Demethylation Process Research Articles

Overview of Methylation and Demethylation Mechanisms and Influencing Factors of Mercury in Water.

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.

Highly energy-efficient degradation of simulated dye wastewater by array type underwater bubble discharge plasma: Key factors identification and degradation pathways

The extensive use of dyes presents a significant safety concern for the reuse of water resources, highlighting the critical need for a rapid and efficient degradation method for dye mixtures in wastewater. This study introduces a degradation system based on an array type underwater bubble discharge plasma specifically designed to treat a dye mixture wastewater containing methylene blue (MB) and methyl violet 2B (MV2B). Analysis of the optical and electrical characteristics reveals that the device experiences minimal temperature increase, with the highest intensity of the band associated with N2 in the emission spectra, and discharges occurring predominantly during the rising and falling edges of a pulse cycle. Experimental results demonstrate that the most effective degradation efficiencies (MB = 94.83%, MV2B = 93.48%) are achieved at an initial dye concentration of 50 mg/L, a power supply frequency of 6 kHz, an air flow rate of 2.5 SLM and an initial electrical conductivity of 50 μS/cm. The degradation of dyes is primarily attributed to the demethylation process of O3(aq) and other species. Toxicity analysis indicates that the plasma degradation process significantly reduces the toxicity of the intermediate products of dyes. This study not only presents a novel approach for treating high concentration mixed dye wastewater, but also provides valuable insights for future research in this area.

The yeast Dothiora sorbi IOJ-3 naturally produced various filamentous sectors with distinct abilities by undergoing DNA demethylation

Some fungi have demonstrated the ability to adapt rapidly to changing environments by exhibiting morphological plasticity, a trait influenced by species and environmental factors. Here, an anamorphic yeast strain IOJ-3 exhibited unique sectorization characteristics, naturally producing diverse filamentous sectors when cultivated on potato dextrose agar (PDA) medium or natural culture medium for durations exceeding 13 days. The strain IOJ-3 and its filamentous sectors were identified as Dothiora sorbi. The morphology of the sectors was consistent and heritable. The life cycle of strain IOJ-3 was investigated through microscopic observation, emphasizing the development of conidiogenous cells as a crucial stage, from which filamentous sectors originate. Some physiological characteristics of IOJ-3 and filamentous sectors are compared, and strain IOJ-3 has a higher antibiotic tolerance than two filamentous sectors, IOJ-3a expands faster on the culture medium, and IOJ-3b can penetrate cellophane. A transcriptomic analysis was conducted to investigate the differentially expressed genes between the yeast form IOJ-3 and its two filamentous sectors, revealing a total of 594 genes that exhibited consistent differential expression relative to IOJ-3, including 44 silencing genes in IOJ-3 that were activated. Gene Ontology analysis indicated that these differentially expressed genes were primarily associated with the cellular component category. Furthermore, adding 5-Azacytidine accelerated filamentous sectorization and increased the proportion of filamentous cells of strain IOJ-3 in PD liquid media, suggesting that the filamentous sectorization observed in strain IOJ-3 is linked to processes of DNA demethylation. In conclusion, this study sheds light on the biological characteristics of D. sorbi regarding morphological transitions and provides substantial direction for exploring genes related to fungal filamentous development.

Oxygen Vacancy Engineering and Constructing Built-In Electric Field in Fe-g-C3N4/Bi2MoO6 Z-Scheme Heterojunction for Boosting Photo-Fenton Catalytic Degradation Performance of Tetracycline.

A novel Fe-g-C3N4/Bi2MoO6 (FCNB) Z-scheme heterojunction enriched with oxygen vacancy is constructed and employed for the photo-Fenton degradation of tetracycline (TC). The 2% FCNB demonstrates prominent catalytic performance and mineralization efficiency for TC wastewater, showing activity of 8.20 times greater than that of pure photocatalytic technology. Density-functional theory (DFT) calculations and degradation experiments confirm that the formation of Fe-N4 sites induces spin-polarization in the material, and the difference in Fermi energy levels results in the formation of built-in electric field at the contact interface, which facilitates the continuous generation and migration of photogenerated carriers to address the issue of insufficient cycling power of Fe (III)/Fe (II).The reactive radicals persistently target the extremely reactive sites anticipated by the Fukui function, causing the mineralization of TC molecules into "non-toxic" compounds through processes of hydroxylation, demethylation, and deamidation. This work holds significant importance in the domain of eliminating organic pollutants from water.

