AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesInformation ScienceHealth Care
Chromatin Assembly Factor-1ChromatinChromatin Assembly and DisassemblyTranscription FactorsTranscription, GeneticHistonesNucleosomesChromosomal Proteins, Non-HistoneNucleosome Assembly Protein 1DNA-Binding ProteinsProtein BindingHistone ChaperonesMolecular Sequence DataNuclear ProteinsPromoter Regions, GeneticChromatin ImmunoprecipitationCell NucleusAcetylationSaccharomyces cerevisiae ProteinsDNA ReplicationDNAHeLa CellsBase SequenceMutationSaccharomyces cerevisiaeApc5 Subunit, Anaphase-Promoting Complex-CyclosomeGene Expression RegulationRetinoblastoma-Binding Protein 4Cell LineAmino Acid SequenceNucleoplasminsBinding SitesCell Cycle ProteinsRepressor ProteinsMolecular ChaperonesDNA, SuperhelicalTranscriptional ActivationMicrococcal NucleaseProtein Structure, TertiaryHeterochromatinTrans-ActivatorsHistone AcetyltransferasesRNA, MessengerGene Expression Regulation, FungalCell ExtractsGene SilencingVirus AssemblySp1 Transcription FactorPlasmidsDrosophilaModels, BiologicalRNA Polymerase IIDrosophila ProteinsCentromereMitosisRecombinant Fusion ProteinsS PhaseDeoxyribonuclease ICloning, MolecularFungal ProteinsHistone DeacetylasesXenopusTranscription Initiation SitePhosphorylationSignal TransductionAcetyltransferasesRecombinant ProteinsCells, CulturedXenopus laevisLysineAdenosine TriphosphatasesDNA DamageTransfectionRetinoblastoma-Binding Protein 7Sequence Homology, Amino AcidModels, GeneticCell CycleMacromolecular SubstancesKineticsEpigenesis, GeneticTemplates, GeneticModels, MolecularTwo-Hybrid System TechniquesProliferating Cell Nuclear AntigenCarrier ProteinsCell-Free SystemOocytesChromosomesDrosophila melanogasterGene Expression Regulation, DevelopmentalPhenotypeProtein SubunitsBlotting, WesternDNA RepairDimerizationMicrotubulesGenes, ReporterGene DeletionHigh Mobility Group ProteinsEnhancer Elements, Genetic
ProteinsNucleosomesGenomeHistonesGenesTranscriptionalUnit of chromatinFactorsOrganizationMethylationReplicationDynamicsConformationLocal chromatinProteinEukaryoticRemodelingAccessibilityModulateGeneticModificationImmunoprecipitationMediatesATPaseRegulateRegulatesVivoIncorporationHistone octamerOccupancyFactorStructuresRegulatorsGene expressionComplexesModificationsKineticsStructuralInitiationStructure
Proteins11
Nucleosomes5
  • In eukaryotic cells, chromatin remodeling factors regulate chromatin structure by altering the assembly, disassembly, and relocalization of nucleosomes, thereby improving the local accessibility of transcription-related factors in their chromatin DNA, which further initiates or suppresses transcription of related genes. (creativebiomart.net)
  • In eukaryotic organisms, nucleosomes function as the most basic unit of chromosome organization directly binding and assembling on DNA to modulate DNA topology, drive compaction, and regulate transcription. (mpg.de)
  • The dynamic events that underlie the disassembly and reassembly of nucleosomes during replication remains a long-standing puzzle in chromosome biology. (mpg.de)
  • In all eukaryotes, including plants, genomic DNA is packaged around octamers of histones, forming the basic structural units of chromatin, the nucleosomes. (cnrs.fr)
  • NAPs participate in the assembly and disassembly of nucleosomes thus contributing to chromatin structure organization. (biomedcentral.com)
Genome8
  • It is mainly manifested in the reduction of whole-genome DNA methylation level, hypermethylation of the promoter region, changes in specific histone modification, abnormal chromatin conformation, changes in non-coding RNA (ncRNA) molecules, etc . (creativebiomart.net)
  • Chromatin compaction protects the genome and maintains genomic integrity. (molcells.org)
  • These results reveal that paternal DNA methylation is remodeled to match the maternal pattern during zygotic genome reprogramming and suggest existence of a chromatin memory allowing parental allelic-specific methylation to be maintained in the hybrid. (bvsalud.org)
  • Our group is interested in characterization of several genes to reveal their roles in deposition of epigenetic marks, in chromatin remodeling, in genome transcription, and in regulation of plant growth and development. (cnrs.fr)
