Hidden codes in mRNA: Control of gene expression by m6A

The role of recurrent somatic mutations that alter conserved m6A motifs in human cancer

N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotes and plays a key role in cellular growth and development. Global changes in cellular methylated RNA and m6A-mediated transcript regulation significantly impact oncogenesis. Here, we investigate how recurrent synonymous and non-synonymous somatic mutations abolishing individual canonical methylated m6A motifs affect transcript levels and survival of patients with cancer. Moreover, we explore the effect of these mutations on creating de novo m6A motifs. To this end, we compared publicly available data on m6A sites with mutations reported in The Cancer Genome Atlas (TCGA). We find that mutations disrupting or creating m6A motifs display a low recurrence and have a negligible impact on RNA abundance. Patients with the highest number of disrupted m6A sites or newly generated m6A motifs did not generally exhibit alterations in mortality risk or outcomes. Hence, our data suggest that mutational alterations in the m6A motif landscape are unlikely to be a primary mechanism for regulating gene function across most cancer types. This may be attributed to the fact that mutations typically affect individual m6A sites, which is likely insufficient to significantly impact gene expression.

Enhancing m6A modification in the motor cortex facilitates corticospinal tract remodeling after spinal cord injury

JOURNAL/nrgr/04.03/01300535-202506000-00026/figure1/v/2024-08-05T133530Z/r/image-tiff Spinal cord injury typically causes corticospinal tract disruption. Although the disrupted corticospinal tract can self-regenerate to a certain degree, the underlying mechanism of this process is still unclear. N6-methyladenosine (m6A) modifications are the most common form of epigenetic regulation at the RNA level and play an essential role in biological processes. However, whether m6A modifications participate in corticospinal tract regeneration after spinal cord injury remains unknown. We found that expression of methyltransferase 14 protein (METTL14) in the locomotor cortex was high after spinal cord injury and accompanied by elevated m6A levels. Knockdown of Mettl14 in the locomotor cortex was not favorable for corticospinal tract regeneration and neurological recovery after spinal cord injury. Through bioinformatics analysis and methylated RNA immunoprecipitation-quantitative polymerase chain reaction, we found that METTL14 regulated Trib2 expression in an m6A-regulated manner, thereby activating the mitogen-activated protein kinase pathway and promoting corticospinal tract regeneration. Finally, we administered syringin, a stabilizer of METTL14, using molecular docking. Results confirmed that syringin can promote corticospinal tract regeneration and facilitate neurological recovery by stabilizing METTL14. Findings from this study reveal that m6A modification is involved in the regulation of corticospinal tract regeneration after spinal cord injury.

Modification of the RNA methylome in neurodevelopmental disorders

RNA metabolism is fundamental to protein synthesis, degradation and transport of molecules. Methylation of RNA influences the processing of mRNA, noncoding RNA, tRNA and rRNA. Here, we review accumulating evidence that disruption to the RNA methylome impairs developmental processes and causes neurodevelopmental conditions. We first describe mutated RNA methylation effector protein genes that give rise to neurodevelopmental syndromes. We consider the biological processes thereby disrupted, including translational dynamics at cytoplasmic and mt-ribosomes, synaptic function, energy production and cellular stress. Finally, we discuss novel forms of methylated RNA, such as R-loops and circular RNAs, which may contribute to disease processes. These findings herald an exciting new era to brain research and highlight the significant potential of manipulating the RNA methylome as a therapeutic target in the treatment of neurodevelopmental disorders.

m6A modification is incorporated into bacterial mRNA without specific functional benefit

N 6-Methyladenosine (m6A), the most abundant modification in eukaryotic messenger RNAs (mRNAs), has also been found at a low level in bacterial mRNAs. However, enzyme(s) that introduce m6A modification on mRNAs in bacteria remain elusive. In this work, we combine deep-sequencing approaches that identify m6A sites with in vitro biochemical studies to identify putative m6A methyltransferases that would modify Escherichia coli mRNAs. We tested four uncharacterized candidates predicted to encode proteins with putative methyltransferase domains, whose deletion decreased the m6A level. However, in vitro analysis with the purified putative methyltransferases revealed that none of them installs m6A on mRNA. Exposure to heat and oxidative stress also changed the m6A level; however, we found no clear correlation between the m6A change and the specific stress. Considering two deep-sequencing approaches with different resolution, we found that m6A methylation on bacterial mRNAs is very low and appears randomly introduced. These results suggest that, in contrast to eukaryotes, the m6A modification in bacterial mRNA lacks a direct enzymatic recognition mechanism and has no clear biological function.

The RNA-binding protein YTHDF3 affects gastric cancer cell migration and response to paclitaxel by regulating EZRIN

BACKGROUND

Gastric cancer (GC) is the fourth most common cause of cancer-related mortality and the fifth most common cancer worldwide. Despite efforts, the identification of biomarkers and new therapeutic approaches for GC remains elusive. Recent studies have begun to reveal the role of N6-adenosine methylation (m6A) in the regulation of gene expression.

METHODS

The expression of the reader YT521-B homology domain-containing family 3 (YTHDF3) in GC was assessed in 331 patients using immunohistochemistry. GC cell lines depleted of YTHDF3 using CRISPR-Cas9 were evaluated for migration, metastasis, orientation of the mitotic spindle, and response to paclitaxel. The association between YTHDF3 and EZRIN (EZR) mRNA was shown using RNA sequencing, immunofluorescence, real-time PCR, and RNA immunoprecipitation. The single-base elongation- and ligation-based qPCR amplification (SELECT) method was used to map m6A in the EZR transcript.

RESULTS

YTHDF3 was significantly overexpressed in GC, and high levels of YTHDF3 were predictive of the response to chemotherapy. In GC cell lines, YTHDF3 was the most highly expressed reader protein. YTHDF3 depletion impaired cytoskeleton organization, cell migration and metastasis, and orientation of the mitotic spindle, leading to an increased response to paclitaxel. EZR was one of the downregulated targets in the YTHDF3 knockout cell models and was associated with the observed phenotype.

CONCLUSION

YTHDF3 contributes to cell motility and response to paclitaxel in GC cell lines, at least in part through EZR regulation. The YTHDF3-EZR regulatory axis is a novel molecular player in GC, with clinical relevance and potential therapeutic utility.

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.

