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ChromatinChromatin Assembly and DisassemblyHistonesChromatin ImmunoprecipitationNucleosomesChromosomal Proteins, Non-HistoneAcetylationMicrococcal NucleaseTranscription, GeneticModels, BiologicalPromoter Regions, GeneticCell NucleusTranscription FactorsDNAProtein BindingDNA-Binding ProteinsChromatin Assembly Factor-1Sex ChromatinNuclear ProteinsMolecular Sequence DataEpigenesis, GeneticHeterochromatinGene Expression RegulationMethylationCell LineDeoxyribonuclease IGene SilencingBase SequenceBinding SitesRepressor ProteinsHistone DeacetylasesHeLa CellsHistone AcetyltransferasesSaccharomyces cerevisiae ProteinsSaccharomyces cerevisiaeChromosomesMutationAmino Acid SequenceBiological ProductsDNA MethylationHistone-Lysine N-MethyltransferaseLysineDNA ReplicationTranscriptional ActivationCell Cycle ProteinsCell Line, TumorModels, GeneticProtein Structure, TertiaryGene Expression ProfilingEuchromatinBiological AssayChickensDrosophila ProteinsCells, CulturedInsulator ElementsMitosisDNA DamageRNA Polymerase IIBiological TherapyCentromereGene Expression Regulation, FungalOligonucleotide Array Sequence AnalysisSignal TransductionEnhancer Elements, GeneticDeoxyribonucleasesRNA, MessengerSpermatozoaDNA HelicasesPolycomb-Group ProteinsAcetyltransferasesDrosophila melanogasterGene Expression Regulation, DevelopmentalCell DifferentiationComputational BiologyTrans-ActivatorsInterphaseProtein Processing, Post-TranslationalNucleic Acid ConformationKineticsDNA RepairRNA InterferenceHistone ChaperonesDrosophilaModels, MolecularAdenosine TriphosphatasesTime FactorsGenomeHigh Mobility Group ProteinsHydroxamic AcidsNucleoproteinsBiological MarkersAlgorithmsBiological WarfareResponse ElementsProteinsPhosphorylationCell CycleRNA, Small InterferingReverse Transcriptase Polymerase Chain ReactionHistone Deacetylase Inhibitors
ProteinsTranscriptionalDissecting chromatin stateImmunoprecipitationEpigenetics ChromatinBivalent chromatinComplexesVivoNucleosomesAccessibilityHistone methyltransferaseRegulationMitoticGeneLociGenesMethylationGenomeModifiersNuclearProcessesModulatesGermlineStructureErythrocyte nucleiReplicationMediateChemistryOrganizationPromoterFunctionMechanismsInteractionStructuralVisualizationStronglyPhysicsExperimentsMagneticChIPActivityImportantBiologyInvestigate
Proteins15
  • Chromatin immunoprecipitation (ChIP) is a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. (wikipedia.org)
  • Briefly, the conventional method is as follows: DNA and associated proteins on chromatin in living cells or tissues are crosslinked (this step is omitted in Native ChIP). (wikipedia.org)
  • citation needed] Cross-linked ChIP is mainly suited for mapping the DNA target of transcription factors or other chromatin-associated proteins, and uses reversibly cross-linked chromatin as starting material. (wikipedia.org)
  • The immunoprecipitated complexes (i.e., the bead-antibody-protein-target DNA sequence complex) are then collected and washed to remove non-specifically bound chromatin, the protein-DNA cross-link is reversed and proteins are removed by digestion with proteinase K. An epitope-tagged version of the protein of interest, or in vivo biotinylation can be used instead of antibodies to the native protein of interest. (wikipedia.org)
  • Knowing how the proteins in the human body interact with DNA to regulate gene expression is a key component of our knowledge of human diseases and biological processes. (wikipedia.org)
  • How the proteins that regulate these processes function in the context of chromatin and its dynamic architectures is an intensive field of study. (rockefeller.edu)
  • Lysine methylation marks manifest their biological effect via so-called 'readers' (or reading domains) which recognize and bind the methylation mark and directly alter the chromatin structure or act as a scaffold for other proteins, which induce biological responses. (europa.eu)
  • Reading domains include Plant homeodomains (PHD) and Chromodomains (CD) found in many chromatin proteins. (europa.eu)
  • The biological system is complex with many regulatory features such as DNA, mRNA, proteins, metabolites, and epigenetic features such as DNA methylation and histone post-translational modifications (PTMs). (rsc.org)
  • The laboratory is particularly interested in studying how specific DNA sequences, DNA binding proteins, and chromatin. (rochester.edu)
  • Chromatin assembly is the assembly of DNA, histone proteins, and other associated proteins into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus. (yeastrc.org)
  • Our results provide new information on the chromatin engagement of two central players in transcription elongation and emphasize the importance of the nucleosome core as a hub for proteins that regulate chromatin during transcription. (biorxiv.org)
