Stem cells. m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation

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.

METTL3 inhibits primed-to-naïve transition of pluripotent stem cells through m6A-YTHDF2-pluripotency/Gstp1 mRNA degradation axis

N6-methyladenosine (m6A) plays crucial roles in development and cellular reprogramming. During embryonic development, pluripotency transitions from a naïve to a primed state, and modeling the reverse primed-to-naïve transition (PNT) provides a valuable framework for investigating pluripotency regulation. Here, we show that inhibiting METTL3 significantly promotes PNT in an m6A-dependent manner. Mechanistically, we found that suppressing METTL3 and YTHDF2 prolongs the lifetimes of pluripotency-associated mRNAs, such as Nanog and Sox2, during PNT. In addition, Gstp1 was identified as a downstream target of METTL3 inhibition and YTHDF2 knockout. Gstp1 overexpression enhances PNT, whereas its inhibition impedes the transition. Overall, our findings suggest that YTHDF2 facilitates the removal of pluripotency gene transcripts and Gstp1, thereby promoting PNT reprogramming through m6A-mediated posttranscriptional control.

Phase transition of WTAP regulates m6A modification of interferon-stimulated genes

N6-methyladenosine (m6A) is the most prevalent modification of mRNA which controls diverse physiological processes. Although m6A modification has been reported to regulate type I interferon (IFN) responses by targeting the mRNA of IFN-β and the interferon-stimulated genes (ISGs), the detailed mechanism of how m6A methyltransferase complex (MTC) rapidly responds to conduct the modification on nascent mRNA during IFN-β stimulation remains largely unclear. Here, we demonstrate that WTAP, the adaptor protein of m6A MTC, undergoes dephosphorylation-regulated phase transition from aggregates to liquid-like condensates under IFN-β stimulation, thereby mediating m6A modification of a subset of ISGs to restrict their expression. The phase transition of WTAP promotes the interaction with nucleus-translocated transcription factor STAT1, recruits MTC to the promoter regions of ISGs and directs the co-transcriptional m6A modification on ISG mRNAs. Collectively, our findings reveal a novel regulatory role of WTAP phase transition in manipulating signaling pathways and fine-tuning immune response by orchestrating dynamic m6A modification through the cooperation of transcription factors and MTC. Our findings unveil a novel mechanism by which WTAP phase transition controls immune homeostasis via transcription factor-MTC-driven dynamic m6A modification, thereby proposing a potential therapeutic target for alleviating immune dysregulation.

The emerging roles of N6-methyladenosine (m6A) deregulation in polycystic ovary syndrome

Polycystic ovary syndrome (PCOS) is an endocrine metabolic syndrome characterized by ovulation disorders, hyperandrogenemia, and polycystic ovaries, which seriously affect the psychological and physical health of childbearing women. N6-methyladenosine (m6A), as the most common mRNA epigenetic modification in eukaryotes, is vital for developing the female reproductive system and reproductive diseases. In recent years, an increasing number of studies have revealed the mechanisms by which m6A modifications and their related proteins are promoting the development of PCOS, including writers, erasers and readers. In this work, we reviewed the research progress of m6A in the pathophysiological development of PCOS from the starting point of PCOS clinical features, included the recent studies or those with significant findings related to m6A and PCOS, summarized the current commonly used therapeutic methods in PCOS and the possible targeted therapies against the m6A mechanism, and looked forward to future research directions of m6A in PCOS. With the gradual revelation of the m6A mechanism, m6A and its related proteins are expected to become a great field for PCOS treatment.

Aberrant downregulation of Y-box binding protein 1 expression impairs the cell cycle in an m5C-dependent manner in human granulosa cells from patients with primary ovarian insufficiency

Y-box binding protein 1 (YBX1) has been reported to play a role in human granulosa cell (GC) dysfunction by binding with long noncoding RNAs in patients with primary ovarian insufficiency (POI). 5-Methylcytosine (m5C) methylation is an abundant RNA epigenetic modification that is widely present in eukaryotic RNAs. However, whether YBX1, an important m5C reader, whether YBX1 participates in POI in an m5C- dependent manner remains unknown. Here, we demonstrated that the expression levels of YBX1 were decreased in GCs from patients with biochemical POI. YBX1 knockdown in a human granulosa cell line (KGN) impaired cell proliferation by preventing the G1 to S transition in the cell cycle. Conversely, YBX1 overexpression promoted the KGN cell proliferation. Integrated analysis of the transcriptome and m5C methylome profiles revealed that in human GCs, knockdown of YBX1 expression destabilized cell cycle-associated transcripts in an m5C-dependent manner, resulting in cell cycle arrest. Our results provide new insights of the pathogenesis of POI, revealing an alternative molecular mechanism in which YBX1 participates in human GC dysfunction by affecting the stability of cell cycle-associated genes in an m5C-dependent manner and thereby modulating GC proliferation.

m6A demethylase FTO/ALKBH5 promotes diabetes-induced endothelial cell dysfunction by negatively regulating lncRNA H19

Endothelial cell dysfunction induced by glucose is the most important cause of diabetic vascular complications, which are the leading causes of blindness, disability, renal failure, heart failure, stroke, and even death in diabetic patients. RNA m6A modification is involved in the pathogenesis of human disease. However, the role and underlying mechanism of RNA m6A modification in high glucose-induced endothelial cell dysfunction is not well understood. Herein, this study first demonstrated that m6A levels were decreased and that the demethylases FTO and ALKBH5 were upregulated in diabetic patients and an STZ-induced diabetic mouse model. This study revealed that high glucose induced decreased m6A levels and increased expression of FTO and ALKBH5, and silencing of FTO and ALKBH5 restored high glucose-induced decreases in m6A levels and dysfunction of HUVECs. Next, this study systematically screened differentially expressed lncRNAs, including H19, in HUVECs under high glucose conditions. This study revealed that FTO-ALKBH5 inhibited H19 expression by decreasing m6A modification in H19 transcripts. In addition, this study demonstrated the role of the FTO/ALKBH5/H19 pathway in high glucose-induced cellular dysfunction of HUVECs. Ultimately, this study uncovered that silencing of H19 promoted the expression of cell cycle-related genes, including PTEN, p21 and p27 via interacting with EZH2 and affecting the H3K27me3 histone modification. Overall, this study is the first to dissect the regulation of lncRNA by m6A modification in hyperglycaemia, identifying a new regulatory pathway in high glucose-induced cellular dysfunction and providing biomarkers with the potential to serve as therapeutic targets for high glucose-induced cellular dysfunction.

