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Science Advances Jun 2020DNA demethylation is important for the erasure of DNA methylation. The role of DNA demethylation in plant development remains poorly understood. Here, we found extensive...
DNA demethylation is important for the erasure of DNA methylation. The role of DNA demethylation in plant development remains poorly understood. Here, we found extensive DNA demethylation in the CHH context around pericentromeric regions and DNA demethylation in the CG, CHG, and CHH contexts at discrete genomic regions during ectopic xylem tracheary element (TE) differentiation. While loss of pericentromeric methylation occurs passively, DNA demethylation at a subset of regions relies on active DNA demethylation initiated by DNA glycosylases ROS1, DML2, and DML3. The and mutations impair ectopic TE differentiation and xylem development in the young roots of seedlings. Active DNA demethylation targets and regulates many genes for TE differentiation. The defect of xylem development in is proposed to be caused by dysregulation of multiple genes. Our study identifies a role of active DNA demethylation in vascular development and reveals an epigenetic mechanism for TE differentiation.
Topics: Arabidopsis; Arabidopsis Proteins; DNA Demethylation; DNA Methylation; Gene Expression Regulation, Plant; Nuclear Proteins; Protein-Tyrosine Kinases; Proto-Oncogene Proteins
PubMed: 32637594
DOI: 10.1126/sciadv.aaz2963 -
Methods in Molecular Biology (Clifton,... 2022Here we describe how to profile the contribution of metabolism and implication of metals to histone methylation and demethylation. The techniques described with the...
Here we describe how to profile the contribution of metabolism and implication of metals to histone methylation and demethylation. The techniques described with the adequate protocols are metabolomics, quantitative proteomics, inductively coupled mass spectrometry and nanoscale secondary ion mass spectrometry.
Topics: Demethylation; Histones; Metals; Methylation; Spectrometry, Mass, Secondary Ion
PubMed: 35733013
DOI: 10.1007/978-1-0716-2481-4_6 -
Clinical Epigenetics Jan 2023Accurate regulation of DNA methylation is necessary for normal cells to differentiate, develop and function. TET2 catalyzes stepwise DNA demethylation in hematopoietic... (Clinical Trial)
Clinical Trial
BACKGROUND
Accurate regulation of DNA methylation is necessary for normal cells to differentiate, develop and function. TET2 catalyzes stepwise DNA demethylation in hematopoietic cells. Mutations in the TET2 gene predispose to hematological malignancies by causing DNA methylation overload and aberrant epigenomic landscape. Studies on mice and cell lines show that the function of TET2 is boosted by vitamin C. Thus, by strengthening the demethylation activity of TET2, vitamin C could play a role in the prevention of hematological malignancies in individuals with TET2 dysfunction. We recently identified a family with lymphoma predisposition where a heterozygous truncating germline mutation in TET2 segregated with nodular lymphocyte-predominant Hodgkin lymphoma. The mutation carriers displayed a hypermethylation pattern that was absent in the family members without the mutation.
METHODS
In a clinical trial of 1 year, we investigated the effects of oral 1 g/day vitamin C supplementation on DNA methylation by analyzing genome-wide DNA methylation and gene expression patterns from the family members.
RESULTS
We show that vitamin C reinforces the DNA demethylation cascade, reduces the proportion of hypermethylated loci and diminishes gene expression differences between TET2 mutation carriers and control individuals.
CONCLUSIONS
These results suggest that vitamin C supplementation increases DNA methylation turnover and provide a basis for further work to examine the potential benefits of vitamin C supplementation in individuals with germline and somatic TET2 mutations.
TRIAL REGISTRATION
This trial was registered at EudraCT with reference number of 2018-000155-41 (01.04.2019).
Topics: Ascorbic Acid; Dioxygenases; DNA Demethylation; DNA Methylation; DNA-Binding Proteins; Germ-Line Mutation; Hematologic Neoplasms; Mutation; Vitamins; Humans
PubMed: 36639817
DOI: 10.1186/s13148-022-01404-6 -
Toxicological Sciences : An Official... Nov 2022Methylmercury (MeHg) persists today as a priority public health concern. Mechanisms influencing MeHg metabolism, kinetics, and toxicity outcomes are therefore essential...