  • The conserved family of Transcription Intermediary Factors (TIF1) proteins consists of key transcriptional regulators that control transcription of target genes by modulating chromatin state. (elifesciences.org)
  • Biological process GO terms and their p-values for co-expressed proteins. (lu.se)
  • Applications are invited for two postdoctoral positions to develop computational approaches to study (1) the phenomena of liquid-liquid phase separation of heterogenous mixtures of nucleic acids and proteins occurring inside the Cell nucleus and (2) the organization of chromatin with subnucleosome resolution inside megabase scale domains. (lu.se)
Transcriptional4
  • Here we identify extensive transcriptional changes that occur during murine astrocyte maturation in vivo that are accompanied by chromatin remodelling at enhancer elements. (nature.com)
  • Culturing astrocytes in a three-dimensional matrix containing FGF2 induces expression of Rorb , Dbx2 and Lhx2 and improves astrocyte maturity based on transcriptional and chromatin profiles. (nature.com)
  • Therefore, extrinsic signals orchestrate the expression of multiple intrinsic regulators, which in turn induce in a modular manner the transcriptional and chromatin changes underlying astrocyte maturation. (nature.com)
  • We subclassified intergenic lncRNAs according to chromatin status at transcriptional initiation regions, defined by relative levels of histone H3K4 mono- and trimethylation. (biomedcentral.com)
Dissecting chromatin state1
  • Our work offers a comprehensive and high-resolution roadmap for dissecting chromatin state transition dynamics during the epigenomic reprogramming of human and mouse FGCs. (nature.com)
Immunoprecipitation2
Epigenetics Chromatin1
Bivalent chromatin3
  • We show that a set of somatic lineage regulators (including Hox, Gata and Sox factors) that carry bivalent chromatin enriched in H3K27me3 and H3K4me2 are selectively targeted by Suv39h1-mediated H3K9me3 and de novo DNA methylation in extra-embryonic versus embryonic (pluripotent) lineages, as assessed both in blastocyst-derived stem cells and in vivo. (cnrs.fr)
  • Using camalexin biosynthesis genes as an example, we confirmed that these two modifications were co-localized to form bivalent chromatin. (biorxiv.org)
  • Our study suggests that this type of bivalent chromatin, which we name a kairostat, controls the precise timing of gene expression upon stimuli. (biorxiv.org)
Complexes3
  • The DNA-protein complexes (chromatin-protein) are then sheared into ~500 bp DNA fragments by sonication or nuclease digestion. (wikipedia.org)
  • Alternatively, chromatin-antibody complexes can be selectively retained and eluted by inert polymer discs. (wikipedia.org)
  • The number of chromatin modifying and remodeling complexes implicated in genome control is growing faster than our understanding of the functional roles they play. (nih.gov)
Vivo3
  • Additional mechanisms that may control DNA accessibility in vivo include chromatin compaction and phase separation - processes that are beginning to be understood. (rockefeller.edu)
  • Although the genome-wide histone modification landscapes of mouse in vivo germ cells and in vitro PGCLCs have been profiled and several germline-specific properties of epigenetic reprogramming have been revealed, the study of genome-scale chromatin states in human FGCs is still challenging, due to the scarcity of materials and technical difficulties. (nature.com)
  • While structural and biochemical studies have shown that the acidic patch controls chromatin factor binding and activity, few studies have elucidated its functions in vivo . (biorxiv.org)
Nucleosomes4
Accessibility4
  • Here, we review the ongoing development of accessibility measurements, we summarize the different molecular and structural mechanisms that shape the accessibility landscape, and we detail the many important biological functions that are linked to chromatin accessibility. (rockefeller.edu)
  • Here we use nucleosome occupancy and methylation sequencing method to analyze both the genome-wide chromatin accessibility and DNA methylome at a series of crucial time points during fetal germ cell development in both human and mouse. (nature.com)
  • The two additional loci, together with two previously reported genome-wide significant loci, 5p15.33 and 9p21.3, were investigated by high-throughput sequencing for chromatin accessibility, histone modification, and promoter capture Hi-C (PCHi-C) profiling. (bvsalud.org)
  • Hofvander J, Jo VY, Fletcher CDM, Puls F, Flucke U, Nilsson J, Magnusson L, Mertens F. PHF1 fusions cause distinct gene expression and chromatin accessibility profiles in ossifying fibromyxoid tumors and mesenchymal cells. (lu.se)