Endotoxin-induced m6A RNA methylation landscape in lung endothelial cells: role of METTL3 in regulating inflammation and injury during acute lung injury

Acute Lung Injury (ALI) involves diffuse alveolar damage, neutrophil infiltration, and pulmonary edema, with unacceptable mortality. Bacterial lipopolysaccharide (LPS) activates inflammatory pathways in ALI, which are then regulated by transcriptional and post-transcriptional pathways to affect gene expression. RNA methylation, N6-methyladenosine, is the main m6A mRNA modification that controls the expression of various genes in different environments. There are very few facts about LPS's effect on m6A RNA methylation. This study will explore the m6A RNA methylation landscape in lung endothelial cells (ECs) to understand its role in lung inflammation. In this study, lung endothelial cells were treated with LPS, and the dynamics of mRNA m6A methylation were examined through m6A-methylated RNA sequencing. RNA abundance was measured with RNA-seq, and global protein expression and m6A-binding proteins were identified using mass spectrometry (MS). Following LPS treatment, global m6A methylation levels increased along with the upregulation and nuclear translocation of METTL3 protein, while demethylase activity remained unchanged. METTL3 drove LPS-induced m6A methylation and endothelial injury, as shown by selective METTL3 siRNA and the inhibitor STM2457. MeRIP-seq analyses revealed increased m6A sites near the 5' UTR in LPS-treated cells, with m6A methylation correlating positively with gene expression. The metabolic and apoptosis pathways were shown to be more enriched in different types of methylated exons. METTL3-mediated m6A methylation targeted inflammatory genes, enhancing protein expression in chemokine signaling and MAPK pathways. STM2457 effectively mitigated LPS- or CLP-induced experimental ALI. According to this paper, LPS-mediated m6A RNA methylation is described in terms of genomic structure. Modulation of m6A methylation exerts influence over LPS-mediated endothelial gene expression and the ensuing inflammatory response.

m6A alters ribosome dynamics to initiate mRNA degradation

Degradation of mRNA containing N6-methyladenosine (m6A) is essential for cell growth, differentiation, and stress responses. Here, we show that m6A markedly alters ribosome dynamics and that these alterations mediate the degradation effect of m6A on mRNA. We find that m6A is a potent inducer of ribosome stalling, and these stalls lead to ribosome collisions that form a unique conformation unlike those seen in other contexts. We find that the degree of ribosome stalling correlates with m6A-mediated mRNA degradation, and increasing the persistence of collided ribosomes correlates with enhanced m6A-mediated mRNA degradation. Ribosome stalling and collision at m6A is followed by recruitment of YTHDF m6A reader proteins to promote mRNA degradation. We show that mechanisms that reduce ribosome stalling and collisions, such as translation suppression during stress, stabilize m6A-mRNAs and increase their abundance, enabling stress responses. Overall, our study reveals the ribosome as the initial m6A sensor for beginning m6A-mRNA degradation.

YTHDF2 suppresses the 2C-like state in mouse embryonic stem cells via the DUX-ZSCAN4 molecular circuit

Mouse embryonic stem cells (ESCs) consist of a rare population of heterogeneous 2-cell-like cells (2CLCs). These cells transiently recapitulate the transcriptional and epigenetic features of the 2-cell embryos, serving as a unique model for studying totipotency acquisition and embryonic development. Accumulating evidence has demonstrated that transcription factors and epigenetic modifications exert crucial functions in the transition of ESCs to 2CLCs. However, the roles of RNA modification in the regulation of the 2C-like state remain elusive. Using a DUX-induced 2CLCs system, we examine N6-methyladenosine (m6A) modification landscape transcriptome-wide and observe dynamic regulation of m6A during DUX-driven 2C-like reprogramming. Notably, many core 2C transcripts like Dux and Zscan4 are highly methylated. We identify the m6A reader protein YTHDF2 as a critical regulator of 2C-like state. Depletion of YTHDF2 facilitates robust expression of 2C-signature genes and ESCs-to-2CLCs transition. Intriguingly, YTHDF2 binds to a subset of m6A-modified 2C transcripts and promotes their decay. We further demonstrate that YTHDF2 suppresses the 2C-like program in a manner that is dependent on both m6A and the DUX-ZSCAN4 molecular circuit. Mechanistically, YTHDF2 interacts with CNOT1, a key component of the RNA deadenylase complex. Consistently, silencing of CNOT1 upregulates the 2C program and promotes ESCs-to-2CLCs transition. Collectively, our findings reveal novel insights into the epitranscriptomic regulation of the 2C-like state in mouse ESCs.

Cigarette smoking modulates m6A modification, affecting the induction of CYP1A1 mRNA by regulating human ARNT and AHRR in A549 cells

N6-Methyladenosine (m6A) modification is a common epitranscriptomic mark of eukaryotic RNAs. This modification is installed by a methyltransferase like 3 (METTL3)-METTL14 complex and is eliminated by fat mass and obesity-associated protein (FTO) and AlkB homolog 5 (ALKBH5). Aberrant m6A modification is associated with the development and progression of cancer. Cigarette smoking is a major lifestyle habit and risk factor for lung cancer. This study aimed to clarify the effects of cigarette smoking on the expression of m6A modification-regulating enzymes and the significance of m6A modification in the biological responses to cigarette smoking. Treatment of cigarette smoke extract (CSE) significantly decreased METTL3 and METTL14 protein levels in human lung adenocarcinoma-derived A549 cells. The induction of CYP1A1 mRNA by 2,3,7,8-tetrachlorodibenzo-p-dioxin, a typical ligand of the aryl hydrocarbon receptor (AHR), was attenuated by the knockdown (KD) of METTL3 or ALKBH5, whereas it was enhanced by the KD of FTO. As the underlying mechanisms, significantly decreased expression of AHR nuclear translocator (ARNT) by the KD of METTL3 or ALKBH5, and significantly decreased expression of AHR repressor (AHRR) by the KD of FTO were demonstrated. Formaldehyde-assisted isolation of regulatory elements assay revealed that the KD of METTL3 or ALKBH5 resulted in the compaction of the chromatin structure of ARNT promoter, suggesting that METTL3 and ALKBH5 promote the transcription of ARNT through the rearrangement of chromatin structure. Collectively, we found that CSE treatment decreased METTL3 and METTL14 protein levels, and m6A modification have impact on the induction of CYP1A1 by modulating ARNT and AHRR expression.