The Role of DNMT Methyltransferases and TET Dioxygenases in the Maintenance of the DNA Methylation Level.

This review deals with the functional characteristics and biological roles of enzymes participating in DNA methylation and demethylation as key factors in epigenetic regulation of gene expression. The set of enzymes that carry out such processes in human cells is limited to representatives of two families, namely DNMT (DNA methyltransferases) and TET (DNA dioxygenases). The review presents detailed information known today about each functionally important member of these families and describes the catalytic activity and roles in the mammalian body while also providing examples of dysregulation of the expression and/or activity of these enzymes in conjunction with the development of some human disorders, including cancers, neurodegenerative diseases, and developmental pathologies. By combining the up-to-date information on the dysfunction of various enzymes that control the DNA "methylome" in the human body, we hope not only to draw attention to the importance of the maintenance of a required DNA methylation level (ensuring epigenetic regulation of gene expression and normal functioning of the entire body) but also to help identify new targets for directed control over the activity of the enzymes that implement the balance between processes of DNA methylation and demethylation.

Thermal degradation of capsaicin and dihydrocapsaicin: Mechanism and hazards of volatile products

Food safety issues have become unprecedentedly notable. To ensure the safe use of capsaicin (CAP) and dihydrocapsaicin (DHCAP) in the food sector, their thermal degradation characteristics was examined for the first time through thermogravimetric analysis (TGA) and pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) analysis. The second major phase occurred within the temperature range of 265–425 ℃, leading to substantial weight reductions of 96.13 % for CAP and 92.76 % for DHCAP. Thermodynamic parameters, calculated using the Flynn–Wall–Ozawa (FWO), Kissinger–Akahira–Sunose (KAS), and Coats–Redfern (C–R) methods, indicated that the thermal decomposition of both CAP and DHCAP was non-spontaneous and followed an F1 mechanism (−ln(1−α)). The pyrolysis of CAP and DHCAP released several volatile compounds, including CAP, DHCAP, Z-9-octadecenamide, octadecanamide, 9-decenenitrile, nonanenitrile, and 8-methylnonanoic acid. These compounds may pose certain toxicological risks and potential hazards to human health. The pyrolytic pathways for CAP and DHCAP are likely to involve the cleavage of alkyl C-N and/or amide bonds, as well as processes of deamidation and demethylation. Therefore, it is prudent to avoid heating food containing CAP and DHCAP above 265 ℃ during culinary preparation.

Assessment of mercury methylation and methylmercury demethylation potentials in water and sediments along the Wabigoon River system

Monomethylmercury (MMHg) plays a crucial role in the accumulation of mercury (Hg) within aquatic food chains. Since ambient levels of methylmercury are governed by the balance of simultaneous methylation and demethylation processes, determining in situ methylation and demethylation rates is critically important to understand the dynamics of methylmercury in the environment. This is especially important in the Wabigoon River system in Ontario, Canada, which is severely contaminated with Hg by a chlor-alkali facility operating in the 1960s, and still exhibits some of the highest recorded fish mercury concentrations in Canada. This work used a simultaneous addition of isotope enriched Hg and MMHg tracers to ascertain Hg methylation and MMHg demethylation potentials. At the locations investigated for this study, the most favourable conditions for Hg methylation were found at the Hydroelectric dam, being able to transform 4.2 % and 4.4 % of added Hg in water and sediments per day, respectively, to MMHg. This could correspond to 1.9 ng/L and 29 ng/g of new MMHg being produced from current ambient Hg. Clay Lake, which is considered a sink for mercury and exhibiting a seasonal anoxic environment at its bottom waters, also demonstrated significant MMHg generation, being able to produce 2.7 ng/L and 13 ng/g of MMHg per day, respectively. Demethylation rates in sediments of riverbed and wetland locations showed an average half-life for methylmercury of 2.1 days, indicating a rapid turnover of MMHg in the Wabigoon River. However, significantly lower demethylation rates were also measured near the inflow of Clay Lake, where it took up to 144 days for MMHg to decrease by 50 %. Generally, most of the investigated locations downstream of the pollution source displayed the potential to generate methylmercury, which could be distributed throughout the Wabigoon River system and therefore require attention with respect to future remediation activities.

