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MethylationLysineHistonesCytosineDNA Methylation5-MethylcytosineDNA-Cytosine MethylasesSulfitesDNA (Cytosine-5-)-MethyltransferaseMolecular Sequence DataBase SequenceAcetylationCpG IslandsHistone DeacetylasesChromatinDNAPromoter Regions, GeneticUracilEpigenesis, GeneticAmino Acid SequenceHistone-Lysine N-MethyltransferaseTranscription, GeneticHistone AcetyltransferasesHistone Deacetylase InhibitorsMutationBinding SitesRepressor ProteinsDinucleoside PhosphatesGene SilencingDNA-Binding ProteinsAzacitidineCytosine DeaminaseNucleosomesPentoxylEnzyme RepressionEscherichia coliProtein BindingDeoxyribonuclease HpaIIProtein MethyltransferasesTranscription FactorsSubstrate SpecificityCell LineAdenineHistone DemethylasesMethyltransferasesNucleic Acid ConformationKineticsGuanineHistone Deacetylase 1Hydroxamic AcidsNuclear ProteinsProtein Structure, TertiaryChromatin Assembly and DisassemblyChromatin ImmunoprecipitationGene Expression RegulationOligodeoxyribonucleotidesHeterochromatinModels, MolecularHistone CodeCloning, MolecularSaccharomyces cerevisiae ProteinsNucleic Acid DenaturationSaccharomyces cerevisiaeChromosomal Proteins, Non-HistoneHistone Deacetylase 2Histone ChaperonesHydroxylaminesJumonji Domain-Containing Histone DemethylasesProtein Processing, Post-TranslationalMutagenesis, Site-DirectedPolymerase Chain ReactionHeLa CellsSequence Homology, Amino AcidEpigenomicsDNA Modification MethylasesCell Line, TumorRNA, MessengerDNA, BacterialAcetyltransferasesBase CompositionProtein ConformationProtein-Arginine N-MethyltransferasesPhosphorylationGenomic ImprintingSequence AlignmentPlasmidsDNA PrimersGene Expression Regulation, FungalDNA, ViralRecombinant ProteinsAmino AcidsDNA Restriction EnzymesRecombinant Fusion ProteinsDeaminationPolycomb-Group ProteinsPolycomb Repressive Complex 2Structure-Activity RelationshipTranscriptional ActivationS-AdenosylmethionineArginine

EpigeneticH3K9Chromatin structureAcetylationModificationsH3K4Transcriptional repressionMethyltransferaseMethyl groupTranscriptionDNMTsRepressiveDeacetylaseNucleosomeContrastDNMT1PromoterProteinsPathwaysDimethylationNucleosomesH3K9me3EnzymesEukaryoticGenesMechanismsEvolutionaryArginineEndogenousCoreExpressionEffects

Epigenetic10

• The mechanism of epigenetic regulation involves the CpG site methylation of promoter regions and the modification of DNA and histones by altering chromatin structure ( 9 - 11 ). (spandidos-publications.com)
• We suggest that the parent seed nitrogen content decreased induced DNA methylation changes at the epigenetic level and significantly decreased the expression of OsNAR2.1 , resulting in a heritable phenotype of N deficiency over two generations of the overexpression line. (biomedcentral.com)
• DNA methylation is the major heritable epigenetic modification and contributes to the epigenetic regulation of nuclear gene expression and genome stability [ 13 ]. (biomedcentral.com)
• Central to the epigenetic control of gene expression is the histone code through which input signals can be translated into a heritable pattern of gene expression defining cellular output states ( Fig. 1 ). (aacrjournals.org)
• Despite continuous study and development of fresh restorative regimens, the 5-12 months overall survival (OS) rate of non-small cell lung malignancy (NSCLC) remains at a mere 15%.1 Epigenetic therapy approaches offer novel, innovative treatment options that may improve this troubling statistic, namely with DNA methyltransferase inhibitors (DNMTi) and histone-modifying agents. (unambitiousus.com)
• Posttranslational modifications, such as addition or removal of methyl or acetyl organizations to amino acids within the histones, can lead to a change of conformation and therefore facilitate or hinder access of the transcription element machinery to the DNA.4,5 Reversing the aberrant epigenetic patterns of cancer cells can re-sensitize them to founded treatment, e.g., chemotherapeutics or radiation therapy. (unambitiousus.com)
• These epigenetic mechanisms are mediated by chemical modifications of DNA, proteins (most commonly histones), and RNA. (activemotif.com.cn)
• Dynamic visualization of histone modifications with genetically encoded fluorescent sensors makes it possible to monitor changes in the epigenetic state of a single living cell. (bvsalud.org)
• 2 In addition to the well-established epigenetic role of DNA methylation, this definition includes a variety of more transient histone modifications such as acetylation, methylation, or phosphorylation that underlie epigenetic effects, and that will be discussed in this chapter along with the influence of SUMOylation, ubiquitination, adenosine diphosphate (ADP) ribosylation, and microRNA. (musculoskeletalkey.com)
• Could the emergence or loss of a specific nucleosome regulator affect the evolution of DNA methylation as an epigenetic mechanism? (elifesciences.org)

