Search Results (46)

Tail docking, serving as an important management intervention in animal husbandry, plays a significant role in regulating tail fat deposition and improving production performance and health status in fat-tailed sheep. This study systematically revealed the reprogramming effects of tail docking on the epigenetic landscape and transcriptome of fat-tailed sheep by integrating whole-genome bisulfite sequencing (WGBS) and RNA m6A methylated immunoprecipitation sequencing (MeRIP-seq). At the DNA level, the tail-docked group exhibited a pronounced trend of hypomethylation across multiple functional genomic regions, including promoters, exons, and introns. Differentially methylated regions (DMRs) were significantly enriched in pathways related to tissue development and stress response, such as the Hippo signaling pathway and adherens junctions. Pyrosequencing validation of the promoter region of the key gene DGAT1 further confirmed the reliability of the WGBS data. At the RNA level, RNA m6A modifications showed an overall up-regulated pattern: the tail-docked group displayed higher numbers of m6A peaks, greater total peak length, and increased genomic coverage compared to the control group, along with better overall prediction of modification sites. Genes associated with differential m6A peaks were closely related to processes such as stem cell pluripotency and cytoskeleton regulation. qPCR validation of several methylation-related enzyme genes (e.g., METTL3, FTO, YTHDF1) yielded results consistent with the sequencing trends. Through integrated analysis of DNA methylation and RNA methylation, we identified 143 genes with concurrent changes in methylation and mRNA expression, among which 41 genes were regulated by both DNA and RNA methylation. These genes were primarily enriched in the adherens junction pathway. Notably, two core genes CITED4 and ZNF644 showed significant changes across all three levels: DNA methylation, RNA methylation, and mRNA expression. This study systematically elucidates the epigenetic mechanism by which tail docking stress induces coordinated DNA hypo-methylation and RNA m6A hyper-methylation to regulate transcriptomic reprogramming in response to environmental intervention. The findings provide novel insights into the molecular basis of trait formation in livestock. Full article

Bacterial and viral diseases significantly reduce soybean (Glycine max) yield and quality. RNA modifications, particularly N⁶-methyladenosine (m⁶A), are increasingly recognized as having a regulatory role in plant–pathogen interactions, but the m⁶A methylome of soybean during viral and bacterial infection has not yet been characterized. Here, we performed transcriptome sequencing and MeRIP-seq (methylated RNA immunoprecipitation followed by high-throughput sequencing) of soybean leaves infected with Soybean mosaic virus (SMV) and/or Pseudomonas syringae pv. glycinea (Psg). In general, m⁶A peaks were highly enriched near stop codons and in 3′-UTR regions of soybean transcripts, and m⁶A methylation was negatively correlated with transcript abundance. Multiple genes showed differential methylation between infected and control plants: 1122 in Psg-infected plants, 539 in SMV-infected plants, and 2269 in co-infected plants; 195 (Psg), 84 (SMV), and 354 (Psg + SMV) of these transcripts were both differentially methylated and differentially expressed. Interestingly, viral infection was predominantly associated with hypermethylation and downregulation, whereas bacterial infection was predominantly associated with hypomethylation and upregulation. GO and KEGG enrichment analysis revealed shared processes likely affected by changes in m⁶A methylation during bacterial and viral infection, including ATP-dependent RNA helicase activity, RNA binding, and endonuclease activity, as well as specific processes affected by only one pathogen. Our findings shed light on the role of m⁶A modifications during pathogen infection and highlight potential targets for epigenetic editing to increase the broad-spectrum disease resistance of soybean. Full article

