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The Myc family is essential for cell proliferation, differentiation, and metabolism, particularly in embryonic development and stem cell functions. However, the specific role of Myc in porcine early embryonic development is not fully understood. This study observed high Myc expression during the four-cell stage of porcine embryos. Inhibition of Myc using 10058-F4 impaired embryonic development, disrupted energy metabolism, and increased DNA methylation. Mechanistically, these effects were dependent on α-KG, a TCA cycle intermediate and cofactor for TET demethylation enzymes. Sequencing analysis of four-cell embryos post- Myc inhibition revealed downregulation of key metabolic enzymes related to α-KG, such as CS, IDH2, leading to reduced α-KG levels. Supplementation with α-Ketoglutarate (α-KG) mitigated the negative effects of Myc inhibition, including lower blastocyst rates, decreased ATP levels, and increased 5 mC levels. In conclusion, Myc regulates the expression of key metabolic enzymes during the four-cell stage, influencing early embryonic metabolism and epigenetic reprogramming. [ABSTRACT FROM AUTHOR]

Background: Head and neck squamous cell carcinoma (HNSCC) has been recognized as the seventh most prevalent malignant tumor globally. It is a malignant neoplasm that arises from the mucosal epithelium of head and neck region. In our previous research, we have demonstrated that MTUS1/ATIP1 exhibits anti-cancer properties in HNSCC. Nevertheless, the underlying mechanism responsible for the reduction of MTUS1/ATIP1 expression has not been investigated. Methods: HNSCC and adjacent normal tissues were collected and examined using m6A MeRIP-seq, qRT-PCR, and IHC to investigate the relationship between MTUS1/ATIP1 and FTO. MeRIP-qPCR, m6A dot blot, RNA and protein stability assays, and RNC-qRT-PCR were employed to elucidate the mechanism by which FTO mediates demethylation of MTUS1/ATIP1 in HNSCC. Functional assays, subcutaneous tumorigenesis, and in situ tongue cancer models were conducted to assess the impact of the FTO-MTUS1/ATIP1 pathway on proliferative capacity of HNSCC tumors. Results: FTO was observed to be markedly upregulated and showed a negative correlation with MTUS1/ATIP1 expression in HNSCC. FTO was responsible for mediating m6A demethylation in the 3'UTR of MTUS1/ATIP1, leading to its degradation. Additionally, silencing MTUS1/ATIP1 successfully reversed the tumor-promoting effects on HNSCC triggered by FTO in in vitro and in vivo. Conclusions: Our research elucidated the functional importance of FTO-mediated m6A demethylation of MTUS1/ATIP1, suggesting that targeting the FTO-MTUS1/ATIP1 axis could be a prospective novel approach for treating HNSCC. [ABSTRACT FROM AUTHOR]

The frequencies and lengths of drought periods are increasing in subtropical and temperate regions worldwide. Epigenetic responses to water stress could be key for plant resilience to these largely unpredictable challenges. Experimental DNA demethylation, together with application of a stress factor is an appropriate strategy to reveal the contribution of epigenetics to plant responses to stress.We analysed leaf cytosine methylation changes in adult plants of the annual Mediterranean herb, Erodium cicutarium, in a greenhouse, after seed demethylation with 5‐Azacytidine and/or recurrent water stress. We used bisulfite RADseq (BsRADseq) and a newly reported reference genome for E. cicutarium to characterize methylation changes in a 2 × 2 factorial design, controlling for plant relatedness.In the long term, 5‐Azacytidine treatment alone caused both hypo‐ and hyper‐methylation at individual cytosines, with substantial hypomethylation in CG contexts. In control conditions, drought resulted in a decrease in methylation in all but CHH contexts. In contrast, the genome of plants that experienced recurrent water stress and had been treated with 5‐Azacytidine increased DNA methylation level by ca. 5%.Seed demethylation and recurrent drought produced a highly significant interaction in terms of global and context‐specific cytosine methylation. Most methylation changes occurred around genic regions and within Transposable Elements. The annotation of these Differentially Methylated Regions associated with genes included several with a potential role in stress responses (e.g., PAL, CDKC, and ABCF), confirming an epigenetic contribution in response to stress at the molecular level. [ABSTRACT FROM AUTHOR]

Cercospora leaf spot (CLS) disease caused by the ascomycete Cercospora beticola is the most widespread fungal leaf disease in sugar beet. Fungicides of two active ingredient classes, quinone-outside inhibitors (QoIs) and demethylation inhibitors (DMIs), were important tools for CLS control. Over the years, C. beticola has become resistant to QoIs and a sensitivity shift has been reported for DMIs. In this study, the mechanisms causing variation in DMI sensitivity in C. beticola isolates from Europe were analyzed. The CYP51 mutations I387M, Y464S, and L144F were detected in many isolates, and most isolates carried the L144F in combination with mutation I309T. Furthermore, single isolates with other mutation combinations have been found. Wildtype isolates were found in low frequency in all European countries. Isolates that contained L144F showed higher EC50 values than those without L144F. Ranges of EC50 values of different CYP51 haplotypes were overlapping, an indication that other resistance mechanisms are present. Mutation L144F is more frequently encoded by codon TTC (96%) than by TTT (4%), and the usage of codon TTC was correlated with increased EC50 values, this being more pronounced for difenoconazole than for mefentrifluconazole. In addition, it could be observed that the usage of codon GAG for E at amino acid position 170, instead of GAA, was more frequently found in isolates with a higher adaptation compared with haplotypes that did not contain L144F. Overall, GAA was present in 67% of all isolates and GAG in 33%, with an unequal distribution within the haplotypes. These data indicate that target site mutations, especially L144F haplotypes, influence DMI sensitivity and that in L144F haplotypes, L144F codon usage might be responsible for variations within L144F haplotypes. The codon usage for E170 may influence sensitivity and increase EC50 variation of wildtype isolates and isolates with "weak" mutations, but not in L144F haplotypes. [ABSTRACT FROM AUTHOR]

Marine prokaryotes are involved in mercury (Hg) speciation in marine environments. However, information regarding the specific microbial lineages contributing to Hg speciation (namely, methylation, demethylation, and reduction) in seawater remains limited. In this study, we investigated the genes involved in methylmercury (MeHg) demethylation (merB), Hg reduction (merA), and Hg methylation (hgcA and hgcB) using a metagenome analysis encompassing free-living (FL; 0.2–3 µm) and particle-attached (PA; > 3 µm) fractions in April and June in Minamata Bay, Japan. We analyzed the total Hg (THg) and MeHg concentrations in dissolved, small particulate (0.2–3 µm), and large particulate (> 3 µm) fractions. Hg analysis showed no significant differences in THg and MeHg concentrations among the three fractions. However, THg and MeHg in the pooled particulate (fractions were higher than those in the dissolved fractions) in June. As for the Hg-related genes, a high merB abundance rather than merA was observed when compared using all samples, suggesting that microbial MeHg demethylation could be prominent rather than Hg reduction in the seawater column. Phylogenetic analyses revealed that Alphaproteobacteria and Actinobacteria were dominant in the total merA and merB-like sequences, respectively. For both merA and merB genes, some lineages appeared in either or both FL and PA fractions. A deltaproteobacteria-like hgcA was also detected in the PA fraction in April. Therefore, the link between distinct phylogenetic lineages within the PA and FL fractions could be significant for Hg speciation in Minamata Bay. [ABSTRACT FROM AUTHOR]

1. Valgus-varus deformity (VVD) is a disease that severely affects leg function in broilers and for which there is no effective control method current available. Although DNA methylation has an important impact on most physiological and pathological processes, its involvement in skeletal muscle growth and development in VVD broilers is unknown. In this study, genome-wide DNA methylation was analysed in VVD-affected and normal broilers using whole genome resulphite sequencing.2. The results showed that in the cytosine-phosphoric acid-guanine (CG) sequence environment there was a methylation rate of about 55% and 4,265 differentially methylated regions (DMRs) were found in the CG. Of these, 550 were located in the promoter, 547 in the exon region, and 1,718 in the intron region.3. All differentially methylated genes (DMGs) were analysed for enrichment of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The GO was enriched in pathways related to protein degradation such as proteasome complex, endopeptidase complex and extracellular region. The KEGG pathways were enriched in signalling pathways related to protein degradation and catabolism such as proteasome, nitrogen metabolism, adherens junction and alanine.4. Protein interactions analysis revealed that FOS, MYL9, and FRAS1 had a high degree of interactions, in which the DNA methylation level of the MYL9 promoter region was negatively correlated with mRNA expression level. Further studies showed that 5-azacytidine (5-AzaC) inhibited DNMT1 and DNMT3A gene expression and promoted MYL9 expression.5. This study systematically investigated overall DNA methylation patterns in the leg muscle of VVD and normal broilers. It screened common differential genes in conjunction with transcriptomic data to further identify genes associated with muscle growth and development. This study provides new insights to better understand the pathogenesis of VVD from an epigenetic perspective. [ABSTRACT FROM AUTHOR]