METTL3-dependent m6A modification of SNAP29 induces "autophagy-mitochondrial crisis" in the ischemic microenvironment after soft tissue transplantation

Necrosis at the ischemic distal end of flap transplants increases patients' pain and economic burden. Reactive oxygen species (ROS) and mitochondrial damage are crucial in regulating parthanatos, but the mechanisms linking disrupted macroautophagic/autophagic flux to parthanatos in ischemic flaps remain unclear. The results of western blotting, immunofluorescence staining, and a proteomic analysis revealed that the autophagic protein SNAP29 was deficient in ischemic flaps, resulting in disrupted autophagic flux, increased ROS-induced parthanatos, and aggravated ischemic flap necrosis. The use of AAV vector to restore SNAP29 in vivo mitigated the disruption of autophagic flux and parthanatos. Additionally, quantification of the total m6A level and RIP-qPCR, MeRIP-qPCR, and RNA stability assessments were performed to determine differential Snap29 mRNA m6A methylation levels and mRNA stability in ischemic flaps. Various in vitro and in vivo tests were conducted to verify the ability of METTL3-mediated m6A methylation to promote SNAP29 depletion and disrupt autophagic flux. Finally, we concluded that restoring SNAP29 by inhibiting METTL3 and YTHDF2 reversed the "autophagy-mitochondrial crisis", defined for the first time as disrupted autophagic flux, mitochondrial damage, mitochondrial protein leakage, and the occurrence of parthanatos. The reversal of this crisis ultimately promoted the survival of ischemic flaps.Abbreviations: AAV = adeno-associated virus; ACTA2/α-SMA = actin alpha 2, smooth muscle, aorta; AIFM/AIF = apoptosis-inducing factor, mitochondrion-associated; ALKBH5 = alkB homolog, RNA demythelase; Baf A1 = bafilomycin A1; CQ = chloroquine; DHE = dihydroethidium; ECs = endothelial cells; F-CHP = 5-FAM-conjugated collagen-hybridizing peptide; GO = gene ontology; HUVECs = human umbilical vein endothelial cells; KEGG = Kyoto Encyclopedia of Genes and Genomes; LC-MS/MS = liquid chromatography-tandem mass spectrometry; LDBF = laser doppler blood flow; m6A = N6-methyladenosine; MAP1LC3/LC3 = microtubule-associated protein 1 light chain 3; MeRIP = methylated RNA immunoprecipitation; METTL3 = methyltransferase 3, N6-adenosine-methyltransferase complex catalytic subunit; NAC = N-acetylcysteine; OGD = oxygen glucose deprivation; PAR = poly (ADP-ribose); PARP1 = poly (ADP-ribose) polymerase family, member 1; PECAM1/CD31 = platelet/endothelial cell adhesion molecule 1; ROS = reactive oxygen species; RT-qPCR = reverse transcription quantitative polymerase chain reaction; RIP = RNA immunoprecipitation; SNAP29 = synaptosomal-associated protein 29; SNARE = soluble N-ethylmaleimide-sensitive factor attachment protein receptor; SQSTM1 = sequestosome 1; SRAMP = sequence-based RNA adenosine methylation site predicting; STX17 = syntaxin 17; TMT = tandem mass tag; TUNEL = terminal deoxynucleotidyl transferase dUTP nick end labeling; VAMP8 = vesicle-associated membrane protein 8; WTAP = WT1 associating protein; YTHDF2 = YTH N6-methyladenosine RNA binding protein 2; 3' UTR = 3'-untranslated region.

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.

Selective Translation Under Heat Shock: Integrating HSP70 mRNA Regulation with Cellular Stress Responses in Yeast and Mammals

Under stress, cells orchestrate a complex regulatory response to maintain protein homeostasis, leveraging differential translational regulation for constitutively expressed mRNAs and the transcriptionally induced heat shock protein HSP70 transcripts. Constitutive mRNAs typically experience partial translational suppression, consistent with their partitioning into stress-induced phase-separated condensates and the global reduction in protein synthesis. In contrast, inducible HSP70 mRNAs bypass this repression to remain in the cytosol where they recruit the available components of the translational machinery to ensure the rapid synthesis of HSP70. Although the components involved in the preferential translation of HSP70 mRNA during heat stress have not been fully elucidated, differences in the mRNA and translation factors between yeast and mammals suggest organism-specific mechanisms of HSP70 mRNA translation. In this review, we consider these differences to discuss the current knowledge on heat shock regulation of translation. We extend the discussion to go beyond the cytosolic needs of HSP70 to ponder the important interplay between the cytosol and mitochondria in activating HSP70 accumulation, which becomes vital for preserving intercompartmental proteostasis and cell survival.

A review of m6A modification in plant development and potential quality improvement

N6-methyladenosine (m6A) represents the most prevalent internal modification observed in eukaryotic mRNAs. As a pivotal regulator of gene expression, m6A exerts influence over a number of processes, including splicing, transport, translation, degradation, and the stability of mRNAs. It thus plays a crucial role in plant development and resistance to biotic and abiotic stressors. The writers, erasers, and readers of m6A, which deposit, eliminate and decode this modification, are also of critical importance and have been identified and characterized in multiple plant species. The advent of next-generation sequencing (NGS) and m6A detection technologies has precipitated a surge in research on m6A in recent years. Extensive research has elucidated the specific roles of m6A in plants and its underlying molecular mechanisms, indicating significant potential for crop improvement. This review presents a comprehensive overview of recent studies on m6A and its regulatory proteins in plant development and stress tolerance. It highlights the potential applications of this modification and its writers, erasers, and readers for plant improvement, with a particular focus on leaf development, floral transition, trichome morphogenesis, fruit ripening, and resilience to pests, diseases and abiotic stresses.

The METTL14-YTHDF1-SAP30 Axis Promotes Glycolysis and Oxaliplatin Resistance in Colorectal Adenocarcinoma via m6A Modification

Colorectal cancer (CRC) is a prevalent cancer with a poor prognosis, especially in advanced metastatic stages. This study identifies SAP30 as a significantly upregulated gene in COAD, linking high SAP30 expression to reduced overall survival. Experimental validation revealed elevated SAP30 levels in CRC cell lines (SW480, RKO, HT29, and HCT15), with the highest expression in oxaliplatin-resistant sublines (HT29-OxR and HCT15-OxR). SAP30 knockdown in oxaliplatin-resistant cells reduced glycolytic activity, glucose consumption, and glycolytic enzyme expression (LDHA, HK1, HK2, GLUT1, and GLUT4), while SAP30 overexpression enhanced glycolysis, partially reversed by the GLUT1 inhibitor WZB117. SAP30 also promoted cell proliferation, inhibited apoptosis, and enhanced migration and invasion in resistant CRC cells. Mechanistically, METTL14, an m6A methyltransferase, upregulates SAP30 mRNA via m6A modification, stabilized by the m6A reader protein YTHDF1. This METTL14-YTHDF1-SAP30 axis sustains SAP30 expression, promoting glycolysis and oxaliplatin resistance. In vivo studies confirmed that SAP30 knockout impairs tumor growth and reduces proliferation and glycolysis markers. This study highlights the METTL14-YTHDF1-SAP30 axis in glycolysis and chemoresistance in CRC, suggesting SAP30 as a potential target to overcome oxaliplatin resistance and improve patient outcomes.

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.