TNC upregulation promotes glioma tumourigenesis through TDG-mediated active DNA demethylation

Gliomas represent the most predominant primary malignant tumor in central nervous system. Thymine DNA glycosylase (TDG) is a central component in active DNA demethylation. However, the specific mechanisms of TDG-mediated active DNA demethylation in gliomas remain unclear. This research indicates TDG expression is overexpressed in gliomas and correlated with poor prognosis. TDG knockdown suppressed the malignant phenotype of gliomas both in vitro and vivo. Notably, RNA-seq analysis revealed a strong association between TDG and tenascin-C (TNC). ChIP-qPCR and MeDIP-qPCR assays were undertaken to confirm that TDG participates in TNC active DNA demethylation process, revealing decreased DNA methylation levels and elevated TNC expression as a result. Silencing TNC expression also suppressed the tumor malignant phenotype in both in vitro and in vivo experiments. Additionally, simultaneous silencing of TNC reduced or even reversed the glioma promotion caused by TDG overexpression. Based on our findings, we conclude that TDG exerts an indispensable role in TNC active DNA demethylation in gliomas. The DNA demethylation process leads to alternations in TNC methylation levels and promotes its expression, thereby contributing to the development of gliomas. These results suggest a novel epigenetic therapeutic strategy targeting active DNA demethylation in gliomas.

TET3 downregulation and low 5-hydroxymethylcytosine are epigenetic signatures of head and neck carcinoma.

Ten-eleven translocases (TETs) are enzymes responsible for demethylation processes, playing a crucial role in maintaining the body's methylation balance. Dysregulation of TET expression can lead to abnormal methylation levels. Isocitrate dehydrogenases (IDH) are upstream genes involved in Kreb cycle responsible for production of α-ketoglutarate (α-KG). α-KG and vitamin C are cofactors of TET3 enzyme. There is limited data on the relationship between TET3 and its cofactor Vitamin C in head and neck carcinoma (H&NC). In this study, we have investigated the expression of the TET3 gene along with IDH1/2 genes involved in the Krebs cycle in the peripheral blood of 32H&NC patients compared to 32 healthy controls. We estimated serum levels of TET3 protein and vitamin C and 5-hydroxymethylcytosine (5-hmC) percentage in DNA isolated from EDTA blood samples. Our findings revealed that TET3 and IDH1/2 were downregulated in H&NC patients compared to healthy controls. Serum levels of TET3 and Vitamin C were low in H&NC patients compared to healthy controls. Diminished levels of percentage 5-hmC were detected in EDTA blood samples of H&NC patients compared to controls. Spearman correlation analysis revealed a significant positive correlation between TET3 levels, vitamin C levels and 5-hmC percentage. The low levels of Vitamin C are believed to contribute to decreased activity of the TET3 gene and less conversion of 5-methylcytosine (5-mC) to 5-hmC. Dietary supplementation of Vitamin C may increase TET3 activity.

Genome-Wide Methylation Analysis Reveals a KCNK3-Prominent Causal Cascade on Hypertension.

