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Cell Reports Mar 2020Histone methyl groups can be removed by demethylases. Although LSD1 and JmjC domain-containing proteins have been identified as histone demethylases, enzymes for many...
Histone methyl groups can be removed by demethylases. Although LSD1 and JmjC domain-containing proteins have been identified as histone demethylases, enzymes for many histone methylation states or sites are still unknown. Here, we perform a screening of a cDNA library containing 2,500 nuclear proteins and identify hHR23A as a histone H4K20 demethylase. Overexpression of hHR23A reduces the levels of H4K20me1/2/3 in cells. In vitro, hHR23A specifically demethylates H4K20me1/2/3 and generates formaldehyde. The enzymatic activity requires Fe(II) and α-ketoglutarate as cofactors and the UBA domains of hHR23A. hHR23B, a protein homologous to hHR23A, also demethylates H4K20me1/2/3 in vitro and in vivo. We further demonstrate that hHR23A/B activate the transcription of coding genes by demethylating H4K20me1 and the transcription of repetitive elements by demethylating H4K20me3. Nuclear magnetic resonance (NMR) analyses demonstrate that an HxxxE motif in the UBA1 domain is crucial for iron binding and demethylase activity. Thus, we identify two hHR23 proteins as histone demethylases.
Topics: Cell Cycle; DNA Repair Enzymes; DNA-Binding Proteins; Demethylation; Formaldehyde; Genetic Loci; Genome, Human; HEK293 Cells; HeLa Cells; Histones; Humans; Iron; Lysine; Peptides; Protein Domains; RNA, Messenger; Repetitive Sequences, Nucleic Acid; Substrate Specificity; Transcription, Genetic
PubMed: 32209475
DOI: 10.1016/j.celrep.2020.03.001 -
The Journal of Biological Chemistry Feb 2022The cytidine deaminase APOBEC3B (A3B) is an endogenous inducer of somatic mutations and causes chromosomal instability by converting cytosine to uracil in...
The cytidine deaminase APOBEC3B (A3B) is an endogenous inducer of somatic mutations and causes chromosomal instability by converting cytosine to uracil in single-stranded DNA. Therefore, identification of factors and mechanisms that mediate A3B expression will be helpful for developing therapeutic approaches to decrease DNA mutagenesis. Arsenic (As) is one well-known mutagen and carcinogen, but the mechanisms by which it induces mutations have not been fully elucidated. Herein, we show that A3B is upregulated and required for As-induced DNA damage and mutagenesis. We found that As treatment causes a decrease of N6-methyladenosine (m6A) modification near the stop codon of A3B, consequently increasing the stability of A3B mRNA. We further reveal that the demethylase FTO is responsible for As-reduced m6A modification of A3B, leading to increased A3B expression and DNA mutation rates in a manner dependent on the m6A reader YTHDF2. Our in vivo data also confirm that A3B is a downstream target of FTO in As-exposed lung tissues. In addition, FTO protein is highly expressed and positively correlates with the protein levels of A3B in tumor samples from human non-small cell lung cancer patients. These findings indicate a previously unrecognized role of A3B in As-triggered somatic mutation and might open new avenues to reduce DNA mutagenesis by targeting the FTO/m6A axis.
Topics: Adenosine; Alpha-Ketoglutarate-Dependent Dioxygenase FTO; Arsenic; Carcinoma, Non-Small-Cell Lung; Cytidine Deaminase; Demethylation; Humans; Lung Neoplasms; Minor Histocompatibility Antigens; Mutagenesis; RNA, Messenger
PubMed: 34998823
DOI: 10.1016/j.jbc.2022.101563 -
Nature Food Jan 2024
Topics: Mercury; Methylmercury Compounds; Methylation; Plants; Demethylation
PubMed: 38177224
DOI: 10.1038/s43016-023-00909-4 -
Stem Cell Research & Therapy Sep 2022Insulin producing cells generated by liver cell transdifferentiation, could serve as an attractive source for regenerative medicine. The present study assesses the...
BACKGROUND
Insulin producing cells generated by liver cell transdifferentiation, could serve as an attractive source for regenerative medicine. The present study assesses the relationship between DNA methylation pTFs induced liver to pancreas transdifferentiation.
RESULTS
The transdifferentiation process is associated with DNA demethylation, mainly at gene regulatory sites, and with increased expression of these genes. Active inhibition of DNA methylation promotes the pancreatic transcription factor-induced transdifferentiation process, supporting a causal role for DNA demethylation in this process.
CONCLUSIONS
Transdifferentiation is associated with global DNA hypomethylation, and with increased expression of specific demethylated genes. A combination of epigenetic modulators may be used to increase chromatin accessibility of the pancreatic transcription factors, thus promoting the efficiency of the developmental process.
Topics: Cell Transdifferentiation; Chromatin; DNA; DNA Demethylation; Insulins; Liver; Pancreas; Transcription Factors
PubMed: 36114514
DOI: 10.1186/s13287-022-03159-6 -
The Plant Cell Mar 2022Cytosine methylation is a reversible epigenetic modification of DNA. In plants, removal of cytosine methylation is accomplished by the four members of the DEMETER (DME)...