Autophagy is a complex cellular process that can either promote or inhibit cancer progression and development, depending on the context and molecular regulation involved. This study investigates how LSD1 regulates autophagy in ovarian cancer by interacting with the autophagy protein LC3B. Utilizing the bioinformatic analysis of TCGA, CPTAC, and GEO datasets, as well as immunohistochemistry in ovarian cancer patients, we explored the expression association between LSD1 and LC3B. Molecular mechanisms were further analyzed using Western blotting, immunoprecipitation, and GST pull-down assays. Our findings reveal that LSD1 binds to LC3B via its SWIRM domain, and high levels of LSD1 are closely associated with aggressive ovarian cancer and poor patient outcomes. Mechanistically, LSD1 demethylates LC3B, leading to decreased LC3B stability. The observed inverse correlation between LSD1 expression and LC3B protein levels in clinical samples underscores the need for further investigation to elucidate how reduced LC3B protein levels induced by LSD1 demethylation may contribute to ovarian cancer. [ABSTRACT FROM AUTHOR]

Histone lysine demethylase 4 A (KDM4A), a non‐heme Fe(II)/2‐oxoglutarate (2OG) dependent oxygenase that catalyzes the demethylation of tri‐methylated lysine residues at the 9, 27, and 36 positions of histone H3 (H3 K9me3, H3 K27me3, and H3 K36me3). These methylated residues show contrasting transcriptional roles; therefore, understanding KDM4A's catalytic mechanisms with these substrates is essential to explain the factors that control the different sequence‐dependent demethylations. In this study, we use molecular dynamics (MD)‐based combined quantum mechanics/molecular mechanics (QM/MM) methods to investigate determinants of KDM4A catalysis with H3 K9me3, H3 K27me3 and H3 K36me3 substrates. In KDM4A‐H3(5–14)K9me3 and KDM4A‐H3(23–32)K27me3 ferryl complexes, the O−H distance positively correlates with the activation barrier of the rate‐limiting step, however in the KDM4A‐H3(32–41)K36me3, no direct one‐to‐one relationship was found implying that the synergistic effects between the geometric parameters, second sphere interactions and the intrinsic electric field contribute for the effective catalysis for this substrate. The intrinsic electric field along the Fe−O bond changes between the three complexes and shows a positive correlation with the HAT activation barrier, suggesting that modulating electric field can be used for fine engineering KDM catalysis with a specific substrate. The results reveal how KDM4A uses a combination of strategies to enable near equally efficient demethylation of different H3Kme3 residues. [ABSTRACT FROM AUTHOR]

Since the mid-1970s, increasingly innovative methods to detect DNA methylation provided detailed information about its distribution, functions, and dynamics. As a result, new concepts were formulated and older ones were revised, transforming our understanding of the associated biology and catalyzing unprecedented advances in biomedical research, drug development, anthropology, and evolutionary biology. In this review, we discuss a few of the most notable advances, which are intimately intertwined with the study of DNA methylation, with a particular emphasis on the past three decades. Examples of these strides include elucidating the intricacies of 5-methylcytosine (5-mC) oxidation, which are at the core of the reversibility of this epigenetic modification; the three-dimensional structural characterization of eukaryotic DNA methyltransferases, which offered insights into the mechanisms that explain several disease-associated mutations; a more in-depth understanding of DNA methylation in development and disease; the possibility to learn about the biology of extinct species; the development of epigenetic clocks and their use to interrogate aging and disease; and the emergence of epigenetic biomarkers and therapies. [ABSTRACT FROM AUTHOR]

Epigenetics plays a pivotal role in regulating gene expression and cellular differentiation. DNA methylation, involving the addition of methyl groups to specific cytosine bases, is a well-known epigenetic modification. The recent discovery of 5-hydroxymethylcytosine (5hmC) has provided new insights into cytosine modifications. 5hmC, derived from the oxidation of 5-methylcytosine (5mC), serves as both an intermediate in demethylation and a stable chemical modification in the genome. In this comprehensive review, we summarize the recent research advancements regarding the functions of 5hmC in development and disease. We discuss its implications in gene expression regulation, cellular differentiation, and its potential role as a diagnostic and prognostic marker in various diseases. Additionally, we highlight the challenges associated with accurately detecting and quantifying 5hmC and present the latest methodologies employed for its detection. Understanding the functional role of 5hmC in epigenetic regulation and further advancing our understanding of gene expression dynamics and cellular processes hold immense promise for the development of novel therapeutic strategies and precision medicine approaches. [ABSTRACT FROM AUTHOR]

The role of oxygen vacancies in enhancing photocatalytic activity has attracted increasing attention. In this work, ZnO nanorods with enriched surface oxygen vacancies were successfully synthesized via a facile hydrothermal process combined with calcination in the presence of urea, and the content of the oxygen vacancies could be tuned by adjusting the calcination temperature and time. The characterization results proved that the content of oxygen vacancies reached 45.47% with a calcination temperature and time of 500 °C and 4 h, respectively. Additionally, the increased oxygen vacancy content was conducive to not only narrowing the ZnO bandgap, but also accelerating the separation and transfer of photoproduced electron–hole pairs, thus enhancing the methylene blue (MB) removal. The maximum removal efficiency of MB reached 97.65% within 120 min under simulated sunlight irradiation, and the catalyst exhibited stable performance after five consecutive cycles. The degradation intermediates of MB determined by liquid chromatograph–mass spectrometer (LC–MS) were the aromatic and ring-opening products of demethylation, desulfurization and hydroxylation. The toxicities of these compounds decreased significantly based on the germination and growth of Vigna radiata. This study provides a controllable and simple strategy for the design of ZnO with abundant oxygen vacancies and high activity in a photocatalytic system under simulated sunlight. [ABSTRACT FROM AUTHOR]

Selenium (Se) serves as a natural detoxifier for the typical toxic heavy metal mercury (Hg), and the interactions between Se and Hg have attracted considerable scholarly attention in the field of Se and Hg. However, there is currently a lack of systematic summaries and discussions about Se–Hg interactions in soil–plant systems. This study summarizes the microscopic processes and macroscopic manifestations of Se–Hg interactions by exploring their characteristics, occurrence and mechanisms, revealing a dual-pump driving mechanism that emphasizes the "soil-root" and "atmosphere-leaf" interface of Se–Hg interactions in soil–plant systems. At the soil–root interface, HS− (H2S), Fe2+ and microorganisms are the key factors that cause the transformation of Se and Hg through oxidation, reduction, methylation and demethylation processes controlled by microbial or abiotic factors. Concurrently, Se reinforces the iron plaque barrier to decrease Hg absorption or to form HgSe complexes to limit Hg transportation into roots. Furthermore, the leaves, as the main plant tissue for Hg/Se uptake and bioaccumulation, are the key sites for the morphological transformation of Hg and Se, where Se–Hg interactions are likely to occur, and thus may constitute the other driving mechanism in the atmosphere–leaf interface. Finally, Se–Hg interactions are outlined after concluding the potential mechanisms, challenges and future research directions. [ABSTRACT FROM AUTHOR]

Ultraviolet (UV) radiation‐triggered production of reactive oxygen species (ROS) is a primary contributor to apoptosis in human lens epithelial cells (HLECs), which can ultimately result in cataract formation. The nuclear factor erythroid‐2‐related factor 2 (Nrf2)‐Kelch ECH associating protein 1 (Keap1) pathway, a fundamental oxidative stress regulation mechanism, plays a crucial role in the development of cataracts. Ferulic acid (FA), recognized for its potent antioxidant properties can activate the Nrf2 signaling pathway to mitigate oxidative damage and cell apoptosis. In this study, we have demonstrated the protective effects of FA in reducing UVA‐induced oxidative damage and apoptosis in HLECs through the modulation of the Keap1/Nrf2 pathway, as evidenced by both cellular and animal experiments. HLECs and Lens were exposed to 10 J/cm2 UVA radiation with or without prior treatment with FA. We found that UVA radiation increased oxidative damage and cell apoptosis in HLECs, ultimately leading to opacification of rat lenses, while FA was able to attenuate both oxidative damage and cell apoptosis in HLECs and reduce the degree of lens opacification. FA upregulated the expression of antioxidant response factors of the Keap1/Nrf2 pathway and downregulated the expression of apoptosis‐related genes in HLECs, as demonstrated by Western blot and RT‐qPCR analyses. We also found that UVA radiation increased the degree of demethylation of the Keap1 promoter in HLECs, whereas FA reduced the level of Keap1 promoter demethylation as determined by DNA sequencing. Additionally, UVA upregulated the expression of DNA active demethylase of the Keap1 promoter in HLECs, Dnmt1, Dnmt3a, and Dnmt3b, as shown by immunofluorescence, Western blot, and RT‐qPCR, however, FA attenuated the activity of the passive demethylase TET1 in addition to the active demethylases. These results demonstrated that UVA radiation can cause oxidative damage, cell apoptosis, and rat lens opacification by increasing the demethylation of the Keap1 promoter in lens epithelial cells. Conversely, FA was shown to reduce oxidative damage, inhibit cell apoptosis, and decrease rat lens opacification by increasing the methylation of the Keap1 promoter. These findings suggest that FA could be therapeutically beneficial in preventing and mitigating cataracts induced by UVA radiation. [ABSTRACT FROM AUTHOR]