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

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

METTL14-mediated m6A RNA methylation promotes the osteogenic differentiation of pPDLSCs by regulating WNT3A

Periodontitis is a chronic inflammatory disease that leads to the loss of periodontal supporting tissue. Furthermore, human periodontal ligament stem cells (hPDLSCs) are identified as candidate cells for the regeneration of periodontal and alveolar bone tissues. N6-Methyladenosine (m6A) performs a vital role in osteoporosis and bone metabolism. However, the role and mechanism of Methyltransferase-like 14 (METTL14) in the osteogenic differentiation of PDLSCs from periodontitis sufferers (pPDLSCs) is unclear. In this research, GSE223924 database analyzed the expression of METTL14 and Wnt Family Member 3A (WNT3A) in gingival tissue samples of 10 healthy subjects, 10 patients with periodontitis and peri-implantitis. RT-qPCR and western blot detected METTL14, COL1A1, Runx2, ALP, and WNT3A mRNA level and protein level. Osteogenic differentiation was evaluated by Alizarin Red S staining and ALP activity. MeRIP and dual-luciferase reporter assays verified interaction between METTL14 and WNT3A. GSE223924 database showed METTL14 was differentially expressed in patients with periodontitis and peri-implantitis. Furthermore, our data verified that METTL14 and WNT3A expression were decreased in pPDLSCs and were upregulated by osteogenic induction. METTL14 promoted osteogenic differentiation of pPDLSCs. METTL14 regulated WNT3A mRNA expression via m6A methylation. METTL14 facilitates osteogenic differentiation of pPDLSCs via modulating WNT3A, providing a possible target for improving alveolar bone regeneration outcomes.Highlights 1. METTL14 expression was decreased in pPDLSCs 2. METTL14 knockdown negatively regulated the osteogenic differentiation of pPDLSCs 3. WNT3A mRNA was a m6A-methylated target by METTL14.

Erasing "bad memories": reversing aberrant synaptic plasticity as therapy for neurological and psychiatric disorders

Dopamine modulates corticostriatal plasticity in both the direct and indirect pathways of the cortico-striato-thalamo-cortical (CSTC) loops. These gradual changes in corticostriatal synaptic strengths produce long-lasting changes in behavioral responses. Under normal conditions, these mechanisms enable the selection of the most appropriate responses while inhibiting others. However, under dysregulated dopamine conditions, including a lack of dopamine release or dopamine signaling, these mechanisms could lead to the selection of maladaptive responses and/or the inhibition of appropriate responses in an experience-dependent and task-specific manner. In this review, we propose that preventing or reversing such maladaptive synaptic strengths and erasing such aberrant "memories" could be a disease-modifying therapeutic strategy for many neurological and psychiatric disorders. We review evidence from Parkinson's disease, drug-induced parkinsonism, L-DOPA-induced dyskinesia, obsessive-compulsive disorder, substance use disorders, and depression as well as research findings on animal disease models. Altogether, these studies allude to an emerging theme in translational neuroscience and promising new directions for therapy development. Specifically, we propose that combining pharmacotherapy with behavioral therapy or with deep brain stimulation (DBS) could potentially cause desired changes in specific neural circuits. If successful, one important advantage of correcting aberrant synaptic plasticity is long-lasting therapeutic effects even after treatment has ended. We will also discuss the potential molecular targets for these therapeutic approaches, including the cAMP pathway, proteins involved in synaptic plasticity as well as pathways involved in new protein synthesis. We place special emphasis on RNA binding proteins and epitranscriptomic mechanisms, as they represent a new frontier with the distinct advantage of rapidly and simultaneously altering the synthesis of many proteins locally.

FTO suppresses DNA repair by inhibiting PARP1

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

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.

Dynamic interplay between RNA N6-methyladenosine modification and porcine reproductive and respiratory syndrome virus infection

N6-methyladenosine (m6A) has attracted significant attention for its role in regulating the complex interaction between viruses and host cells. Porcine reproductive and respiratory syndrome virus (PRRSV) is a significant pathogen affecting swine health worldwide. Here, we first identified seven m6A-enriched peaks in PRRSV genomic RNA by m6A RNA immunoprecipitation sequencing (m6A-seq). Moreover, functional analyses revealed a positive correlation between the m6A modification level and PRRSV replication. Treatment with the universal methylation inhibitor 3-deazaadenosine (3-DAA) effectively suppressed PRRSV replication in a dose-dependent manner. Furthermore, m6A-seq was also used to determine the m6A landscape of the transcriptome in PAMs infected with pandemic or highly pathogenic PRRSV strains. Among the 4677 transcripts exhibiting altered m6A modification levels, the MAPK14 gene and the p38/MAPK signalling pathway emerged as preliminary targets of m6A-mediated epigenetic regulation during PRRSV infection. These findings provide new insights into the epigenetic mechanisms underlying PRRSV infection and may facilitate the development of anti-PRRSV therapeutics.

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

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

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

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

The m6A modification regulates the composition of myofiber types in chicken skeletal muscle

As a widespread epigenetic RNA modification, N6-methyladenosine (m6A) plays essential regulatory roles in multiple biological processes. However, its function in maintaining and modulating myofiber-type properties remains largely unknown. To investigate the post-transcriptional modification underlying the myofiber type diversity in chicken skeletal muscle, we evaluated the m6A methylation levels of chicken skeletal muscles with different phenotypic traits, and profiled a transcriptome-wide m6A map in the oxidative and glycolytic skeletal muscles by methylated RNA immunoprecipitation sequencing (MeRIP-seq). Our results showed that the levels of m6A methylation in chicken skeletal muscles were closely related to the composition of myofiber types. The m6A methylation level of anterior latissimus dorsi (ALD, typical oxidative skeletal muscle) was the highest among the three muscles and significantly higher than that of the pectoralis major (PM, typical glycolytic skeletal muscle) (P<0.05). We found that about 24.77 % and 33.50 % of genes were modified by m6A methylation in the PM and ALD, respectively, and identified 6,530 and 9,965 m6A peaks, which were mainly located in the coding sequence (CDS) and stop codon. About 3.14 % of m6A modified genes showed significantly differential methylation levels between these two muscles. Intriguingly, the myofiber type-related genes, such as MYOT, TPM3, TPM1, PDK1, MBNL1, and MYH1G, showed differences in m6A methylation and mRNA expression. Further analysis revealed that the m6A methylation was positively correlated with gene expression homeostasis. It is exciting we found that the expression level of ALKBH5 mRNA and protein, was closely related to the composition of myofiber types. ALKBH5 over-expression could regulate the expression levels of genes related to muscle contraction and metabolism, including MYH1E, MYH1G, MYH7B, PDK1, and TPM1, suggesting the effect of ALKBH5 on the formation of myofiber-type properties in chicken skeletal muscle. Our results contribute to a better understanding of epigenetic factors involved in forming chicken myofiber-type properties and provide new targets for further investigation into chicken's growth development and meat quality.

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.

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.

Phenotypic screens identify SCAF1 as critical activator of RNAPII elongation and global transcription

Transcripts produced by RNA polymerase II (RNAPII) are fundamental for cellular responses to environmental changes. It is therefore no surprise that there exist multiple avenues for the regulation of this process. To explore the regulation mediated by RNAPII-interacting proteins, we used a small interfering RNA (siRNA)-based screen to systematically evaluate their influence on RNA synthesis. We identified several proteins that strongly affected RNAPII activity. We evaluated one of the top hits, SCAF1 (SR-related C-terminal domain-associated factor 1), using an auxin-inducible degradation system and sequencing approaches. In agreement with our screen results, acute depletion of SCAF1 decreased RNA synthesis, and showed an increase of Serine-2 phosphorylated-RNAPII (pS2-RNAPII). We found that the accumulation of pS2-RNAPII within the gene body occurred at GC-rich regions and was indicative of stalled RNAPII complexes. The accumulation of stalled RNAPII complexes was accompanied by reduced recruitment of initiating RNAPII, explaining the observed global decrease in transcriptional output. Furthermore, upon SCAF1 depletion, RNAPII complexes showed increased association with components of the proteasomal-degradation machinery. We concluded that in cells lacking SCAF1, RNAPII undergoes a rather interrupted passage, resulting in intervention by the proteasomal-degradation machinery to clear stalled RNAPII. While cells survive the compromised transcription caused by absence of SCAF1, further inhibition of proteasomal-degradation machinery is synthetically lethal.

