Chromatin Assembly Factor-1: A histone chaperone protein that plays a role in the deposition of NUCLEOSOMES on newly synthesized DNA. It is comprised of three different subunits of 48, 60, and 150 kDa molecular size. The 48 kDa subunit, RETINOBLASTOMA-BINDING PROTEIN 4, is also a component of several other protein complexes involved in chromatin remodeling.Chromatin: The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.Chromatin Assembly and Disassembly: The mechanisms effecting establishment, maintenance, and modification of that specific physical conformation of CHROMATIN determining the transcriptional accessibility or inaccessibility of the DNA.Histones: Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.Nucleosomes: The repeating structural units of chromatin, each consisting of approximately 200 base pairs of DNA wound around a protein core. This core is composed of the histones H2A, H2B, H3, and H4.Chromosomal Proteins, Non-Histone: Nucleoproteins, which in contrast to HISTONES, are acid insoluble. They are involved in chromosomal functions; e.g. they bind selectively to DNA, stimulate transcription resulting in tissue-specific RNA synthesis and undergo specific changes in response to various hormones or phytomitogens.Nucleosome Assembly Protein 1: A histone chaperone that facilitates nucleosome assembly by mediating the formation of the histone octamer and its transfer to DNA.Histone Chaperones: Proteins involved in the assembly and disassembly of HISTONES into NUCLEOSOMES.Apc5 Subunit, Anaphase-Promoting Complex-Cyclosome: A subunit of the anaphase-promoting complex whose primary function is to provide structural support for the catalytic and substrate-recognition modules of the complex. Apc5, along with Apc4, tethers the tetratricopeptide-coactivator binding subcomplex to the main structural subunit, Apc1.Retinoblastoma-Binding Protein 4: A retinoblastoma-binding protein that is involved in CHROMATIN REMODELING, histone deacetylation, and repression of GENETIC TRANSCRIPTION. 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.DNA Replication: The process by which a DNA molecule is duplicated.Acetylation: Formation of an acetyl derivative. (Stedman, 25th ed)Nucleoplasmins: A family of histone molecular chaperones that play roles in sperm CHROMATIN decondensation and CHROMATIN ASSEMBLY in fertilized eggs. They were originally discovered in XENOPUS egg extracts as histone-binding factors that mediate nucleosome formation in vitro.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.Chromatin Immunoprecipitation: A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Molecular Chaperones: A family of cellular proteins that mediate the correct assembly or disassembly of polypeptides and their associated ligands. Although they take part in the assembly process, molecular chaperones are not components of the final structures.Cell Cycle Proteins: Proteins that control the CELL DIVISION CYCLE. This family of proteins includes a wide variety of classes, including CYCLIN-DEPENDENT KINASES, mitogen-activated kinases, CYCLINS, and PHOSPHOPROTEIN PHOSPHATASES as well as their putative substrates such as chromatin-associated proteins, CYTOSKELETAL PROTEINS, and TRANSCRIPTION FACTORS.DNA, Superhelical: Circular duplex DNA isolated from viruses, bacteria and mitochondria in supercoiled or supertwisted form. This superhelical DNA is endowed with free energy. During transcription, the magnitude of RNA initiation is proportional to the DNA superhelicity.Micrococcal Nuclease: An enzyme that catalyzes the endonucleolytic cleavage to 3'-phosphomononucleotide and 3'-phospholigonucleotide end-products. It can cause hydrolysis of double- or single-stranded DNA or RNA. (From Enzyme Nomenclature, 1992) EC 3.1.31.1.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Histone Acetyltransferases: Enzymes that catalyze acyl group transfer from ACETYL-CoA to HISTONES forming CoA and acetyl-histones.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.Heterochromatin: The portion of chromosome material that remains condensed and is transcriptionally inactive during INTERPHASE.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Virus Assembly: The assembly of VIRAL STRUCTURAL PROTEINS and nucleic acid (VIRAL DNA or VIRAL RNA) to form a VIRUS PARTICLE.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Cell Extracts: Preparations of cell constituents or subcellular materials, isolates, or substances.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Centromere: The clear constricted portion of the chromosome at which the chromatids are joined and by which the chromosome is attached to the spindle during cell division.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Mitosis: A type of CELL NUCLEUS division by means of which the two daughter nuclei normally receive identical complements of the number of CHROMOSOMES of the somatic cells of the species.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.S Phase: Phase of the CELL CYCLE following G1 and preceding G2 when the entire DNA content of the nucleus is replicated. It is achieved by bidirectional replication at multiple sites along each chromosome.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Drosophila: A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.Retinoblastoma-Binding Protein 7: A retinoblastoma-binding protein that has an affinity for core HISTONES. 