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Biology Direct May 2024The enzymes performing protein post-translational modifications (PTMs) form a critical post-translational regulatory circuitry that orchestrates literally all cellular... (Review)
Review
The enzymes performing protein post-translational modifications (PTMs) form a critical post-translational regulatory circuitry that orchestrates literally all cellular processes in the organism. In particular, the balance between cellular stemness and differentiation is crucial for the development of multicellular organisms. Importantly, the fine-tuning of this balance on the genetic level is largely mediated by specific PTMs of histones including lysine methylation. Lysine methylation is carried out by special enzymes (lysine methyltransferases) that transfer the methyl group from S-adenosyl-L-methionine to the lysine residues of protein substrates. Set7/9 is one of the exemplary protein methyltransferases that however, has not been fully studied yet. It was originally discovered as histone H3 lysine 4-specific methyltransferase, which later was shown to methylate a number of non-histone proteins that are crucial regulators of stemness and differentiation, including p53, pRb, YAP, DNMT1, SOX2, FOXO3, and others. In this review we summarize the information available to date on the role of Set7/9 in cellular differentiation and tissue development during embryogenesis and in adult organisms. Finally, we highlight and discuss the role of Set7/9 in pathological processes associated with aberrant cellular differentiation and self-renewal, including the formation of cancer stem cells.
Topics: Histone-Lysine N-Methyltransferase; Cell Differentiation; Humans; Animals; Protein Processing, Post-Translational; Methylation; Stem Cells
PubMed: 38812048
DOI: 10.1186/s13062-024-00484-z -
Proceedings of the National Academy of... Jun 2020The development of methyl-transverse relaxation-optimized spectroscopy (methyl-TROSY)-based NMR methods, in concert with robust strategies for incorporation of...
The development of methyl-transverse relaxation-optimized spectroscopy (methyl-TROSY)-based NMR methods, in concert with robust strategies for incorporation of methyl-group probes of structure and dynamics into the protein of interest, has facilitated quantitative studies of high-molecular-weight protein complexes. Here we develop a one-pot in vitro reaction for producing NMR quantities of methyl-labeled DNA at the C5 and N6 positions of cytosine (5mC) and adenine (6mA) nucleobases, respectively, enabling the study of high-molecular-weight DNA molecules using TROSY approaches originally developed for protein applications. Our biosynthetic strategy exploits the large number of naturally available methyltransferases to specifically methylate DNA at a desired number of sites that serve as probes of structure and dynamics. We illustrate the methodology with studies of the 153-base pair Widom DNA molecule that is simultaneously methyl-labeled at five sites, showing that high-quality C-H spectra can be recorded on 100 μM samples in a few minutes. NMR spin relaxation studies of labeled methyl groups in both DNA and the H2B histone protein component of the 200-kDa nucleosome core particle (NCP) establish that methyl groups at 5mC and 6mA positions are, in general, more rigid than Ile, Leu, and Val methyl probes in protein side chains. Studies focusing on histone H2B of NCPs wrapped with either wild-type DNA or DNA methylated at all 26 CpG sites highlight the utility of NMR in investigating the structural dynamics of the NCP and how its histone core is affected through DNA methylation, an important regulator of transcription.
Topics: Adenine; Carbon Isotopes; CpG Islands; Cytosine; DNA; DNA Methylation; DNA-Binding Proteins; Molecular Dynamics Simulation; Molecular Weight; Nuclear Magnetic Resonance, Biomolecular; Nucleosomes; Spectrum Analysis
PubMed: 32457157
DOI: 10.1073/pnas.2004317117 -
Genes Feb 2023Epigenetics is a gene-environment interaction mechanism, manifested mostly through changes in regulatory gene expression. Stress is an established environmental factor...
Epigenetics is a gene-environment interaction mechanism, manifested mostly through changes in regulatory gene expression. Stress is an established environmental factor known to induce epigenetic changes. This study aimed to assess the long-term effect of stress as juveniles, or juvenile and adult stress, on alterations in glutamic acid decarboxylase genes (, ). We assessed DNA methylation and RNA expression in four rat groups: (1) control group, (2) juvenile stress group sacrificed two days following stress exposure (JSe) (RNA only), (3) juvenile stress group sacrificed as adults (JS), and (4) juvenile and adult stress group (JS + AS). Three different areas of the brain were examined in each group: the dorsal dentate gyrus (dDG), the dorsal CA1 (dCA1), and the basolateral amygdala (BLA). A significantly low methylation level of in the BLA was observed among the JS group, followed by almost complete recovery among the JS + AS group. However, in dDG, an opposite trend was captured, and higher methylation was found in JS. In addition, RNA levels were found to be decreased in JS compared to JSe and JS + AS. These findings can point to a possible mechanism: while juvenile stress may enhance a better coping strategy with life challenges, additional stress in adulthood may trigger a contradictory response, either beneficial or harmful.