Transmissible gastroenteritis virus (TGEV) represents a critical intestinal pathogen responsible for acute enteritis in pigs, posing significant challenges to global swine production biosecurity. N⁶-methyladenosine (m⁶A), the most abundant epitranscriptomic mark in eukaryotic messenger RNA, has emerged as a regulatory factor in host–virus interactions. Despite its recognized importance, the functional significance of m⁶A modifications during TGEV infection of porcine jejunal epithelial (IPEC-J2) cells remains unexplored. Here, we established a TGEV-infected IPEC-J2 cell model and we employed methylated RNA immunoprecipitation sequencing (MeRIP-seq) to comprehensively profile the m⁶A epitranscriptomic landscape and identify N⁶-methyladenosine-bearing transcripts in IPEC-J2 cells following TGEV challenge. A total of 14,813 m⁶A peaks were identified in the IPEC-J2, distributed in 7728 genes, mainly enriched in the CDS and 3′-UTRs. After TGEV infection, we identified 832 m⁶A peaks and 1660 genes with significant changes. Integrative analysis revealed a direct positive relationship between N⁶-methyladenosine modification abundance and transcript expression levels. Through integrated examination of MeRIP-Seq and RNA-Seq datasets, we identified 105 transcripts bearing m⁶A modifications, which were mainly enriched in the mTOR signaling pathway. Protein–protein interaction (PPI) network and RT-qPCR analysis demonstrated that SOS2 probably acts an important moderator in TGEV infection. This work contributes to understanding the m⁶A modification landscape in the TGEV-swine model and suggests SOS2 as potential target for future antiviral strategies. Full article

Epstein–Barr virus (EBV) infection is closely associated with gastric cancer, yet its role in m6A-dependent gene regulation remains poorly understood. In this study, we investigated how EBV infection alters the m6A methylation pattern in gastric cancer cells and examined its impact on TSC22D1 mRNA stability through interaction with the m6A reader protein YTHDF1. m6A RNA immunoprecipitation sequencing (MeRIP-seq) revealed a significant reduction in m6A methylation of TSC22D1 in EBV-infected gastric cancer cells (AGS-EBV) compared with EBV-negative cells (AGS). Moreover, YTHDF1 knockdown increased both the stability and expression of TSC22D1. These findings demonstrate that YTHDF1 binds to TSC22D1 mRNA and promotes its m6A-dependent degradation. Collectively, our results suggest that EBV infection modulates m6A modification to regulate gene stability and identify the YTHDF1–TSC22D1 axis as a potential therapeutic target in EBV-associated gastric cancer. Full article

RNA methylation, particularly N6-methyladenosine (m⁶A) and 5-methylcytosine (m⁵C), functions as a pivotal post-transcriptional regulatory mechanism and plays a central role in plant growth, development, and stress responses. This review provides a systematic summary of recent advances in RNA methylation research in cucurbit crops. To date, high-throughput technologies such as MeRIP-seq and nanopore direct RNA sequencing have enabled the preliminary construction of RNA methylation landscapes in cucurbit species, revealing their potential regulatory roles in key agronomic traits, including fruit development, responses to biotic and abiotic stresses, and disease resistance. Nevertheless, this field remains in its early stages for cucurbit crops and faces several major challenges: First, mechanistic understanding is still limited, with insufficient knowledge regarding the composition and biological functions of the core protein families involved in methylation dynamics—namely, “writers,” “erasers,” and “readers.” Second, functional validation remains inadequate, as direct evidence linking specific RNA methylation events to downstream gene regulation and phenotypic outcomes is largely lacking. Third, resources are scarce; compared to model species such as Arabidopsis thaliana and rice, cucurbit crops possess limited species-specific genetic data and genetic engineering tools (e.g., CRISPR/Cas9-based gene editing systems), which significantly hampers comprehensive functional studies. To overcome these limitations, future research should prioritize the development and application of more sensitive detection methods, integrate multi-omics datasets—including transcriptomic and methylomic profiles—to reconstruct regulatory networks, and conduct rigorous functional assays to establish causal relationships between RNA methylation modifications and phenotypic variation. The ultimate objective is to fully elucidate the biological significance of RNA methylation in cucurbit plants and harness its potential for crop improvement through genetic and biotechnological approaches. Full article