Methylmercury (MeHg) persists today as a priority public health concern. Mechanisms influencing MeHg metabolism, kinetics, and toxicity outcomes are therefore essential knowledge for informing exposure risks. Evidence points to different toxic potencies of MeHg and inorganic mercury (Hg2+), highlighting the role for biotransformation (demethylation) in regulating MeHg toxicokinetics/dynamics. Whereas microbial MeHg demethylation in the gut is seen to influence elimination kinetics, the potential for systemic demethylation in tissues and target organs to influence MeHg toxicity remains uncertain. To investigate the consequences of systemic MeHg demethylation across development, we engineered transgenic Drosophila to express the bacterial organomercurial lyase enzyme (merB) in a targeted and tissue-specific manner. With all combinations of merB-induced demethylation, ubiquitously (via an actin promoter) or in a tissue-specific manner (ie, gut, muscle, neurons), we observe a rescue of MeHg-induced eclosion failure at the pupal to adult transition. In MeHg-fed larvae with ubiquitous or targeted (gut and muscle) merB expression, we see a significant decrease in MeHg body burden at the pupal stage relative to control flies. We also observe a significant increase in the MeHg elimination rate with merB demethylation induced in adults (control, t1/2 = 7.2 days; merB flies, t1/2 = 3.1 days). With neuronal-specific merB expression, we observe a rescue of MeHg-induced eclosion failure without a decrease in Hg body burden, but a redistribution of Hg away from the brain. These results demonstrate the previously unidentified potential for intracellular MeHg demethylation to promote transport and elimination of Hg, and reduce developmental MeHg toxicity. Impact Statement: These findings demonstrate the potential for MeHg demethylation in situ to contribute significantly to the MeHg elimination and distribution kinetics of whole animals and thereby affords a means of protection against the toxic insult of MeHg. Therefore, this study reveals important insight into processes that can determine an individual's resistance or susceptibility to MeHg and provides rationale for therapies targeting a novel metabolism-based pathways to alleviate toxicity risk stemming from MeHg exposure.
Topics: Animals; Methylmercury Compounds; Kinetics; Drosophila; Mercury; Animals, Genetically Modified; Demethylation
PubMed: 36200918
DOI: 10.1093/toxsci/kfac105 -
The Science of the Total Environment Sep 2023Terrestrial ecosystems store large amounts of mercury (Hg), which may be subject to methylation, mobilization and uptake into downstream aquatic ecosystems. Mercury...
Terrestrial ecosystems store large amounts of mercury (Hg), which may be subject to methylation, mobilization and uptake into downstream aquatic ecosystems. Mercury concentrations, methylation and demethylation potentials are not well characterized simultaneously across different habitats in boreal forest ecosystems, particularly not so in stream sediment, leading to uncertainties about the importance of various habitats as primary production areas of the bioaccumulative neurotoxin methylmercury (MeHg). In this study, we collected soil and sediment samples from 17 undisturbed, central Canadian boreal forested watersheds during spring, summer and fall to robustly characterize the spatial (upland and riparian/wetland soils, and stream sediment) and seasonal patterns of total Hg (THg) and MeHg concentrations. Mercury methylation and MeHg demethylation potentials (K and K) in the soils and sediment were also assessed using enriched stable Hg isotope assays. We found the highest K and %-MeHg in stream sediment. In both riparian and wetland soils, Hg methylation was lower and less seasonally variable compared to stream sediment, but had comparable MeHg concentrations, suggesting longer-term storage of MeHg produced in these soils. Soil and sediment carbon content, and THg and MeHg concentrations were strong covariates across habitats. Additionally, sediment carbon content was important for delineating between stream sediment with relatively high vs. relatively low Hg methylation potential, which generally separated between different landscape physiographies. Broadly, this large and spatiotemporally diverse dataset is an important baseline for understanding Hg biogeochemistry in boreal forests both in Canada and possibly in many other boreal systems globally. This work is particularly important with respect to future possible impacts from natural and anthropogenic perturbations, which are increasingly straining boreal ecosystems in various parts of the world.