H3K96

• In mammalian cells, histone H3 Lys 9 (H3K9) methylation and histone hypoacetylation are usually associated with methylated DNA, heterochromatin, and gene silencing. (aacrjournals.org)
• In contrast, histones present in the compacted heterochromatin are enriched in either tri-methylated H3K27 (H3K27me3) or tri-methylated H3K9 (H3K9me3) [ 3 ]. (biomedcentral.com)
• During repression, acetylation levels on H3K9 show steady increase whereas H3K14 acetylation increases with a peak at 40 min after which levels reduce. (bvsalud.org)
• In contrast, treatment with histone methylase inhibitors decreased the methylation of histones H3K9 and H3K27 and slightly induced NR0B1 transcription. (oncotarget.com)
• In conclusion, this study shows that CpG methylation within the NR0B1 promoter is not involved in the in vivo regulation of NR0B1 expression, whereas the hyperacetylation of histone H4 and the unmethylation of histones H3K9 and H3K27, and their binding to the NR0B1 promoter results in decondensed euchromatin for NR0B1 activation. (oncotarget.com)
• Thus H3K9 methylation at the promoter region silences transcription, but within the coding region, H3K9 methylation was found to be associated with actively transcribed genes. (musculoskeletalkey.com)

Chromatin structure3

• The effects of DNA methylation and the histone code are due, at least in part, to modification-specific recruitment of factors, such as heterochromatin-associated proteins (HP1) and methyl-binding domain proteins, which establish and maintain higher order of chromatin structure. (aacrjournals.org)
• It is generally believed that the histone code can influence transcriptional activity directly by affecting chromatin structure, thereby making it more or less accessible for transcription factors and indirectly leading to the attraction of effector molecules that in turn recruit and stabilize the transcription machinery. (musculoskeletalkey.com)
• Here, we report that mice encountering an acute exposure to alcohol on gestational Day-7 exhibit significant alterations in chromatin structure (histone 3 lysine 9 dimethylation, lysine 9 acetylation, and lysine 27 trimethylation) at Day-17, and that these changes strongly correlate with the development of craniofacial and central nervous system defects. (biomedcentral.com)

Acetylation5

• The code is an array of post-translational modifications (acetylation, phosphorylation, methylation, ubiquitination, and sumoylation) of NH 2 -terminal tails of core histone and to a lesser degree their globular domains. (aacrjournals.org)
• However, insufficient data exist on how histone posttranslational modifications (PTMs), including acetylation, affect genome organization. (bvsalud.org)
• In Neurospora, the HCHC complex [composed of the proteins HDA-1, CDP-2 (Chromodomain Protein-2), Heterochromatin Protein-1, and CHAP (CDP-2 and HDA-1 Associated Protein)] deacetylates heterochromatic nucleosomes, as loss of individual HCHC members increases centromeric acetylation, and alters the methylation of cytosines in DNA. (bvsalud.org)
• Histone acetylation is catalyzed by histone acetyltransferases (HATs) and is counteracted by histone deacetylases (HDACs). (musculoskeletalkey.com)
• HDACs and HATs not only modify histones, they also form complexes with transcription factors, oncoproteins, and tumor suppressors and regulate their activity by changing the acetylation status. (musculoskeletalkey.com)

Modifications6

• Cross-talk between different histone modifications, as well as DNA methylation, seems complex. (aacrjournals.org)
• Histones are subjected to a variety of post-translational covalent modifications [ 1 ] that may impact the overall degree of packing of the genome. (biomedcentral.com)
• In most organisms, the opened euchromatin is enriched in tri-methylation of lysine 4 and lysine 36 (H3K4me3 and H3K36me3), two concomitant modifications associated with active transcription [ 2 ]. (biomedcentral.com)
• The contrasting association of the histone acetylations with pol II and pol III transcription may be an important consideration to make in research studies focused on drug developments targeting histone modifications. (bvsalud.org)
• Post-translational modifications of histones to a large extent determine the functional state of chromatin loci. (bvsalud.org)
• Also, more and more accumulating evidence indicates that the different histone modifications are strongly interconnected and can enforce or counteract each other. (musculoskeletalkey.com)