To date, more than 170 chemical modifications have been identified in RNA. m⁶A (N⁶-methyladenine) RNA methylation is the most abundant form of mRNA modification in eukaryotes, playing an important role in RNA post-transcriptional processes. To investigate the function of m⁶A methylation modification in the development and lactation of dairy goat mammary glands, mammary gland tissue samples were collected in the early (20 days postpartum), peak (90 days postpartum), and late period (210 days postpartum) of three dairy goats. MeRIP-seq and RNA-seq were used to explore m⁶A methylation modification events. We identified 1638 differential peaks in the MeRIP-seq data across 1539 differentially methylated genes, which were enriched in ribosome biogenesis in eukaryotes, Toll-like receptor signaling pathway, TNF signaling pathway, MAPK, and other pathways related to mammary gland development and lactation. A conjoint analysis revealed that 179 common differential expressed genes were obtained, of which 150 were negatively regulated by their m⁶A modifications, while 5 common differentially expressed genes—PPARG, HSPA2, CDK5, ACTB and NOTCH3, were screened out in the two groups. In conclusion, m⁶A modification involves the pathways related to mammary gland development and lactation by modifying gene expression. This studyprovides new insights into m⁶A epigenetic regulation, mammary epithelial gene networks, and actionable molecular targets for high-value dairy product production and the breeding of new varieties. Full article

Resveratrol (RES), a natural polyphenol with lipid metabolism-regulating properties, also demonstrates remarkable efficacy in strengthening intestinal barrier integrity. In order to elucidate the mechanism by which RES ameliorates intestinal damage and lipid metabolism disturbances in Megalobrama amblycephala under a high-fat (HF) diet, a conventional diet (CON), an HF diet (HF), or an HF diet supplemented with 0.6, 3, or 6 g/kg RES (HF + 0.06%, 0.3%, or 0.6% RES) was fed to fish. After 8 weeks, RES supplementation in the HF diet significantly improved the growth performance and alleviated hepatic lipid deposition. Microbiota profiling revealed RES improved intestinal barrier function by reducing α-diversity, Actinobacteria and Bosea abundances, and enriching Firmicutes abundance. RES also maintained the integrity of the intestinal physical barrier and inhibited the inflammatory response. MeRIP-seq analysis indicated that RES modulated intestinal mRNA m⁶A methylation by upregulating methyltransferase-like 3 (mettl3) and downregulating fat mass and obesity-associated gene (fto) and Alk B homolog 5 (alkbh5). Combined RNA-seq and MeRIP-seq data revealed that RES alleviated endoplasmic reticulum stress (ERS) by upregulating the m⁶A methylation and gene level of heat shock protein 70 (hsp70). Correlation analyses identified significant associations between intestinal microbiota composition and ERS, tight junction, and inflammation. In summary, RES ameliorates lipid dysregulation via a synergistic mechanism involving intestinal microbiota, m⁶A modification, ERS, barrier function, and inflammatory response. Full article

Background: The function and mechanism of N6-methyladenosine (m6A) methylation in pressure-overload cardiac fibrosis remains limited and unclear. This study aims to analyze and predict m6A modifications present in mouse hearts because of transverse aortic constriction (TAC). Materials and Methods: Twelve male C57BL/6 mice were randomly assigned to two groups, TAC group and sham group. The RNA Dot Blot assay was employed to evaluate the overall m6A methylation levels in both TAC and sham mice. The expression level of m6A-related enzymes were investigated through RT-PCR and Western blotting. MeRIP-seq and RNA-seq analyses were conducted to identify differentially modified m6A genes and mRNA expression genes. The protein–protein interaction (PPI) network was carried out to choose potential hub genes. Additionally, the transcription factor (TF)–microRNA (miRNA) coregulatory network and the drug–hub gene interaction network were built based on these hub genes. Furthermore, molecular docking simulations were also performed to analyze the interactions between drugs and hub genes. Results: Compared with the sham group, the TAC group demonstrated elevated levels of global m6A methylation. METTL3 and METTL14 were significantly upregulated, whereas FTO and ALKBH5 were significantly downregulated following TAC. MeRIP-seq analysis identified 17,806 m6A peaks associated with 9184 genes and 16,392 m6A peaks associated with 8550 genes in the TAC and sham groups, respectively. In conjunction with RNA-seq data, 66 genes were identified as exhibiting concurrent differences in both m6A methylation levels and mRNA expression. Six hub genes, Cd33, Irf4, Nr4a2, Hspa1b, Nr4a1, and Adcy1, were identified through the construction of a PPI network. The TF-miRNA coregulatory network contains six hub genes, 31 miRNAs, and 24 TFs. The drug–hub genes interaction network included five hub genes and 36 candidate drugs. Conclusions: The m6A modification is prevalent in TAC-induced cardiac fibrosis and significantly contributes to the fibrotic process by regulating critical genes. In the future, it may emerge as one of the potential cardiac fibrosis therapeutic targets. Full article

