pathology by influencing various cellular processes. However, the degree to which these mechanisms are shared across different cancer types remains unclear. In this study, we analyze an expansive array of 167 m6A epitranscriptome profiles covering 12 distinct cancer types and their originating normal tissues. We trained 12 distinct, cancer type-specific interpretable deep cross network models, which successfully distinguish between specific pairs of normal and cancer m6A contexts using integrated information from both the sequences and curated genomic knowledge. Interestingly, cross-cancer type testing indicated the existence of shared genomic patterns across various cancers at the epitranscriptome level. A pan-cancer model was subsequently developed to identify these shared patterns that could not be observed in a single cancer type. Our analysis uncovered, for the first time, a common epitranscriptome signature shared across multiple cancer types, particularly associated with RNA hybridization process and aberrant splicing. This highlights the importance of a comprehensive understanding of the pan-cancer epitranscriptome and holding potential implications in the development of RNA methylation-based therapeutics for various cancers.

Chromatin accessibility: biological functions, molecular mechanisms and therapeutic application

The dynamic regulation of chromatin accessibility is one of the prominent characteristics of eukaryotic genome. The inaccessible regions are mainly located in heterochromatin, which is multilevel compressed and access restricted. The remaining accessible loci are generally located in the euchromatin, which have less nucleosome occupancy and higher regulatory activity. The opening of chromatin is the most important prerequisite for DNA transcription, replication, and damage repair, which is regulated by genetic, epigenetic, environmental, and other factors, playing a vital role in multiple biological progresses. Currently, based on the susceptibility difference of occupied or free DNA to enzymatic cleavage, solubility, methylation, and transposition, there are many methods to detect chromatin accessibility both in bulk and single-cell level. Through combining with high-throughput sequencing, the genome-wide chromatin accessibility landscape of many tissues and cells types also have been constructed. The chromatin accessibility feature is distinct in different tissues and biological states. Research on the regulation network of chromatin accessibility is crucial for uncovering the secret of various biological processes. In this review, we comprehensively introduced the major functions and mechanisms of chromatin accessibility variation in different physiological and pathological processes, meanwhile, the targeted therapies based on chromatin dynamics regulation are also summarized.