Histone methyltransferase2
  • The histone methyltransferase Setd8 alters the chromatin landscape and regulates the expression of key transcription factors during erythroid differentiation. (rochester.edu)
  • We show that Bonus associates with the histone methyltransferase SetDB1 and the chromatin remodeler NuRD and depletion of either component releases Bonus-induced repression. (elifesciences.org)
Regulation2
Mitotic3
  • Confocal microscopy demonstrated nanotube s within the nucleus that were in association with cellular and mitotic tubulin as well as the chromatin. (cdc.gov)
  • The narrow diame- association with cellular and mitotic tubulin as ter and great length of single-walled carbon nano- well as the chromatin. (cdc.gov)
  • Our results are the first to tubes (SWCNT) suggest the potential to interact report disruption of the mitotic spindle by with critical biological structures. (cdc.gov)
Gene3
  • Protein methylation at lysine residues modulates chromatin structure, affects gene expression and mammalian development. (europa.eu)
  • Pharmacological reversal of the effects on chromatin structure completely eliminates the effects of maternal care on glucocorticoid receptor expression and hypothalamic-pituitary-adrenal (HPA) responses to stress, thus suggesting a causal relation between the maternally induced, epigenetic modification of the glucocorticoid receptor gene and the effects on stress responses in the offspring. (deepdyve.com)
  • In parallel, molecular measurements such as gene expression and chromatin activity across individuals are being collected at an unprecedented rate. (dana-farber.org)
Loci2
  • The striking differences between the precise sequence of action by various cofactors observed in these studies may be - at least in part - due to differences between the specific promoters studied, and distinct requirements exhibited by specific loci for chromatin remodeling based on their pre-existing nucleoprotein architecture. (nih.gov)
  • Large-scale genetic association studies have identified multiple susceptibility loci for nasopharyngeal carcinoma (NPC), but the underlying biological mechanisms remain to be explored. (bvsalud.org)
Genes1
  • Collectively, our results suggest a mutually exclusive role for Ring1B and Suv39h1 in regulating distinct chromatin states at key developmental genes and propose a novel mechanism by which lineage specification can be reinforced during early development. (cnrs.fr)
Methylation1
Genome1
Modifiers1
  • These chromatin modifiers are important regulators of development and deregulated in cancer. (edu.au)
Nuclear1
  • The new discovery was made possible by a new and technically challenging nuclear magnetic resonance (NMR) method, which discerns features of chromatin dynamics that are invisible to other commonly used approaches. (ucsf.edu)
Processes3
  • Integrated function analysis showed dCTCF-binding sites of different classes might be involved in different biological processes, and IM sites were more conserved and more intensely bound. (biomedcentral.com)
  • We now apply our workflow to decipher signaling by ubiquitin and UBLs and elucidate how ubiquitin and UBLs switch the functions of their targets to regulate numerous biological processes. (mpg.de)
  • Despite this, there is a significant gap between these established associations and studies that examine the role of repetitive elements in biological processes and disease development " shares Christopher Douse. (lu.se)
Modulates1
Germline1
  • Although the global and thorough DNA demethylation patterns of human FGCs have been revealed, the accompanying chromatin states in human germline remains unexplored. (nature.com)
Structure4
  • In addition, it appears that in specific cases one type of chromatin structure alteration (e.g., histone hyperacetylation) is contingent upon prior alterations of a different sort (i.e. (nih.gov)
  • In this study, we have determined the crystal structure of one subunit in an ATP-dependent chromatin remodeling factor and suggested the overall shape combined with a lot of physicochemical, biochemical and molecular biological methods. (nii.ac.jp)
  • The proposal will apply an interdisciplinary approach in an international environment to maximize its chances of success: the biological role of reading domains will be evaluated with molecular biology (histone and chromatin pulldowns, ChIP-seq, confocal microscopy), biochemistry (Peptide arrays, mass spectrometry, methyltransferase activity assays) and biophysics techniques (fluorescence anisotropy, circular dichroism spectroscopy) as well as crystallography (solving the structure of reading domains). (europa.eu)