Colchicine is commonly prescribed for inflammation and gout, but its nephrotoxicity and underlying mechanisms remain incompletely understood. The objective of this research was to clarify the association between m6A methylation modifications and nephrotoxicity caused by colchicine. A significant decrease in HK2 cell viability was observed following colchicine treatment, and mRNA sequencing (mRNA-seq) revealed the differential expression of genes associated with DNA damage and autophagy. Further methylated RNA immunoprecipitation sequencing (MeRIP-seq) analysis revealed an association between N6-methyladenosine (m6A) modifications and the expression of genes involved in DNA damage and autophagy after colchicine exposure. Molecular docking and a molecular dynamics (MD) analysis identified ZC3H13 as a potential regulator of colchicine-induced cytotoxicity in HK2. Experimental validation confirmed that colchicine induces DNA damage and autophagy in HK2 cells, with ZC3H13 playing a significant role in these processes. In conclusion, the findings suggested that colchicine-induced damage in HK2 cells is associated with changes in m6A methylation levels in target genes and the altered expression of m6A regulator. Full article

N6-methyladenosine (m6A) represents the most common and thoroughly investigated RNA modification and exerts essential functions in regulating gene expression through influencing the RNA stability, the translation efficiency, alternative splicing, and nuclear export processes. The rapid development of high-throughput sequencing approaches, including miCLIP and MeRIP-seq, has profoundly transformed epitranscriptomics research. These techniques facilitate the detailed transcriptome-wide profiling of m6A modifications, shedding light on their crucial roles in diverse biological pathways. This review comprehensively examines the identification, mechanisms of regulation, and functional consequences of m6A modifications. It emphasizes their critical roles in physiological contexts, encompassing immune function, neuronal development, and the differentiation of stem cells. Additionally, the review discusses the contributions of m6A dysregulation to pathological conditions, including cancer, neurodegenerative diseases, and disorders of metabolism. We also discuss the development and application of machine-learning algorithms for m6A site prediction, emphasizing the integration of sequence-based, structural, and evolutionary conservation features to enhance the predictive accuracy. Furthermore, the potential of applying the findings from m6A research in precision medicine and drug development is examined. By synthesizing the current knowledge and emerging trends, this review aims to provide a comprehensive understanding of m6A biology and its translational potential, offering new perspectives for future research and therapeutic innovation. Full article