  • By applying whole genome and quantitative chromatin conformation analysis {chromatin interaction analysis with paired end tag sequencing (ChIA-PET), and real time chromosome conformation capture (3C) assay}, we observed that the MEF2C-bound enhancer and transcription start site (TSS) of KLF4 came into closer spatial proximity by pitavastatin treatment. (soken.ac.jp)
  • Finally, we observed nucleosome disruption and disorganization emanating from replication origins and traveling with the elongating replication forks across the genome in S phase, likely reflecting the disassembly and assembly of chromatin ahead of and behind the replication fork, respectively. (duke.edu)
  • Eukaryotic cells compact their large genome into highly ordered chromatin structures within the nucleus. (aging-us.com)
  • Incorporation of histone variants confers variability to the chromatin and expands the repertoire of epigenetic marks in a functional alphabet that controls genome plasticity and dynamics [ 4 ]. (aging-us.com)
Histones6
Genes6
  • Trimethylation of histone H3 lysine 4 (H3K4me3) marks transcription start sites of virtually all active genes. (ox.ac.uk)
  • Similarly, the single-cell assay for transposase-accessible chromatin sequencing showed increased chromatin accessibility at genes associated with myeloid differentiation, including CD11b, CD11c, and IRF8. (nih.gov)
  • In this work, we show that the rice DELLA protein SLENDER RICE1 (SLR1) forms a tripartite complex with Polycomb-repressive complex 2 (PRC2) and the histone deacetylase HDA702 to repress downstream genes by establishing a silent chromatin state. (bvsalud.org)
  • However, in the context of mixed tissues, rather than on individual loci, the ALKBH1 mutation or overexpression mainly affects the expression of genes with a specific combination of chromatin modifications in the body region marked with H3K4me3 and H3K27me3 but depleted of DNA CG methylation. (bvsalud.org)
  • In the similar context of mixed tissues, further analysis reveals that the ALKBH1 protein preferentially binds to genes marked by the chromatin signature and has a function to maintain a high H3K4me3/H3K27me3 ratio by impairing the binding of Polycomb repressive complex 2 (PRC2) to the targets, which is required for both the basal and stress-induced expression of the genes. (bvsalud.org)
  • Transcription of inflammatory genes in innate immune cells is coordinately regulated by transcription factors, including NF-κB, and chromatin modifiers. (cnrs.fr)
Transcriptional4
  • The mechanisms effecting establishment, maintenance, and modification of that specific physical conformation of CHROMATIN determining the transcriptional accessibility or inaccessibility of the DNA. (lookformedical.com)
  • This study shows that CRISPRi mediates precise transcriptional pausing, which can be followed by transcription termination. (nature.com)
  • Collectively, these results establish a general epigenetic mechanism for DELLA-mediated gene repression and reveal details of the chromatin dynamics during transcriptional activation stimulated by GA signaling. (bvsalud.org)
  • By recruiting SWI/SNF chromatin remodellers to IκB-ζ, transcriptional coactivator for NF-κB, the conserved nuclear protein Akirin2 stimulates pro-inflammatory gene promoters in mouse macrophages during innate immune responses to viral or bacterial infection. (cnrs.fr)
Unit of chromatin3
  • The elementary unit of chromatin is a nucleosome in which approximately 147 bp DNA is wrapped 1.67 turns around a histone octamer ( Fierz and Poirier, 2019 ). (molcells.org)
  • The repeating unit of chromatin is the nucleosome, formed from two histone H2A-H2B dimers and one histone H3-H4 tetramer around which 147 bp of DNA are wrapped [ 1 ]. (biomedcentral.com)
  • The nucleosome is the basic packaging unit of chromatin. (aging-us.com)
Factors6
  • Chromatin dynamics is regulated by many factors, including histone tail modifiers, remodeling complexes, and histone chaperones ( Peterson and Almouzni, 2013 ). (molcells.org)