Topics: Rats; Animals; Brain; DNA Methylation; Epigenesis, Genetic; RNA
PubMed: 36980837
DOI: 10.3390/genes14030565 -
International Journal of Molecular... 2011Individual variations in inorganic arsenic metabolism may influence the toxic effects. Arsenic (+3 oxidation state) methyltransferase (AS3MT) that can catalyze the... (Review)
Review
Individual variations in inorganic arsenic metabolism may influence the toxic effects. Arsenic (+3 oxidation state) methyltransferase (AS3MT) that can catalyze the transfer of a methyl group from S-adenosyl-l-methionine (AdoMet) to trivalent arsenical, may play a role in arsenic metabolism in humans. Since the genetic polymorphisms of AS3MT gene may be associated with the susceptibility to inorganic arsenic toxicity, relationships of several single nucleotide polymorphisms (SNPs) in AS3MT with inorganic arsenic metabolism have been investigated. Here, we summarize our recent findings and other previous studies on the inorganic arsenic metabolism and AS3MT genetic polymorphisms in humans. Results of genotype dependent differences in arsenic metabolism for most of SNPs in AS3MT were Inconsistent throughout the studies. Nevertheless, two SNPs, AS3MT 12390 (rs3740393) and 14458 (rs11191439) were consistently related to arsenic methylation regardless of the populations examined for the analysis. Thus, these SNPs may be useful indicators to predict the arsenic metabolism via methylation pathways.
Topics: Arsenic; Gene Frequency; Humans; Methylation; Methyltransferases; Polymorphism, Single Nucleotide; Racial Groups; S-Adenosylmethionine
PubMed: 21731446
DOI: 10.3390/ijms12042351 -
Molecules (Basel, Switzerland) Jun 2021The almiramide -methylated lipopeptides exhibit promising activity against trypanosomatid parasites. A structure-activity relationship study has been performed to...
The almiramide -methylated lipopeptides exhibit promising activity against trypanosomatid parasites. A structure-activity relationship study has been performed to examine the influences of -methylation and conformation on activity against various strains of leishmaniasis protozoan and on cytotoxicity. The synthesis and biological analysis of twenty-five analogs demonstrated that derivatives with a single methyl group on either the first or fifth residue amide nitrogen exhibited greater activity than the permethylated peptides and relatively high potency against resistant strains. Replacement of amino amide residues in the peptide, by turn inducing α amino γ lactam (Agl) and -aminoimidazalone (Nai) counterparts, reduced typically anti-parasitic activity; however, peptide amides possessing Agl residues at the second residue retained significant potency in the unmethylated and permethylated series. Systematic study of the effects of methylation and turn geometry on anti-parasitic activity indicated the relevance of an extended conformer about the central residues, and conformational mobility by tertiary amide isomerization and turn geometry at the extremities of the active peptides.
Topics: Amides; Isomerism; Leishmania; Lipopeptides; Methylation; Protein Conformation; Structure-Activity Relationship
PubMed: 34204673
DOI: 10.3390/molecules26123606 -
Annual Review of Nutrition Aug 2018Exposure to inorganic arsenic (InAs) via drinking water and/or food is a considerable worldwide problem. Methylation of InAs generates monomethyl (MMAs)- and dimethyl... (Review)
Review
Exposure to inorganic arsenic (InAs) via drinking water and/or food is a considerable worldwide problem. Methylation of InAs generates monomethyl (MMAs)- and dimethyl (DMAs)-arsenical species in a process that facilitates urinary As elimination; however, MMAs is considerably more toxic than either InAs or DMAs. Emerging evidence suggests that incomplete methylation of As to DMAs, resulting in increased MMAs, is associated with increased risk for a host of As-related health outcomes. The biochemical pathway that provides methyl groups for As methylation, one-carbon metabolism (OCM), is influenced by folate and other micronutrients, including choline and betaine. Individuals and species differ widely in their ability to methylate As. A growing body of research, including cell-culture, animal-model, and epidemiological studies, has demonstrated the role of OCM-related micronutrients in As methylation. This review examines the evidence that nutritional status and nutritional interventions can influence the metabolism and toxicity of As, with a primary focus on folate.
Topics: Animals; Arsenic; Carbon; Dietary Exposure; Humans; Methylation; Nutritional Physiological Phenomena
PubMed: 29799766
DOI: 10.1146/annurev-nutr-082117-051757 -
Clinical Epigenetics Mar 2023Few studies have examined epigenetic age acceleration (AA), the difference between DNA methylation (DNAm) predicted age and chronological age, in relation to somatic...