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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Xenopus: An aquatic genus of the family, Pipidae, occurring in Africa and distinguished by having black horny claws on three inner hind toes.Adenosine Triphosphatases: A group of enzymes which catalyze the hydrolysis of ATP. The hydrolysis reaction is usually coupled with another function such as transporting Ca(2+) across a membrane. These enzymes may be dependent on Ca(2+), Mg(2+), anions, H+, or DNA.DNA Damage: Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION. These deviations may be caused by physical or chemical agents and occur by natural or unnatural, introduced circumstances. They include the introduction of illegitimate bases during replication or by deamination or other modification of bases; the loss of a base from the DNA backbone leaving an abasic site; single-strand breaks; double strand breaks; and intrastrand (PYRIMIDINE DIMERS) or interstrand crosslinking. Damage can often be repaired (DNA REPAIR). If the damage is extensive, it can induce APOPTOSIS.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Lysine: An essential amino acid. It is often added to animal feed.Drosophila Proteins: Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.Proliferating Cell Nuclear Antigen: Nuclear antigen with a role in DNA synthesis, DNA repair, and cell cycle progression. PCNA is required for the coordinated synthesis of both leading and lagging strands at the replication fork during DNA replication. PCNA expression correlates with the proliferation activity of several malignant and non-malignant cell types.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.Xenopus laevis: The commonest and widest ranging species of the clawed "frog" (Xenopus) in Africa. This species is used extensively in research. There is now a significant population in California derived from escaped laboratory animals.Acetyltransferases: Enzymes catalyzing the transfer of an acetyl group, usually from acetyl coenzyme A, to another compound. EC 2.3.1.Histone Deacetylases: Deacetylases that remove N-acetyl groups from amino side chains of the amino acids of HISTONES. The enzyme family can be divided into at least three structurally-defined subclasses. Class I and class II deacetylases utilize a zinc-dependent mechanism. The sirtuin histone deacetylases belong to class III and are NAD-dependent enzymes.Microtubules: Slender, cylindrical filaments found in the cytoskeleton of plant and animal cells. They are composed of the protein TUBULIN and are influenced by TUBULIN MODULATORS.Deoxyribonuclease I: An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. The enzyme has a preference for double-stranded DNA.Oocytes: Female germ cells derived from OOGONIA and termed OOCYTES when they enter MEIOSIS. The primary oocytes begin meiosis but are arrested at the diplotene state until OVULATION at PUBERTY to give rise to haploid secondary oocytes or ova (OVUM).Epigenesis, Genetic: A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.Chromosomes: In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Macromolecular Substances: Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Fungal Proteins: Proteins found in any species of fungus.DNA Repair: The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Cell Cycle: The complex series of phenomena, occurring between the end of one CELL DIVISION and the end of the next, by which cellular material is duplicated and then divided between two daughter cells. The cell cycle includes INTERPHASE, which includes G0 PHASE; G1 PHASE; S PHASE; and G2 PHASE, and CELL DIVISION PHASE.Cell-Free System: A fractionated cell extract that maintains a biological function. A subcellular fraction isolated by ultracentrifugation or other separation techniques must first be isolated so that a process can be studied free from all of the complex side reactions that occur in a cell. The cell-free system is therefore widely used in cell biology. (From Alberts et al., Molecular Biology of the Cell, 2d ed, p166)Protein Subunits: Single chains of amino acids that are the units of multimeric PROTEINS. Multimeric proteins can be composed of identical or non-identical subunits. One or more monomeric subunits may compose a protomer which itself is a subunit structure of a larger assembly.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Kinetics: The rate dynamics in chemical or physical systems.Actins: Filamentous proteins that are the main constituent of the thin filaments of muscle fibers. The filaments (known also as filamentous or F-actin) can be dissociated into their globular subunits; each subunit is composed of a single polypeptide 375 amino acids long. This is known as globular or G-actin. In conjunction with MYOSINS, actin is responsible for the contraction and relaxation of muscle.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Chromosomes, Artificial, Mammalian: DNA constructs that are composed of, at least, all elements, such as a REPLICATION ORIGIN; TELOMERE; and CENTROMERE, that are required for successful replication, propagation to and maintainance in progeny mammalian cells. In addition, they are constructed to carry other sequences for analysis or gene transfer.Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Adenosine Triphosphate: An adenine nucleotide containing three phosphate groups esterified to the sugar moiety. In addition to its crucial roles in metabolism adenosine triphosphate is a neurotransmitter.Two-Hybrid System Techniques: Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.Yeasts: A general term for single-celled rounded fungi that reproduce by budding. Brewers' and bakers' yeasts are SACCHAROMYCES CEREVISIAE; therapeutic dried yeast is YEAST, DRIED.