Objective: We currently face a sharp increase of T-cell acute lymphoblastic leukemia (T-ALL) incidence and a challenge of unmasking its complex etiology. The deoxycytidine analog 5-Aza-2'-deoxycytidine (5-Aza-dC) is currently the most common nucleoside methyltransferase inhibitor. The objective of this study was to clarify the role of 5-Aza-dC in T-ALL cell biological behaviors and phosphatase and tensin homolog deleted on chromosome ten (PTEN) expression. Material and Methods: T-ALL cell lines were divided into the experimental group with 5-Aza-dC solution treatment, and the control group without treatment. PTEN methylation was detected using methylation-specific polymerase chain reaction (MS-PCR). Following the measurement of cell proliferation, viability, apoptosis, invasion, migration, etc., quantitative reverse transcription-polymerase chain reaction (PCR) was conducted to detect PTEN, DNA methyl-transferases (DNMT1), DNMT3a, MBD2, and MeCP2 expressions; Western blot to detect PTEN, PI3K, AKT, and mTOR protein expressions. In addition, rescue experiments to inhibit and restore the expression of PTEN in different groups were performed for further identification of the results in the former parts. Results: MS-PCR results showed that in Jurkat cells, the target band was amplified using methylated primers for the PTEN gene promoter region; moreover, at 10 μmol/L of 5-Aza-dC for 24 h, PTEN methylation was completely removed without any un-methylated band observed. The experimental group had significantly lower cell proliferation and viability rates, higher apoptosis rates, decreased cell proportion in S phase, reduced invasion and migration; increased PTEN expression, decreased DNMT1, DNMT3a, MBD2, and MeCP2 mRNA expressions; and decreased PI3K, AKT, and mTOR protein expressions than those in the control group (all P < 0.05). Furthermore, according to the rescue experiment, silenced PTEN expression weakened the beneficial roles of 5-Aza-dC treatment, and resulted in significantly higher cell proliferation and viability rates, lower apoptosis rates, increased cell proportion in S phase, increased cell invasion and migration; decreased PTEN expression, elevated DNMT1, DNMT3a, MBD2, and MeCP2 mRNA expressions, and higher PI3K, AKT, and mTOR protein expressions (all P < 0.05). While restored PTEN expression enhanced functions of 5-Aza-dC treatment, leading to obviously lower cell proliferation and viability rates, higher apoptosis rates, increased cell proportion in G1 phase, and reduced cell invasion and migration; as well as increased PTEN expression, decreased DNMT1, DNMT3a, MBD2, and MeCP2 mRNA expressions, and lower PI3K, AKT, and mTOR protein expressions (all P < 0.05). Conclusion: Demethylation treatment with 5-Aza-dC can inhibit T-ALL cell malignant biological behaviors and enhance the sensitivity to chemotherapy agents possibly, which may be related to the inhibited expressions of DNMT1, DNMT3a, MBD2, and MeCP2, and restored expression activity of PTEN to negatively regulate the PI3K/AKT signal transduction. Our silencing and restoration of PTEN expressions further support our findings, highlighting that demethylation with 5-Aza-dC to restore the anti-tumor activity of the tumor suppressor gene PTEN may be a promising therapeutic option for treating T-ALL. [ABSTRACT FROM AUTHOR]

Mercury, particularly in its methylated form, poses a significant environmental and health risk in aquatic ecosystems. While the toxicity and bioaccumulation of mercury are well documented, there remains a critical gap in our understanding of the mechanisms governing mercury methylation and demethylation in aquatic environments. This review systematically examines the complex interplay of chemical, biological, and physical factors that influence mercury speciation and transformation in natural water systems. We provide a comprehensive analysis of methylation and demethylation processes, specifically focusing on the dominant role of methanogenic bacteria. Our study highlights the crucial function of hgcAB genes in facilitating mercury methylation by anaerobic microorganisms, an area that represents a frontier in current research. By synthesizing the existing knowledge and identifying key research priorities, this review offers novel insights into the intricate dynamics of mercury cycling in aquatic ecosystems. Our findings provide a theoretical framework to inform future studies and guide pollution management strategies for mercury and its compounds in aquatic environments. [ABSTRACT FROM AUTHOR]

Okra is a common vegetable in the African cuisine, known for its distinctive slimy texture. Plant cell walls include hydrocolloids, especially pectin, which contribute to their sliminess. This textural property is known to become lost during thermal treatment. In this research, okra hydrocolloid is extracted and used to produce a model medium at a pH of 6.0, representing okra's natural state. This medium is subjected to various controlled thermal treatments (70–130 °C) to evaluate their impact on pectin degradation. At the same time, the texture of okra puree is also assessed using an instrumental method under the same conditions. The two main products of pectin degradation—reducing end sugars from depolymerization and methanol from a demethylation—are measured and found to show an increase as a function of time and temperature. Kinetic modeling indicates that a first-order reaction fits well with the experimental concentrations of both products. The rate constants, as a function of temperature, aligns with the Arrhenius model, confirming the chemical basis of the degradation. Instrumental results correlate well with the production of methanol and reducing end sugars, indicating that pectin degradation is the primary cause of texture changes during the thermal treatment of okra and that this change can be controlled by adjusting the temperature. [ABSTRACT FROM AUTHOR]

Abstract Background Head and neck squamous cell carcinoma (HNSCC) has been recognized as the seventh most prevalent malignant tumor globally. It is a malignant neoplasm that arises from the mucosal epithelium of head and neck region. In our previous research, we have demonstrated that MTUS1/ATIP1 exhibits anti-cancer properties in HNSCC. Nevertheless, the underlying mechanism responsible for the reduction of MTUS1/ATIP1 expression has not been investigated. Methods HNSCC and adjacent normal tissues were collected and examined using m6A MeRIP-seq, qRT-PCR, and IHC to investigate the relationship between MTUS1/ATIP1 and FTO. MeRIP-qPCR, m6A dot blot, RNA and protein stability assays, and RNC-qRT-PCR were employed to elucidate the mechanism by which FTO mediates demethylation of MTUS1/ATIP1 in HNSCC. Functional assays, subcutaneous tumorigenesis, and in situ tongue cancer models were conducted to assess the impact of the FTO-MTUS1/ATIP1 pathway on proliferative capacity of HNSCC tumors. Results FTO was observed to be markedly upregulated and showed a negative correlation with MTUS1/ATIP1 expression in HNSCC. FTO was responsible for mediating m6A demethylation in the 3’UTR of MTUS1/ATIP1, leading to its degradation. Additionally, silencing MTUS1/ATIP1 successfully reversed the tumor-promoting effects on HNSCC triggered by FTO in in vitro and in vivo. Conclusions Our research elucidated the functional importance of FTO-mediated m6A demethylation of MTUS1/ATIP1, suggesting that targeting the FTO-MTUS1/ATIP1 axis could be a prospective novel approach for treating HNSCC.