Writers, readers, and erasers of N6-Methyladenosine (m6A) methylomes in oilseed rape: identification, molecular evolution, and expression profiling

BACKGROUND

m6A RNA modifications are the most prevalent internal modifications in eukaryotic mRNAs and are crucial for plant growth and development, as well as for responses to biotic or abiotic stresses. The modification is catalyzed by writers, removed by erasers, and decoded by various m6A-binding proteins, which are readers. Brassica napus is a major oilseed crop. The dynamic regulation of m6A modifications by writers, erasers, and readers offers potential targets for improving the quality of this crop.

RESULTS

In this study, we identified 92 m6A-regulatory genes in B. napus, including 13 writers, 29 erasers, and 50 readers. A phylogenetic analysis revealed that they could be further divided into four, three, and two clades, respectively. The distribution of protein motifs and gene structures among members of the same clade exhibited notable similarity. During the course of evolution, whole genome duplication (WGD) and segmental duplication were the primary drivers of the expansion of m6A-related gene families. The genes were subjected to rigorous purification selection. Additionally, several sites under positive selection were identified in the proteins. RNA-seq and quantitative real-time PCR (qRT-PCR) expression analyses revealed that the identified Bnam6As exhibit tissue-specific expression patterns, as well as their expression patterns in response to various abiotic and biotic stresses. The 2000 bp sequence upstream of Bnam6As contained a number of cis-acting elements that regulate plant growth and environmental response. Furthermore, the protein interaction network revealed their interactions with a number of proteins of significant functional importance.

CONCLUSION

The identification of m6A modifiers in oilseed rape and their molecular evolution and expression profiling have revealed potential functions and molecular mechanisms of m6A, thus establishing a foundation for further functional validation and molecular breeding.

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.

RBM15 Knockdown Impairs the Malignancy of Cervical Cancer by Mediating m6A Modification of Decorin

Cervical cancer (CC) is considered to be the most prevalent female malignancies across the globe and a prime cause of mortality among women. RNA-binding motif protein 15 (RBM15) has been elucidated to participate in tumorigenesis in various cancers by regulating RNA N6-methyladenosine (m6A) methylation. However, its significance and detailed molecular mechanisms remain uncertain in CC. Using CGA database and qRT-PCR, the RBM15 expression was found to be elevated in CC tissues. After performing EdU, wound healing, Transwell migration, and xenograft tumor assays, RBM15 knockdown inhibited the malignant properties of CC cells along with the tumor development of CC cells in vivo. Moreover, qRT-PCR, MeRIP, and western blotting experiments were also confirmed that decorin (DCN) downregulated in CC was a direct substrate of RBM15 m6A methylation, and RBM15 knockdown could enhance DCN expression in CC cells. The anti-tumor effects of RBM15 knockdown could be abolished by DCN silencing. Overall, RBM15 knockdown lowered the tumorigenesis of CC both in vitro and in vivo, and it does so via mediating m6A modification of DCN mRNA in CC cells.

Oestrogen suppresses the adipogenesis of fibro/adipogenic progenitors through reactivating the METTL3-ESR1-mediated loop in post-menopausal females

BACKGROUND

Post-menopausal women experience more severe muscular fatty infiltration, though the mechanisms remain unclear. The decline in estrogen levels is considered as a critical physiological alteration during post-menopause. Fibro/adipogenic progenitors (FAPs) are identified as major contributors to muscular fatty infiltration. This study aimed to investigate the detailed mechanism underlying the excessive muscular fatty infiltration in postmenopausal females.

METHODS

Supraspinatus muscle samples were collected from female patients with or without menopause, and from mice with or without ovariectomy (OVX), to evaluate muscular fatty infiltration and isolated FAPs. The expressions of (estrogen receptor 1) ESR1, methyltransferase-like 3 (METTL3), and adipogenesis ability in FAPs from post-menopausal women and OVX mice were investigated. RNA sequencing (RNA-Seq) was performed to explore the gene expression profiles and potential mechanisms in FAPs from Pdgfrα-CreERT2; Esr1 knockout (Esr1 KO) mice and Esr1 flox/flox (Esr1 f/f) mice. The interplay of the METTL3-ESR1 mediated loop and its role in regulating adipogenesis in FAPs were investigated using dual luciferase reporter assays, chromatin immunoprecipitation (ChIP), and protein and RNA stability assays. The effects of estrogen supplementation on muscular fatty infiltration and locomotor function in OVX mice were evaluated by immunofluorescent staining and functional analysis.

RESULTS

Decreased expression of ESR1/METTL3 and increased adipogenesis ability in FAPs was found in post-menopausal female. METTL3-mediated m6A methylation promoted ESR1 mRNA stability at the post-transcriptional level in FAPs. METTL3-mediated m6A modification promoted ESR1 expression by stabilizing ESR1 mRNA, while ESR1 acted as a transcription factor that enhanced METTL3 transcription in turn. ESR1 also suppressed the transcription of the adipogenic transcription factor peroxisome proliferator-activated receptor gamma (PPARγ), thereby inhibiting adipogenesis in FAPs. Reactivation of the METTL3-ESR1 mediated loop by estrogen alleviated excessive adipogenesis in FAPs from post-menopausal women, and it also reduced muscular fatty infiltration, and improved locomotor function in OVX mice.

CONCLUSION

Excessive muscular fatty infiltration in post-menopausal women arose from the disruption of the METTL3-ESR1 mediated loop of FAPs due to estrogen deficiency. Reactivation of the METTL3-ESR1 mediated loop by estrogen may serve as a novel intervention to inhibit excessive adipogenesis of post-menopausal female FAPs, thereby ameliorating muscular fatty infiltration and improving locomotor function in post-menopausal females.

KEY POINTS

Oestrogen insufficiency disrupted the METTL3ESR1 loop in post-menopausal FAPs, causing excessive muscular fatty infiltration. METTL3-mediated m6A modification stabilized ESR1 mRNA and enhanced ESR1 expression, while increased ESR1 further promoted METTL3 transcription. ESR1 inhibited the transcription of adipogenic factor PPARγ, ameliorating adipogenesis in FAPs. Reactivating the METTL3ESR1 loop via oestrogen in FAPs reduced muscular fatty infiltration and improved locomotor function.