Effects of circPICALM-miR-132-PHKB regulated by METTL3 on proliferation of porcine skeletal muscle satellite cells

Circular RNA (circRNA) is ubiquitously expressed in highly differentiated eukaryotes, playing an extremely vital regulatory role in muscle growth and development. In this study, we identified circPICALM, a novel circRNA which consists of exons 5 to 9 of the PICALM gene, exhibiting differential expression in the longissimus dorsi muscle (LD) of adult (QA) and newborn (QN) Queshan Black pigs. CircPICALM is resistant to RNase R, mainly located in the cytoplasm with potential coding capacities. When circPICALM was over-expressed in porcine skeletal muscle satellite cells (PSMSCs), there was a significant decrease in the expression levels of PCNA, CDK4, CDK1 and CCND1, which consequently inhibited the proliferation of PSMSCs. Conversely, miR-132, a target molecule of circPICALM, was found to promote the proliferation of PSMSCs. In addition, circPICALM can up-regulate the expression of the target gene PHKB by competitively adsorbing miR-132. The circPICALM-ssc-miR-132-PHKB regulatory axis is regulated by METTL3, which increases the m6A level of both PSMSCs and circPICALM, thereby promoting the proliferation of PSMSCs. Overall, this study furnishes a fundamental reference for further in-depth exploration of the specific molecular mechanisms underlying m6A modification and circPICALM in muscle development and progression.

The m6A demethylase FTO promotes C/EBPβ-LIP translation to perform oncogenic functions in breast cancer cells

N6-methyladenosine (m6A) is a prevalent posttranscriptional mRNA modification involved in the regulation of transcript turnover, translation, and other aspects of RNA fate. The modification is mediated by multicomponent methyltransferase complexes (so-called writers) and is reversed through the action of the m6A-demethylases fat mass and obesity-associated (FTO) and alkB homolog 5 (ALKBH5) (so-called erasers). FTO promotes cell proliferation, colony formation and metastasis in models of triple-negative breast cancer (TNBC). However, little is known about genome-wide or specific downstream regulation by FTO. Here, we examined changes in the genome-wide transcriptome and translatome following FTO knockdown in TNBC cells. Unexpectedly, FTO knockdown had a limited effect on the translatome, while transcriptome analysis revealed that genes related to extracellular matrix (ECM) and epithelial-mesenchymal transition (EMT) are regulated through yet unidentified mechanisms. Differential translation of CEBPB mRNA into the C/EBPβ transcription factor isoform C/EBPβ-LIP is known to act in a pro-oncogenic manner in TNBC cells through regulation of EMT genes. Here we show that FTO is required for efficient C/EBPβ-LIP expression, suggesting that FTO has oncogenic functions through regulation of C/EBPβ-LIP.

METTL14 regulates chondrogenesis through the GDF5-RUNX-extracellular matrix gene axis during limb development

m6A RNA methylation is essential for many aspects of mammalian development but its roles in chondrogenesis remain largely unknown. Here, we show that m6A is necessary for chondrogenesis and limb morphogenesis using limb progenitor-specific knockout mice of Mettl14, an essential subunit in the m6A methyltransferase complex. The knockout disrupts cartilage anlagen formation in limb buds with 11 downregulated proteins known to dysregulate chondrogenesis and shorten limb skeletons upon mutation in mice and humans. Further studies show a gene regulatory hierarchy among the 11 proteins. m6A stabilizes the transcript and increases the protein level of GDF5, a BMP family member. This activates the chondrogenic transcription factor genes Runx2 and Runx3, whose mRNAs are also stabilized by m6A. They promote the transcription of six collagen genes and two other chondrogenic genes, Ddrgk1 and Pbxip1. Thus, this study uncovers an m6A-based cascade essential for chondrogenesis during limb skeletal development.

Epigenetic regulation in oogenesis and fetal development: insights into m6A modifications

The unique physiological structure of women has led to a variety of diseases that have attracted the attention of many people in recent years. Disturbances in the reproductive system microenvironment lead to the progression of various female tumours and pregnancy disorders. Numerous studies have shown that epigenetic modifications crucially influence both oogenesis and foetal development. m6A, a modification at the mRNA level, consists of three parts, namely, writers, erasers, and readers, which are involved in several biological functions, such as the nucleation and stabilisation of mRNAs, thereby regulating the development of reproductive system diseases. In this manuscript, we delineate the constituents of m6A, their biological roles, and advancements in understanding m6A within the maternal-foetal immunological context. In addition, we summarise the mechanism of m6A in gynaecological diseases and provide a new perspective for targeting m6A to delay the progression of reproductive system diseases in clinical practice.

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.

METTL14-Induced M6A Methylation Increases G6pc Biosynthesis, Hepatic Glucose Production and Metabolic Disorders in Obesity

METTL14 dimerizes with METTL3 to install N6-methyladenosine (m6A) on mRNA (m6A writers). Subsequently, m6A readers bind to m6A-marked RNA to influence its metabolism. RNA m6A emerges to critically regulate multiple intracellular processes; however, there is a gap in our understanding of m6A in liver metabolism. Glucose-6-phosphatase catalytic subunit (G6pc) mediates hepatic glucose production (HGP) and serves as the gatekeeper for glycogenolysis and gluconeogenesis; however, G6pc regulation is not fully understood. Here, METTL14 is identified as a posttranscriptional regulator of G6pc. Liver METTL14, METTL3, and m6A-methylated G6pc mRNA are upregulated in mice with diet-induced obesity. Deletion of Mettl14 decreases, whereas overexpression of METTL14 increases, G6pc mRNA m6A in hepatocytes in vitro and in vivo. Five m6A sites are identified, and disruption of them (G6pcΔ 5A) blocks METTL14-induced m6A methylation of G6pcΔ 5A mRNA. METTL14 increases both stability and translation of G6pc but not G6pcΔ 5A mRNA. YTHDF1 and YTHDF3 but not YTHDF2 (m6A readers) bind to m6A-marked G6pc mRNA to increase its synthesis. Deletion of hepatic Mettl14 decreases gluconeogenesis in primary hepatocytes, liver slices, and mice. Hepatocyte-specific restoration of G6pc reverses defective HGP in Mettl14 knockout mice. These results unveil a METTL14/G6pc mRNA m6A/G6pc biosynthesis/HGP axis governing glucose metabolism in health and metabolic disease.

tRNA modifications tune m6A-dependent mRNA decay

Chemically modified nucleotides in mRNA are critical regulators of gene expression, primarily through interactions with reader proteins that bind to these modifications. Here, we present a mechanism by which the epitranscriptomic mark N6-methyladenosine (m6A) is read by tRNAs during translation. Codons that are modified with m6A are decoded inefficiently by the ribosome, rendering them "non-optimal" and inducing ribosome collisions on cellular transcripts. This couples mRNA translation to decay. 5-Methoxycarbonylmethyl-2-thiouridine (mcm5s2U) in the tRNA anticodon loop counteracts this effect. This unanticipated link between the mRNA and tRNA epitranscriptomes enables the coordinated decay of mRNA regulons, including those encoding oncogenic signaling pathways. In cancer, dysregulation of the m6A and mcm5s2U biogenesis pathways-marked by a shift toward more mcm5s2U-is associated with more aggressive tumors and poor prognosis. Overall, this pan-epitranscriptomic interaction represents a novel mechanism of post-transcriptional gene regulation with implications for human health.