  • Mechanistically, Acly deficiency altered chromatin accessibility and expression of multiple C/EBP family transcription factors known to regulate myeloid differentiation and cell metabolism, with increased Cebpe and decreased Cebpa and Cebpb. (nih.gov)
  • Early accomplishments of the SNCGE in this area include discovering the novel regulatory mechanism that induces translation of GCN4 mRNA via small upstream ORFs (uORFs) in the mRNA leader by phosphorylation and inhibition of eIF2 by the kinase Gcn2, now understood to regulate expression of key transcription factors (Atf4 and Atf5) in mammals and implicated in learning and memory. (nih.gov)
  • ii) identifying a higher-order assembly of initiation factors 1, 2, 3, and 5-the multifactor complex (MFC)-and elucidating its roles in PIC assembly and accurate start codon selection. (nih.gov)
  • In endothelial cells, statin-dependent atheroprotective gene up-regulation is mediated by Kruppel-like factor (KLF) family transcription factors. (soken.ac.jp)
  • Trans -acting splicing factors, pre-mRNA secondary structure and chromatin organization are now known to directly affect alternative splicing decisions [ 6 ]. (biomedcentral.com)
Organization4
  • Chromatin organization is dynamically altered for diverse DNA metabolic transactions such as replication, transcription, and repair. (molcells.org)
  • Link to all annotated objects annotated to chromatin organization. (planteome.org)
  • Link to all direct and indirect annotations to chromatin organization. (planteome.org)
  • We also studied the roles of other classes of protein kinases (Cla4) and additional post-translational modifications (SUMOylation) in septin complex assembly, formation of different septin-based supramolecular ensembles, disassembly of septin-containing structures, and the function of septin organization in the events required for cell division and membrane septation during cytokinesis. (berkeley.edu)
Methylation5
  • To understand what dictates the emerging patterns of de novo DNA methylation in the male germline, we mapped DNA methylation, chromatin, and transcription changes in purified fetal mouse germ cells by using methylated CpG island recovery assay (MIRA)-chip, chromatin immunoprecipitation (ChIP)-chip, and strand-specific RNA deep sequencing, respectively. (nih.gov)
  • Global de novo methylation occurred by default in prospermatogonia without any apparent trigger from preexisting repressive chromatin marks but was preceded by broad, low-level transcription along the chromosomes, including the four known paternally imprinted differentially methylated regions (DMRs). (nih.gov)
  • Similarly, each maternally imprinted DMR was protected from default DNA methylation among highly methylated DNA by an H3K4me2 peak and transcription initiation at least in one strand. (nih.gov)
  • Our results suggest that the pattern of de novo DNA methylation in prospermatogonia is dictated by opposing actions of broad, low-level transcription and dynamic patterns of active chromatin. (nih.gov)
  • AlkB homolog1 (ALKBH1) is shown to demethylate DNA adenine methylation (6mA) preferentially from single-stranded or unpaired DNA, while its demethylase activity and function in the chromatin context are unclear. (bvsalud.org)
Replication7
  • Chromosome replication is performed by a large multisubunit assembly, known as the replisome, which couples the unpackaging of parental DNA with the synthesis of new daughter strands. (mpg.de)
  • These intricate structures must likewise allow for efficient disassembly and reassembly during replication. (mpg.de)
  • By reconstituting the S. Cerevisiae replication machinery at the single complex level we are able to study critical transient intermediates formed during chromatin replication. (mpg.de)
  • While the double-helical structure of duplex DNA is advantageous for the storage and maintenance of genetic information, it poses major challenges during essential cellular processes, such as transcription and replication, when the information-rich DNA bases must be accessed. (mpg.de)
  • Scholars@Duke publication: Cell-Cycle-Dependent Chromatin Dynamics at Replication Origins. (duke.edu)