Acute inflammation induces acute megakaryopoiesis with impaired platelet production during fetal hematopoiesis

Hematopoietic development is tightly regulated by various factors. The role of RNA m6A modification during fetal hematopoiesis, particularly in megakaryopoiesis, remains unclear. Here, we demonstrate that loss of m6A methyltransferase METTL3 induces formation of double-stranded RNAs (dsRNAs) and activates acute inflammation during fetal hematopoiesis in mouse. This dsRNA-mediated inflammation leads to acute megakaryopoiesis, which facilitates the generation of megakaryocyte progenitors but disrupts megakaryocyte maturation and platelet production. The inflammation and immune response activate the phosphorylation of STAT1 and IRF3, and upregulate downstream interferon-stimulated genes (ISGs). Inflammation inhibits the proliferation rate of hematopoietic progenitors and further skews the cell fate determination toward megakaryocytes rather than toward erythroid from megakaryocyte-erythroid progenitors (MEPs). Transcriptional-wide gene expression analysis identifies IGF1 as a major factor whose reduction is responsible for the inhibition of megakaryopoiesis and thrombopoiesis. Restoration of IGF1 with METTL3-deficient hematopoietic cells significantly increases megakaryocyte maturation. In summary, we elucidate that the loss of RNA m6A modification-induced acute inflammation activates acute megakaryopoiesis, but impairs its final maturation through the inhibition of IGF1 expression during fetal hematopoiesis.

Two dynamic N-terminal regions are required for function in ribosomal RNA adenine dimethylase family members

Prominent members of the ribosomal RNA adenine dimethylase (RRAD) family of enzymes facilitate ribosome maturation by dimethylating 2 nt of small subunit rRNA, including the human DIMT1 and bacterial KsgA enzymes. A subgroup of RRAD enzymes, named erythromycin resistance methyltransferases (Erm), dimethylate a specific nucleotide in large subunit rRNA to confer antibiotic resistance. How these enzymes regulate methylation so that it only occurs on the specific substrate is not fully understood. While performing random mutagenesis on the catalytic domain of ErmE, we discovered that mutants in an N-terminal region of the protein that is disordered in the ErmE crystal structure are associated with a loss of antibiotic resistance. By subjecting site-directed mutants of ErmE and KsgA to phenotypic and in vitro assays, we found that the N-terminal region is critical for activity in RRAD enzymes: The N-terminal basic region promotes rRNA binding, and the conserved motif likely assists in juxtaposing the adenosine substrate and the S-adenosylmethionine cofactor. Our results and emerging structural data suggest that this dynamic, N-terminal region of RRAD enzymes becomes ordered upon rRNA binding, forming a cap on the active site required for methylation.

Mutability and hypermutation antagonize immunoglobulin codon optimality

The efficacy of antibody responses is inherently linked to paratope diversity, as generated through V(D)J recombination and somatic hypermutation. Despite this, it is unclear how genetic diversification mechanisms evolved alongside codon optimality and affect antibody expression. Here, we analyze germline immunoglobulin (IG) genes, natural V(D)J repertoires, serum IgG, and monoclonal antibody (mAb) expression through the lens of codon optimality. Germline variable genes (IGVs) exhibit diverse optimality that is inversely related to mutability. Hypermutation deoptimizes heavy-chain (IGH) VDJ repertoires within human tonsils, bone marrow, lymph nodes (including SARS-CoV-2-specific clones), blood (HIV-1-specific clones), mice, and zebrafish. Analyses of mutation-affected codons show that targeting to complementarity-determining regions constrains deoptimization. Germline IGHV optimality correlates with serum variable fragment (VH) usage after influenza vaccination, while synonymous deoptimization attenuated mAb yield. These findings provide unanticipated insights into an antagonistic relationship between diversification mechanisms and codon optimality. Ultimately, the need for diversity takes precedence over that for the most optimal codon usage.

ALKBH5 controlled autophagy of peripheral blood mononuclear cells by regulating NRG1 mRNA stability in ankylosing spondylitis

Ankylosing spondylitis (AS) is a chronic inflammatory rheumatic disease which is characterized by pathological osteogenesis. N6-methyladenosine (m6A) RNA modification is pivotal in immunity and inflammation. In this study, the peripheral blood mononuclear cells (PBMCs) were isolated from healthy or AS patients blood samples in Fuyang People's Hospital, which was utilized to clarify the role of m6A modification in AS pathogenesis. The results showed that the autophagy levels showed a decreasing trend; meanwhile, the m6A demethylase ALKBH5 expression was downregulation in AS-PBMCs. The RNA-seq analysis identified 201 significantly altered genes including NRG1, FOS, CAMKK2, NLRC4, and DAPK1; and NRG1 mRNA expression levels showed significant improvement in AS. After ALKBH5 knockdown, the autophagy levels significantly decreased through increasing NRG1 m6A modification and enhancing its mRNA stability, while ALKBH5 overexpression promoted autophagy by reduceing NRG1 mRNA stability. Additionally, the results found that the "reader" IGF2BP3 substantially enhanced NRG1 expression and mRNA stability in AS patients PBMCs. Silencing ALKBH5 increased IGF2BP3 binding to the m6A-enriched NRG1 transcript, and enhancing NRG1 mRNA stability and protein expression. However, ALKBH5 modification site mutation may increase IGF2BP3 binding to NRG1 mRNA. These finding suggested that ALKBH5 downregulation inhibited AS-PBMCs autophagy leves through regulating post-transcriptional m6A modification to upregulate NRG1 protein expression, which provided novel and effective approaches for AS clinical therapy.

m 6 A-mediated gluconeogenic enzyme PCK1 upregulation protects against hepatic ischemia-reperfusion injury

BACKGROUND AND AIMS

Ischemia-reperfusion (I/R) injury frequently occurs during liver surgery, representing a major reason for liver failure and graft dysfunction after operation. The metabolic shift from oxidative phosphorylation to glycolysis during ischemia increased glucose consumption and accelerated lactate production. We speculate that donor livers will initiate gluconeogenesis, the reverse process of glycolysis in theory, to convert noncarbohydrate carbon substrates (including lactate) to glucose to reduce the loss of hepatocellular energy and foster glycogen storage for use in the early postoperative period, thus improving post-transplant graft function.

APPROACH AND RESULTS

By analyzing human liver specimens before and after hepatic I/R injury, we found that the rate-limiting enzyme of gluconeogenesis, PCK1, was significantly induced during liver I/R injury. Mouse models with liver I/R operation and hepatocytes treated with hypoxia/reoxygenation confirmed upregulation of PCK1 during I/R stimulation. Notably, high PCK1 level in human post-I/R liver specimens was closely correlated with better outcomes of liver transplantation. However, blocking gluconeogenesis with PCK1 inhibitor aggravated hepatic I/R injury by decreasing glucose level and deepening lactate accumulation, while overexpressing PCK1 did the opposite. Further mechanistic study showed that methyltransferase 3-mediated RNA N6-methyladinosine modification contributes to PCK1 upregulation during hepatic I/R injury, and hepatic-specific knockout of methyltransferase 3 deteriorates liver I/R injury through reducing the N6-methyladinosine deposition on PCK1 transcript and decreasing PCK1 mRNA export and expression level.

CONCLUSIONS

Our study found that activation of the methyltransferase 3/N6-methyladinosine-PCK1-gluconeogenesis axis is required to protect against hepatic I/R injury, providing potential intervention approaches for alleviating hepatic I/R injury during liver surgery.

Knockdown of IGF2BP2 overcomes cisplatin-resistance in lung cancer through downregulating Spon2 gene

BACKGROUND

Cisplatin (DDP) resistance has long posed a challenge in the clinical treatment of lung cancer (LC). Insulin-like growth factor 2 binding protein 2 (IGF2BP2) has been identified as an oncogenic factor in LC, whereas its specific role in DDP resistance in LC remains unclear.