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.

Understanding epigenetic regulation in the endometrium - lessons from mouse models with implantation defects

Endometrial function, crucial for successful embryo implantation, is significantly influenced by epigenetic regulation. This review investigates the crucial roles of DNA methylation, histone modifications, chromatin remodeling, and RNA methylation in endometrial receptivity and implantation, based on a survey of recent literature on knockout mouse models with implantation defects. These models illuminate how epigenetic disruptions contribute to implantation failure, a significant human reproductive health concern. DNA methylation and histone modifications modulate endometrial receptivity by affecting gene silencing and chromatin structure, respectively. Chromatin remodeling factors also play a critical role in endometrial dynamics, influencing gene expression. Furthermore, RNA methylation emerges as critical in implantation through transcriptional and translational control. While human studies provide limited epigenetic snapshots, mouse models with suppressed epigenetic regulators reveal direct causal links between epigenetic alterations and implantation failure. Understanding these epigenetic interactions offers potential for novel therapies addressing reproductive disorders.

Tailoring and reversing m6A editing with sequential RNA bioorthogonal chemistry

Many existing methods for post-transcriptional RNA modification rely on a single-step approach, limiting the ability to reversibly control m6A methylation at specific sites. Here, we address this challenge by developing a multi-step system that builds on the concept of sequential RNA bioorthogonal chemistry. Our strategy uses an azide-based reagent (NAI-N3) capable of both cleavage and ligation reactions, thereby allowing iterative and reversible modifications of RNA in living cells. By applying this approach in CRISPR (clustered regularly interspaced short palindromic repeats)-based frameworks, we demonstrate tailored editing of m6A marks at targeted RNA sites, overcoming the one-way restriction of conventional bioorthogonal methods. This sequential protocol not only broadens the scope for fine-tuned RNA regulation but also provides a versatile platform for exploring dynamic m6A function in genetic and epigenetic research.

Epigenome dynamics in early mammalian embryogenesis

During early embryonic development in mammals, the totipotency of the zygote - which is reprogrammed from the differentiated gametes - transitions to pluripotency by the blastocyst stage, coincident with the first cell fate decision. These changes in cellular potency are accompanied by large-scale alterations in the nucleus, including major transcriptional, epigenetic and architectural remodelling, and the establishment of the DNA replication programme. Advances in low-input genomics and loss-of-function methodologies tailored to the pre-implantation embryo now enable these processes to be studied at an unprecedented level of molecular detail in vivo. Such studies have provided new insights into the genome-wide landscape of epigenetic reprogramming and chromatin dynamics during this fundamental period of pre-implantation development.

N6-methyladenosine modification of host Hsc70 attenuates nucleopolyhedrovirus infection in the lepidopteran model insect Bombyx mori

N6-methyladenosine (m6A) is the most prevalent internal modification on mRNA and plays critical roles in various biological processes including virus infection. It has been shown that m6A methylation is able to regulate virus proliferation and host innate immunity in mammals and plants, however, this antiviral defense in insects is largely unknown. Here we investigated function of m6A and its associated methyltransferases in nucleopolyhedrovirus (BmNPV) infection in silkworm. We reported significant changes of m6A methyltransferases METTL3 and METTL14 upon BmNPV treatment. Knockdown of METTL3 and METTL14 enhanced BmNPV infection and promoted viral proliferation, whereas overexpression of these enzymes could prevent viral replication. Further study revealed that host heat shock cognate 70 (Hsc70) as a target gene of m6A would contribute to BmNPV proliferation. CRISPR-dCas9-targeted methylation of Hsc70 by METTL3/METTL14 decreased its expression and further attenuated BmNPV infection. Consistently, knockout of METTL3 in silkworm individuals by CRISPR-Cas9 reduced overall m6A levels, which led to rapid death of silkworms and increase of BmNPV upon virus infection likely due to upregulated expression of Hsc70. Collectively, these findings provided a novel insight into antiviral activity of m6A and demonstrated a distinct immune response via attenuating host Hsc70 expression to counteract BmNPV replication in lepidopteran silkworm.

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.

The landscape of N6-methyladenosine in localized primary prostate cancer

N6-methyladenosine (m6A), the most abundant internal RNA modification in humans, regulates most aspects of RNA processing. Prostate cancer is characterized by widespread transcriptomic dysregulation; therefore, we characterized the m6A landscape of 162 localized prostate tumors with matched DNA, RNA and protein profiling. m6A abundance varied dramatically across tumors, with global patterns emerging via complex germline-somatic cooperative regulation. Individual germline polymorphisms regulated m6A abundance, cooperating with somatic mutation of cancer driver genes and m6A regulators. The resulting complex patterns were associated with prognostic clinical features and established the biomarker potential of global and locus-specific m6A patterns. Tumor hypoxia dysregulates m6A profiles, bridging prior genomic and proteomic observations. Specific m6A sites, such as those in VCAN, drive disease aggression, associating with poor outcomes, tumor growth and metastasis. m6A dysregulation is thus associated with key events in the natural history of prostate cancer: germline risk, microenvironmental dysregulation, somatic mutation and metastasis.

The epitranscriptome: reshaping the DNA damage response

Genomic instability poses a formidable threat to cellular vitality and wellbeing, prompting cells to deploy an intricate DNA damage response (DDR) mechanism. Recent evidence has suggested that RNA is intricately linked to the DDR by serving as template, scaffold, or regulator during the repair of DNA damage. Additionally, RNA molecules undergo modifications, contributing to the epitranscriptome, a dynamic regulatory layer influencing cellular responses to genotoxic stress. The intricate interplay between RNA and the DDR sheds new light on how the RNA epigenome contributes to the maintenance of genomic integrity and ultimately shapes the fate of damaged cells.