Cytosine methylation is a reversible epigenetic modification of DNA. In plants, removal of cytosine methylation is accomplished by the four members of the DEMETER (DME) family of 5-methylcytosine DNA glycosylases, named DME, DEMETER-LIKE2 (DML2), DML3, and REPRESSOR OF SILENCING1 (ROS1) in Arabidopsis thaliana. Demethylation by DME is critical for seed development, preventing experiments to determine the function of the entire gene family in somatic tissues by mutant analysis. Here, we bypassed the reproductive defects of dme mutants to create somatic quadruple homozygous mutants of the entire DME family. dme; ros1; dml2; and dml3 (drdd) leaves exhibit hypermethylated regions compared with wild-type leaves and rdd triple mutants, indicating functional redundancy among all four demethylases. Targets of demethylation include regions co-targeted by RNA-directed DNA methylation and, surprisingly, CG gene body methylation, indicating dynamic methylation at these less-understood sites. Additionally, many tissue-specific methylation differences are absent in drdd, suggesting a role for active demethylation in generating divergent epigenetic states across wild-type tissues. Furthermore, drdd plants display an early flowering phenotype, which involves 5'-hypermethylation and transcriptional down-regulation of FLOWERING LOCUS C. Active DNA demethylation is therefore required for proper methylation across somatic tissues and defines the epigenetic landscape of intergenic and coding regions.
Topics: Arabidopsis Proteins; DNA Demethylation; DNA Methylation; Gene Expression Regulation, Plant; Protein-Tyrosine Kinases; Proto-Oncogene Proteins
PubMed: 34954804
DOI: 10.1093/plcell/koab319 -
JCI Insight Oct 2023Abnormal macrophage polarization is generally present in autoimmune diseases. Overwhelming M1 macrophage activation promotes the continuous progression of inflammation,...
Abnormal macrophage polarization is generally present in autoimmune diseases. Overwhelming M1 macrophage activation promotes the continuous progression of inflammation, which is one of the reasons for the development of autoimmune diseases. However, the underlying mechanism is still unclear. Here we explore the function of Regulatory factor X1 (RFX1) in macrophage polarization by constructing colitis and lupus-like mouse models. Both in vivo and in vitro experiments confirmed that RFX1 can promote M1 and inhibit M2 macrophage polarization. Furthermore, we found that RFX1 promoted DNA demethylation of macrophage polarization-related genes by increasing APOBEC3A/Apobec3 expression. We identified a potential RFX1 inhibitor, adenosine diphosphate (ADP), providing a potential strategy for treating autoimmune diseases.
Topics: Animals; Mice; Autoimmune Diseases; DNA Demethylation; Inflammation; Macrophage Activation; Macrophages; Regulatory Factor X1
PubMed: 37733446
DOI: 10.1172/jci.insight.165546 -
Environmental Pollution (Barking, Essex... Mar 2024Photodemethylation is the major pathway of methylmercury (MeHg) demethylation in surface water before uptake by the food chain, whose mechanisms and influence factors... (Review)
Review
Photodemethylation is the major pathway of methylmercury (MeHg) demethylation in surface water before uptake by the food chain, whose mechanisms and influence factors are still not completely understood. Here, we review the current knowledge on photodemethylation of MeHg and divide MeHg photolysis into three pathways: (1) direct photodemethylation, (2) free radical attack, and (3) intramolecular electron or energy transfer. In aquatic environments, dissolved organic matter is involved into all above pathways, and due to its complex compositions, properties and concentrations, DOM poses multiple functions during the PD of MeHg. DOM-MeHg complex (mainly by sulfur-containing molecules) might weaken the C-Hg bond and enhance PD through both direct and indirect pathways. In special, synergistic effects of both strong binding sites and chromophoric moieties in DOM might lead to intramolecular electron or energy transfer. Moreover, DOM might play a role of radical scavenger; while triplet state DOM, which is generated by chromophoric DOM under light, might become a source of free radicals. Apart from DOMs, transition metals, halides, NO, NO, and carbonates also act as radical initialaters or scavengers, and significantly pose effects on radical demethylation, which is generally mediated by hydroxyl radicals and singlet oxygen. Environmental factors such as pH, light wavelength, light intensity, dissolved oxygen, salinity, and suspended particles also affect the PD of MeHg. This study assessed previously published works on three major mechanisms, with the goal of providing general estimates for photodemethylation under various environment factors according to know effects, and highlighting the current uncertainties for future research directions.
Topics: Methylmercury Compounds; Mercury; Light; Photolysis; Free Radicals; Demethylation; Water Pollutants, Chemical
PubMed: 38195023
DOI: 10.1016/j.envpol.2024.123297 -
Science Advances Dec 2022DNA methylation [5-methylcytosine (5mC)] is a repressive gene-regulatory mark required for vertebrate embryogenesis. Genomic 5mC is tightly regulated through the action...
