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MethylationHistonesAcetylationDNA MethylationCytosineHistone-Lysine N-MethyltransferaseHistone DeacetylasesEpigenesis, GeneticDNA-Cytosine MethylasesDNA (Cytosine-5-)-Methyltransferase5-MethylcytosineCpG IslandsLysineChromatinHistone AcetyltransferasesSulfitesProtein MethyltransferasesHistone DemethylasesHistone Deacetylase InhibitorsMolecular Sequence DataGene SilencingBase SequenceJumonji Domain-Containing Histone DemethylasesPromoter Regions, GeneticMethyltransferasesNucleosomesDNAHydroxamic AcidsTranscription, GeneticChromatin ImmunoprecipitationAzacitidineChromatin Assembly and DisassemblyHeterochromatinAmino Acid SequenceHistone CodeEpigenomicsHistone Deacetylase 1DNA-Binding ProteinsUracilProtein Processing, Post-TranslationalMutationRepressor ProteinsAcetyltransferasesDinucleoside PhosphatesNuclear ProteinsPolycomb Repressive Complex 2Oxidoreductases, N-DemethylatingProtein BindingTranscription FactorsBinding SitesEuchromatinCell LineProtein-Arginine N-MethyltransferasesHistone Deacetylase 2p300-CBP Transcription FactorsChromosomal Proteins, Non-HistoneGene Expression RegulationGenomic ImprintingDeoxyribonuclease HpaIISubstrate SpecificityHistone ChaperonesProtein Structure, TertiarySaccharomyces cerevisiae ProteinsCytosine DeaminaseCell Line, TumorPentoxylDNA Modification MethylasesHeLa CellsPolycomb-Group ProteinsAdenineEscherichia coliSaccharomyces cerevisiaeNucleic Acid ConformationPolymerase Chain ReactionKineticsGuanineModels, MolecularRetinoblastoma-Binding Protein 2Gene Expression Regulation, NeoplasticEpigenetic RepressionRNA Polymerase IITranscriptional ActivationRNA, MessengerReverse Transcriptase Polymerase Chain ReactionS-AdenosylmethionineOligodeoxyribonucleotidesRetinoblastoma-Binding Protein 4PhosphorylationNucleic Acid DenaturationCells, CulturedBlotting, WesternLong Interspersed Nucleotide ElementsArabidopsisHydroxylaminesDNA PrimersCloning, MolecularRNA InterferenceEnzyme InhibitorsOligonucleotide Array Sequence AnalysisGene Expression Profiling

EpigeneticChromatin structureModificationsLysineH3K9DeacetylaseDeacetylasesHyperacetylationPromoterNovoHDACsContrastDNMT1HeterochromatinProteinsEukaryotesMethyl groupDeacetylationMRNATranscriptionalReplicationRepressiveMechanismPathwaysEnzymesNucleosomeFungusInterplayAffinitySequencesEndogenousCorrelationRegulationExpressionRoleSpecificProcessMarksFunction

Epigenetic11

• His fields of research comprise RNA-mediated gene silencing processes with a focus on epigenetic phenomena, including studies on RNA-directed DNA methylation, the characterization of virus silencing suppressor proteins, the development of plant bioreactor platforms and viroid research. (degruyter.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)
• The aberrant expression of methylation and ncRNAs, two crucial regulators of epigenetic modifications, has been widely demonstrated in cancer. (ijbs.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)
• 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)
• These epigenetic mechanisms are mediated by chemical modifications of DNA, proteins (most commonly histones), and RNA. (activemotif.com.cn)
• 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)
• Bromodomains recognize acetylated histone lysine residues and function as 'readers' of these epigenetic histone marks to regulate chromatin structure and gene expression by linking associated proteins to the acetylated nucleosomal targets. (activemotif.com)
• Could the emergence or loss of a specific nucleosome regulator affect the evolution of DNA methylation as an epigenetic mechanism? (elifesciences.org)
• Among the 140 modified RNA nucleotide variants identified, methylation of adenosine at the N6 position (m6A) is the most prevalent epigenetic mark in eukaryotic mRNA. (pharmaceuticalintelligence.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)

Modifications8

• 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)
• Cross-talk between different histone modifications, as well as DNA methylation, seems complex. (aacrjournals.org)
• Kong M, Yu X, Guo W, Guo R. The bidirectional interplay between ncRNAs and methylation modifications in gastrointestinal tumors. (ijbs.com)
• Therefore, we summarize the interrelation process between ncRNAs and methylation modifications in GI tumors, including the detailed mechanism of methylation enzyme regulation of ncRNAs, the molecular mechanism of ncRNAs regulation of methylation modifications, and the correlation between the interactions between ncRNAs and methylation modifications and clinical features of tumors. (ijbs.com)
• Finally, we discuss the potential value of ncRNAs and methylation modifications in clinical diagnosis and therapy. (ijbs.com)
• A large number of covalent modifications on histone, such as different types, residues, and amount, will affect the inhibition or activation of gene expression. (gjkqyxzz.cn)
• Characterization of histone modifications at subtelomeric regions revealed H3 trimethyl-K9, H3 trimethyl-K27, and H4 trimethyl-K20 enrichment. (biomedcentral.com)
• Also, more and more accumulating evidence indicates that the different histone modifications are strongly interconnected and can enforce or counteract each other. (musculoskeletalkey.com)

Lysine5

• 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)
• 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)
• We demonstrate the presence of telomeric silencing in Neurospora and show a dependence on histone deacetylases and methylation of histone H3 lysine 9. (biomedcentral.com)
• The fission yeast S. pombe lacks Sir3p and Sir4p but employs methylation of histone H3 lysine 9 (K9) plus a Sir2p homologue (Sir2) for silencing [ 15 ]. (biomedcentral.com)
• BPTF also specifically recognizes H3 tails trimethylated on lysine 4 ( H3K4me3 ), which mark transcription start sites of virtually all active genes. (activemotif.com)