Melatonin via MTNR1B regulates METTL3 to protect ileum cell differentiation

Intestinal stem cells rapidly differentiate into various epithelial cells, playing a crucial role in maintaining intestinal homeostasis. Melatonin, a known endogenous molecule with anti-inflammatory and antioxidant properties, has its potential efficacy in ileum stem cells differentiation not fully understood to date. This study indicates that melatonin suppresses ileum inflammation and maintains normal differentiation of ileum stem cells through MTNR1B. Subsequent outcomes following treatment with MTNR1B inhibitors further substantiate these findings. Additionally, overexpression of METTL3 protein appears to be a potential instigator for promoting ileum inflammation and disruptions in cell differentiation. Treatment with the METTL3 inhibitor SAH significantly inhibits ileum inflammation and Wnt/β-catenin activity, thereby sustaining normal cellular differentiation functions. In summary, this study showed that melatonin may improve ileum inflammation and maintain cell differentiation functions by inhibiting abnormal METTL3 expression via MTNR1B.

m6A-Modified GATA2 Enhances Odontogenic Differentiation in Stem Cells from the Apical Papilla

Epigenetic modifications play a crucial role in regulating stem cell differentiation. Among these, N6-methyladenosine (m6A) modification significantly impacts mRNA stability and translation. However, its role in dental stem cell differentiation remains largely unexplored. Functional assays, including ALP activity, alizarin red S staining, qPCR, and Western blot, were conducted to assess odontogenic differentiation. Then, an in vivo dentin formation model was used to validate our findings. Additionally, we employed RNA stability assays and m6A site mutagenesis to investigate the regulatory mechanism of m6A modification in GATA2-mediated differentiation. Our results demonstrated that overexpression of GATA2 significantly promoted SCAP odontogenic differentiation. Moreover, in vivo studies confirmed that GATA2 overexpression enhances dentin formation in mouse models. Conversely, knockdown of GATA2 or mutation of its m6A sites led to reduced mRNA stability and decreased odontogenic differentiation. m6A modification is enriched in the 3' untranslated region (3'UTR) of GATA2 mRNA, regulating its stability and expression. Our findings indicate that m6A modification contributes to the post-transcriptional regulation of GATA2, enhancing its stability and promoting SCAP-mediated odontogenic differentiation and dentin formation. This study provides new insights into the epigenetic regulation of dental stem cells and suggests a potential molecular target for dental tissue regeneration.

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.

Targeting m6A RNA Modification in Tumor Therapeutics

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

Gut dysbiosis conveys psychological stress to activate LRP5/β-catenin pathway promoting cancer stemness

Psychological stress causes gut microbial dysbiosis and cancer progression, yet how gut microbiota determines psychological stress-induced tumor development remains unclear. Here we showed that psychological stress promotes breast tumor growth and cancer stemness, an outcome that depends on gut microbiota in germ-free and antibiotic-treated mice. Metagenomic and metabolomic analyses revealed that psychological stress markedly alters the composition and abundance of gut microbiota, especially Akkermansia muciniphila (A. muciniphila), and decreases short-chain fatty acid butyrate. Supplement of active A. muciniphila, butyrate or a butyrate-producing high fiber diet dramatically reversed the oncogenic property and anxiety-like behavior of psychological stress in a murine spontaneous tumor model or an orthotopic tumor model. Mechanistically, RNA sequencing analysis screened out that butyrate decreases LRP5 expression to block the activation of Wnt/β-catenin signaling pathway, dampening breast cancer stemness. Moreover, butyrate as a HDAC inhibitor elevated histone H3K9 acetylation level to transcriptionally activate ZFP36, which further accelerates LRP5 mRNA decay by binding adenine uridine-rich (AU-rich) elements of LRP5 transcript. Clinically, fecal A. muciniphila and serum butyrate were inversely correlated with tumoral LRP5/β-catenin expression, poor prognosis and negative mood in breast cancer patients. Altogether, our findings uncover a microbiota-dependent mechanism of psychological stress-triggered cancer stemness, and provide both clinical biomarkers and potential therapeutic avenues for cancer patients undergoing psychological stress.

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

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

Capturing short-range and long-range dependencies of nucleotides for identifying RNA N6-methyladenosine modification sites

N6-methyladenosine (m6A) plays a crucial role in enriching RNA functional and genetic information, and the identification of m6A modification sites is therefore an important task to promote the understanding of RNA epigenetics. In the identification process, current studies are mainly concentrated on capturing the short-range dependencies between adjacent nucleotides in RNA sequences, while ignoring the impact of long-range dependencies between non-adjacent nucleotides for learning high-quality representation of RNA sequences. In this work, we propose an end-to-end prediction model, called m6ASLD, to improve the identification accuracy of m6A modification sites by capturing the short-range and long-range dependencies of nucleotides. Specifically, m6ASLD first encodes the type and position information of nucleotides to construct the initial embeddings of RNA sequences. A self-correlation map is then generated to characterize both short-range and long-range dependencies with a designed map generating block for each RNA sequence. After that, m6ASLD learns the global and local representations of RNA sequences by using a graph convolution process and a designed dependency searching block respectively, and finally achieves its identification task under a joint training scheme. Extensive experiments have demonstrated the promising performance of m6ASLD on 11 benchmark datasets across several evaluation metrics.

M6A Demethyltransferase FTO Attenuates Meniscus Degeneration and Osteoarthritis via Orchestrating Autophagy and Energetic Metabolism

Impaired autophagy is reported to promote osteoarthritis (OA). However, the mechanism by which autophagy in regulating meniscus degeneration and OA remains unclear. Here, unconvered aberrant energetic metabolism pattern in meniscus cells with OA is uncovered first, which results in lower adenosine triphosphate (ATP) production. And these phenomena are induced by impaired autophagy in meniscus cells with OA. It is further revealed that the suppression of m6A demethylase fat mass and obesity-associated protein (FTO) inhibits autophagy and causing lower ATP production by reducing oxidative phosphorylation. Specific deletion of FTO in meniscus cells by generating FTOflox/flox; COL1A1-CreERT2 (FTOcko) mice impair autophagy and promote meniscus degeneration and OA, while intra-articular injection of adeno-associated virus of FTO (AAV-FTO) restores autophagy and alleviates meniscus degeneration and OA. Mechanistically, FTO regulates the mRNA stability of ATG16L1 by targeting the m6A methylation sites on ATG16L1 in a YTHDF2-dependent manner, thereby inhibiting the formation of autophagosomes and causing an imbalance in energetic metabolism. Intra-articular injection of AAV-FTO reverses the catabolic phenotype of meniscus degeneration and OA in FTOcko mice. In summary, these findings reveal FTO orchestrates autophagy and energetic metabolism by regulating ATG16L1 in a m6A-dependent manner. Therefore, targeting FTO might be a potential therapeutic strategy for meniscus degeneration and early-stage OA.