Exercise is a well-recognized non-pharmacological strategy for preventing and managing metabolic dysfunction-associated steatotic liver disease (MASLD, formerly known as NAFLD). While the benefits of exercise are thought to involve epigenetic mechanisms, the precise role of RNA m6A methylation remains unclear. This study investigates how treadmill exercise modulates RNA m6A methylation to prevent MASLD in a high-fat diet (HFD)-induced mouse model. Male C57BL/6 mice were fed either a standard diet (SD) or HFD for 12 weeks, with a subset of HFD-fed mice undergoing treadmill exercise (HFD + Ex). Liver pathology and biochemical markers were assessed. RNA sequencing (RNA-Seq) and methylated RNA immunoprecipitation sequencing (MeRIP-seq) were performed to identify differentially expressed genes (DEGs) and m6A methylation changes. Key candidate gene Paqr7 was validated through siRNA-mediated knockdown in AML-12 cells to assess its role in lipid metabolism. Treadmill exercise alleviated MASLD-related pathology and biochemical abnormalities. RNA-Seq identified 984 DEGs in the HFD vs. SD comparison and 544 in the HFD + Ex vs. HFD comparison. Intersection analysis identified 155 genes upregulated in MASLD and downregulated following exercise. MeRIP-seq revealed 225 hypermethylated and 208 hypomethylated m6A peaks in HFD + Ex vs. HFD groups. Integrative analysis highlighted Adra2b, Lipa, and Paqr7 as key exercise-responsive genes. Silencing Paqr7 through siRNA-mediated knockdown reduced lipid accumulation and suppressed lipogenic gene expression, suggesting its role in exercise-mediated MASLD improvement. Treadmill exercise prevents MASLD by modulating RNA m6A methylation, with Paqr7 emerging as a potential regulator of lipid metabolism. These findings highlight epigenetic modulation as a key mechanism in exercise-induced liver protection. Full article

m⁶A methylation modification is an important genetic modification involved in biological processes such as sexual maturation, antibacterial, and antiviral in aquatic animals. However, few studies have been conducted in aquatic animals on the relationship between m⁶A methylation modification and autophagy-inflammation induced by lipid metabolism disorders. In the present study, a high-fat (HF) group and HF-MLP group (1 g mulberry leaf polysaccharides (MLPs)/1 kg HF diet) were set up. The mid-hind intestines of Megalobrama amblycephala juveniles from the two groups were collected for MeRIP-seq and RNA-seq after an 8-week feeding trial. The m⁶A peaks in the HF and HF-MLP groups were mainly enriched in the 3′ Untranslated Region (3′UTR), Stop codon, and coding sequence (CDS) region. Compared with the HF group, the m⁶A peaks in the HF-MLP group were shifted toward the 5′UTR region. ‘RRACH’ was the common m⁶A methylation motif in the HF and HF-MLP groups. Methyltransferase mettl14 and wtap expression in the intestines of the HF-MLP group were significantly higher compared with the HF group (p < 0.05). A total of 21 differentially expressed genes(DEGs) with different peaks were screened by the combined MeRIP-seq and RNA-seq analysis. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis enriched BCL2 interacting protein 3 (bnip3) to autophagy–animal and mitophagy–animal signaling pathways, etc., and nucleotide-binding domain leucine-rich repeat protein 1 (nlrp1) was enriched to the Nucleotide-binding oligomerization domain (NOD)-like receptor signaling pathway. Combined MeRIP-seq and RNA-seq analysis indicated that the expression pattern of bnip3 was hyper-up and that of nlrp1 was hyper-down. Gene Set Enrichment Analysis (GSEA) analysis confirmed that the intestinal genes of HF-MLP group positively regulate lysosomal and autophagy–animal signaling pathways. In the present study, we demonstrated that m⁶A methylation modification plays a role in regulating autophagy-inflammatory responses induced by HF diets by MLPs, and further explored the molecular mechanisms by which MLPs work from the epigenetic perspective. Full article

