Search Results (412)

Mastitis remains the most economically damaging disease in the global dairy industry, and conventional genetic selection based on somatic cell score (SCS) has produced only limited gains in resistance. Epigenetic mechanisms—mitotically heritable yet environmentally responsive and largely reversible modifications that regulate gene expression without altering the DNA sequence—are now emerging as a complementary layer of biological information that can sharpen the prediction of disease susceptibility. This review summarizes current evidence on three classes of epigenetic markers associated with bovine mastitis resistance: DNA methylation, non-coding RNAs (with emphasis on microRNAs, long non-coding RNAs, circular RNAs, and small nucleolar RNAs), and histone modifications, alongside the increasingly important epitranscriptomic layer of N6-methyladenosine (m6A) RNA modification. Particular attention is given to differentially methylated regions and discriminant methylation haplotype blocks in immune-related genes, circulating and milk-derived non-coding RNA biomarkers, m6A-mediated regulation of inflammatory transcripts, and histone-mark dynamics in mammary epithelial cells challenged with Staphylococcus aureus and Escherichia coli. We conclude with current limitations and perspectives on translating these markers into selection tools and therapeutic targets. Across all marker classes, current evidence remains constrained by small cohort sizes, breed-specific study designs, a scarcity of longitudinal and multi-generational data, and limited functional validation, so most candidate markers are still at the discovery stage and require cautious interpretation before deployment. Full article

Perioperative stress induces profound molecular and cellular responses that contribute to postoperative complications, including perioperative neurocognitive disorders (PND), chronic postsurgical pain, organ dysfunction, immunothrombosis, fibrosis, and cancer progression. Increasing evidence demonstrates that epigenetic mechanisms act as central regulators linking surgical trauma, inflammation, metabolic stress, ischemia–reperfusion injury, and immune activation to long-term alterations in gene expression and tissue remodeling. DNA methylation, histone modifications, chromatin remodeling, non-coding RNAs, and RNA epitranscriptomic mechanisms such as N6-methyladenosine (m6A) collectively orchestrate perioperative responses across multiple organ systems. Recent translational studies have identified histone deacetylases (HDACs), histone methyltransferases, NETosis-associated chromatin signaling, HMGB1/NF-κB activation, and epigenetic regulation of neuroimmune pathways as major contributors to postoperative cognitive dysfunction, chronic pain, cardiac dysfunction, pulmonary injury, and fibrosis. In parallel, advances in liquid biopsy, circulating tumor DNA (ctDNA), and single-cell epigenomics have opened new opportunities for biomarker-guided perioperative precision medicine. This review summarizes current evidence regarding epigenetic regulation in perioperative medicine with special emphasis on neuroepigenetics, NETosis, fibrosis, cardiac epigenetics, immune remodeling, and perioperative oncological outcomes. Furthermore, we discuss emerging therapeutic strategies targeting HDACs, DNA methylation, m6A pathways, and chromatin-associated inflammatory signaling as potential future interventions for perioperative complications. Full article

Aims: Treatment of higher-risk myelodysplastic syndromes (HR-MDS) with azacytidine (AZA) exerts significant effects on the epigenome, primarily through DNA demethylation and reactivation of epigenetically silenced genes. Beyond this established mechanism, molecular AZA-linked effects are increasingly being recognized. Materials and methods: Liquid chromatography combined with mass spectrometry (LC-MS/MS) was employed for the accurate assessment of various RNA and DNA modifications pre- and post-AZA treatment of an HR-MDS cohort (N = 8). Mapping of the AZA treatment-responsive regulatory pathways was performed by miRNA-next generation sequencing (NGS), followed by a multi-layered bioinformatic pipeline, integrating miRNA differential expression, gene set enrichment, and network analyses. The precise number of mitochondrial (mt)DNA copies pre- and post-AZA was evaluated by a digital PCR assay. Results: Cell pathways affected by miRNA differential expression patterns pre- and post-AZA treatment discriminated the clinical phenotypes of Responders against Non-Responders to therapy. Intracellular RNA modifications: N6-methyladenosine (m6A), 5-methylcytidine (m5C), N1-methyladenosine (m1A), 2′-O-methylguanosine (Gm) and adenosine-to-inosine (A → I) editing were evaluated for their potential impact in treatment response. Nuclear DNA/mtDNA methylation profiles and mtDNA copy number reduction manifested the mitochondrial features affected by AZA. Our results suggest that neoplastic HSPCs in HR-MDS Responders to AZA adapt by normalizing glycolytic metabolism and enhancing ribosomal activity. The observed reduction of mtDNA content can be associated with improved survival and suppression of malignant progression. Non-Responders, despite experiencing mtDNA depletion, seem unable to coordinate such metabolic reprogramming and remain disadvantaged to AZA therapy. Full article