  • Chromatin is highly dynamic, a characteristic that is vital in regulating nuclear processes such as transcription and replication which require access to DNA. (biomedcentral.com)
  • The dynamic nature of chromatin establishes the access to the genetic material and, as a consequence, influences a large number of biological processes, such as DNA replication, repair and transcription [ 1 , 2 ]. (aging-us.com)
Dynamics4
  • Chromatin dynamics is essential for maintaining genomic integrity and regulating gene expression. (molcells.org)
  • The authors use this approach to study how NuRD assembles on chromatin and how it regulates enhancer dynamics. (nature.com)
  • These results provide insights into cell-cycle-regulated chromatin dynamics and how they relate to the regulation of origin activity. (duke.edu)
  • The large ~280-kDa U5 snRNP protein PRPF8 is central to the dynamics of spliceosome assembly [ 11 ]. (biomedcentral.com)
Conformation2
  • In the study of Ras-induced tumor development, the importance of chromatin remodeling changes in cancer is also evident, with the observation that chromatin conformation is more open in early-developing tumors and more accessible in late-stage tumor development. (creativebiomart.net)
  • Taken together, dynamic chromatin conformation change was shown to mediate pitavastatin-responsive gene induction in endothelial cells. (soken.ac.jp)
Local chromatin1
  • however, the interplay between the assembly of these complexes and the local chromatin environment is less well understood. (duke.edu)
Protein5
  • The 48 kDa subunit, RETINOBLASTOMA-BINDING PROTEIN 4, is also a component of several other protein complexes involved in chromatin remodeling. (lookformedical.com)
  • A retinoblastoma-binding protein that is involved in CHROMATIN REMODELING, histone deacetylation, and repression of GENETIC TRANSCRIPTION. (lookformedical.com)
  • The repeating structural units of chromatin, each consisting of approximately 200 base pairs of DNA wound around a protein core. (lookformedical.com)
  • As the assembly was carried out in the absence of ATP, this suggests that formation of the holoenzyme from the individual subcomplexes is solely driven by protein-protein interactions at the interface. (upstate.edu)
  • Unlike reversible disassembly, which requires ATP hydrolysis on V 1 to break protein-protein interactions, Oxr1p mediated disassembly of V-ATPase is ATP independent and therefore a novel mode of activity regulation. (upstate.edu)
Eukaryotic1
Remodeling4
  • These events facilitate remodeling of the chromatin landscape and efficient repair. (nature.com)
  • However, it remains unclear how microbial sensing initiates chromatin remodeling. (cnrs.fr)
  • Furthermore, Akirin2 and IκB-ζ recruitment to the Il6 promoter depend upon the presence of IκB-ζ and Akirin2, respectively, for regulation of chromatin remodeling. (cnrs.fr)
  • The Cardiac TBX5 Interactome Reveals a Chromatin Remodeling Network Essential for Cardiac Septation. (princeton.edu)
Accessibility1
  • In this study, we demonstrate that ATP citrate lyase (Acly), which metabolizes citrate to generate cytosolic acetyl-CoA and is of clinical interest, can regulate chromatin accessibility to limit myeloid differentiation. (nih.gov)
Modulate1
  • May modulate chromatin structure by regulation of nucleosome assembly/disassembly (By similarity). (gao-lab.org)
Genetic1
  • Chromatin represents the physiological template of genetic information. (cnrs.fr)
Modification1
  • Loss-of-function or downregulation of the chromatin regulators impaired SLR1-dependent histone modification and gene repression. (bvsalud.org)
Immunoprecipitation1
  • We focused on MEF2C among the MEF2 family members and identified a novel functional MEF2C binding site 148 kb upstream of the KLF4 gene by chromatin immunoprecipitation along with deep sequencing (ChIP-seq) followed by luciferase assay. (soken.ac.jp)
Mediates2
  • Homeodomain transcription factor that mediates jasmonic acid (JA)-mediated COI1-dependent and abscisic acid (ABA)-mediated PMR4-dependent resistance to infection by necrotrophic fungal pathogens (e.g. (gao-lab.org)