N-6 methyladenosine is the most abundant nucleic acid modification in eukaryotes and plays a crucial role in gene regulation. The AlkB family of alpha-ketoglutarate-dependent dioxygenases is responsible for nucleic acid demethylation. Recent studies have discovered that a chemical demethylation system using hydrogen peroxide and ammonium bicarbonate can effectively demethylate nucleic acids. The addition of ferrous ammonium sulfate boosts the oxidation rate by forming a Fenton reagent with hydrogen peroxide. However, the specific mechanism and key steps of this process remain unclear. In this study, we investigate the influence of ferrous ammonium sulfate concentration on the kinetic isotope effect (KIE) of the chemical demethylation system using LC-MS. As the concentration of ferrous ions increases, the observed KIE decreases from 1.377 ± 0.020 to 1.120 ± 0.016, indicating a combination of the primary isotope effect and inverse α-secondary isotope effect with the ion pairing effect. We propose that the initial hydrogen extraction is the rate-limiting step and observe a tight transition state structure in the formation of the hm6A process through the analysis of KIE trends. The concentration-dependent KIE provides a novel perspective on the mechanism of chemical demethylation and offers a chemical model for enzyme-catalyzed demethylation. [ABSTRACT FROM AUTHOR]

DNA methylation is environment-sensitive and can mediate stress responses. In trees, changes in the environment might cumulatively shape the methylome landscape over time. However, because high-resolution methylome studies usually focus on single environmental cues, the stress-specificity and long-term stability of methylation responses remain unclear. Here, we studied the methylome plasticity of a Populus nigra cv. 'Italica' clone widely distributed across Europe. Adult trees from different geographic locations were clonally propagated in a common garden experiment and exposed to cold, heat, drought, herbivory, rust infection, and salicylic acid treatments. Whole-genome bisulfite sequencing revealed stress-induced and naturally occurring DNA methylation variants. In CG/CHG contexts, the same genomic regions were often affected by multiple stresses, suggesting a generic methylome response. Moreover, these variants showed striking overlap with naturally occurring methylation variants between trees from different locations. Drought treatment triggered CHH hypermethylation of transposable elements, affecting entire superfamilies near drought-responsive genes. Thus, we revealed genomic hotspots of methylation change that are not stress-specific and that contribute to natural DNA methylation variation, and identified stress-specific hypermethylation of entire transposon superfamilies with possible functional consequences. Our results underscore the importance of studying multiple stressors in a single experiment for recognizing general versus stress-specific methylome responses. [ABSTRACT FROM AUTHOR]

Although arginine methylation (R-methylation) is one of the most important post-translational modifications (PTMs) conserved in eukaryotes, it has not been studied to the same extent as phosphorylation and ubiquitylation. Technical constraints, which are in the process of being resolved, may partly explain this lack of success. Our knowledge of R-methylation has recently evolved considerably, particularly in metazoans, where misregulation of the enzymes that deposit this PTM is implicated in several diseases and cancers. Indeed, the roles of R-methylation have been highlighted through the analyses of the main actors of this pathway: the PRMT writer enzymes, the TUDOR reader proteins, and potential "eraser" enzymes. In contrast, R-methylation has been much less studied in plants. Even so, it has been shown that R-methylation in plants, as in animals, regulates housekeeping processes such as transcription, RNA silencing, splicing, ribosome biogenesis, and DNA damage. R-methylation has recently been highlighted in the regulation of membrane-free organelles in animals, but this role has not yet been demonstrated in plants. The identified R-met targets modulate key biological processes such as flowering, shoot and root development, and responses to abiotic and biotic stresses. Finally, arginine demethylases activity has mostly been identified in vitro, so further studies are needed to unravel the mechanism of arginine demethylation. [ABSTRACT FROM AUTHOR]

Both DNA 5-methylcytosine (5mC) and RNA N6-methyladenosine (m6A) modifications are reported to participate in cellular stress responses including inflammation. Phosphoenolpyruvate carboxykinase 2 (PCK2) is upregulated in Kupffer cells (KCs) to facilitate the proinflammatory phosphorylation signaling cascades upon LPS stimulation, yet the role of 5mC and m6A in PCK2 upregulation remain elusive. Here, we report that the significantly augmented PCK2 mRNA and protein levels are associated with global 5mC demethylation coupled with m6A hypermethylation in LPS-activated KCs. The suppression of 5mC demethylation or m6A hypermethylation significantly alleviates the upregulation of PCK2 and proinflammatory cytokines in LPS-challenged KCs. Further reciprocal tests indicate 5mC demethylation is upstream of m6A hypermethylation. Specifically, CpG islands in the promoters of PCK2 and RNA methyltransferase (METTL3 and METTL14) genes are demethylated, while the 3′UTR of PCK2 mRNA is m6A hypermethylated, in LPS-stimulated KCs. These modifications contribute to the transactivation of the PCK2 gene as well as increased PCK2 mRNA stability and protein production via a m6A-mediated mechanism with IGF2BP1 as the reader protein. These results indicate that DNA 5mC and RNA m6A collaborate to upregulate PCK2 expression, respectively, at the transcriptional and post-transcriptional levels during KC activation. [ABSTRACT FROM AUTHOR]

Background: Elevated extracellular matrix (ECM) accumulation is a major contributing factor to the pathogenesis of fibrotic diseases. Recent studies have indicated that N6‐methyladenosine (m6A) RNA modification plays a pivotal role in modulating RNA stability and contribute to the initiation of various pathological conditions. Howbeit, the precise mechanism by which m6A influences ECM deposition remains unclear. Methods: In this study, we used hypertrophic scars (HTSs) as a paradigm to investigate ECM‐related diseases. We focused on the role of ALKBH5‐mediated m6A demethylation within the pathological progression of HTSs and examined its correlation with clinical stages. The effects of ALKBH5 ablation on ECM components were studied both in vivo and in vitro. Downstream targets of ALKBH5, along with their underlying mechanisms, were identified using integrated high‐throughput analysis, RNA‐binding protein immunoprecipitation and RNA pull‐down assays. Furthermore, the therapeutic potential of exogenous ALKBH5 overexpression was evaluated in fibrotic scar models. Results: ALKBH5 was decreased in fibroblasts derived from HTS lesions and was negatively correlated with their clinical stages. Importantly, ablation of ALKBH5 promoted the expression of COL3A1, COL1A1, and ELN, leading to pathological deposition and reconstruction of the ECM both in vivo and in vitro. From a therapeutic perspective, the exogenous overexpression of ALKBH5 significantly inhibited abnormal collagen deposition in fibrotic scar models. As determined by integrated high‐throughput analysis, key ECM components including COL3A1, COL1A1, and ELN are direct downstream targets of ALKBH5. By means of its mechanism, ALKBH5 inhibits the expression of COL3A1, COL1A1, and ELN by removing m6A from mRNAs, thereby decreasing their stability in a YTHDF1‐dependent manner. Conclusions: Our study identified ALKBH5 as an endogenous suppressor of pathological ECM deposition, contributing to the development of a reprogrammed m6A‐targeted therapy for HTSs. [ABSTRACT FROM AUTHOR]

The collection, storage, and transport of samples prior to and during analysis is of utmost importance, especially for highly potent analogs that may not be present in high concentrations and are susceptible to pH or thermally mediated degradation. An accelerated stability study was performed on 17 fentanyl analogs (fentalogs) over a wide range of pH (2–10) and temperature (20–60°C) conditions over 24 h. Dilute aqueous systems were used to investigate temperature and pH‐dependent kinetics using liquid chromatography–tandem mass spectrometry (LC–MS/MS). Liquid chromatography‐quadrupole/time‐of‐flight‐mass spectrometry (LC‐Q/TOF–MS) was used for structural elucidation of degradants. With the exception of remifentanil, all fentalogs evaluated were stable at pH 6 or lower. Fentalogs were generally unstable in strongly alkaline environments and at elevated temperatures. Remifentanil was the least stable drug and N‐dealkylated fentalogs were the most stable. Fentanyl degraded to acetylfentanyl, norfentanyl, fentanyl N‐oxide, and 1‐phenethylpyridinium salt (1‐PEP). A total of 26 unique breakdown products were observed for 15 of the fentanyl derivatives studied. Common degradation pathways involved N‐dealkylation, oxidation of the piperidine nitrogen, and β‐elimination of N‐phenylpropanamide followed by oxidation/dehydration of the piperidine ring. Ester and amide hydrolysis, demethylation at the propanamide, and O‐demethylation were observed for selected fentalogs only. The potential for analyte loss should be considered during the pre‐analytical phase (i.e., shipping and transport) where environmental conditions may not be controlled, as well as during the analysis itself. [ABSTRACT FROM AUTHOR]

Prostate cancer (PCa) is one of the most common and prevalent cancers in men worldwide. The majority of PCa-related deaths result from metastasis rather than primary tumors. Several studies have focused on the relationship between male-specific genes encoded on the Y chromosome and PCa metastasis; however, the relationship between the male specific protein encoded on the Y chromosome and tumor suppression has not been fully clarified. Here, we report a male specific protein of this type, the histone H3 lysine 4 (H3K4) demethylase JARID1D, which has the ability to inhibit the gene expression program related to cell invasion, and can thus form a phenotype that inhibits the invasion of PCa cells. However, JARID1D exhibits low expression level in advanced PCa, and which is related to rapid invasion and metastasis in patients with PCa. Curcumin, as a multi-target drug, can enhance the expression and demethylation activity of JARID1D, affect the androgen receptor (AR) and epithelial-mesenchymal transition (EMT) signaling cascade, and inhibit the metastatic potential of castration resistant cancer (CRPC). These findings suggest that using curcumin to increase the expression and demethylation activity of JARID1D may be a feasible strategy to inhibit PCa metastasis by regulating EMT and AR. Highlights: Knockdown of JARID1D can enhance the invasion and metastasis ability of prostate cancer cells. Curcumin improves the expression and demethylation activity of JARID1D. Curcumin can stimulate the JARID1D/AR/EMT signaling cascade through demethylation to inhibit the metastatic potential of castration-resistant prostate cancer. [ABSTRACT FROM AUTHOR]