RESULTS

In this study, we investigated the role of IGF2BP2 on DDP resistance in DDP-resistant A549 cells (A549/DDP) in vitro and in a DDP-resistant lung tumor-bearing mouse model in vivo. Additionally, methylated RNA immunoprecipitation sequencing (MeRIP-seq) was conducted to identify the potential mRNAs regulated by IGF2BP2, an N6-methyladenosine (m6A) regulator, in the tumor tissues of mice. Compared to normal tissues, IGF2BP2 levels were increased in LC tissues and in relapsed/resistant LC tissues. Most importantly, IGF2BP2 levels were significantly higher in relapsed/resistant LC tissues than in LC tissues. Significantly, knockdown of IGF2BP2 or DDP treatment inhibited A549 cell viability, migration, and cell cycle progression. Consistently, DDP treatment suppressed the viability and migration and triggered cell cycle arrest in A549/DDP cells in vitro, as well as reduced tumor volume and weight of A549/DDP tumor-bearing mice; meanwhile, the combination of DDP and IGF2BP2 siRNA further significantly inhibited A549/DDP cell growth in vitro and in vivo compared to DDP treatment alone. Furthermore, MeRIP-seq data showed that IGF2BP2 downregulation remarkably elevated m6A levels of spondin 2 (Spon2) and reduced mRNA levels of Spon2 in tumor tissues from A549 tumor-bearing mice. Meanwhile, the combination of DDP and IGF2BP2 siRNA notably reduced Spon2 levels, as well as inhibited the viability and induced apoptosis in A549/DDP cells; however, these effects were reversed by Spon2 overexpression.

CONCLUSION

Collectively, downregulation of IGF2BP2 could overcome DDP resistance in LC through declining the Spon2 gene expression in an m6A-dependent manner. These results may provide a new strategy for overcoming DDP resistance in LC.

SERRATE drives phase separation behaviours to regulate m6A modification and miRNA biogenesis

The methyltransferase complex (MTC) deposits N6-adenosine (m6A) onto RNA, whereas the microprocessor produces microRNA. Whether and how these two distinct complexes cross-regulate each other has been poorly studied. Here we report that the MTC subunit B tends to form insoluble condensates with poor activity, with its level monitored by the 20S proteasome. Conversely, the microprocessor component SERRATE (SE) forms liquid-like condensates, which in turn promote the solubility and stability of the MTC subunit B, leading to increased MTC activity. Consistently, the hypomorphic lines expressing SE variants, defective in MTC interaction or liquid-like phase behaviour, exhibit reduced m6A levels. Reciprocally, MTC can recruit the microprocessor to the MIRNA loci, prompting co-transcriptional cleavage of primary miRNA substrates. Additionally, primary miRNA substrates carrying m6A modifications at their single-stranded basal regions are enriched by m6A readers, which retain the microprocessor in the nucleoplasm for continuing processing. This reveals an unappreciated mechanism of phase separation in RNA modification and processing through MTC and microprocessor coordination.

Unlocking epigenetic breeding potential in tomato and potato

Tomato (Solanum lycopersicum) and potato (Solanum tuberosum), two integral crops within the nightshade family, are crucial sources of nutrients and serve as staple foods worldwide. Molecular genetic studies have significantly advanced our understanding of their domestication, evolution, and the establishment of key agronomic traits. Recent studies have revealed that epigenetic modifications act as "molecular switches", crucially regulating phenotypic variations essential for traits such as fruit ripening in tomatoes and tuberization in potatoes. This review summarizes the latest findings on the regulatory mechanisms of epigenetic modifications in these crops and discusses the integration of biotechnology and epigenomics to enhance breeding strategies. By highlighting the role of epigenetic control in augmenting crop yield and adaptation, we underscores its potential to address the challenges posed by a growing global population as well as changing climate.

Comprehensive analysis of m6A methylome alterations after azacytidine plus venetoclax treatment for acute myeloid leukemia by nanopore sequencing

N6 adenosine methylation (m6A), one of the most prevalent internal modifications on mammalian RNAs, regulates RNA transcription, stabilization, and splicing. Growing evidence has focused on the functional role of m6A regulators on acute myeloid leukemia (AML). However, the global m6A levels after azacytidine (AZA) plus venetoclax (VEN) treatment in AML patients remain unclear. In our present study, bone marrow (BM) sample pairs (including pre-treatment [AML] and post-treatment [complete remission (CR)] samples) were harvested from three AML patients who had achieved CR after AZA plus VEN treatment for Nanopore direct RNA sequencing. Notably, the amount of m6A sites and the m6A levels in CR BMs was significantly lower than those in the AML BMs. Such a significant reduction in the m6A levels was also detected in AZA-treated HL-60 cells. Thirteen genes with decreased m6A and expression levels were identified, among which three genes (HPRT1, SNRPC, and ANP32B) were closely related to the prognosis of AML. Finally, we speculated the mechanism via which m6A modifications affected the mRNA stability of these three genes. In conclusion, we illustrated for the first time the global landscape of m6A levels in AZA plus VEN treated AML (CR) patients and revealed that AZA had a significant demethylation effect at the RNA level in AML patients. In addition, we identified new biomarkers for AZA plus VEN-treated AML via Nanopore sequencing technology in RNA epigenetics.

ZC3H13 promotes autophagy in bladder cancer through m6A methylation modification of PJA2 and ubiquitination of KSR1

The N6-methyladenine (m6A) modification is the most common modification of messenger RNAs in eukaryotes and has crucial roles in multiple cancers, including bladder cancer (BLCA). This paper aimed to probe the molecular mechanism of zinc-finger CCCH-type containing 13 (ZC3H13)-mediated N6-methyladenine (m6A) modification in BLCA progression via autophagy. Differential expression of ZC3H13 in BLCA was analyzed by the bioinformatics database. ZC3H13 expression in BLCA tissues and cell lines was determined, and malignant behaviors of BLCA cells were examined in vitro and in vivo. ZC3H13 was decreased in BLCA tissues and cell lines relative to adjacent tissues and normal uroepithelial cells. ZC3H13 overexpression restricted BLCA cell growth in vitro and curbed BLCA development in vivo. ZC3H13 promoted the mRNA stability of paraja ring finger 2 (PJA2) through m6A modification, leading to the ubiquitination degradation of the kinase suppressor of Ras 1 (KSR1). Knockdown of PJA2 and overexpression of KSR1 reversed the inhibitory effect of ZC3H13 on BLCA progression. ZC3H13 degraded KSR1 through m6A modification of PJA2, promoted cell autophagy, and repressed BLCA progression. Overall, ZC3H13 promotes the mRNA stability of PJA2 through m6A modification to degrade KSR1, thereby promoting autophagy in BLCA.

Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework

Direct nanopore-based RNA sequencing can be used to detect posttranscriptional base modifications, such as N6-methyladenosine (m6A) methylation, based on the electric current signals produced by the distinct chemical structures of modified bases. A key challenge is the scarcity of adequate training data with known methylation modifications. We present Xron, a hybrid encoder-decoder framework that delivers a direct methylation-distinguishing basecaller by training on synthetic RNA data and immunoprecipitation (IP)-based experimental data in two steps. First, we generate data with more diverse modification combinations through in silico cross-linking. Second, we use this data set to train an end-to-end neural network basecaller followed by fine-tuning on IP-based experimental data with label smoothing. The trained neural network basecaller outperforms existing methylation detection methods on both read-level and site-level prediction scores. Xron is a standalone, end-to-end m6A-distinguishing basecaller capable of detecting methylated bases directly from raw sequencing signals, enabling de novo methylome assembly.

Methyltransferase-like 3 represents a prospective target for the diagnosis and treatment of kidney diseases

Kidney disease is marked by complex pathological mechanisms and significant therapeutic hurdles, resulting in high morbidity and mortality rates globally. A deeper understanding of the fundamental processes involved can aid in identifying novel therapeutic targets and improving treatment efficacy. Current comprehensive data analyses indicate the involvement of methyltransferase-like 3 (METTL3) and its role in RNA N6-methyladenosine methylation in various renal pathologies, including acute kidney injury, renal fibrosis, and chronic kidney disease. However, there is a paucity of thorough reviews that clarify the functional mechanisms of METTL3 and evaluate its importance in enhancing therapeutic outcomes. This review seeks to systematically examine the roles, mechanisms, and potential clinical applications of METTL3 in renal diseases. The findings presented suggest that METTL3 is implicated in the etiology and exacerbation of kidney disorders, affecting their onset, progression, malignancy, and responsiveness to chemotherapeutic agents through the regulation of specific genetic pathways. In conclusion, this review underscores a detrimental correlation between METTL3 and kidney diseases, highlighting the therapeutic promise of targeting METTL3. Additionally, it offers critical insights for researchers concerning the diagnosis, prognosis, and treatment strategies for renal conditions.

Dynamic multilayered control of m6A RNA demethylase activity

Similar to DNA and histone, RNA can also be methylated. In its most common form, a N6-methyladenosine (m6A) chemical modification is introduced into nascent messenger ribonucleic acid (mRNA) by a specialized methyltransferase complex and removed by the RNA demethylases, Fat mass and obesity-associated (FTO), and ALKBH5. The fate of m6A-marked mRNA is uniquely diverse, ranging from degradation to stabilization/translation, which has been suggested to be largely dependent on its interaction with the family of YT521-B homology (YTH) domain-containing proteins. Here, we highlight a series of control levers that impinge on the RNA demethylases. We present evidence to indicate that intermediary metabolism and various posttranslation modifications modulate the activity, stability, and the subcellular localization of FTO and ALKBH5, further dispelling the notion that m6A methylation is not a dynamic process. We also discuss how examination of these underappreciated regulatory nodes adds a more nuanced view of the role of FTO and ALKBH5 and should guide their study in cancer and nonmalignant conditions alike.

ALKBH5 activates CEP55 transcription through m6A demethylation in FOXP2 mRNA and expedites cell cycle entry and EMT in ovarian cancer

BACKGROUND

Centrosomal protein of 55 kDa (CEP55) overexpression has been linked to tumor stage, aggressiveness of the tumor, poor prognosis, and metastasis. This study aims to elucidate the action of CEP55 in ovarian cancer (OC) and the regulation by the alpha-ketoglutarate-dependent dioxygenase alkB homolog 5 (ALKBH5)/Forkhead box protein P2 (FOXP2) axis.

METHODS

Differentially expressed genes in OC were identified using in silico identification, followed by prognostic value assessment. Lentiviral vectors were constructed to downregulate CEP55 in OC cells, and colony formation, EdU, TUNEL, flow cytometry, Transwell assays, and Phalloidin staining were conducted. Transcription factors regulating CEP55 were predicted and verified, and rescue experiments were performed. The effect of ALKBH5-mediated demethylation on FOXP2 mRNA stability and OC cell cycle and EMT were analyzed.

RESULTS

High expression of CEP55 in OC was linked to unsatisfactory prognosis of patients. Knockdown of CEP55 repressed proliferation, invasiveness, and epithelial-mesenchymal transition (EMT) while inducing apoptosis and cell cycle arrest in OC cells. FOXP2 bound to the promoter of CEP55 to repress CEP55 transcription. FOXP2 regulated transcriptional repression of CEP55 to impede the malignant progression of OC and inhibit tumor metastasis. ALKBH5-mediated demethylation modification induced mRNA degradation of FOXP2. Knockdown of ALKBH5 induced cell cycle arrest and inhibited EMT in OC cells.

CONCLUSIONS

ALKBH5 hinders FOXP2-mediated transcriptional repression of CEP55 to promote the malignant progression of OC via cell cycle and EMT.

Systematic perturbation screens identify regulators of inflammatory macrophage states and a role for TNF mRNA m6A modification

Macrophages exhibit remarkable functional plasticity, a requirement for their central role in tissue homeostasis. During chronic inflammation, macrophages acquire sustained inflammatory 'states' that contribute to disease, but there is limited understanding of the regulatory mechanisms that drive their generation. Here we describe a systematic functional genomics approach that combines genome-wide phenotypic screening in primary murine macrophages with transcriptional and cytokine profiling of genetic perturbations in primary human macrophages to uncover regulatory circuits of inflammatory states. This process identifies regulators of five distinct states associated with key features of macrophage function. Among these regulators, loss of the N6-methyladenosine (m6A) writer components abolishes m6A modification of TNF transcripts, thereby enhancing mRNA stability and TNF production associated with multiple inflammatory pathologies. Thus, phenotypic characterization of primary murine and human macrophages describes the regulatory circuits underlying distinct inflammatory states, revealing post-transcriptional control of TNF mRNA stability as an immunosuppressive mechanism in innate immunity.

m6A modification of mutant huntingtin RNA promotes the biogenesis of pathogenic huntingtin transcripts

In Huntington's disease (HD), aberrant processing of huntingtin (HTT) mRNA produces HTT1a transcripts that encode the pathogenic HTT exon 1 protein. The mechanisms behind HTT1a production are not fully understood. Considering the role of m6A in RNA processing and splicing, we investigated its involvement in HTT1a generation. Here, we show that m6A methylation is increased before the cryptic poly(A) sites (IpA1 and IpA2) within the huntingtin RNA in the striatum of Hdh+/Q111 mice and human HD samples. We further assessed m6A's role in mutant Htt mRNA processing by pharmacological inhibition and knockdown of METTL3, as well as targeted demethylation of Htt intron 1 using a dCas13-ALKBH5 system in HD mouse cells. Our data reveal that Htt1a transcript levels are regulated by both METTL3 and the methylation status of Htt intron 1. They also show that m6A methylation in intron 1 depends on expanded CAG repeats. Our findings highlight a potential role for m6A in aberrant splicing of Htt mRNA.