BACKGROUND
Few studies have examined epigenetic age acceleration (AA), the difference between DNA methylation (DNAm) predicted age and chronological age, in relation to somatic genomic features in paired cancer and normal tissue, with less work done in non-European populations. In this study, we aimed to examine DNAm age and its associations with breast cancer risk factors, subtypes, somatic genomic profiles including mutation and copy number alterations and other aging markers in breast tissue of Chinese breast cancer (BC) patients from Hong Kong.
METHODS
We performed genome-wide DNA methylation profiling of 196 tumor and 188 paired adjacent normal tissue collected from Chinese BC patients in Hong Kong (HKBC) using Illumina MethylationEPIC array. The DNAm age was calculated using Horvath's pan-tissue clock model. Somatic genomic features were based on data from RNA sequencing (RNASeq), whole-exome sequencing (WES), and whole-genome sequencing (WGS). Pearson's correlation (r), Kruskal-Wallis test, and regression models were used to estimate associations of DNAm AA with somatic features and breast cancer risk factors.
RESULTS
DNAm age showed a stronger correlation with chronological age in normal (Pearson r = 0.78, P < 2.2e-16) than in tumor tissue (Pearson r = 0.31, P = 7.8e-06). Although overall DNAm age or AA did not vary significantly by tissue within the same individual, luminal A tumors exhibited increased DNAm AA (P = 0.004) while HER2-enriched/basal-like tumors exhibited markedly lower DNAm AA (P = < .0001) compared with paired normal tissue. Consistent with the subtype association, tumor DNAm AA was positively correlated with ESR1 (Pearson r = 0.39, P = 6.3e-06) and PGR (Pearson r = 0.36, P = 2.4e-05) gene expression. In line with this, we found that increasing DNAm AA was associated with higher body mass index (P = 0.039) and earlier age at menarche (P = 0.035), factors that are related to cumulative exposure to estrogen. In contrast, variables indicating extensive genomic instability, such as TP53 somatic mutations, high tumor mutation/copy number alteration burden, and homologous repair deficiency were associated with lower DNAm AA.
CONCLUSIONS
Our findings provide additional insights into the complexity of breast tissue aging that is associated with the interaction of hormonal, genomic, and epigenetic mechanisms in an East Asian population.
Topics: Humans; Female; DNA Methylation; Breast Neoplasms; East Asian People; Breast; Epigenesis, Genetic; Aging
PubMed: 36991516
DOI: 10.1186/s13148-023-01465-1 -
Biophysical Journal Dec 1995The molecular order and hydration properties of the amine group in phosphatidylethanolamine and its N-methyl derivatives were studied by 2H-NMR at subzero temperatures.... (Comparative Study)
Comparative Study
The molecular order and hydration properties of the amine group in phosphatidylethanolamine and its N-methyl derivatives were studied by 2H-NMR at subzero temperatures. Three coexisting signals with 2H-NMR quadrupolar splittings of 146, 106, and 28.8 KHz were detected from the fully hydrated phosphatidylethanolamine/D2O at the lowest studied temperature of -120 degrees C by using short recycle time in the applied NMR pulse sequence. These signals have been assigned to originate from frozen D2O in the interbilayer space and the deuterated amine group, i.e., -ND, with and without threefold symmetric motions. Comparative 2H-NMR studies of phosphatidylethanolamine/D2O with different degrees of methylation over a temperature range between -40 and -120 degrees C lead to the following conclusions. First, the bond angle of -D attached to the nitrogen atom of the amine group may be determined by the 2H-NMR quadrupolar splittings, i.e., 106 and 28.8 KHz, of the two coexisting signals of the deuterated amine group and found to be 112.9 for the gel-state phosphatidylethanolamine. Second, assuming the applicability of the empirical equation for the hydrogen bond distance of N+D--O with deuteron quadrupole coupling constants and using the intermolecular hydrogen bond distance of the amine group determined in single crystals of phosphatidylethanolamine bilayers, the largest measured quadrupolar splitting (delta nu Q) of N-D in this study, i.e., 106 KHz, is close to the static value. This interpretation is also consistent with the fact that the delta nu Q value determined remains constant in the temperature range between -70 and -120 degrees C. Third, the molecular order parameter of the amine group, as calculated from the ratio of the libration-averaged and static delta nu Q value for the lipid with different degrees of methylation, suggests that the perturbation of the headgroup interaction is most significant for the final methylation step. Finally, measurement of the spectral intensity of isotropic unfrozen D2O signals in D2O/phospholipid dispersions at temperatures below the homogeneous nucleation temperature of ice formation for D2O, i.e., below -34 degrees C, suggests that the first methylation step perturbs the neighboring water most significantly. Assuming that the molecular order of the amine group and the amount of unfrozen water detected under the present experimental condition can be taken as a measure of the hydrogen-bonding ability and the extent of perturbation caused by the methyl group, respectively, the gradual methylation of the amine group perturbs the interactions of the N-methylated headgroups in a nonlinear fashion. The results provide a molecular explanation for the phase behavior of phospholipids with different degrees of methylation.