Utilizing kraft technical lignin to produce value-added products is one of the obstacles associated with kraft mill work as an operational biorefinery. The objective of this work was to evaluate chemical modification in eucalypt kraft lignin after heat treatment of black liquor. To prove possible structural changes, advanced analytical tools were used, such as pyrolysis coupled to gas chromatography and mass spectrometry (Py-GC/MS), Fourier transform infrared spectroscopy (FTIR), and two-dimensional nuclear magnetic resonance spectroscopy (2D NMR). Kraft lignins extracted from heat-treated liquors compared with the untreated liquors showed a high total lignin content, varying between 96.4 and 98.3 %, and a lower content of sugars and ash. Py-GC/MS, FTIR and 2D NMR analyses showed interesting modification on the lignin structure, such as a reduction in S-type and G-type lignin and an increase in H-type and Ca-type lignin with heat treatment of the black liquor. The heat treatment of the black liquor proved to be efficient in the chemical modification of the extracted kraft lignins. Demethylation and demethoxylation reactions occurred and they generated kraft lignin with free phenolic groups and that were rich in catechol groups. [ABSTRACT FROM AUTHOR]

Ultrasound‐assisted extraction of pectin from Saba banana (Musa acuminata x balbisiana (BBB Group) "Saba") peels produced crude pectin that requires further purification. Two downstream processes (alcohol washing (AW) and acid demethylation (AD)) were compared. AW involved gelatinous precipitate washing with 85% alcohol and pressing to squeeze out liquids, while AD involved a sequential AW of the dried pectin with 60% acidified alcohol, and 60% and 95% alcohol solutions. Results showed that both methods produced low methoxyl pectins with similar color, yield, and moisture content, with no significant (p > 0.05) differences observed. AD, however, produced pectin with better quality in terms of ash content and anhydrouronic acid (AUA) content relative to the control. Fourier transform infrared spectra revealed that the samples contain ‐OH, C‐H, COO−, COO, and C‐O groups, but only AD has COO‐R due to structural modification. Overall, AD has the potential to improve the quality of crude ultrasound‐extracted pectin from Saba banana peels. Yet, pre‐extraction processing methods are necessary to meet FAO color standards for pectin. [ABSTRACT FROM AUTHOR]

Histone deacetylases 1 and 2 play a major role in the transcriptional regulation of T-regulatory (Treg) cells via interactions with a myriad of coregulatory factors. Sin3a has been well established as a Hdac1/2 cofactor, while its role within Tregs has not been established. In this study, the effects of conditional deletion of Sin3a within Foxp3+ Tregs were evaluated. Developmental deletion of Sin3a from Foxp3+ Tregs resulted in the rapid onset of fatal autoimmunity. Treg numbers were greatly reduced, while residual Tregs had impaired suppressive function. Mice also showed effector T-cell activation, autoantibody production, and widespread tissue injury. Mechanistically, Sin3a deletion resulted in decreased transcription of Foxp3 with a complete lack of CNS2 CpG demethylation. In addition, Foxp3 protein stability was impaired with an increased ex-Treg population. Thus, Sin3a plays a critical role in the maintenance of Treg identity and function and is essential for the expression and stability of Foxp3. [ABSTRACT FROM AUTHOR]

The human alkylation B (AlkB) homologs, ALKBH2 and ALKBH3, respond to methylation damage to maintain genomic integrity and cellular viability. Both ALKBH2 and ALKBH3 are direct reversal repair enzymes that remove 1-methyladenine (1meA) and 3-methylcytosine (3meC) lesions commonly generated by alkylating chemotherapeutic agents. Thus, the existence of deficiencies in ALKBH proteins can be exploited in synergy with chemotherapy. In this study, we investigated possible interactions between ALKBH2 and ALKBH3 with other proteins that could alter damage response and discovered an interaction with the mismatch repair (MMR) system. To test whether the lack of active MMR impacts ALKBH2 and/or ALKBH3 response to methylating agents, we generated cells deficient in ALKBH2, ALKBH3, or both in addition to Mlh homolog 1 (MLH1), another MMR protein. We found that MLH1koALKBH3ko cells showed enhanced resistance toward SN1- and SN2-type methylating agents, whereas MLH1koALKBH2ko cells were only resistant to SN1-type methylating agents. Concomitant loss of ALKBH2 and ALKBH3 (ALKBH2ko3ko) rendered cells sensitive to SN1- and SN2-agents, but the additional loss of MLH1 enhanced resistance to both types of damage. We also showed that ALKBH2ko3ko cells have an ATR-dependent arrest at the G2/M checkpoint, increased apoptotic signaling, and replication fork stress in response to methylation. However, these responses were not observed with the loss of functional MLH1 in MLH1koALKBH2ko3ko cells. Finally, in MLH1koALKBH2ko3ko cells, we observed elevated mutant frequency in untreated and temozolomide treated cells. These results suggest that obtaining a more accurate prognosis of chemotherapeutic outcome requires information on the functionality of ALKBH2, ALKBH3, and MLH1. [ABSTRACT FROM AUTHOR]

A new method for the intramolecular electrophilic ipso -cyclization of alkynes with triflic anhydride-activated sulfoxides, followed by demethylation with triethylamine in one pot, is described for the synthesis of 3-thiospiro[4.5]-decatrienones in moderate to good yields. This method provides a facile strategy for assembling the sulfur-substituted spirocyclic compounds. [ABSTRACT FROM AUTHOR]

Rice bakanae disease (RBD) is a typical seed-borne fungal disease caused by Fusarium fujikuroi. Prochloraz is a sterol demethylation inhibitor, which is among the most important classes of active ingredients for the management of RBD. In 2022, the total resistance frequency of F. fujikuroi to prochloraz in Zhejiang Province was 62.67%. The fitness of the prochloraz-resistant population was lower than that of the susceptible population, but its pathogenicity was slightly stronger. The S312T and F511S double mutations of Ffcyp51b were detected in the resistant isolates. Loop-mediated isothermal amplification (LAMP) technology based on S312T was established to rapidly determine prochloraz resistance in F. fujikuroi. LAMP primer mismatch design was performed based on the cyp51b gene, and 100–300 bp sequences containing a mutation at codon 312 were amplified. In a 25 µL reaction tube, 1 pg/µL DNA of F. fujikuroi could be detected. The detection limit for the frequency of prochloraz resistance was 0.498% using this method. We performed LAMP detection on rice seedlings inoculated with prochloraz-sensitive and -resistant isolates and treated them with prochloraz. Prochloraz demonstrated good control in rice seedlings. A chromogenic reaction was observed in seedlings treated with prochloraz-resistant isolates, and the results were verified using electrophoresis. It has been demonstrated that LAMP technology based on the S312T genotype can quickly and specifically detect prochloraz-resistant isolates in rice seedlings. [ABSTRACT FROM AUTHOR]

Chronic pain is a prevalent condition with a multifaceted pathogenesis, where epigenetic modifications, particularly DNA methylation, might play an important role. This review delves into the intricate mechanisms by which DNA methylation and demethylation regulate genes associated with nociception and pain perception in nociceptive pathways. We explore the dynamic nature of these epigenetic processes, mediated by DNA methyltransferases (DNMTs) and ten-eleven translocation (TET) enzymes, which modulate the expression of pro- and anti-nociceptive genes. Aberrant DNA methylation profiles have been observed in patients with various chronic pain syndromes, correlating with hypersensitivity to painful stimuli, neuronal hyperexcitability, and inflammatory responses. Genome-wide analyses shed light on differentially methylated regions and genes that could serve as potential biomarkers for chronic pain in the epigenetic landscape. The transition from acute to chronic pain is marked by rapid DNA methylation reprogramming, suggesting its potential role in pain chronicity. This review highlights the importance of understanding the temporal dynamics of DNA methylation during this transition to develop targeted therapeutic interventions. Reversing pathological DNA methylation patterns through epigenetic therapies emerges as a promising strategy for pain management. [ABSTRACT FROM AUTHOR]