N6-methyladenosine (m6A) is the most prevalent internal modification of eukaryotic mRNA and a central regulator of plant development and stress adaptation. The plant m6A writer complex requires two MT-A70 family proteins, the catalytic subunit MTA70 and its non-catalytic partner MTB, yet the evolutionary basis and structural logic underlying this functional division remain unresolved across land plant lineages. Here, we present an integrative computational analysis of MTA70 and MTB across 15 phylogenetically representative species spanning bryophytes, lycophytes, charophyte algae, monocots, and dicots. Phylogenomic reconstruction resolved three strongly supported clades, namely MTA70, MTB, and an intermediate MTA70-like group, demonstrating that catalytic-to-regulatory divergence predates the separation of major land plant lineages. MTA70 proteins exhibited strict conservation of gene structure, catalytic motifs, and domain architecture, reflecting selective constraint at functionally critical residues, whereas MTB showed extensive divergence in exon–intron organization and surface-exposed residues, consistent with relaxed structural constraints. AlphaFold2-based structural modeling and data-driven protein–protein docking predicted a stable MTA70–MTB heterodimer with a buried surface area of 1435 Ų and a binding free energy of −8.1 kcal/mol, with Lys746 and Lys637 of MTB identified as primary interface hotspots by computational alanine scanning. Expression profiling across six species revealed preferential MTB accumulation in reproductive tissues, while promoter analysis identified statistically significant enrichment of jasmonate-responsive elements (TGACG-motif) in MTB promoters (Mann–Whitney U, p = 0.025) and a 3.4-fold higher abundance of ABA-responsive elements (ABRE) in MTB relative to MTA70, suggesting potential responsiveness to multiple phytohormone signals. Together, these findings establish an evolutionary and regulatory framework for MTB as a conserved scaffold coupling m6A deposition to developmental and environmental signaling in land plants. Full article

Skeletal homeostasis relies on coordinated interactions among osteoblasts, osteoclasts, osteocytes, chondrocytes, and bone marrow stromal cells. Disruption of this balance contributes to the development of osteoporosis, osteoarthritis, impaired skeletal repair, and bone malignancies. Fat mass and obesity-associated protein (FTO), an RNA demethylase that removes N6-methyladenosine (m6A) and related RNA modifications, has emerged as a key context-dependent regulator of skeletal biology. Rather than acting uniformly as either a pro-osteogenic or disease-promoting factor, FTO exerts diverse effects that depend on the cell type, disease stage, target transcript, reader-protein context, and mode of therapeutic modulation. This narrative review summarizes current evidence on the role of FTO in osteoblast differentiation, osteoclast activity, bone marrow mesenchymal stem cell (BMSC) lineage commitment, cartilage homeostasis, osteosarcoma, multiple myeloma, and bone-related metastasis. We highlight areas of consensus, unresolved controversies, the strength of the available evidence, and major translational challenges. Collectively, FTO represents a promising therapeutic target in skeletal diseases; however, the current evidence remains largely preclinical and should be interpreted with caution until its efficacy and safety are validated in clinical settings. Full article

Background: As a major regulator, methyltransferase-like 3 (METTL3) catalyzes N6-methyladenosine (m⁶A) modification in mRNA. The m⁶A modifications mediated by METTL3 influence RNA splicing, nucleocytoplasmic distribution, stability, and other functions, thereby playing a vital and indispensable role in genetic regulatory network. Although several studies have shown its critical role in mRNA fate, the global pattern of mRNA methylation alteration driven by METTL3 remain unclear. Methods: Here, a HEK293T cell line with METTL3 depletion was constructed, and RNA sequencing (RNA-seq) and methylated RNA Immunoprecipitation Sequencing (MeRIP-seq) were implemented. Additionally, quantitative Reverse Transcription PCR (qRT-PCR) technology was used to confirm some of the differentially expressed genes. Result: The mRNA methylation alteration landscape was clarified and the regions altered by m⁶A modification due to METTL3 deletion that was annotated and characterized, with 5763 hypomethylated/269 hypermethylated genes after METTL3 silence. Several methylation-related innate anti-infection immune genes, including MYD88, RIG-1, CYLD and IRF9, were exposed through comprehensive analysis to MeRIP-seq and RNA-seq data, and these genes were principally enriched in pathogen infection and innate immune response pathways such as Shigellosis, Yersinia infection, and the HIV-1 viral life cycle. Conclusion: Our study discovered that the METTL3 association with differentially expressed genes, suggested that METTL3 and the genes it regulates might serve as targets for defense against infection. Full article