Topics: Deuterium; Freezing; Magnetic Resonance Spectroscopy; Methylation; Molecular Conformation; Phosphatidylcholines; Phosphatidylethanolamines; Structure-Activity Relationship
PubMed: 8599659
DOI: 10.1016/S0006-3495(95)80123-2 -
Biological Research For Nursing Jan 2022Cardiovascular disease disproportionately affects African Americans as the leading cause of morbidity and mortality. Among African Americans, compared to other racial...
BACKGROUND
Cardiovascular disease disproportionately affects African Americans as the leading cause of morbidity and mortality. Among African Americans, compared to other racial groups, cardiovascular disease onset occurs at an earlier age due to a higher prevalence of cardiometabolic risk factors, particularly obesity, hypertension and type 2 diabetes. Emerging evidence suggests that heritable epigenetic processes are related to increased cardiovascular disease risk, but this is largely unexplored in adolescents or across generations.
MATERIALS AND METHODS
In a cross-sectional descriptive pilot study in low-income African American mother-adolescent dyads, we examined associations between DNA methylation and the cardiometabolic indicators of body mass index, waist circumference, and insulin resistance.
RESULTS
Four adjacent cytosine and guanine nucleotides (CpG) sites were significantly differentially methylated and associated with C-reactive protein (CRP), 62 with waist circumference, and none to insulin resistance in models for both mothers and adolescents.
CONCLUSION
Further study of the relations among psychological and environmental stressors, indicators of cardiovascular disease, risk, and epigenetic factors will improve understanding of cardiovascular disease risk so that preventive measures can be instituted earlier and more effectively. To our knowledge this work is the first to examine DNA methylation and cardiometabolic risk outcomes in mother-adolescent dyads.
Topics: Adolescent; Black or African American; Body Mass Index; Cardiovascular Diseases; Cross-Sectional Studies; DNA Methylation; Diabetes Mellitus, Type 2; Female; Humans; Insulin Resistance; Mothers; Pilot Projects; Risk Factors; Waist Circumference
PubMed: 34719281
DOI: 10.1177/10998004211039017 -
Chemical Research in Toxicology Dec 2020Inorganic arsenic is one of the most toxic and carcinogenic substances in the environment, but many organisms, including humans, methylate inorganic arsenic to mono-,...
Inorganic arsenic is one of the most toxic and carcinogenic substances in the environment, but many organisms, including humans, methylate inorganic arsenic to mono-, di-, and trimethylated arsenic metabolites, which the organism can excrete. In humans and other eukaryotic organisms, the arsenite methyltransferase (AS3MT) protein methylates arsenite. AS3MT sequences from eukaryotic organisms group phylogenetically with predicted eubacterial AS3MT sequences, which has led to the suggestion that AS3MT was acquired from eubacteria by multiple events of horizontal gene transfer. In this study, we evaluated whether 55 (out of which 47 were predicted based on protein sequence similarity) sequences encoding putative AS3MT orthologues in 47 species from different kingdoms can indeed methylate arsenic. Fifty-three of the proteins showed arsenic methylating capacity. For example, the predicted AS3MT of the human gut bacterium methylated arsenic efficiently. We performed a kinetic analysis of 14 AS3MT proteins representing two phylogenetically distinct clades (Group 1 and 2) that each contain both eubacterial and eukaryotic sequences. We found that animal and bacterial AS3MTs in Group 1 rarely produce trimethylated arsenic, whereas and the bacterium in Group 2 produce trimethylated arsenic metabolites. These findings suggest that animals during evolution have acquired different arsenic methylating phenotypes from different bacteria. Further, it shows that humans carry two bacterial systems for arsenic methylation: one bacterium-derived AS3MT from Group 1 incorporated in the human genome and one from Group 2 in present in the gut microbiome.
Topics: Animals; Arsenic; Faecalibacterium prausnitzii; Gastrointestinal Microbiome; Humans; Hydra; Methylation; Methyltransferases; Phylogeny; Rhodopseudomonas
PubMed: 33156617
DOI: 10.1021/acs.chemrestox.0c00375