Despite advances in understanding hypertension's genetic structure, how noncoding genetic variants influence it remains unclear. Studying their interaction with DNA methylation is crucial to deciphering this complex disease's genetic mechanisms. We investigated the genetic and epigenetic interplay in hypertension using whole-genome bisulfite sequencing. Methylation profiling in 918 males revealed allele-specific methylation and methylation quantitative trait loci. We engineered rs1275988T/C mutant mice using CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9), bred them for homozygosity, and subjected them to a high-salt diet. Telemetry captured their cardiovascular metrics. Protein-DNA interactions were elucidated using DNA pull-downs, mass spectrometry, and Western blots. A wire myograph assessed vascular function, and analysis of the Kcnk3 gene methylation highlighted the mutation's role in hypertension. We discovered that DNA methylation-associated genetic effects, especially in non-cytosine-phosphate-guanine (non-CpG) island and noncoding distal regulatory regions, significantly contribute to hypertension predisposition. We identified distinct methylation quantitative trait locus patterns in the hypertensive population and observed that the onset of hypertension is influenced by the transmission of genetic effects through the demethylation process. By evidence-driven prioritization and in vivo experiments, we unearthed rs1275988 in a cell type-specific enhancer as a notable hypertension causal variant, intensifying hypertension through the modulation of local DNA methylation and consequential alterations in Kcnk3 gene expression and vascular remodeling. When exposed to a high-salt diet, mice with the rs1275988C/C genotype exhibited exacerbated hypertension and significant vascular remodeling, underscored by increased aortic wall thickness. The C allele of rs1275988 was associated with elevated DNA methylation levels, driving down the expression of the Kcnk3 gene by attenuating Nr2f2 (nuclear receptor subfamily 2 group F member 2) binding at the enhancer locus. Our research reveals new insights into the complex interplay between genetic variations and DNA methylation in hypertension. We underscore hypomethylation's potential in hypertension onset and identify rs1275988 as a causal variant in vascular remodeling. This work advances our understanding of hypertension's molecular mechanisms and encourages personalized health care strategies.

A disposable electrochemical magnetic immunosensor for the rapid and sensitive detection of 5-formylcytosine and 5-carboxylcytosine in DNA

5-formylcytosine (5 fC) and 5-carboxylcytosine (5caC) serve as key intermediates in DNA demethylation process with significant implications for gene regulation and disease progression. In this study, we introduce a novel electrochemical sensing platform specifically designed for the sensitive and selective detection of 5 fC and 5caC in DNA. Protein A-modified magnetic beads (ProtA-MBs) coupled with specific antibodies facilitate the immunorecognition and enrichment of these modified bases. Signal amplification is achieved through several chemical reactions involving the interaction between N3-kethonaxl and guanine, copper-free click chemistry for the attachment of dibenzocyclooctyne (DBCO)-Biotin, and the subsequent recognition by streptavidin-conjugated horseradish peroxidase (SA-HRP). The assay's readout is performed on a disposable laser-induced graphene (LIG) electrode, modified with the bead-antibody-DNA complex in a magnetic field, and analyzed using differential pulse voltammetry in a system employing hydroquinone (HQ) as the redox mediator and H2O2 as the substrate. This immunosensor displayed excellent sensitivity, with detection limits of 14.8 fM for 5 fC across a 0.1–1000 pM linear range and 87.4 fM for 5caC across a 0.5–5000 pM linear range, and maintained high selectivity even in the presence of interferences from other DNA modifications. Successful application in quantifying 5 fC and 5caC in genomic DNA from cell extracts, with recovery rates between 97.7% to 102.9%, underscores its potential for clinical diagnostics. N3-kethoxal was used for the first time in an electrochemical sensor. This work not only broadens the toolkit for detecting DNA modifications but also provides a fresh impetus for the development of point-of-care testing (POCT) technologies.

24-epibrassinolide as a multidimensional regulator of rice (Oryza sativa) physiological and molecular responses under isoproturon stress