Background/Objectives: N6-methyladenosine (m⁶A) is a prevalent RNA modification that significantly influences various biological processes. AlkB homologs (ALKBHs) belong to the family of specific demethylases and, by regulating m⁶A methylation, are known to be involved in the modulation of plant stress responses. However, the ALKBH gene family has not been systematically characterized in ginseng. Methods: A genome-wide identification and characterization of the ALKBH gene family in ginseng were performed using a telomere-to-telomere reference genome. Phylogenetic relationships, gene structures, conserved motifs, 3D structures, chromosomal distribution, syntenic relationships, cis-acting regulatory elements, protein-protein interaction (PPI) networks, and expression profiles were analyzed. Transcriptome datasets covering multiple tissues, developmental stages, cultivars, and abiotic stress treatments were examined. Candidate stress-responsive genes were further validated by qRT-PCR. Results: A total of 17 PgALKBH genes were identified and classified into seven subfamilies. Structural analyses revealed conserved motifs, exon–intron organization, and 3D structures among members within the same subfamily. Chromosomal localization and synteny analyses suggested that the PgALKBH family has been evolutionarily conserved between ginseng and Arabidopsis and has primarily undergone purifying selection during its expansion. Promoter analysis identified abundant light-, hormone-, and stress-responsive cis-elements. Expression profiling revealed distinct tissue- and developmental stage-specific patterns. The PPI analysis suggested that PgALKBH proteins, especially PgALKBH10, may play a central role in m⁶A-mediated RNA regulation in ginseng. Transcriptome and qRT-PCR analyses further showed that PgALKBH genes respond differentially to drought, cold, and salt stresses. Notably, PgALKBH10 was induced under all three stress conditions. Conclusions: This study provides a comprehensive characterization of the ALKBH gene family in ginseng and identifies PgALKBH10 as a promising candidate involved in multiple abiotic stress responses. These findings establish a foundation for elucidating the roles of RNA m⁶A demethylation in ginseng and provide valuable genetic resources for developing stress-tolerant ginseng cultivars. Full article

RNA N⁶-methyladenosine (m⁶A) modification is a pivotal post-transcriptional regulator of diverse biological processes. Despite the growing interest in insect epitranscriptomics, a systematic evaluation of research trends and hotspots remains lacking. Here, we conducted a bibliometric analysis to map the global landscape of METTL3 and m⁶A research in entomology over the past decade. Our results reveal a steady increase in publications, signaling a phase of rapid expansion in this field. Notably, the number of studies on METTL3 is significantly lower than that of general m⁶A research, suggesting that current efforts prioritize phenotypic over the mechanistic roles of core regulatory components. Keyword co-occurrence analysis identifies Bombyx mori, Locusta migratoria, and Drosophila melanogaster as the primary model systems. Research hotspots predominantly center on METTL3-mediated regulation of development, behavioral plasticity, immunity, and host–pathogen interactions. These findings highlight insect METTL3 as a burgeoning research frontier. Future studies should emphasize cross-species comparisons and the systematic dissection of regulatory networks to provide novel theoretical frameworks and molecular targets for sustainable pest management and resource insect utilization. Full article

More than 160 types of post-transcriptional RNA modifications have been identified, revealing considerable diversity in their types, abundances, distributions, and functional roles across different RNAs, cells, and tissues in humans. Recent advances in high-throughput sequencing technologies have enabled the systematic detection of dynamic RNA modifications, including N6-methyladenosine (m⁶A) and inosine (I). In this review, we focus on RNA modifications in eukaryotic mRNA and provide an overview of current high-throughput methodologies for detecting the most abundant adenosine-related modifications, including m⁶A and adenosine-to-inosine (A-to-I) RNA editing. Finally, we discuss the major challenges that remain in the field and highlight key directions for future research. Full article