Background/Objectives: Epigenetic regulation plays a critical role in diabetes research, with N6-methyladenosine (m6A) modification emerging as a key factor in disease progression. METTL14, an essential epigenetic regulator, may influence the effects of thiamine on intensive insulin therapy in diabetic patients. Methods: Blood samples from twenty diabetic patients were collected before and after intensive insulin therapy for MeRIP-seq and RNA-seq analysis. Genes with m6A modifications and corresponding mRNAs were identified and functionally analyzed using Gene Ontology (GO) and KEGG pathway analysis. RT-qPCR was used to confirm the overexpression of METTL14, PIK3R1, TPK1, and IPMK, while METTL14 overexpression was further validated in THP1 cells. Results: GO analysis revealed a significant enrichment of overlapping genes in metabolic pathways. A reduction in m6A modification levels was observed post intensive insulin therapy, indicating METTL14’s involvement in regulating TPK1, IPMK, and PIK3R1 expression. TPK1 levels showed a positive correlation with thiamine levels. Clinical validation demonstrated that combining thiamine with insulin therapy significantly reduced glucose and triglyceride levels compared to insulin alone. Conclusions: Thiamine supplementation alongside intensive insulin therapy offers therapeutic potential by downregulating TPK1 expression and mitigating lipid-related complications in diabetic patients. These findings highlight the pivotal role of METTL14-mediated m6A modification in regulating key metabolic genes during diabetes treatment. Full article

Background: N6-methyladenosine (m⁶A) modification plays a crucial role in the regulation of diverse cellular processes influenced by environmental factors. Nevertheless, the involvement of m⁶A-modified long noncoding RNAs (lncRNAs) in the pathogenesis of lung injury induced by particulate matter (PM) remains largely unexplored. Methods: Here, we establish a mouse model of PM-induced lung injury. We utilized m6A-modified RNA immunoprecipitation sequencing (MeRIP-seq) to identify differentially expressed m6A peaks on long non-coding RNAs (lncRNAs). Concurrently, we performed lncRNA sequencing (lncRNA-seq) to determine the differentially expressed lncRNAs. The candidate m6A-modified lncRNAs in the lung tissues of mice were identified through the intersection of the data obtained from these two sequencing approaches. Results: A total of 664 hypermethylated m⁶A peaks on 644 lncRNAs and 367 hypomethylated m⁶A peaks on 358 lncRNAs are confirmed. We use bioinformatic tools to analyze the potential functions and pathways of these m⁶A-modified lncRNAs, revealing their involvement in regulating inflammation, immune response, and metabolism-related pathways. Three key m⁶A-modified lncRNAs (lncRNA NR_003508, lncRNA uc008scb.1, and lncRNA ENSMUST00000159072) are identified through a joint analysis of the MeRIP-seq and lncRNA-seq data, and their validation is carried out using MeRIP-PCR and qRT-PCR. Analysis of the coding-non-coding gene co-expression network reveals that m⁶A-modified lncRNAs NR_003508 and uc008scb.1 participate in regulating pathways associated with inflammation and immune response. Conclusions: This study first provides a comprehensive transcriptome-wide analysis of m⁶A methylation profiling in lncRNAs associated with PM-induced lung injury and identifies three pivotal candidate m⁶A-modified lncRNAs. These findings shed light on a novel regulatory mechanism underlying PM-induced lung injury. Full article

Traumatic brain injury (TBI) poses a major global health challenge, leading to serious repercussions for those affected and imposing considerable financial strains on families and healthcare systems. RNA methylation, especially 5-methylcytosine (m⁵C), plays a crucial role as an epigenetic modification in regulating RNA at the level of post-transcriptional regulation. However, the impact of TBI on the m⁵C methylation profile of long non-coding RNAs (lncRNAs) remains unexplored. In the present study, we conducted a thorough transcriptome-wide examination of m⁵C methylation in lncRNAs in a rat TBI model utilizing MeRIP-Seq. Our results revealed significant differences in the amount and distribution of m⁵C methylation in lncRNAs between TBI and control groups, indicating profound changes in m⁵C methylation following TBI. Bioinformatic analyses linked these specifically methylated transcripts to pathways involved in immune response, neural repair, and lipid metabolism, providing insight into possible mechanisms underlying TBI pathology. These findings offer novel perspectives on the post-transcriptional modifications in lncRNA m⁵C methylation following TBI, which may contribute to understanding the disease mechanisms and developing targeted therapeutic strategies. Full article