Brassinosteroids (BRs) can regulate various processes in plant development and defense against environmental stress. In this study, the contribution of BRs in the degradation of isoproturon (IPU) in rice has been established. IPU has a significant effect on rice growth, chlorophyll content, and membrane permeability. When treated with 1.0 μmol/L 24-epibrassinolide (EBR), a BR analogue, the associated symptoms of rice poisoning were alleviated as the IPU levels in the rice and growth media were decreased. In the presence of EBR, the activities of several IPU-related detoxification enzymes were enhanced to cope with the stress due to IPU. An RNA-sequencing (RNA-Seq) has been performed to determine the variation of transcriptomes and metabolic mechanisms in rice treated with EBR, IPU, or IPU+EBR. Some of the differentially expressed genes (DEGs) were Phase I-III reaction components of plants, such as cytochrome P450 (CYP450), glutathione S-transferase (GST), glycosyltransferases (GTs), and the ATP-binding cassette transporter (ABC transporter). The expression of some signal transduction genes was significantly up-regulated. The relative content of low-toxicity IPU metabolites increased due to the presence of EBR as determined by UPLC/Q-TOF-MS/MS. The IPU metabolic pathways include enzyme-catalyzed demethylation, hydroxylation, hydrolysis, glycosylation, and amino acid conjugation processes. The results suggest that EBR plays a key role in the degradation and detoxification of IPU. This study has provided evidence that BRs regulate the metabolism and detoxification of IPU in rice, and offers a new approach to ensuring cleaner crops by eliminating pesticide residues in the environment.

Functional genes and microorganisms controlling in situ methylmercury production and degradation in marine sediments: A case study in the Eastern China Coastal Seas

Dominant microorganisms and functional genes, including hgcA, hgcB, merA, and merB, have been identified to be responsible for mercury (Hg) methylation or methylmercury (MeHg) demethylation. However, their in situ correlation with MeHg levels and the processes of Hg methylation and MeHg demethylation in coastal areas remains poorly understood. In this study, four functional genes related to Hg methylation and MeHg demethylation (hgcA, hgcB, merA, and merB) were all detected in the sediments of the Eastern China Coastal Seas (ECCSs) (representative coastal seas highly affected by human activities) using metagenomic approaches. HgcA was identified to be the key gene controlling the in situ net production of MeHg in the ECCSs. Based on metagenomic analysis and incubation experiments, sulfate-reducing bacteria were identified as the dominant microorganisms controlling Hg methylation in the ECCSs. In addition, hgcA gene was positively correlated with the MeHg content and Hg methylation rates, highlighting the potential roles of Hg methylation genes and microorganisms influenced by sediment physicochemical properties in MeHg cycling in the ECCSs. These findings highlighted the necessity of conducting similar studies in other natural systems for elucidating the molecular mechanisms underlying MeHg production in aquatic environments.

Discovery of novel natural-product-derived mutant isocitrate dehydrogenases 1 inhibitors: Structure-based virtual screening, biological evaluation and structure-activity relationship study

Mutations in IDH1 are commonly observed across various cancers, causing the conversion of α-KG to 2-HG. Elevated levels of 2-HG disrupt histone and DNA demethylation processes, promoting tumor development. Consequently, there is substantial interest in developing small molecule inhibitors targeting the mutant enzymes. Herein, we report a structure-based high-throughput virtual screening strategy using a natural products library, followed by hit-to-lead optimization. Through this process, we discover a potent compound, named 11s, which exhibited significant inhibition to IDH1 R132H and IDH1 R132C with IC50 values of 124.4 and 95.7 nM, respectively. Furthermore, 11s effectively reduced 2-HG formation, with EC50 values of 182 nM in U87 R132H cell, and 84 nM in HT-1080 cell. In addition, 11s significantly reduced U87 R132H and HT-1080 cell proliferation with GC50 values of 3.48 and 1.38 μM, respectively. PK-PD experiments further confirmed that compound 11s significantly decreased 2-HG formation in an HT-1080 xenograft mouse model, resulting in notable suppression of tumor growth without apparent loss in body weight.

Small Molecule‐Inducible and Photoactivatable Cellular RNA N1‐Methyladenosine Editing