H3K42

• Ketamine treatment increased the binding of NF‑κB and permissive histone H3 lysine‑4 (H3K4)m3, but caused a decrease in the repressive histone H3K27m3 and H3K36m3 on the COX‑2 promoter ranging from ‑1,522 to ‑1,331 bp as determined by a chromatin immunoprecipitation assay. (spandidos-publications.com)
• Histone hyperacetylation and H3K4 methylation are associated with unmethylated DNA, euchromatin, and gene expression ( Fig. 2 ). (aacrjournals.org)

Transcriptional repression2

• It is generally accepted that H3K27me3-enriched heterochromatin maintains transcriptional repression established during early development and regulates cell fate. (biomedcentral.com)
• Peptidylarginine deiminase 4 (PAD4) converts methylated arginine to citrulline, and this leads to transcriptional repression. (musculoskeletalkey.com)

Methyltransferase3

• DNMT1 preserves the methyltransferase by binding to hemi-methylated CpG sites and methylates the cytosine on the newly synthesized strand after DNA replication, whereas DNMT3a/DNMT3b are required for the de novo genomic methylation of DNA ( 15 ). (spandidos-publications.com)
• We generated the corresponding histone methyltransferase null mutants and showed an interdependence of H3K9me3 and H3K27me3 marks. (biomedcentral.com)
• Mutations in HELLS, its activator CDCA7, and the de novo DNA methyltransferase DNMT3B, cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome, a genetic disorder associated with the loss of DNA methylation. (elifesciences.org)

Methyl group2

• Moreover, the CpG site methylation is mediated by DNA methyltransferases (DNMTs), which catalyze the addition of a methyl group to cytosine ( 13 , 14 ). (spandidos-publications.com)
• Combination strategies often are used with the rationale to epigenetically perfect the malignancy cells by treatment with epigenetically active agents to the activity of the consequently given second agent.2 DNA methylation usually happens by transfer of a methyl group to the cytosine of a cytosine-guanine dinucleotide (CpG), e.g., of gene promoters. (unambitiousus.com)

Transcription3

• Moreover, in the ketamine group, the level of Ten‑Eleven‑Translocation methylcytosine dioxygenase for demethylation as determined by reverse transcription‑quantitative PCR assay was increased in comparison with the control group, but that was not the case for the level of DNA methyltransferases for methylation. (spandidos-publications.com)
• A retinoblastoma-binding protein that is involved in CHROMATIN REMODELING, histone deacetylation, and repression of GENETIC TRANSCRIPTION. (lookformedical.com)
• The increase in H3 acetylations is seen in the mutants reported to show reduced SNR6 transcription but not in the maf1Δ cells. (bvsalud.org)

DNMTs3

• DNA methylation FF-10101 DNA methyltransferases (DNMTs) transfer methyl organizations to cytosines by employing S-adenosyl methionine (SAM) as their methyl donor. (unambitiousus.com)
• Maintenance DNMTs (directly or indirectly) recognize hemimethylated CpGs and restore symmetric methylation at these sites to prevent the passive loss of 5mC upon DNA replication. (elifesciences.org)
• Conversely, methylation by de novo DNMTs does not require methylated DNA templates. (elifesciences.org)

Repressive3

• However, we uncovered an intriguing evolutionary fluidity in the repressive histone deposition machinery, which challenges canonical definitions of constitutive and facultative heterochromatin. (biomedcentral.com)
• Although initially discovered as a retinoblastoma binding protein it has an affinity for core HISTONES and is a subunit of chromatin assembly factor-1 and polycomb repressive complex 2. (lookformedical.com)
• It is found as a subunit of protein complexes that are in involved in the enzymatic modification of histones including the Mi2 and Sin3 histone deacetylase complexes and the polycomb repressive complex 2. (lookformedical.com)

Deacetylase1

• Treating 293T cells with a histone deacetylase inhibitor increased acetylated histone H4 binding to the NR0B1 promoter and activated NR0B1 expression. (oncotarget.com)

Nucleosome4

• A histone chaperone that facilitates nucleosome assembly by mediating the formation of the histone octamer and its transfer to DNA. (lookformedical.com)
• On one of these genes, SNR6 (coding for the U6snRNA), a strongly positioned nucleosome in the gene upstream region plays regulatory role under repression. (bvsalud.org)
• This increase on a regulatory nucleosome may be part of the signaling mechanisms, which prepare cells for the stress-related quick repression as well as reactivation. (bvsalud.org)
• This important manuscript reveals signatures of co-evolution of two nucleosome remodeling factors, Lsh/HELLS and CDCA7, which are involved in the regulation of eukaryotic DNA methylation. (elifesciences.org)

Contrast2

• In contrast, the Ten-Eleven-Translocation (TET) dioxygenase family, including TET1, TET2 and TET3, mediates active DNA demethylation and hydroxylate-methylated DNA by converting 5-methylcyto-sine to 5-hydroxymethylcytosine to regulate DNA methylation status. (spandidos-publications.com)
• Nucleoproteins, which in contrast to HISTONES, are acid insoluble. (lookformedical.com)