Topics: Mercury; Ecosystem; Soil; Methylation; Seasons; Canada; Water Pollutants, Chemical; Environmental Monitoring; Methylmercury Compounds; Demethylation
PubMed: 37245803
DOI: 10.1016/j.scitotenv.2023.164447 -
TET Enzymes in the Immune System: From DNA Demethylation to Immunotherapy, Inflammation, and Cancer.Annual Review of Immunology Jun 2024Ten-eleven translocation (TET) proteins are iron-dependent and α-ketoglutarate-dependent dioxygenases that sequentially oxidize the methyl group of 5-methylcytosine... (Review)
Review
Ten-eleven translocation (TET) proteins are iron-dependent and α-ketoglutarate-dependent dioxygenases that sequentially oxidize the methyl group of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). All three epigenetic modifications are intermediates in DNA demethylation. TET proteins are recruited by transcription factors and by RNA polymerase II to modify 5mC at enhancers and gene bodies, thereby regulating gene expression during development, cell lineage specification, and cell activation. It is not yet clear, however, how the established biochemical activities of TET enzymes in oxidizing 5mC and mediating DNA demethylation relate to the known association of TET deficiency with inflammation, clonal hematopoiesis, and cancer. There are hints that the ability of TET deficiency to promote cell proliferation in a signal-dependent manner may be harnessed for cancer immunotherapy. In this review, we draw upon recent findings in cells of the immune system to illustrate established as well as emerging ideas of how TET proteins influence cellular function.
Topics: Humans; Neoplasms; Animals; Inflammation; Immunotherapy; Dioxygenases; DNA Demethylation; Immune System; Epigenesis, Genetic; Proto-Oncogene Proteins; DNA Methylation; DNA-Binding Proteins; Mixed Function Oxygenases
PubMed: 38360546
DOI: 10.1146/annurev-immunol-080223-044610 -
The EMBO Journal Oct 2023Dermal Fibroblast Progenitors (DFPs) differentiate into distinct fibroblast lineages during skin development. However, the epigenetic mechanisms that regulate DFP...
Dermal Fibroblast Progenitors (DFPs) differentiate into distinct fibroblast lineages during skin development. However, the epigenetic mechanisms that regulate DFP differentiation are not known. Our objective was to use multimodal single-cell approaches, epigenetic assays, and allografting techniques to define a DFP state and the mechanism that governs its differentiation potential. Our initial results indicated that the overall transcription profile of DFPs is repressed by H3K27me3 and has inaccessible chromatin at lineage-specific genes. Surprisingly, the repressive chromatin profile of DFPs renders them unable to reform the skin in allograft assays despite their multipotent potential. We hypothesized that chromatin derepression was modulated by the H3K27me3 demethylase, Kdm6b/Jmjd3. Dermal fibroblast-specific deletion of Kdm6b/Jmjd3 in mice resulted in adipocyte compartment ablation and inhibition of mature dermal papilla functions, confirmed by additional single-cell RNA-seq, ChIP-seq, and allografting assays. We conclude that DFPs are functionally derepressed during murine skin development by Kdm6b/Jmjd3. Our studies therefore reveal a multimodal understanding of how DFPs differentiate into distinct fibroblast lineages and provide a novel publicly available multiomics search tool.
Topics: Animals; Mice; Chromatin; Histones; Jumonji Domain-Containing Histone Demethylases; Cell Differentiation; Demethylation; Fibroblasts
PubMed: 37602956
DOI: 10.15252/embj.2023113880 -
The New England Journal of Medicine Aug 2022
Topics: Azacitidine; Demethylation; Humans; Myelodysplastic Syndromes; Oncogenes; Up-Regulation
PubMed: 35921465
DOI: 10.1056/NEJMc2208134 -
Inflammation Research : Official... Feb 2023The present study was designed to explore the potential regulatory mechanism between mitophagy and pyroptosis during sepsis-associated acute lung injury (ALI).
BACKGROUND
The present study was designed to explore the potential regulatory mechanism between mitophagy and pyroptosis during sepsis-associated acute lung injury (ALI).