Altered N6-methyladenosine methylation level in spermatozoa messenger RNA of the male partners is related to unexplained recurrent pregnancy loss

BACKGROUND

Understanding the pathogenesis of unexplained recurrent pregnancy loss is paramount for advancing effective treatments. Various biological processes, including spermatogenesis and embryo development, are tightly regulated by N6-methyladenosine modifications. However, few studies have focused on the impact of sperm N6-methyladenosine modifications on embryonic development. Therefore, we aimed to study altered N6-methyladenosine-mediated messenger RNA methylation modifications in the spermatozoa of male partners from couples experiencing unexplained recurrent pregnancy loss, to identify potential diagnostic markers and explore their potential molecular mechanisms in pregnancy loss and embryogenesis.

METHODS

Methylated RNA immunoprecipitation (MeRIP) sequencing and RNA sequencing were conducted on the spermatozoa of men from couples in the 'unexplained recurrent pregnancy loss' group (n = 6), and the fertility control group (n = 6). To identify the role of the detected key genes, zebrafish model embryos were studied, and multi-omics (transcriptomics, proteomics, and metabolomics) analyses helped to explore the molecular mechanism of abnormal embryogenesis.

FINDINGS

Comparing unexplained recurrent pregnancy loss with the fertility control group, 217 N6-methyladenosine peaks were significantly upregulated, and 40 were downregulated in the spermatozoa. The combined analyses of spermatozoa-methylated RNA immunoprecipitation sequencing and RNA sequencing indicated that N6-methyladenosine methylation and the expression of SEMA5A, MT-ATP6, ZNF662, and KDM4C were significantly different. In zebrafish embryos, the altered expression of the four genes increased embryonic mortality and malformations by disturbing several key signaling pathways and zygotic genome activation.

INTERPRETATION

This study highlights the paternal epigenome, which could be one of the reasons for faulty embryogenesis leading to pregnancy loss. The N6-methyladenosine modification, the most prevalent RNA modification, contributes to the exploration and understanding of the paternal epigenome in the maintenance of pregnancy and fetal growth and development. The four genes identified in this study may serve as potential diagnostic markers and elucidate novel molecular mechanisms of embryogenesis.

Transcriptomic Regulation by Astrocytic m6A Methylation in the mPFC

Astrocytes, the most prevalent type of glial cells, have been found to play a crucial part in numerous physiological functions. By offering metabolic and structural support, astrocytes are vital for the proper functioning of the brain and regulating information processing and synaptic transmission. Astrocytes located in the medial prefrontal cortex (mPFC) are highly responsive to environmental changes and have been associated with the development of brain disorders. One of the primary mechanisms through which the brain responds to environmental factors is epitranscriptome modification. M6-methyladenosine methylation is the most prevalent internal modification of eukaryotic messenger RNA (mRNA), and it significantly impacts transcript processing and protein synthesis. However, the effects of m6A on astrocyte transcription and function are still not well understood. Our research demonstrates that ALKBH5, an RNA demethylase of m6A found in astrocytes, affects gene expression in the mPFC. These findings suggest that further investigation into the potential role of astrocyte-mediated m6A methylation in the mPFC is warranted.

Transcriptome-wide mapping of N3-methylcytidine modification at single-base resolution

3-Methylcytidine (m3C), a prevalent modification of transfer RNAs (tRNAs), was recently identified in eukaryotic messenger RNAs (mRNAs). However, its precise distribution and formation mechanisms in mRNAs remain elusive. Here, we develop a novel approach, m3C immunoprecipitation and sequencing (m3C-IP-seq), utilizing antibody enrichment to profile the m3C methylome at single-nucleotide resolution. m3C-IP-seq captures 12 cytoplasmic tRNA isoacceptors and 2 mitochondrial tRNA isoacceptors containing m3C modifications. Moreover, m3C-IP-seq permits the comprehensive profiling of m3C sites in mRNAs and long noncoding RNAs, with their presence reliant on a nuclear isoform of METTL8. A significant proportion of m3C sites is concentrated in the 3' untranslated region (3' UTR) of mRNAs and is associated with mRNA degradation. Additionally, m3C methylation is dynamic and responds to hypoxia. Collectively, our data demonstrate the widespread presence of m3C modification in the human transcriptome and provide a resource for functional studies of m3C-mediated RNA metabolism.

De novo basecalling of RNA modifications at single molecule and nucleotide resolution

RNA modifications influence RNA function and fate, but detecting them in individual molecules remains challenging for most modifications. Here we present a novel methodology to generate training sets and build modification-aware basecalling models. Using this approach, we develop the m6ABasecaller, a basecalling model that predicts m6A modifications from raw nanopore signals. We validate its accuracy in vitro and in vivo, revealing stable m6A modification stoichiometry across isoforms, m6A co-occurrence within RNA molecules, and m6A-dependent effects on poly(A) tails. Finally, we demonstrate that our method generalizes to other RNA and DNA modifications, paving the path towards future efforts detecting other modifications.

Injecting structure-aware insights for the learning of RNA sequence representations to identify m6A modification sites

N6-methyladenosine (m6A) represents one of the most prevalent methylation modifications in eukaryotes and it is crucial to accurately identify its modification sites on RNA sequences. Traditional machine learning based approaches to m6A modification site identification primarily focus on RNA sequence data but often incorporate additional biological domain knowledge and rely on manually crafted features. These methods typically overlook the structural insights inherent in RNA sequences. To address this limitation, we propose M6A-SAI, an advanced predictor for RNA m6A modifications. M6A-SAI leverages a transformer-based deep learning framework to integrate structure-aware insights into sequence representation learning, thereby enhancing the precision of m6A modification site identification. The core innovation of M6A-SAI lies in its ability to incorporate structural information through a multi-step process: initially, the model utilizes a Transformer encoder to learn RNA sequence representations. It then constructs a similarity graph based on Manhattan distance to capture sequence correlations. To address the limitations of the smooth similarity graph, M6A-SAI integrates a structure-aware optimization block, which refines the graph by defining anchor sets and generating an awareness graph through PageRank. Following this, M6A-SAI employs a self-correlation fusion graph convolution framework to merge information from both the similarity and awareness graphs, thus producing enriched sequence representations. Finally, a support vector machine is utilized for classifying these representations. Experimental results validate that M6A-SAI substantially improves the recognition of m6A modification sites by incorporating structure-aware insights, demonstrating its efficacy as a robust method for identifying RNA m6A modification sites.

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.

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.