  • Here we show that a plant homeodomain (PHD) finger of nucleosome remodelling factor (NURF), an ISWI-containing ATP-dependent chromatin-remodelling complex, mediates a direct preferential association with H3K4me3 tails. (ox.ac.uk)
ATPase3
  • Depletion of H3K4me3 causes partial release of the NURF subunit, BPTF (bromodomain and PHD finger transcription factor), from chromatin and defective recruitment of the associated ATPase, SNF2L (also known as ISWI and SMARCA1), to the HOXC8 promoter. (ox.ac.uk)
  • Biochemical experiments showed that Oxr1p binds and promotes V-ATPase disassembly. (upstate.edu)
  • Journal cover: V-ATPase is regulated by disassembly into soluble V 1 (shown in cyan) and membrane integral V o (shown in gold) subcomplexes. (upstate.edu)
Regulate1
  • Acly inhibition thus can promote myelopoiesis through deprivation of acetyl-CoA and altered histone acetylome to regulate C/EBP transcription factor family activity for myeloid differentiation. (nih.gov)
Regulates1
  • Sequential assembly of the human spliceosome on RNA transcripts regulates splicing across the human transcriptome. (biomedcentral.com)
Vivo1
  • These results strongly suggest that WDR5 and NURF function in a common biological pathway in vivo, and that NURF-mediated ATP-dependent chromatin remodelling is directly coupled to H3K4 trimethylation to maintain Hox gene expression patterns during development. (ox.ac.uk)
Incorporation1
  • Consequently, H3.3 incorporation and turnover represent an additional layer in the regulation of the chromatin landscape during aging. (aging-us.com)
Histone octamer1
  • A histone chaperone that facilitates nucleosome assembly by mediating the formation of the histone octamer and its transfer to DNA. (lookformedical.com)
Occupancy1
  • We also found that the strongest correlation between chromatin occupancy at the ACS and origin efficiency occurred in early S phase, consistent with the rate-limiting formation of the Cdc45-Mcm2-7-GINS (CMG) complex being a determinant of origin activity. (duke.edu)
Factor2
  • Chromatin assembly factor 1. (lookformedical.com)
  • Human mutations in the cardiac transcription factor gene TBX5 cause congenital heart disease (CHD), although the underlying mechanism is unknown. (princeton.edu)
Structures1
Regulators2
  • Histone deacetylases (HDACs) are important chromatin regulators essential for plant tolerance to adverse environments. (bvsalud.org)
  • In such a crowded molecular picture, recent exciting insights have uncovered the role of histone variants as key regulators of the chromatin structure. (aging-us.com)
Gene expression1
  • Competition for PRPF8 availability alters the transcription-coupled splicing of RNAs in which weak 5′ splice sites predominate, enabling diversification of human gene expression during biological processes like mitosis. (biomedcentral.com)
Complexes1
  • The core spliceosome component PRPF8 is essential for spliceosome assembly through its participation in ribonucleoprotein (RNP) complexes for splice-site recognition, branch-point formation and catalysis. (biomedcentral.com)
Modifications1
  • Histone modifications related to both active and inhibitory chromatin can be observed during cancer progression, and these modifications can occur simultaneously. (creativebiomart.net)
Kinetics1
  • Experimental enhancement of splice-site strength in mini-gene constructs overcomes the effects of PRPF8 depletion on the kinetics and fidelity of splicing during transcription. (biomedcentral.com)
Structural1
  • In the present study, the structural basis of nucleosome assembly activity in P. falciparum was addressed by determining and analysing the crystal structure of smaller NAP in the parasite called PfNapS. (biomedcentral.com)
Initiation1
  • These findings have helped to illuminate the molecular mechanism of TC recruitment and assembly of 43S PICS at an early stage of the initiation pathway. (nih.gov)
Structure1
  • item_titles": {"attribute_name": "タイトル", "attribute_value_mlt": [{"subitem_title": "Direct evidence for pitavastatin induced chromatin structure change in the KLF4 gene in endothelial cells. (soken.ac.jp)