DNA methylation [5-methylcytosine (5mC)] is a repressive gene-regulatory mark required for vertebrate embryogenesis. Genomic 5mC is tightly regulated through the action of DNA methyltransferases, which deposit 5mC, and ten-eleven translocation (TET) enzymes, which participate in its active removal through the formation of 5-hydroxymethylcytosine (5hmC). TET enzymes are essential for mammalian gastrulation and activation of vertebrate developmental enhancers; however, to date, a clear picture of 5hmC function, abundance, and genomic distribution in nonvertebrate lineages is lacking. By using base-resolution 5mC and 5hmC quantification during sea urchin and lancelet embryogenesis, we shed light on the roles of nonvertebrate 5hmC and TET enzymes. We find that these invertebrate deuterostomes use TET enzymes for targeted demethylation of regulatory regions associated with developmental genes and show that the complement of identified 5hmC-regulated genes is conserved to vertebrates. This work demonstrates that active 5mC removal from regulatory regions is a common feature of deuterostome embryogenesis suggestive of an unexpected deep conservation of a major gene-regulatory module.
Topics: Animals; DNA Demethylation; Vertebrates; Gene Regulatory Networks; Embryonic Development; DNA Methylation; Mammals
PubMed: 36459547
DOI: 10.1126/sciadv.abn2258 -
Pathology International Oct 2022Overexpression of OCIAD2 in lung adenocarcinoma has already been reported in several research articles, but the molecular mechanism involved remains unknown. Promoter...
Overexpression of OCIAD2 in lung adenocarcinoma has already been reported in several research articles, but the molecular mechanism involved remains unknown. Promoter CpG methylation is a representative form of epigenetic gene regulation, and a considerable number of tumor suppressor genes show hypermethylation in many cancers. In contrast, promoter CpG hypomethylation causes oncogene overexpression, resulting in carcinogenesis and malignant progression. In the present study, we investigated the CpG methylation and expression status of OCIAD2 using tumor tissues and adjacent normal tissues from seven cases of lung adenocarcinoma. We also examined the relationship between CpG methylation status and outcome in 58 patients with adenocarcinoma. Pyrosequencing showed that CpG sites in OCIAD2 promoter regions were more frequently demethylated in tumor tissues than in adjacent normal tissues, and reverse transcription-quantitative polymerase chain reaction revealed overexpression of OCIAD2 in lung adenocarcinoma. There was a correlation between OCIAD2 CpG demethylation and the level of mRNA expression, and statistical analysis showed that CpG hypomethylation of OCIAD2 was associated with poor outcomes. Our results suggest that overexpression of OCIAD2 might be caused mainly by CpG hypomethylation and that OCIAD2 methylation status might be a useful prognostic indicator in lung adenocarcinoma.
Topics: Adenocarcinoma of Lung; CpG Islands; DNA Methylation; Demethylation; Gene Expression Regulation, Neoplastic; Humans; Lung Neoplasms; Neoplasm Proteins; RNA, Messenger
PubMed: 35920378
DOI: 10.1111/pin.13262 -
Epigenetics & Chromatin Oct 2023Vitamin C (vitC) enhances the activity of 2-oxoglutarate-dependent dioxygenases, including TET enzymes, which catalyse DNA demethylation, and Jumonji-domain histone...
BACKGROUND
Vitamin C (vitC) enhances the activity of 2-oxoglutarate-dependent dioxygenases, including TET enzymes, which catalyse DNA demethylation, and Jumonji-domain histone demethylases. The epigenetic remodelling promoted by vitC improves the efficiency of induced pluripotent stem cell derivation, and is required to attain a ground-state of pluripotency in embryonic stem cells (ESCs) that closely mimics the inner cell mass of the early blastocyst. However, genome-wide DNA and histone demethylation can lead to upregulation of transposable elements (TEs), and it is not known how vitC addition in culture media affects TE expression in pluripotent stem cells.
RESULTS
Here we show that vitC increases the expression of several TE families, including evolutionarily young LINE-1 (L1) elements, in mouse ESCs. We find that TET activity is dispensable for L1 upregulation, and that instead it occurs largely as a result of H3K9me3 loss mediated by KDM4A/C histone demethylases. Despite increased L1 levels, we did not detect increased somatic insertion rates in vitC-treated cells. Notably, treatment of human ESCs with vitC also increases L1 protein levels, albeit through a distinct, post-transcriptional mechanism.
CONCLUSION
VitC directly modulates the expression of mouse L1s and other TEs through epigenetic mechanisms, with potential for downstream effects related to the multiple emerging roles of L1s in cellular function.
Topics: Humans; Animals; Mice; Ascorbic Acid; Mouse Embryonic Stem Cells; Long Interspersed Nucleotide Elements; DNA Methylation; Histone Demethylases; DNA; Demethylation; Jumonji Domain-Containing Histone Demethylases
PubMed: 37845773
DOI: 10.1186/s13072-023-00514-6