Background: Hypertension-induced vascular injury involves endothelial dysfunction, inflammation, and oxidative stress, leading to vascular remodeling and cardiovascular complications. Flavin-containing monooxygenase 2 (FMO2) has been implicated in redox regulation, but its role in hypertensive vascular injury remains unclear. This study investigated whether KuJiang GanLuoYin (KJGLY) protects against hypertensive vascular injury and whether FMO2-associated Fat mass and obesity-associated protein (FTO)/N6-methyladenosine (m⁶A) signaling is involved. Methods: Spontaneously hypertensive rats (SHRs) were treated with KJGLY for eight weeks. Blood pressure, vascular remodeling, inflammation, oxidative stress, and global m⁶A RNA methylation were assessed. Integrated metabolomic and proteomic analyses were performed to identify treatment-associated molecular alterations and candidate proteins. AAV9-mediated FMO2 knockdown in SHRs and gain- and loss-of-function approaches in angiotensin II (Ang II)-stimulated human umbilical vein endothelial cells were used to examine the functional involvement of FMO2. Ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS)-based chemical profiling and High-performance liquid chromatography–tandem mass spectrometry (HPLC–MS/MS) quantification were performed to characterize the major constituents of KJGLY. Results: KJGLY significantly reduced blood pressure and alleviated vascular remodeling in SHRs. Metabolomic and proteomic analyses revealed treatment-associated alterations in inflammatory and lipid metabolic pathways and identified FMO2 as a treatment-responsive candidate. KJGLY restored FMO2 expression, reduced FTO abundance and NF-κB activation, increased global m⁶A levels, and attenuated inflammatory and oxidative stress responses in hypertensive aortas. Conversely, AAV9-mediated FMO2 knockdown aggravated vascular injury, enhanced inflammation and oxidative stress, reduced global m⁶A levels, and increased NF-κB activation. Co-immunoprecipitation showed an association between FMO2 and FTO, and MeRIP-qPCR indicated that FMO2 manipulation altered m⁶A enrichment of VCAM-1 mRNA. In Ang II-stimulated endothelial cells, linarin, the most abundant quantified constituent of KJGLY, partially recapitulated the cellular effects of KJGLY, including restoration of FMO2/FTO-associated signaling and attenuation of inflammatory activation. Conclusions: These findings support a functional role for FMO2 in hypertensive vascular injury and suggest that FMO2-associated modulation of FTO/m⁶A signaling may contribute to the vascular protective effects of KJGLY. Linarin recapitulated key protective effects in vitro, although its in vivo contribution to the formula remains to be determined. Full article

Epitranscriptomic modifications, particularly RNA methylations, have emerged as regulators of gene expression, with their dysregulation acting as a key factor in tumorigenesis and metastatic progression. This review evaluates the therapeutic landscapes of N⁶-methyladenosine (m⁶A) and N¹-methyladenosine (m¹A) modifications in cancer. While the m⁶A machinery predominantly dictates mRNA turnover and stability, the m¹A network is uniquely positioned to drive translational reprogramming, allowing malignant cells to endure severe microenvironmental stress and evade cell death. Despite positional and chemical differences, these modifications exhibit profound epitranscriptomic crosstalk through shared regulatory proteins. Here, we comprehensively analyze current pharmacological strategies targeting the m⁶A axis, highlighting the transition from classical small-molecule inhibitors of regulatory proteins of these methylations, such as methyltransferase-like 3 (METTL3), fat mass and obesity-associated protein (FTO), and AlkB homolog 5 (ALKBH5), to the novel event-driven approach of proteolysis-targeting chimeras (PROTACs). Furthermore, we assess the emerging therapeutic potential of the m¹A regulatory machinery, positioning tRNA methyltransferase 6/61A (TRMT6/61A) writers and AlkB homolog 1 to 3 (ALKBH1-3) erasers as promising therapeutic targets. Finally, we discuss clinical successes and current translational obstacles, including off-target toxicity, pharmacokinetic limitations, and epitranscriptomic escape, emphasizing that site-specific modulation and smart precision therapies will dictate the future of oncology. Full article

Splicing factor 3b1 (SF3B1), a component of U2 small nuclear ribonucleoprotein (U2 snRNP), has been known for its essential roles in pre-mRNA splicing and alternative splicing. Here we show that knocking down (KD) of SF3B1 broadly induced a significant reduction in mRNA expression in the genome. One of the genes whose expression is reduced by SF3B1 KD is methyl-transferase-like 3 (METTL3), a writer of N6-methyladenosine (m⁶A). We demonstrate that expression of both METTL3 mRNA and protein is affected by SF3B1 KD, which further decreases the m⁶A RNA expression level. m⁶A-seq indicates that SF3B1 KD affects m⁶A distribution within multiple genes in the genome. In addition, a high proportion of hypo-methylation events by SF3B1 KD (~70%) are overlapped in METTL3 KD cells, and a conserved m⁶A motif is observed in the hypo-methylated regions as in SF3B1 KD cells, suggesting the m⁶A decrease by SF3B1 is a direct effect of the reduced METTL3 expression. Furthermore, RT-qPCR using unlabeled RNA and 5-Bromouridine (BrU)-labeled nascent RNA and actinomycin D treatment demonstrates that transcription of METTL3 is significantly reduced but the mRNA decay rate is not altered, suggesting that METTL3 expression is altered at the transcription level. We further show that SF3B1 interacts with RNA polymerase (Pol) II in the RNA independent manner, further indicating the involvement of SF3B1 in transcription. Lastly, we demonstrate that the transcription inactive H3K27me3 on the METTL3 promoter was significantly increased whereas transcription active H3K4me3 was not changed by SF3B1 KD. Taken together, we conclude that reduced SF3B1 expression suppresses the transcription of METTL3 and inhibits m⁶A RNA expression. Full article