METHODS
In vitro or in vivo models of sepsis-associated ALI were established by administering lipopolysaccharide (LPS) or performing caecal ligation and puncture (CLP) surgery. Pyroptosis levels were detected by electron microscopy, immunofluorescence, flow cytometry, western blotting and immunohistochemistry. Dual-luciferase reporter gene assay was applied to verify the targeting relationship between miR-138-5p and NLRP3. Methylation-specific PCR and chromatin immunoprecipitation assays were used to determine methylation of the miR-138-5p promoter. Mitophagy levels were examined by transmission electron microscopy and western blotting.
RESULTS
NLRP3 inflammasome silencing alleviated alveolar macrophage (AM) pyroptosis and septic lung injury. In addition, we confirmed the direct targeting relationship between miR-138-5p and NLRP3. Overexpressed miR-138-5p alleviated AM pyroptosis and the pulmonary inflammatory response. Moreover, the decreased expression of miR-138-5p was confirmed to depend on promoter methylation, while inhibition of miR-138-5p promoter methylation attenuated AM pyroptosis and pulmonary inflammation. Here, we discovered that an increased cytoplasmic mtDNA content in sepsis-induced ALI models induced the methylation of the miR-138-5p promoter, thereby decreasing miR-138-5p expression, which may activate the NLRP3 inflammasome and trigger AM pyroptosis. Mitophagy, a form of selective autophagy that clears damaged mitochondria, reduced cytoplasmic mtDNA levels. Furthermore, enhanced mitophagy might suppress miR-138-5p promoter methylation and relieve the pulmonary inflammatory response, changes that were reversed by treatment with isolated mtDNA.
CONCLUSIONS
In summary, our study indicated that mitophagy induced the demethylation of the miR-138-5p promoter, which may subsequently inhibit NLRP3 inflammasome, AM pyroptosis and inflammation in sepsis-induced lung injury. These findings may provide a promising therapeutic target for sepsis-associated ALI.
Topics: Humans; Inflammasomes; Pyroptosis; NLR Family, Pyrin Domain-Containing 3 Protein; MicroRNAs; Mitophagy; Acute Lung Injury; Sepsis; Demethylation; Lipopolysaccharides
PubMed: 36538076
DOI: 10.1007/s00011-022-01675-y -
The European Journal of Neuroscience Jul 2023It has been confirmed that BTB domain and CNC homologue 1 (BACH1) are involved in ferroptosis-related diseases. However, the function of BACH1 in cerebral...
It has been confirmed that BTB domain and CNC homologue 1 (BACH1) are involved in ferroptosis-related diseases. However, the function of BACH1 in cerebral ischemia-reperfusion injury (CIRI)-induced ferroptosis remains to be largely unrevealed. First, analysis of differentially expressed genes in CIRI based on the GEO dataset GSE119121 revealed that BACH1 was upregulated in CIRI. BACH1 level was prominently increased in middle cerebral artery occlusion (MCAO)/reperfusion model and oxygen-glucose deprivation/reoxygenation cell model. Further, knock-down of BACH1 markedly reduced iron ion concentration, ROS production, 4-HNE and lipid peroxidation levels and facilitated GSH content, cell viability and protein levels of GPX4 and SLC7A11, while an pcDNA-KDM4C or pcDNA-COX2 combined with BACH1 siRNA could not enhance this effect. Mechanistically, BACH1 bound on the KDM4C promoter to transcriptionally activate its expression. Besides, KDM4C could occupy the promoter locus of the COX2 gene, promoting the COX2 expression by eliminating H3K9me3. Overexpression of KDM4C or COX2 overturned the effects of BACH1 inhibition. In vivo findings displayed that brain infraction, pathological damage and neuronal loss rate in MCAO mice were conspicuously decreased after BACH1 knock-down. This study reveals that BACH1 encourages ferroptosis in neuroblastoma cells and CIRI mouse brain tissues by activating KDM4C-mediated COX2 demethylation.
Topics: Animals; Mice; BTB-POZ Domain; Cyclooxygenase 2; Ferroptosis; Reperfusion Injury; Cinacalcet; Demethylation; Brain Ischemia; Infarction, Middle Cerebral Artery
PubMed: 37161649
DOI: 10.1111/ejn.16035