Background: Aberrant DNA methylation alterations are implicated in amyotrophic lateral sclerosis (ALS). Nevertheless, the influence of genetic variants in genes regulating DNA methylation on ALS patients is not well understood. Therefore, we aim to provide a comprehensive variant profile of genes related to DNA methylation (DNMT1, DNMT3A, DNMT3B, DNMT3L) and demethylation (TET1, TET2, TET3, TDG) and to investigate the association of these variants with ALS. Methods: Variants were screened in a cohort of 2240 ALS patients from Southwest China, using controls from the Genome Aggregation Database (n = 9976) and the China Metabolic Analytics Project (n = 10,588). The over-representation of rare variants and their association with ALS risk were evaluated using Fisher's exact test with Bonferroni correction at both allele and gene levels. Kaplan–Meier analysis and Cox regression analysis were employed to explore the relationship between variants and survival. Results: A total of 210 variants meeting the criteria were identified. Gene-based burden analysis identified a significant increase in ALS risk associated with rare variants in the TET2 gene (OR = 1.95, 95% CI = 1.29–2.88, P = 0.001). Survival analysis demonstrated that patients carrying variants in demethylation-related genes had a higher risk of death compared to those with methylation-related gene variants (HR = 1.29, 95% CI = 1.03–1.86, P = 0.039). Conclusions: This study provides a genetic variant profile of genes involved in DNA methylation and demethylation regulation, along with the clinical characteristics of ALS patients carrying these variants. The findings offer genetic evidence implicating disrupted DNA methylation dynamics in ALS. [ABSTRACT FROM AUTHOR]

Electron-rich pyridines with π donor groups at the para position play an important role as nucleophiles in organocatalysis, but their ligand properties and utilization in coordination chemistry have received little attention. Herein, we report the synthesis of two electron-rich pyridines 1 and 2 bearing N-heterocyclic imine groups at the para position and explore their coordination chemistry. Experimental and computational methods were used to assess the donor ability of the new pyridines showing that they are stronger donors than aminopyridines and guanidinyl pyridines, and that the nature of the N-heterocyclic backbone has a strong influence on the pyridine donor strength. Coordination compounds with Lewis acids including the CO2, SO2, BCl3 and PdII ions were synthesized and characterized. Despite the ambident character of the new pyridines, coordination preferentially occurs at the pyridine-N atom. Methyl transfer experiments reveal that 1 and 2 can act as demethylation reagents. [ABSTRACT FROM AUTHOR]

• Two-hit model of schizophrenia-induced hippocampal Slc6a4 promoter methylation. • EE over 50 days alleviated sensorimotor gating deficits and working memory impairments in mice exposed to the two-hit. • EE normalized hippocampal Iba-1 expression induced by the two-hit model pointing to a reduction in microglial activation. • Hippocampal Slc6a4 promoter demethylation was observed in two-hit animals subjected to EE. Here, we explored the impact of prolonged environmental enrichment (EE) on behavioral, neurochemical, and epigenetic changes in the serotonin transporter gene in mice subjected to a two-hit schizophrenia model. The methodology involved administering the viral mimetic PolyI:C to neonatal Swiss mice as a first hit during postnatal days (PND) 5–7, or a sterile saline solution as a control. At PND21, mice were randomly assigned either to standard environment (SE) or EE housing conditions. Between PND35-44, the PolyI:C-treated group was submitted to various unpredictable stressors, constituting the second hit. Behavioral assessments were conducted on PND70, immediately after the final EE exposure. Following the completion of behavioral assessments, we evaluated the expression of proteins in the hippocampus that are indicative of microglial activation, such as Iba-1, as well as related to neurogenesis, including doublecortin (Dcx). We also performed methylation analysis on the serotonin transporter gene (Slc6a4) to investigate alterations in serotonin signaling. The findings revealed that EE for 50 days mitigated sensorimotor gating deficits and working memory impairments in two-hit mice and enhanced their locomotor and exploratory behaviors. EE also normalized the overexpression of hippocampal Iba-1 and increased the expression of hippocampal Dcx. Additionally, we observed hippocampal demethylation of the Slc6a4 gene in the EE-exposed two-hit group, indicating epigenetic reprogramming. These results contribute to the growing body of evidence supporting the protective effects of long-term EE in counteracting behavioral disruptions caused by the two-hit schizophrenia model, pointing to enhanced neurogenesis, diminished microglial activation, and epigenetic modifications of serotonergic pathways as underlying mechanisms. [ABSTRACT FROM AUTHOR]

Introduction: Epigenetics play a vital role in stratifying CNS tumors and gliomas. The importance of studying Secreted frizzled-related protein 4 (SFRP4) in gliomas is to improve diffuse glioma methylation profiling. Here we examined the methylation status of SFRP4 promoter and the level of its protein expression in diffuse gliomas WHO grades 2-4. Methods: SFRP4 expression was detected by immunohistochemistry and evaluated semi-quantitatively. In the tumor hot-spot area, the intensity of protein expression in 200 cells was determined using ImageJ (National Institutes of Health, United States). The assessment of immunopositivity was based on the IRS score (Immunoreactivity Score). Promoter methylation was examined by methylation specific-PCR (MSP) in fifty-one diffuse glioma samples and appropriate controls. Isolated DNA was treated with bisulfite conversion and afterwards used for MSP. Public databases (cBioPortal, COSMIC and LOVD) were searched to corroborate the results. Results and discussion: SFRP4 protein expression in glioblastomas was very weak or non-existent in 86.7% of samples, moderate in 13.3%, while strong expression was not observed. The increase in astrocytoma grade resulted in SFRP4 protein decrease (p = 0.008), indicating the loss of its antagonistic role in Wnt signaling. Promoter methylation of SFRP4 gene was found in 16.3% of cases. Astrocytomas grade 2 had significantly more methylated cases compared to grade 3 astrocytomas (p = 0.004) and glioblastomas (p < 0.001), which may indicate temporal niche of methylation in grade 2. Furthermore, the expression levels of SFRP4 were high in samples with methylated SFRP4 promoter and low or missing in unmethylated cases (Pearson's R = -0.413; p = 0.003). We also investigated the association of SFRP4 changes to key Wnt regulators GSK3β and DKK3 and established a positive correlation between methylations of SFRP4 and GSK3β (Pearson's R = 0.323; p = 0.03). Furthermore, SFRP4 expression was correlated to unmethylated DKK3 (Chi square = 7.254; p = 0.027) indication that Wnt signaling antagonist is associated to negative regulator's demethylation. Conclusion: The study contributes to the recognition of the significance of epigenetic changes in diffuse glioma indicating that restoring SFRP4 protein holds potential as therapeutic avenue. Reduced expression of SFRP4 in glioblastomas, not following promoter methylation pattern, suggests another mechanism, possible global methylation, that turns off SFRP4 expression in higher grades. [ABSTRACT FROM AUTHOR]

Background: N1-Methyladenosine (m1A) is an abundant modification of transcripts regulating mRNA structure and translation efficiency. However, the characteristics and biological functions of mRNA m1A modification in adult hippocampal neurogenesis remain enigmatic. Results: We found that m1A demethylase Alkbh3 was dramatically enriched in neurons and neuronal genesis. Functionally, depletion of Alkbh3 in neural stem cells (NSCs) significantly decreased m1A modification, neuronal differentiation and proliferation coupling with increasing gliogenesis, whereas overexpressing Alkbh3 facilitated neuronal differentiation and proliferation. Mechanistically, the m1A demethylation of Mmp15 mRNA by Alkbh3 improved its RNA stability and translational efficacy, which promoted neurogenesis. Therapeutically, the silencing of Alkbh3 reduced hippocampal neurogenesis and impaired spatial memory in the adult mice. Conclusions: We reveal a novel function of m1A demethylation on Mmp15 mRNA in Alkbh3-mediated neurogenesis, which shed light on advancing Alkbh3 regulation of neurogenesis as a novel neurotherapeutic strategy. [ABSTRACT FROM AUTHOR]

New 2‐(di)methoxythienyl substituted ligands of the 2,2′‐bipyridine series containing various aromatic substituents at the C3 position were obtained in yields of up to 90 %. A "1,2,4‐triazine" methodology involving an SNH reaction in 1,2,4‐triazine followed by an aza‐Diels‐Alder reaction with 2,5‐norbornadiene was used to synthesize the target compounds. When the Diels‐Alder reaction was carried out in an autoclave, an unexpected demethylation reaction was observed, leading to the formation of oxo‐thienyl substituted products. A mechanism for the reaction that occurred has been proposed on the basis of identified byproducts. Preliminary studies on the photophysical and coordination properties of the obtained compounds were also carried out. In particular, the possibility of obtaining a platinum(II) complex with the demethylation product was demonstrated. [ABSTRACT FROM AUTHOR]