Succinate, a tricarboxylic acid (TCA) cycle intermediate, is the essential signal molecule that links metabolic signals and inflammation. Dietary succinate supplementation has been reported to prevent obesity induced by a high-fat diet (HFD). However, the underlying mechanism remains elusive. Here, we found that dietary succinate elevated the serum succinate levels. Meanwhile, we found succinate increased methyltransferaselike 3 (METTL3) protein expression in brown adipocytes, thereby elevating N⁶-methyladenosine (m⁶A) levels in Hypoxia-inducible factor1-alpha (Hif1a) mRNA. Hif1a mRNA is recognized by the m⁶A-binding protein YTH domain-containing family protein 1 (YTHDF1), facilitating HIF1A protein expression. HIF1A activates the transcription of thermogenic genes, ultimately increasing brown adipose energy expenditure. Together, our research provided new insights into the effect of succinate on m⁶A modification in brown adipose tissue thermogenesis. Full article

Cardiovascular remodeling, encompassing vascular remodeling, myocardial remodeling, and fibrosis-associated tissue remodeling, underlies atherosclerosis, pulmonary hypertension, myocardial infarction, myocardial fibrosis, and other cardiovascular diseases. Its regulation has traditionally been studied through transcriptional, inflammatory, metabolic, mechanical, and intercellular signaling mechanisms. Recent advances in epitranscriptomics have identified N6-methyladenosine (m⁶A) RNA methylation as an additional post-transcriptional layer that interacts with microRNA (miRNA) pathways during cardiovascular disease progression. This review summarizes current evidence for m⁶A-miRNA crosstalk in cardiovascular remodeling, focusing on epitranscriptomic checkpoints that regulate miRNA fate, feedback-like regulatory circuits involving miRNAs and the m⁶A machinery, and cell-type-specific programs across endothelial cells, vascular smooth muscle cells, fibroblasts, and cardiomyocytes. We further discuss emerging analytical technologies and translational implications of this regulatory axis. Future studies should clarify causal mechanisms, cell-type and disease-stage specificity, and translational feasibility. Together, this multilayered framework provides a systems-level perspective on how RNA regulatory networks may shape pathological remodeling in cardiovascular disease. Full article

Background/Objectives: N6-methyladenosine (m⁶A) is the most prevalent and functionally significant internal modification within eukaryotic mRNA. While m⁶A is known to be regulated at internal sites by factors such as splice junctions, the mechanisms governing deposition within the cap-proximal region remain poorly understood. This study aims to determine the patterns of m⁶A stoichiometry in cap-proximal regions and to investigate whether the choice of the specific transcription start site (TSS) can affect m⁶A stoichiometry. Methods: We re-analyzed our published single-nucleotide-resolution CROWN-seq data to quantify m⁶A stoichiometry across transcript isoforms with different TSSs, and assessed the relationship between specific TSSs and specific m⁶A sites (“TSS-m⁶A-site pairs”). Results: We established the first single-nucleotide-resolution dataset of m⁶A stoichiometry across the transcriptome in cap proximal regions, including stoichiometry of m⁶A across 5′ isoforms for each gene. We found that m⁶A deposition is markedly inhibited within a narrow cap-proximal region in a distance-sensitive manner. m⁶A sites located close to both 5′ and 3′ exon ends exhibit low methylation due to the overlap between the cap-proximal and 3′ exon-end exclusion zones. Conclusions: We find that the first exon contains a narrow m⁶A exclusion zone at its 5′ end. As a result, cap-proximal m⁶A sites can have different stoichiometries depending on the TSS choice. As the m⁶A site is positioned farther from the TSS, m⁶A stoichiometry increases. These results reveal that TSS switching is a regulatory mechanism for m⁶A stoichiometry in cap-proximal regions and provide a mechanism for fine-tuning gene expression and mRNA fate through isoform-specific m⁶A modification stoichiometry. Full article