AbstractN1‐methyladenosine (m1A) modification is one of the most prevalent epigenetic modifications on RNA. Given the vital role of m1A modification in RNA processing such as splicing, stability and translation, developing a precise and controllable m1A editing tool is pivotal for in‐depth investigating the biological functions of m1A. In this study, we developed an abscisic acid (ABA)‐inducible and reversible m1A demethylation tool (termed AI‐dm1A), which targets specific transcripts by combining the chemical proximity‐induction techniques with the CRISPR/dCas13b system and ALKBH3. We successfully employed AI‐dm1A to selectively demethylate the m1A modifications at A8422 of MALAT1 RNA, and this demethylation process could be reversed by removing ABA. Furthermore, we validated its demethylation function on various types of cellular RNAs including mRNA, rRNA and lncRNA. Additionally, we used AI‐dm1A to specifically demethylate m1A on ATP5D mRNA, which promoted ATP5D expression and enhanced the glycolysis activity of tumor cells. Conversely, by replacing the demethylase ALKBH3 with methyltransferase TRMT61A, we also developed a controllable m1A methylation tool, namely AI‐m1A. Finally, we caged ABA by 4,5‐dimethoxy‐2‐nitrobenzyl (DMNB) to achieve light‐inducible m1A methylation or demethylation on specific transcripts. Collectively, our m1A editing tool enables us to flexibly study how m1A modifications on specific transcript influence biological functions and phenotypes.

Small Molecule-Inducible and Photoactivatable Cellular RNA N1-Methyladenosine Editing.

N1-methyladenosine (m1A) modification is one of the most prevalent epigenetic modifications on RNA. Given the vital role of m1A modification in RNA processing such as splicing, stability and translation, developing a precise and controllable m1A editing tool is pivotal for in-depth investigating the biological functions of m1A. In this study, we developed an abscisic acid (ABA)-inducible and reversible m1A demethylation tool (termed AI-dm1A), which targets specific transcripts by combining the chemical proximity-induction techniques with the CRISPR/dCas13b system and ALKBH3. We successfully employed AI-dm1A to selectively demethylate the m1A modifications at A8422 of MALAT1 RNA, and this demethylation process could be reversed by removing ABA. Furthermore, we validated its demethylation function on various types of cellular RNAs including mRNA, rRNA and lncRNA. Additionally, we used AI-dm1A to specifically demethylate m1A on ATP5D mRNA, which promoted ATP5D expression and enhanced the glycolysis activity of tumor cells. Conversely, by replacing the demethylase ALKBH3 with methyltransferase TRMT61A, we also developed a controllable m1A methylation tool, namely AI-m1A. Finally, we caged ABA by 4,5-dimethoxy-2-nitrobenzyl (DMNB) to achieve light-inducible m1A methylation or demethylation on specific transcripts. Collectively, our m1A editing tool enables us to flexibly study how m1A modifications on specific transcript influence biological functions and phenotypes.

Prenatal exposure to low-dose bisphenol A disrupts hippocampal DNA methylation and demethylation in male rat offspring.

Earlier research has demonstrated that developmental exposure to bisphenol A (BPA) has persistent impacts on both adult brain growth and actions. It has been suggested that BPA might obstruct the methylation coding of the genes in the brain. In this study, the methylation changes in the hippocampus tissue of male rat pups were examined following prenatal BPA exposure. Pregnant Sprague-Dawley rats were treated with either vehicle (tocopherol-stripped corn oil) or BPA (4, 40, or 400μg/kg·body weight/day) throughout the entire duration of gestation and lactation. At 3weeks of age, the male rat offspring were euthanized, and the hippocampus were dissected out for analysis. The expression levels of DNA methyltransferases (DNMT1, DNMT3A, and DNMT3B) and DNA demethylases (TET1, Gadd45a, Gadd45b, and Apobec1) were analyzed in the hippocampus by means of quantitative real-time polymerase chain reaction and Western blotting, respectively. The results showed that prenatal exposure to BPA upregulated the expression of enzymes associated with DNA methylation and demethylation processes in the hippocampus of male rat offspring. These findings suggest that prenatal exposure to a low dose of BPA could potentially disrupt the balance of methylation and demethylation in the hippocampus, thereby perturbing epigenetic modifications. This may represent a neurotoxicity mechanism of BPA.