Ultrafine Particulate Matter Exacerbates the Risk of Delayed Neural Differentiation: Modulation Role of METTL3-Mediated m6A Modification

Air pollution, especially from ultrafine particles (PM0.1, ≤0.1 μm), is increasingly recognized for its detrimental effects on health. The influence of PM0.1 on neurodevelopmental disorders and its underlying mechanisms remain incompletely understood but are of significant concern. Through an investigation using mouse embryonic stem cells (mESCs), our study has uncovered disruptions in cell cycle dynamics, reduced neural precursor formation, and impaired neurogenesis during mESC neural differentiation as a result of PM0.1-induced neurodevelopmental toxicity. By employing N6-methyladenosine (m6A) methylated RNA immunoprecipitation sequencing and bioinformatics, we identified Zic1 as a key target of PM0.1-induced developmental disturbances. Our mechanistic findings indicate that PM0.1 enhances m6A methylation of Zic1 by upregulating Mettl3, leading to decreased mRNA stability and expression of this gene. Furthermore, the efficacy of the METTL3 inhibitor in alleviating nerve differentiation impairments emphasizes the significance of this pathway. In addition, source analysis, molecular docking, and toxicity analyses show that PAHs with higher ring structures in PM0.1 from combustion sources competitively bind to METTL3, potentially exacerbating neurodevelopmental toxicity. This study not only underscores the severe impact of PM0.1 on neurodevelopment but also reveals the pivotal role of m6A modification in mediating these effects, providing valuable insights and potential therapeutic targets for mitigating PM0.1-related health risks.

Molecular Regulation of Palatogenesis and Clefting: An Integrative Analysis of Genetic, Epigenetic Networks, and Environmental Interactions

Palatogenesis is a complex developmental process requiring temporospatially coordinated cellular and molecular events. The following review focuses on genetic, epigenetic, and environmental aspects directing palatal formation and their implication in orofacial clefting genesis. Essential for palatal shelf development and elevation (TGF-β, BMP, FGF, and WNT), the subsequent processes of fusion (SHH) and proliferation, migration, differentiation, and apoptosis of neural crest-derived cells are controlled through signaling pathways. Interruptions to these processes may result in the birth defect cleft lip and/or palate (CL/P), which happens in approximately 1 in every 700 live births worldwide. Recent progress has emphasized epigenetic regulations via the class of non-coding RNAs with microRNAs based on critically important biological processes, such as proliferation, apoptosis, and epithelial-mesenchymal transition. These environmental risks (maternal smoking, alcohol, retinoic acid, and folate deficiency) interact with genetic and epigenetic factors during palatogenesis, while teratogens like dexamethasone and TCDD inhibit palatal fusion. In orofacial cleft, genetic, epigenetic, and environmental impact on the complex epidemiology. This is an extensive review, offering current perspectives on gene-environment interactions, as well as non-coding RNAs, in palatogenesis and emphasizing open questions regarding these interactions in palatal development.

Epigenetic regulation in female reproduction: the impact of m6A on maternal-fetal health

With the development of public health, female diseases have become the focus of current concern. The unique reproductive anatomy of women leads to the development of gynecological diseases gradually become an important part of the socio-economic burden. Epigenetics plays an irreplaceable role in gynecologic diseases. As an important mRNA modification, m6A is involved in the maturation of ovum cells and maternal-fetal microenvironment. At present, researchers have found that m6A is involved in the regulation of gestational diabetes and other reproductive system diseases, but the specific mechanism is not clear. In this manuscript, we summarize the components of m6A, the biological function of m6A, the progression of m6A in the maternal-fetal microenvironment and a variety of gynecological diseases as well as the progression of targeted m6A treatment-related diseases, providing a new perspective for clinical treatment-related diseases.

The role of methyltransferase-like 3 (METTL3) in immune response modulation in bivalve (Mytilus coruscus) during bacterial infection

N6-methyladenosine (m6A) modification is a prevalent mRNA modification that regulates diverse biological processes in eukaryotes, including immune responses. While the role of m6A in mammalian immunity has been explored, its involvement in the immune defense of invertebrates, particularly marine bivalves which face constant pathogen challenges, remains largely unknown. Here, we investigated the function of methyltransferase-like 3 (METTL3), a key m6A "writer" enzyme, in the immune response of the marine bivalve Mytilus coruscus against Vibrio alginolyticus infection. M. coruscus METTL3 (McMETTL3) expression in the digestive gland increased (3-fold) after V. alginolyticus infection, coinciding with elevated m6A levels. Silencing McMETTL3 reduced both m6A levels and V. alginolyticus-induced apoptosis in digestive gland cells. In silico analysis identified a C1q-like protein family member (McC1QL) as a potential downstream target of McMETTL3, exhibiting an increase (7.2-fold) in m6A modification and an increase (1.5-fold) in expression during infection. Functional experiments confirmed that McC1QL knockdown inhibited McMETTL3-driven apoptosis (10.83 %). These findings demonstrate that METTL3 regulates apoptosis and immune responses in invertebrates via m6A modification of target genes like McC1QL. This study provides novel insights into the m6A-mediated immune regulation mechanisms in marine bivalves and may offer potential avenues for developing innovative disease control strategies in aquaculture.

An iPSC model of fragile X syndrome reflects clinical phenotypes and reveals m 6 A- mediated epi-transcriptomic dysregulation underlying synaptic dysfunction

Fragile X syndrome (FXS), the leading genetic cause of intellectual disability, arises from FMR1 gene silencing and loss of the FMRP protein. N6-methyladenosine (m 6 A) is a prevalent mRNA modification essential for post-transcriptional regulation. FMRP is known to bind to and regulate the stability of m 6 A-containing transcripts. However, how loss of FMRP impacts on transcriptome-wide m 6 A modifications in FXS patients remains unknown. To answer this question, we generated cortical neurons differentiated from induced pluripotent stem cells (iPSC) derived from healthy subjects and FXS patients. In electrophysiology recordings, we validated that synaptic and neuronal network defects in iPSC-derived FXS neurons corresponded to the clinical EEG data of the patients from which the corresponding iPSC line was derived. In analysis of transcriptome-wide methylation, we show that FMRP deficiency led to increased translation of m 6 A writers, resulting in hypermethylation that primarily affecting synapse-associated transcripts and increased mRNA decay. Conversely, in the presence of an m 6 A writer inhibitor, synaptic defects in FXS neurons were rescued. Taken together, our findings uncover that an FMRP-dependent epi-transcriptomic mechanism contributes to FXS pathogenesis by disrupting m 6 A modifications in FXS, suggesting a promising avenue for m 6 A- targeted therapies.