H3K94

• 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, 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)

Deacetylase3

• Treating 293T cells with a histone deacetylase inhibitor increased acetylated histone H4 binding to the NR0B1 promoter and activated NR0B1 expression. (oncotarget.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)
• We show that NST-1 is an H4-specific histone deacetylase. (biomedcentral.com)

Deacetylases1

• Histone acetylation is catalyzed by histone acetyltransferases (HATs) and is counteracted by histone deacetylases (HDACs). (musculoskeletalkey.com)

Hyperacetylation1

• Histone hyperacetylation and H3K4 methylation are associated with unmethylated DNA, euchromatin, and gene expression ( Fig. 2 ). (aacrjournals.org)

Promoter3

• 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)
• 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)
• Expression of both isoforms negatively correlated with methylation at specific regions of the Mecp2 promoter, both at D2 and D8. (biomedcentral.com)

Novo5

• At least in plants, DNA regions that become de novo methylated can be defined by homologous RNA molecules in a process termed RNA-directed DNA methylation (RdDM). (degruyter.com)
• 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)
• Our studies also reveal silencing functions for DIM-5 and HP1 that appear independent of their role in de novo DNA methylation. (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)
• Conversely, methylation by de novo DNMTs does not require methylated DNA templates. (elifesciences.org)

HDACs1

• 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)

Contrast4

• 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)
• In contrast, acetylation of histones H3 and H4 increased. (biomedcentral.com)
• In contrast, decitabine withdrawal downregulated both Mecp2 isoforms to different extents at D8, without affecting DNA methylation at the Mecp2 REs. (biomedcentral.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)

Heterochromatin1

• dim-5 , which encodes a histone H3 K9 methyltransferase and hpo , which encodes heterochromatin protein-1. (biomedcentral.com)

Proteins2

• 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)

Eukaryotes3

• In eukaryotes, DNA methylation refers to the addition of a methyl group to the fifth atom in the six-atom ring of cytosine residues. (degruyter.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)
• DNA methylation, particularly 5-methylcytosine (5mC) at CpG sequences, is widely conserved in eukaryotes. (elifesciences.org)

Methyl group1

• 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)

Deacetylation1

• A retinoblastoma-binding protein that is involved in CHROMATIN REMODELING, histone deacetylation, and repression of GENETIC TRANSCRIPTION. (lookformedical.com)

MRNA1

• Identified in bacterial rRNAs and tRNAs as early as the 1950s, this type of methylation was subsequently found in other RNA molecules, including mRNA, in animal and plant cells as well. (pharmaceuticalintelligence.com)

Transcriptional1

• DNA methylation typically causes gene transcriptional silencing, whereas demethylation leads to transcription activation. (gjkqyxzz.cn)

Replication1

• 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)

Repressive1

• 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)

Mechanism1

• On the mechanism of inhibition of DNA-cytosine methyltransferases by cytosine analogs[J]. Cell, 1983, 33(1):9-10. (gjkqyxzz.cn)

Pathways1

• 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)

Enzymes1

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

Nucleosome3

• A histone chaperone that facilitates nucleosome assembly by mediating the formation of the histone octamer and its transfer to DNA. (lookformedical.com)
• BPTF (Bromodomain PHD finger transcription factor) is a histone-binding component of NuRF (nucleosome-remodeling factor), a complex which catalyzes ATP-dependent nucleosome sliding and facilitates transcription of chromatin. (activemotif.com)
• 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)

Fungus1

• We initiated a study of telomeric silencing in Neurospora crassa , a fungus that sports DNA methylation, unlike most other organisms in which telomeric silencing has been characterized. (biomedcentral.com)

Interplay1

• We used a previously characterized in vitro differentiating neural stem cell (NSC) system to investigate the interplay between Mecp2 isoform-specific expression and DNA methylation at the Mecp2 REs. (biomedcentral.com)

Affinity1

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

Sequences1

• The recruitment of this machinery results in the production of viroid-derived small RNAs (vd-sRNAs) that mediate RNA degradation and DNA methylation of cognate sequences. (degruyter.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)

Correlation2

• Further, we performed correlation analysis between DNA methylation at the Mecp2 REs and the expression of Mecp2 isoforms after decitabine exposure and withdrawal. (biomedcentral.com)
• Our results show the correlation between the expression of Mecp2 isoforms and DNA methylation in differentiating NSC, providing insights on the potential role of DNA methylation at the Mecp2 REs in Mecp2 isoform-specific expression. (biomedcentral.com)

Regulation1

• 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)

Expression3

• Similar histone occupancies were confirmed in a comparison of cancerous tissues with strong, moderate and negative NR0B1 expression. (oncotarget.com)
• We hypothesized that DNA methylation at these REs may impact the expression of Mecp2 isoforms. (biomedcentral.com)
• At different stages of NSC differentiation, Mecp2 isoforms showed reciprocal expression patterns associated with minor, but significant changes in DNA methylation at the Mecp2 REs. (biomedcentral.com)

Role2

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

Specific1

• 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)

Process1

• 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)

Marks1

• the m 6 A-containing fragments are then sequenced and aligned to the genome, thus allowing us to locate the positions of methylation marks. (pharmaceuticalintelligence.com)

Function2

• 12] Schubeler D. Function and information content of DNA methylation[J]. Nature, 2015, 517(7534):321-326. (gjkqyxzz.cn)
• CpG-rich islands and the function of DNA methylation[J]. Nature, 1986, 321(6067):209-213. (gjkqyxzz.cn)