DNA methylation is an important molecular modification that plays a key role in the expression of cancer genes. Evaluation of epigenetic changes, hypomethylation and hypermethylation, in specific genes are applied for cancer diagnosis. Numerous studies have concentrated on describing DNA methylation patterns as biomarkers for cancer diagnosis monitoring and predicting response to cancer therapy. Various techniques for detecting DNA methylation status in cancers are based on sodium bisulfite treatment. According to the application of these methods in research and clinical studies, they have a number of advantages and disadvantages. The current review highlights sodium bisulfite treatment-based techniques, as well as, the advantages, drawbacks, and applications of these methods in the evaluation of human cancers. [ABSTRACT FROM AUTHOR]

Deoxynivalenol (DON) is a prevalent toxin causing severe liver damage through hepatocellular oxidative stress. However, the underlying mechanisms and effective therapeutic approaches remain unknown. Here, the unique role of the xenobiotic metabolism factor pregnane X receptor (PXR) in mediating DON‐induced hepatocellular oxidative stress is investigated. Treatment with the PXR agonist 3‐indole‐propionic acid (IPA) alleviates DON‐induced oxidative stress and liver injury both in vitro and in vivo. Mechanistically, it is discovered for the first time that PXR agonist IPA directly transactivates the m6A demethylase FTO expression, leading to site‐specific demethylation and decreased abundance of YTHDC1‐bound Malat1 lncRNA at single‐nucleotide resolution. The diminished m6A modification of Malat1 lncRNA reduces its stability and augments antioxidant pathways governed by NRF2, consequently mitigating DON‐induced liver injury. Furthermore, Malat1 knockout mice exhibit decreased DON‐induced liver injury, emphasizing the role of Malat1 lncRNA in oxidative stress. Collectively, the findings establish that PXR‐mediated m6A‐dependent Malat1 lncRNA expression determines hepatocyte oxidative stress via m6A demethylase FTO, providing valuable insights into the potential mechanisms underlying DON‐induced liver injury and offers potential therapeutic strategies for its treatment. [ABSTRACT FROM AUTHOR]

Sesbania gum (SG), as an environmentally friendly natural polymer, was chemically modified in heterogeneoususing systems using a combination of cross-linking, carboxymethylation and oxidation to broaden its applications. The experimental results showed that the cross-linking was chiefly conducted on the smaller particles of SG, while the carboxymethylation and oxidation were primarily carried out on the larger particles. The carboxymethylation and oxidation obviously increased the average size of SG. The dialdehyde oxidation destroyed the crystalline structure of SG more severely than cross-linking and carboxymethylation. The cross-linking, carboxymethylation and oxidation increased the thermal stability of SG, but decreased its enthalpy change. The pasting properties of tapioca starch were influenced by the addition of SG and modified SG. The crystalline structure of polyethylene oxide (PEO) was influenced by addition of SG and modified SG. The reduction in crystallinity degree and introduction of dialdehyde carboxymethyl cross-linked sesbania gum (DCCLSG) with aldehyde groups were beneficial for ameliorating the ion migration through the solid electrolyte membrane. [ABSTRACT FROM AUTHOR]

N‐methyladenosine (m6A) represents a prevalent RNA modification observed in colorectal cancer. Despite its abundance, the biological implications of m6A methylation on the lncRNA CARMN remain elusive in colorectal cancer, especially for mutant p53 gain‐of‐function. Here, we elucidate that CARMN exhibits diminished expression levels in colorectal cancer patients with mutant p53, attributed to its rich m6A methylation, which promotes cancer proliferation, invasion and metastasis in vitro and in vivo. Further investigation illustrates that ALKBH5 acts as a direct demethylase of CARMN, targeting 477 methylation sites, thereby preserving CARMN expression. However, the interaction of mutant p53 with the ALKBH5 promoter impedes its transcription, enhancing m6A methylation levels on CARMN. Subsequently, YTHDF2/YTHDF3 recognise and degrade m6A‐modified CARMN. Concurrently, overexpressing CARMN significantly suppressed colorectal cancer progression in vitro and in vivo. Additionally, miR‐5683 was identified as a direct downstream target of lncRNA CARMN, exerting an antitumour effect by cooperatively downregulating FGF2 expression. Our findings revealed the regulator and functional mechanism of CARMN in colorectal cancer with mutant p53, potentially offering insights into demethylation‐based strategies for cancer diagnosis and therapy. The m6A methylation of CARMN that is prime for mutant p53 gain‐of‐function‐induced malignant progression of colorectal cancer, identifying a promising approach for cancer therapy. [ABSTRACT FROM AUTHOR]

Background: DNA methylation can change rapidly to regulate the expression of stress-responsive genes. Previous studies have shown that there are significant differences in the cold resistance of winter rapeseed (Brassica rapa L.) after being domesticated in different selection environments; however, little is known about the epigenetic regulatory mechanisms of its cold resistance formation. Methods: Four winter rapeseed materials ('CT-2360', 'MXW-1', '2018-FJT', and 'DT-7') domesticated in different environments were selected to analyze the DNA methylation level and pattern changes under low temperature using methylation-sensitive amplified polymorphism technology with 60 primer pairs. Results: A total of 18 pairs of primers with good polymorphism were screened, and 1426 clear bands were amplified, with 594 methylation sites, accounting for 41.65% of the total amplified bands. The total methylation ratios of the four materials were reduced after low-temperature treatment, in which the DNA methylation level of 'CT-2360' was higher than that of the other three materials; the analysis of methylation patterns revealed that the degree of demethylation was higher than that of methylation in 'MXW-1', '2018-FJT', and 'DT-7', which were 22.99%, 19.77%, and 24.35%, respectively, and that the methylation events in 'CT-2360' were predominantly dominant at 22.95%. Fifty-three polymorphic methylated DNA fragments were randomly selected and further analyzed, and twenty-nine of the cloned fragments were homologous to genes with known functions. The candidate genes VQ22 and LOC103871127 verified the existence of different expressive patterns before and after low-temperature treatment. Conclusions: Our work implies the critical role of DNA methylation in the formation of cold resistance in winter rapeseed. These results provide a comprehensive insight into the adaptation epigenetic regulatory mechanism of Brassica rapa L. to low temperature, and the identified differentially methylated genes can also be used as important genetic resources for the multilateral breeding of winter-resistant varieties. [ABSTRACT FROM AUTHOR]

Objective: Non‐small cell lung cancer (NSCLC) is a prevailing LC characterized by poor outcomes. AlkB homolog 5 (ALKBH5) functions as a tumor suppressor in several cancers. This study delved into the role of ALKBH5 in NSCLC development. Methods: TCGA database predicted ALKBH5 expression in NSCLC patients. ALKBH5 levels in NSCLC and human bronchial epithelial cells were determined. pcDNA3.1‐ALKBH5/NC, pcDNA3.1‐SLC7A11/NC, and ferrostatin‐1 were used to explore the interactions among ALKBH5, SLC7A11, and ferroptosis. SLC7A11 mRNA and its protein levels were measured by RT‐qPCR and Western blot. Cell viability, apoptosis, migration, and invasion were assessed by CCK‐8, flow cytometry, and Transwell. Total N6‐methyladenosine (m6A) quantification and its enrichment on SLC7A11 mRNA were determined, followed by the observation of Ki67, ALKBH5 and SLC7A11‐positive cell numbers. Glutathione (GSH), lipid reactive oxygen species (lipid‐ROS), malondialdehyde (MDA), and iron ion contents were determined. Animal experiments further analyzed the role of ALKBH5 in tumor development and glutathione peroxidase 4 (GPX4) expression. Results: Bioinformatics analysis revealed the lowly‐expressed ALKBH5 in LC patients. ALKBH5 was downregulated in NSCLC cells and its upregulation repressed proliferation activity, invasion, and migration, and facilitated apoptosis. ALKBH5 upregulation decreased GSH, increased lipid‐ROS, MDA, and iron ion contents, and downregulated SLC7A11 by reducing m6A modification. SLC7A11 upregulation partly annulled the effect of ALKBH5 overexpression on cell ferroptosis and malignant behaviors. In vivo assays elucidated the suppression of ALKBH5 upregulation on tumor development and GPX4 levels. Conclusion: ALKBH5 upregulation downregulates SLC7A11 transcription by decreasing m6A modification, thus promoting NSCLC cell ferroptosis and ultimately repressing NSCLC progression. [ABSTRACT FROM AUTHOR]