Understanding hydropyrolysis mechanism of β-O-4 type lignin dimer

Hydropyrolysis has been demonstrated as a highly effective method in the production of fuels and high-value chemicals. However, limited research has been conducted on the reaction mechanism under hydrogen conditions, which necessitates further investigation. In order to examine the impact of hydrogen, experiments were conducted on a high-pressure pyrolyzer using 1-methoxy-2-phenethoxybenzenene with β-O-4 linkage. The results indicated that hydrogen promoted the depolymerization and reduced the formation of heavier compounds, leading to an increase in the production of the monomer phenols and aromatic compounds. Experiments were further conducted at different pressures. The results obtained from reactive molecular dynamics simulations exhibited the pyrolysis mechanisms. The cleavage of Cβ-O, Cph-O, and Cα-Cβ bonds, as well as demethylation and demethoxylation processes during hydropyrolysis were observed. The initial reaction commenced with Cβ-O bond cleavage, which was enhanced by the presence of hydrogen. Subsequent reactions were categorized into three types: decomposition or isomerization reaction, coupling with radical groups containing carbon, and combination with hydrogen molecules or hydrogen radicals. The direct reactions between the model compound molecules and hydrogen molecules or hydrogen radicals, as well as primary hydrogen abstraction reactions and hydrogen elimination reactions were explored. These simulations offer valuable insights into understanding the influence of hydrogen at the molecular level.

The level of active DNA demethylation compounds in leukocytes and urine samples as potential epigenetic biomarkers in breast cancer patients

The active DNA demethylation process, which involves TET proteins, can affect DNA methylation pattern. TET dependent demethylation results in DNA hypomethylation by oxidation 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) and its derivatives. Moreover, TETs’ activity may be upregulated by ascorbate. Given that aberrant DNA methylation of genes implicated in breast carcinogenesis may be involved in tumor progression, we wanted to determine whether breast cancer patients exert changes in the active DNA demethylation process. The study included blood samples from breast cancer patients (n = 74) and healthy subjects (n = 71). We analyzed the expression of genes involved in the active demethylation process (qRT-PCR), and 5–mC and its derivatives level (2D-UPLC MS/MS). The ascorbate level was determined using UPLC-MS. Breast cancer patients had significantly higher TET3 expression level, lower 5-mC and 5-hmC DNA levels. TET3 was significantly increased in luminal B breast cancer patients with expression of hormone receptors. Moreover, the ascorbate level in the plasma of breast cancer patients was decreased with the accompanying increase of sodium-dependent vitamin C transporters (SLC23A1 and SLC23A2). The presented study indicates the role of TET3 in DNA demethylation in breast carcinogenesis.

Functional significance of DNA methylation: epigenetic insights into Sjögren's syndrome.

Sjögren's syndrome (SjS) is a systemic, highly diverse, and chronic autoimmune disease with a significant global prevalence. It is a complex condition that requires careful management and monitoring. Recent research indicates that epigenetic mechanisms contribute to the pathophysiology of SjS by modulating gene expression and genome stability. DNA methylation, a form of epigenetic modification, is the fundamental mechanism that modifies the expression of various genes by modifying the transcriptional availability of regulatory regions within the genome. In general, adding a methyl group to DNA is linked with the inhibition of genes because it changes the chromatin structure. DNA methylation changes the fate of multiple immune cells, such as it leads to the transition of naïve lymphocytes to effector lymphocytes. A lack of central epigenetic enzymes frequently results in abnormal immune activation. Alterations in epigenetic modifications within immune cells or salivary gland epithelial cells are frequently detected during the pathogenesis of SjS, representing a robust association with autoimmune responses. The analysis of genome methylation is a beneficial tool for establishing connections between epigenetic changes within different cell types and their association with SjS. In various studies related to SjS, most differentially methylated regions are in the human leukocyte antigen (HLA) locus. Notably, the demethylation of various sites in the genome is often observed in SjS patients. The most strongly linked differentially methylated regions in SjS patients are found within genes regulated by type I interferon. This demethylation process is partly related to B-cell infiltration and disease progression. In addition, DNA demethylation of the runt-related transcription factor (RUNX1) gene, lymphotoxin-α (LTA), and myxovirus resistance protein A (MxA) is associated with SjS. It may assist the early diagnosis of SjS by serving as a potential biomarker. Therefore, this review offers a detailed insight into the function of DNA methylation in SjS and helps researchers to identify potential biomarkers in diagnosis, prognosis, and therapeutic targets.