  • Understanding this question is complicated by the diversity of chromatin structure and the heterogeneity of replication reactions. (mskcc.org)
Erythrocyte nuclei1
  • Here, chromatin fibers were isolated from N. maculosus erythrocyte nuclei using mild micrococcal nuclease digestion, fixed briefly with glutaraldehyde, applied to thin carbon films and negatively stained with aurothioglucose. (cellimagelibrary.org)
Replication2
  • One fundamental question is: how do replication forks efficiently progress through chromatin? (mskcc.org)
  • Such limitations have significantly hampered our ability to understand how the replication machinery progresses through chromatin and how replication forks are processed when they are stalled by impediments such as DNA damage. (mskcc.org)
Mediate1
  • It is possible that CTCF, through using different combinations of zinc fingers, interacting with different protein partners, and the last but not the least, employing various post-translational modifications, could mediate extensive intra- and inter-chromatin interactions [ 7 , 8 ]. (biomedcentral.com)
Chemistry4
  • We offer a selection of recent papers on a variety of topics from the Journal of Biological Chemistry , the Journal of Lipid Research and Molecular & Cellular Proteomics . (asbmb.org)
  • The results of their research were reported in the Journal of Biological Chemistry . (asbmb.org)
  • The study , published in the Journal of Biological Chemistry , is a step forward in creating precision medicine approaches to diabetes prevention and treatment. (asbmb.org)
  • The successful candidate will have strong experience in molecular modelling and simulations and statistical mechanics and will hold a PhD/DPhil in physics, chemistry, quantitative biology, applied mathematics, or a closely related field, with a strong interest in biological systems. (lu.se)
Organization1
Promoter1
  • A consensus emerging from all these experiments is that the joint action by several types of chromatin remodeling machines can lead to a more profound alteration of the infrastructure of chromatin over a target promoter than could be obtained by these enzymes acting independently. (nih.gov)
Function1
Mechanisms2
  • However, structural bases for enzyme mechanisms through chromatin remodeling are not known. (nii.ac.jp)
  • Disentangling the underlying biological mechanisms poses the next great challenge for large-scale genetics. (dana-farber.org)
Interaction2
  • SUMOylation influences Bonus's subnuclear localization, its association with chromatin and interaction with SetDB1. (elifesciences.org)
  • Thus, our study indicates that direct interaction between chromatin and SWCNTs may contribute to genetic changes in somatic cells. (cdc.gov)
Structural1
  • It had seemed to me for some time that a nucleosome capable of adopting alternate conformations in response to its surrounding molecular environment could more efficiently ensure the structural integrity and fluidity chromatin needs for its biological role. (ucsf.edu)
Visualization2
  • 7,5 credits Course description There has been a dramatic development of microscopical methods for visualization of biological structures and physiological events. (lu.se)
  • Microscopic diagnosis of D. fragilis was based on visualization of pleomorphic trophozoites, ranging in size from 4 µm to 20 µm, with fragmented chromatin and pale gray-blue finely vacuolated cytoplasm after Giemsa staining ( Figure 1 ). (cdc.gov)
Strongly1
Physics2
  • The Physical Biology Circle Meeting will bring together European researchers at the leading edge of research in experimental and theoretical biological physics. (mpg.de)
  • After completing his Bachelors in Physics at UC Berkeley, where he was awarded the University Medal, Mekhail received his medical degree at UC San Francisco, and Ph.D. in Electrical Engineering and Computer Science from the Massachusetts Institute of Technology where his research focused on using micro-fabricated devices for biological detection. (nih.gov)
Experiments2
Magnetic1
  • The lab's model qubit is the Nitrogen-Vacancy center in diamond, which they use to image magnetic phenomena in condensed-matter and biological systems over a broad range of length scales. (nih.gov)
ChIP3
Activity1
Important1
  • Chromatin remodeling is important for the epigenetic reprogramming of human primordial germ cells. (nature.com)
Biology1
  • 7,5 credits This course is well suited for masters students at the department of Biology interested in biological modelling, how models work and what they are good for. (lu.se)
Investigate1
  • KMET-READ plans to investigate the biological role of these reading domains in essential histone lysine methyltransferases - PHDs in MLL2 and MLL3 and CDs in SUV39H1 and SUV39H2. (europa.eu)