Human cytochrome P450 3A4 (CYP3A4) is a major drug-metabolizing enzyme that shows extreme substrate promiscuity. Moreover, its large and malleable active site can simultaneously accommodate several substrate molecules of the same or different nature, which may lead to cooperative binding and allosteric behavior. Due to difficulty of crystallization of CYP3A4-substrate complexes, it remains unknown how multiple substrates can arrange in the active site. We determined crystal structures of CYP3A4 bound to three and six molecules of caffeine, a psychoactive alkaloid serving as a substrate and modulator of CYP3A4. In the ternary complex, one caffeine binds to the active site suitably for C8-hydroxylation, most preferable for CYP3A4. In the senary complex, three caffeine molecules stack parallel to the heme with the proximal ligand poised for 3-N-demethylation. However, the caffeine stack forms extensive hydrophobic interactions that could preclude product dissociation and multiple turnovers. In both complexes, caffeine is also bound in the substrate channel and on the outer surface known as a peripheral site. At all sites, aromatic stacking with the caffeine ring(s) is likely a dominant interaction, while direct and water-mediated polar contacts provide additional stabilization for the substrate-bound complexes. Protein-ligand interactions via the active site R212, intrachannel T224, and peripheral F219 were experimentally confirmed, and the latter two residues were identified as important for caffeine association. Collectively, the structural, spectral, and mutagenesis data provide valuable insights on the ligand binding mechanism and help better understand how purine-based pharmaceuticals and other aromatic compounds could interact with CYP3A4 and mediate drug-drug interactions.

DNA and RNA methylation are essential epigenetic modifications that play a pivotal role in various physiological processes by modulating gene expression at the post-transcriptional level. Abnormal DNA/RNA methylation is closely linked to a range of human diseases, including cancer and neurological disorders. Therefore, the accurate and sensitive detection of DNA/RNA methylation is of great importance in both epigenetic biology research and disease diagnosis. Technological advancements have led to the comprehensive development of methylation detection methods. Among these, electrochemical techniques have garnered significant attention owing to their simplicity and effectiveness in detection. This review provides an overview of methylation detection technologies based on electrochemical principles developed over the past five years, including electrochemical, photoelectrochemical, electrochemiluminescence, and fluorescence methodologies. Additionally, it discusses the advantages and disadvantages of these approaches, challenges and advancements in methylation detection.

The Myc family is essential for cell proliferation, differentiation, and metabolism, particularly in embryonic development and stem cell functions. However, the specific role of Myc in porcine early embryonic development is not fully understood. This study observed high Myc expression during the four-cell stage of porcine embryos. Inhibition of Myc using 10058-F4 impaired embryonic development, disrupted energy metabolism, and increased DNA methylation. Mechanistically, these effects were dependent on α-KG, a TCA cycle intermediate and cofactor for TET demethylation enzymes. Sequencing analysis of four-cell embryos post-Myc inhibition revealed downregulation of key metabolic enzymes related to α-KG, such as CS, IDH2, leading to reduced α-KG levels. Supplementation with α-Ketoglutarate (α-KG) mitigated the negative effects of Myc inhibition, including lower blastocyst rates, decreased ATP levels, and increased 5 mC levels. In conclusion, Myc regulates the expression of key metabolic enzymes during the four-cell stage, influencing early embryonic metabolism and epigenetic reprogramming.

Arabidopsis telomeric repeat binding factors (TRBs) can bind telomeric DNA sequences to protect telomeres from degradation. TRBs can also recruit Polycomb Repressive Complex 2 (PRC2) to deposit tri-methylation of H3 lysine 27 (H3K27me3) over certain target loci. Here, we demonstrate that TRBs also associate and colocalize with JUMONJI14 (JMJ14) and trigger H3K4me3 demethylation at some loci. The trb1/2/3 triple mutant and the jmj14-1 mutant show an increased level of H3K4me3 over TRB and JMJ14 binding sites, resulting in up-regulation of their target genes. Furthermore, tethering TRBs to the promoter region of genes with an artificial zinc finger (TRB-ZF) successfully triggers target gene silencing, as well as H3K27me3 deposition, and H3K4me3 removal. Interestingly, JMJ14 is predominantly recruited to ZF off-target sites with low levels of H3K4me3, which is accompanied with TRB-ZFs triggered H3K4me3 removal at these loci. These results suggest that TRB proteins coordinate PRC2 and JMJ14 activities to repress target genes via H3K27me3 deposition and H3K4me3 removal.

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and irreversible interstitial lung disease with a prognosis worse than lung cancer. It is a fatal lung disease with largely unknown etiology and pathogenesis, and no effective therapeutic drugs render its treatment largely unsuccessful. With continuous indepth research efforts, the epigenetic mechanisms in IPF pathogenesis have been further discovered and concerned. As a widely studied mechanism of epigenetic modification, DNA methylation is primarily facilitated by DNA methyltransferases (DNMTs), resulting in the addition of a methyl group to the fifth carbon position of the cytosine base, leading to the formation of 5-methylcytosine (5-mC). Dysregulation of DNA methylation is intricately associated with the advancement of respiratory disorders. Recently, the role of DNA methylation in IPF pathogenesis has also received considerable attention. DNA methylation patterns include methylation modification and demethylation modification and regulate a range of essential biological functions through gene expression regulation. The Ten-Eleven-Translocation (TET) family of DNA dioxygenases is crucial in facilitating active DNA demethylation through the enzymatic conversion of the modified genomic base 5-mC to 5-hydroxymethylcytosine (5-hmC). TET2, a member of TET proteins, is involved in lung inflammation, and its protein expression is downregulated in the lungs and alveolar epithelial type II cells of IPF patients. This review summarizes the current knowledge of pathologic features and DNA methylation mechanisms of pulmonary fibrosis, focusing on the critical roles of abnormal DNA methylation patterns, DNMTs, and TET proteins in impacting IPF pathogenesis. Researching DNA methylation will enchance comprehension of the fundamental mechanisms involved in IPF pathology and provide novel diagnostic biomarkers and therapeutic targets for pulmonary fibrosis based on the studies involving epigenetic mechanisms. [ABSTRACT FROM AUTHOR]

Molybdate inhibits sulfate respiration in sulfate-reducing bacteria (SRB). It is used as an inhibitor to indirectly evaluate the role of SRB in mercury methylation in the environment. Here, the SRB Pseudodesulfovibrio hydrargyri BerOc1 was used to assess the effect of molybdate on cell growth and mercury methylation under various metabolic conditions. Geobacter sulfurreducens PCA was used as the non-SRB counterpart strain with the ability to methylate mercury. While PCA growth and methylation are not affected by molybdate, 1 mM of molybdate inhibits BerOc1 growth under sulfate respiration (50% inhibition) but also under fumarate respiration (complete inhibition). Even more surprising, mercury methylation of BerOc1 is totally inhibited at 0.1 mM of molybdate when grown under sulfate or fumarate respiration with pyruvate as the electron donor. As molybdate is expected to reduce cellular ATP level, the lower Hg methylation observed with pyruvate could be the consequence of lower energy production. Although molybdate alters the expression of hgcA (mercury methylation marker) and sat (involved in sulfate reduction and molybdate sensitivity) in a metabolism-dependent manner, no relationship with mercury methylation rates could be found. Our results show, for the first time, a specific mercury methylation inhibition by molybdate in SRB. [ABSTRACT FROM AUTHOR]

Tissue biopsy remains the standard for diagnosing gastrointestinal stromal tumors (GISTs), although liquid biopsy is emerging as a promising alternative in oncology. In this pilot study, we advocate for droplet digital PCR (ddPCR) to diagnose GIST in tissue samples and explore its potential for early diagnosis via liquid biopsy, focusing on the PDGFRA D842V mutation and SEPT9 hypermethylated gene. We utilized ddPCR to analyze the predominant PDGFRA mutation (D842V) in surgical tissue samples from 15 GIST patients, correlating with pathologists' diagnoses. We expanded our analysis to plasma samples to compare DNA alterations between tumor tissue and plasma, also investigating SEPT9 gene hypermethylation. We successfully detected the PDGFRA D842V mutation in GIST tissues by ddPCR. Despite various protocols to enhance mutation detection in early-stage disease, it remained challenging, likely due to the low concentration of DNA in plasma samples. Additionally, the results of Area Under the Curve (AUC) for the hypermethylated SEPT9 gene, analyzing concentration, ratio, and abundance were 0.74 (95% Confidence Interval (CI): 0.52 to 0.97), 0.77 (95% CI: 0.56 to 0.98), and 0.79 (95% CI: 0.59 to 0.99), respectively. As a rare disease, the early detection of GIST through such biomarkers is particularly crucial, offering significant potential to improve patient outcomes. [ABSTRACT FROM AUTHOR]