Abundant mRNA m1A modification in dinoflagellates: a new layer of gene regulation

Dinoflagellates, a class of unicellular eukaryotic phytoplankton, exhibit minimal transcriptional regulation, representing a unique model for exploring gene expression. The biosynthesis, distribution, regulation, and function of mRNA N1-methyladenosine (m1A) remain controversial due to its limited presence in typical eukaryotic mRNA. This study provides a comprehensive map of m1A in dinoflagellate mRNA and shows that m1A, rather than N6-methyladenosine (m6A), is the most prevalent internal mRNA modification in various dinoflagellate species, with an asymmetric distribution along mature transcripts. In Amphidinium carterae, we identify 6549 m1A sites characterized by a non-tRNA T-loop-like sequence motif within the transcripts of 3196 genes, many of which are involved in regulating carbon and nitrogen metabolism. Enriched within 3'UTRs, dinoflagellate mRNA m1A levels negatively correlate with translation efficiency. Nitrogen depletion further decreases mRNA m1A levels. Our data suggest that distinctive patterns of m1A modification might influence the expression of metabolism-related genes through translational control.

Effects of METTL3-METTL14 on primary microRNA processing by Drosha-DGCR8

MicroRNAs modulate most protein-coding genes, and many are regulated during maturation. Chemical modifications of primary transcripts containing microRNAs have been implicated in altering Microprocessor processing efficiency, a key initiating endonucleolytic step performed by Drosha and DGCR8. METTL3-METTL14 produces N 6 -methyladenosine which is the most common methylation for mRNAs. Genetic experiments suggested that METTL3-METTL14 promotes primary microRNA processing by Microprocessor, but the molecular mechanism still needs to be elucidated. We tested the hypothesis that METTL3-METTL14 or m 6 A may directly impact Drosha or DGCR8 function during primary microRNA processing. After reconstituting the methyltransferase and processing activities, we show that the presence of METTL3-METTL14 complexes does not affect the processing efficiency of Drosha-DGCR8. We also established a method to prepare m 6 A-modified primary microRNAs and used them to show that the processing of the transcripts with m 6 A is similar to those without any modification. Recombinant METTL3-METTL14 and DGCR8 do not form stable complexes, challenging the previous model that depends on enhanced DGCR8 recruitment. Therefore, METTL3-METTL14 or m 6 A modification does not generally promote Microprocessor-mediated microRNA processing, although they may impact certain cases.

PSAT1 is upregulated by METTL3 to attenuate high glucose-induced retinal pigment epithelial cell apoptosis and oxidative stress

BACKGROUND

Diabetic retinopathy (DR) is a major ocular complication of diabetes mellitus, and a significant cause of visual impairment and blindness in adults. Phosphoserine aminotransferase 1 (PSAT1) is an enzyme participating in serine synthesis, which might improve insulin signaling and insulin sensitivity. Furthermore, it has been reported that the m6A methylation in mRNA controls gene expression under many physiological and pathological conditions. Nevertheless, the influences of m6A methylation on PSAT1 expression and DR progression at the molecular level have not been reported.

METHODS

High-glucose (HG) was used to treat human retinal pigment epithelial cells (ARPE-19) to construct a cell injury model. PSAT1 and Methyltransferase-like 3 (METTL3) levels were detected by real-time quantitative polymerase chain reaction (RT-qPCR). PSAT1, B-cell lymphoma-2 (Bcl-2), Bcl-2 related X protein (Bax), and METTL3 protein levels were examined by western blot assay. Cell viability and apoptosis were detected by Cell Counting Kit-8 (CCK-8) and TUNEL assays. Reactive oxygen species (ROS), malondialdehyde (MDA), and Glutathione peroxidase (GSH-Px) levels were examined using special assay kits. Interaction between METTL3 and PSAT1 was verified using methylated RNA immunoprecipitation (MeRIP) and dual-luciferase reporter assay.

RESULTS

PSAT1 and METTL3 levels were decreased in DR patients and HG-treated ARPE-19 cells. Upregulation of PSAT1 might attenuate HG-induced cell viability inhibition and apoptosis and oxidative stress promotion in ARPE-19 cells. Moreover, PSAT1 was identified as a downstream target of METTL3-mediated m6A modification. METTL3 might improve the stability of PSAT1 mRNA via m6A methylation.

CONCLUSION

METTL3 might mitigate HG-induced ARPE-19 cell damage partly by regulating the stability of PSAT1 mRNA, providing a promising therapeutic target for DR.

Epitranscriptome in action: RNA modifications in the DNA damage response

Complex pathways involving the DNA damage response (DDR) contend with cell-intrinsic and -extrinsic sources of DNA damage. DDR mis-regulation results in genome instability that can contribute to aging and diseases including cancer and neurodegeneration. Recent studies have highlighted key roles for several RNA species in the DDR, including short RNAs and RNA/DNA hybrids (R-loops) at DNA break sites, all contributing to efficient DNA repair. RNAs can undergo more than 170 distinct chemical modifications. These RNA modifications have emerged as key orchestrators of the DDR. Here, we highlight the function of enzyme- and non-enzyme-induced RNA modifications in the DDR, with particular emphasis on m6A, m5C, and RNA editing. We also discuss stress-induced RNA damage, including RNA alkylation/oxidation, RNA-protein crosslinks, and UV-induced RNA damage. Uncovering molecular mechanisms that underpin the contribution of RNA modifications to DDR and genome stability will have direct application to disease and approaches for therapeutic intervention.

ALKBH5 Regulates Osteogenic Differentiation via the lncRNA/mRNA Complex

Human adipose-derived stem cells (hASCs) are commonly used in bone tissue regeneration. The N6-methyladenosine (m6A) modification has emerged as a novel regulatory mechanism for gene expression, playing a critical role in osteogenic differentiation of stem cells. However, the precise role and mechanism of alkylation repair homolog 5 (ALKBH5) in hASC osteogenesis remain incompletely elucidated and warrant further investigation. Herein, we employed methylated RNA immunoprecipitation sequencing, RNA sequencing, and weighted gene coexpression network analysis to identify a key long noncoding RNA (lncRNA) in hASCs: lncRNA AK311120. Functional experiments demonstrated that lnc-AK311120 promoted the osteogenic differentiation of hASCs, while a mutation at the m6A central site A of lnc-AK311120 was found to decrease the level of m6A modification. The osteogenic effect of ALKBH5 was confirmed both in vitro and in vivo using a mandibular defect model in nude mice. Subsequent investigations revealed that knockdown of ALKBH5 resulted in a significant increase in the m6A modification level of lnc-AK311120, accompanied by a downregulation in the expression level of lnc-AK311120. Additional rescue experiments demonstrated that overexpression of lnc-AK311120 could restore the phenotype after ALKBH5 knockdown. We observed that AK311120 interacted with the RNA-binding proteins DExH-Box helicase 9 (DHX9) and YTH domain containing 2 (YTHDC2) to form a ternary complex, while mitogen-activated protein kinase kinase 7 (MAP2K7) served as the shared downstream target gene of DHX9 and YTHDC2. Knockdown of AK311120 led to a reduction in the binding affinity between DHX9/YTHDC2 and the target gene MAP2K7. Furthermore, ALKBH5 facilitated the translation of MAP2K7 and activated the downstream JNK signaling pathway through the AK311120-DHX9-YTHDC2 complex, without affecting its messenger RNA level. Collectively, we have investigated the regulatory effect and mechanism of ALKBH5-mediated demethylation of lncRNA in hASC osteogenesis for the first time, offering a promising approach for bone tissue engineering.