Dynamics and regulatory roles of RNA m6A methylation in unbalanced genomes

N6-methyladenosine (m6A) in eukaryotic RNA is an epigenetic modification that is critical for RNA metabolism, gene expression regulation, and the development of organisms. Aberrant expression of m6A components appears in a variety of human diseases. RNA m6A modification in Drosophila has proven to be involved in sex determination regulated by Sxl and may affect X chromosome expression through the MSL complex. The dosage-related effects under the condition of genomic imbalance (i.e. aneuploidy) are related to various epigenetic regulatory mechanisms. Here, we investigated the roles of RNA m6A modification in unbalanced genomes using aneuploid Drosophila. The results showed that the expression of m6A components changed significantly under genomic imbalance, and affected the abundance and genome-wide distribution of m6A, which may be related to the developmental abnormalities of aneuploids. The relationships between methylation status and classical dosage effect, dosage compensation, and inverse dosage effect were also studied. In addition, we demonstrated that RNA m6A methylation may affect dosage-dependent gene regulation through dosage-sensitive modifiers, alternative splicing, the MSL complex, and other processes. More interestingly, there seems to be a close relationship between MSL complex and RNA m6A modification. It is found that ectopically overexpressed MSL complex, especially the levels of H4K16Ac through MOF, could influence the expression levels of m6A modification and genomic imbalance may be involved in this interaction. We found that m6A could affect the levels of H4K16Ac through MOF, a component of the MSL complex, and that genomic imbalance may be involved in this interaction. Altogether, our work reveals the dynamic and regulatory role of RNA m6A modification in unbalanced genomes, and may shed new light on the mechanisms of aneuploidy-related developmental abnormalities and diseases.

O-GlcNAcylated FTO promotes m6A modification of SOX4 to enhance MDS/AML cell proliferation

Fat mass and obesity-associated protein (FTO) was the first m6A demethylase identified, which is responsible for eliminating m6A modifications in target RNAs. While it is well-established that numerous cytosolic and nuclear proteins undergo O-GlcNAcylation, the possibility of FTO being O-GlcNAcylated and its functional implications remain unclear. This study found that a negative correlation between FTO expression and O-GlcNAcylation in patients with myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). The decreased O-GlcNAcylation on FTO can result in diminished m6A modification of SRY-related high mobility group box 4 (SOX4). This led to the promotion of cell apoptosis and inhibition of cell proliferation in MDS/AML. The O-GlcNAcylation of FTO stabilized SOX4 transcripts in an m6A-dependent manner, resulting in increased AKT and MAPK phosphorylation and decreased cell apoptosis. Inhibiting FTO O-GlcNAcylation significantly slowed AML progression in vitro, a finding supported by clinical data in MDS/AML patients. In conclusion, our study highlights the crucial role of FTO O-GlcNAcylation in RNA m6A methylation and the progression of MDS/AML, thereby providing a potential therapeutic avenue for these formidable diseases.

ALKBH5, an m6A demethylase, attenuates tumor growth and inhibits metastasis in papillary thyroid carcinoma

The significance of ALKBH5 in erasing mRNA methylation in mRNA biogenesis, decay, and translation control has emerged as a prominent research focus. Additionally, ALKBH5 is associated with the development of numerous human cancers. However, it remains unclear whether ALKBH5 regulates the growth and metastasis of papillary thyroid carcinoma (PTC). Here, we compared cancer tissues and paracancerous tissues from PTC patients, along with cultured cells expressing ALKBH5 (overexpression, silent gene expression, normal stable expression). Our primary objective was to investigate the impact of ALKBH5 on PTC. Selected 30 cases of PTC tissues and their adjacent noncancerous tissues to compare the protein expression levels of ALKBH5 between the two groups using immunohistochemical analysis. qRT-PCR and western blot were used to detect the expression of ALKBH5 in normal thyroid follicular epithelial cells (Nthy-ori3-1) and 4 PTC cell lines (human PTC cell lines K1, BCPAP, IHH4, and TPC1). Appropriate cell lines were screened for subsequent experiments. Immunofluorescence staining was used to localize the high accumulation of ALKBH5 in cells. Construct the ALKBH5 knockdown vector and ALKBH5 overexpression vector separately, and construct the overexpression ALKBH5-mut vector with m6A domain mutation. The impact of different levels of ALKBH5 in the three cell lines on RNA m6A methylation levels was compared using qRT-PCR and western blot methods. Furthermore, cell viability was assessed using the CCK-8 assay, while the impact on cell proliferation was examined using plate colony formation assay. Cell invasion was evaluated using the Transwell assay. Immunohistochemical staining results showed that the expression of ALKBH5 protein in PTC cancer tissue was significantly lower than in adjacent non-cancerous tissue (P < 0.05). Lymph node metastasis in PTC patients may have been linked to ALKBH5 protein levels in their cancerous tissues (P = 0.034). The expression of ALKBH5 in PTC cell lines BCPAP, IHH4, and TPC1 was significantly lower than Nthy-ori3-1 (P < 0.05). IHH4 and TPC1 cell lines were selected for subsequent experiments. Immunofluorescence single staining results showed a high accumulation of ALKBH5 protein in the cell nucleus. Cell viability results suggested that compared to the overexpression-negative control group, cell proliferation, and invasion were significantly decreased in the ALKBH5 overexpression group (P < 0.05) and the mut-ALKBH5 overexpression group (P < 0.05). Additionally, compared to the ALKBH5 overexpression group, cell proliferation and invasion were significantly more decreased in the mut-ALKBH5 overexpression group (P < 0.05). However, compared to the interference-negative control group, cell proliferation and invasion were significantly increased in the ALKBH5 interference group (P < 0.05). The presented findings suggested that m6A demethylase ALKBH5 inhibits tumor growth and metastasis in PTC. Moreover, effective inhibition of m6A modification of ALKBH5 might constitute a potential treatment strategy for PTC.

Detecting a wide range of epitranscriptomic modifications using a nanopore-sequencing-based computational approach with 1D score-clustering

To date, over 40 epigenetic and 300 epitranscriptomic modifications have been identified. However, current short-read sequencing-based experimental methods can detect <10% of these modifications. Integrating long-read sequencing technologies with advanced computational approaches, including statistical analysis and machine learning, offers a promising new frontier to address this challenge. While supervised machine learning methods have achieved some success, their usefulness is restricted to a limited number of well-characterized modifications. Here, we introduce Modena, an innovative unsupervised learning approach utilizing long-read nanopore sequencing capable of detecting a broad range of modifications. Modena outperformed other methods in five out of six benchmark datasets, in some cases by a wide margin, while being equally competitive with the second best method on one dataset. Uniquely, Modena also demonstrates consistent accuracy on a DNA dataset, distinguishing it from other approaches. A key feature of Modena is its use of 'dynamic thresholding', an approach based on 1D score-clustering. This methodology differs substantially from the traditional statistics-based 'hard-thresholds.' We show that this approach is not limited to Modena but has broader applicability. Specifically, when combined with two existing algorithms, 'dynamic thresholding' significantly enhances their performance, resulting in up to a threefold improvement in F1-scores.