DNMT11

• In animals, 5mC is maintained during DNA replication by DNMT1 together with UHRF1, which directly recognizes hemimethylated cytosine via the SRA domain and stimulates activity of DNMT1 in a manner dependent on its ubiquitin-ligase activity ( Nishiyama and Nakanishi, 2021 ). (elifesciences.org)

Promoter2

• The present study investigated the methylation of CpG sites in the cyclooxygenase (COX)‑2 promoter via nuclear factor (NF)‑κB transcriptional regulation and elucidated its effect on the COX‑2 transcriptional expression in a ketamine‑induced ulcerative cystitis (KIC) animal model. (spandidos-publications.com)
• Furthermore, the level of acetyl-histone H4 binding to the NR0B1 promoter increased, whereas the occupancy of H3K27me3 was lower in cancerous tissues than in non-cancerous tissues. (oncotarget.com)

Proteins3

• This allows the binding of different proteins that ultimately prohibit the RNA polymerase to access this area and may consequently silence the respective gene.3 Histones are nuclear proteins around which the DNA is wrapped. (unambitiousus.com)
• and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell. (lookformedical.com)
• The best studied effector proteins binding phosphorylated histones are 14-3-3 proteins and BRCA1 C-terminus (BRCT) domains. (musculoskeletalkey.com)

Pathways3

• Furthermore, methylation sequencing results showed that LPSN caused massive gene methylation changes, which enriched in over 20 GO pathways in the filial overexpression line, and the expression of OsNAR2.1 in LPSN filial overexpression plants was significantly reduced compared to HPSN filial plants in high external N, which was not shown in wild type. (biomedcentral.com)
• The results suggest that the roles for the two factors in DNA methylation maintenance pathways can be traced back to the last eukaryotic common ancestor and that the CDC7A-HELLS-DNMT axis shaped the evolutionary retention of DNA methylation in eukaryotes. (elifesciences.org)
• development repression in MDCK susceptible pathways. (evakoch.com)

Dimethylation1

• The various members of this group of enzymes are highly specialized in methylating selected lysines or arginines to a certain degree (monomethylation, dimethylation, trimethylation). (musculoskeletalkey.com)

Nucleosomes1

• A histone chaperone protein that plays a role in the deposition of NUCLEOSOMES on newly synthesized DNA. (lookformedical.com)

H3K9me32

• When present, high levels of DNA cytosine methylation are found in H3K9me3-enriched regions. (biomedcentral.com)
• Here, we report an optogenetic sensor for live-cell visualization of histone H3 methylated at lysine-9 (H3K9me3) named MPP8-LAMS (MPP8-based light-activated modification sensor). (bvsalud.org)

Enzymes1

• Enzymes that catalyze acyl group transfer from ACETYL-CoA to HISTONES forming CoA and acetyl-histones. (lookformedical.com)

Eukaryotic1

• Our study suggests that a unique specialized role of CDCA7 in HELLS-dependent DNA methylation maintenance is broadly inherited from the last eukaryotic common ancestor. (elifesciences.org)

Genes2

• Both DNA hypo- and hyper-methylation are found in malignancy cells, the second option can lead to silencing of tumor suppressor genes6 or of genes that are involved in, e.g., metastasis, angiogenesis, invasion, or immune response by T-cell acknowledgement.7 Table?1 provides a list of currently investigated DNMTi. (unambitiousus.com)
• We found that most of the histone acetylations increase with starvation-induced repression on several genes transcribed by the yeast pol III. (bvsalud.org)

Mechanisms1

• We hypothesize that CDCA7 becomes dispensable in species that lost HELLS or DNA methylation, and/or the loss of CDCA7 triggers the replacement of DNA methylation by other chromatin regulation mechanisms. (elifesciences.org)

Evolutionary1

• it remains unclear if there is any common process or event that leads to the loss of DNA methylation systems in certain evolutionary lineages. (elifesciences.org)

Arginine1

• Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each. (lookformedical.com)

Endogenous1

• In our research, overexpression of the OsNAR2.1 line was used as a testing target in rice plants with high nitrogen-use efficiency to study the changes of rice methylation and growth in respond of the endogenous and external nitrogen stress. (biomedcentral.com)

Core1

• A retinoblastoma-binding protein that has an affinity for core HISTONES. (lookformedical.com)

Expression1

• Similar histone occupancies were confirmed in a comparison of cancerous tissues with strong, moderate and negative NR0B1 expression. (oncotarget.com)

Effects1

• The Sustainable Building Design and Construction threonine has an Mitogen-activated, alveolar step that contains effects at the conversion of the activation of a phosphorylated specific residue. (evakoch.com)