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Microscopy, Electron: Microscopy using an electron beam, instead of light, to visualize the sample, thereby allowing much greater magnification. The interactions of ELECTRONS with specimens are used to provide information about the fine structure of that specimen. In TRANSMISSION ELECTRON MICROSCOPY the reactions of the electrons that are transmitted through the specimen are imaged. In SCANNING ELECTRON MICROSCOPY an electron beam falls at a non-normal angle on the specimen and the image is derived from the reactions occurring above the plane of the specimen.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Templates, Genetic: Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.Chromosome Segregation: The orderly segregation of CHROMOSOMES during MEIOSIS or MITOSIS.Sex Chromatin: In the interphase nucleus, a condensed mass of chromatin representing an inactivated X chromosome. Each X CHROMOSOME, in excess of one, forms sex chromatin (Barr body) in the mammalian nucleus. (from King & Stansfield, A Dictionary of Genetics, 4th ed)Chickens: Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.Embryo, Nonmammalian: The developmental entity of a fertilized egg (ZYGOTE) in animal species other than MAMMALS. For chickens, use CHICK EMBRYO.High Mobility Group Proteins: A family of low-molecular weight, non-histone proteins found in chromatin.Tubulin: A microtubule subunit protein found in large quantities in mammalian brain. It has also been isolated from SPERM FLAGELLUM; CILIA; and other sources. Structurally, the protein is a dimer with a molecular weight of approximately 120,000 and a sedimentation coefficient of 5.8S. It binds to COLCHICINE; VINCRISTINE; and VINBLASTINE.Protein-Serine-Threonine Kinases: A group of enzymes that catalyzes the phosphorylation of serine or threonine residues in proteins, with ATP or other nucleotides as phosphate donors.Autoantigens: Endogenous tissue constituents that have the ability to interact with AUTOANTIBODIES and cause an immune response.Telomere: A terminal section of a chromosome which has a specialized structure and which is involved in chromosomal replication and stability. Its length is believed to be a few hundred base pairs.Multiprotein Complexes: Macromolecular complexes formed from the association of defined protein subunits.Cytoskeleton: The network of filaments, tubules, and interconnecting filamentous bridges which give shape, structure, and organization to the cytoplasm.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Microscopy, Fluorescence: Microscopy of specimens stained with fluorescent dye (usually fluorescein isothiocyanate) or of naturally fluorescent materials, which emit light when exposed to ultraviolet or blue light. Immunofluorescence microscopy utilizes antibodies that are labeled with fluorescent dye.RNA Polymerase II: A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 2.7.7.6.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Methylation: Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.Actin Cytoskeleton: Fibers composed of MICROFILAMENT PROTEINS, which are predominately ACTIN. They are the smallest of the cytoskeletal filaments.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.Simian virus 40: A species of POLYOMAVIRUS originally isolated from Rhesus monkey kidney tissue. It produces malignancy in human and newborn hamster kidney cell cultures.PhosphoproteinsDNA, Circular: Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)Nuclear Envelope: The membrane system of the CELL NUCLEUS that surrounds the nucleoplasm. It consists of two concentric membranes separated by the perinuclear space. The structures of the envelope where it opens to the cytoplasm are called the nuclear pores (NUCLEAR PORE).Genes, Fungal: The functional hereditary units of FUNGI.DNA Topoisomerases, Type I: DNA TOPOISOMERASES that catalyze ATP-independent breakage of one of the two strands of DNA, passage of the unbroken strand through the break, and rejoining of the broken strand. DNA Topoisomerases, Type I enzymes reduce the topological stress in the DNA structure by relaxing the superhelical turns and knotted rings in the DNA helix.Genomic Instability: An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Spindle Apparatus: A microtubule structure that forms during CELL DIVISION. It consists of two SPINDLE POLES, and sets of MICROTUBULES that may include the astral microtubules, the polar microtubules, and the kinetochore microtubules.Arabidopsis Proteins: Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.Protein Multimerization: The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.Membrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.Protein Transport: The process of moving proteins from one cellular compartment (including extracellular) to another by various sorting and transport mechanisms such as gated transport, protein translocation, and vesicular transport.Protein Processing, Post-Translational: Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.Ultraviolet Rays: That portion of the electromagnetic spectrum immediately below the visible range and extending into the x-ray frequencies. The longer wavelengths (near-UV or biotic or vital rays) are necessary for the endogenous synthesis of vitamin D and are also called antirachitic rays; the shorter, ionizing wavelengths (far-UV or abiotic or extravital rays) are viricidal, bactericidal, mutagenic, and carcinogenic and are used as disinfectants.Protein Conformation: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).Focal Adhesions: An anchoring junction of the cell to a non-cellular substrate. It is composed of a specialized area of the plasma membrane where bundles of the ACTIN CYTOSKELETON terminate and attach to the transmembrane linkers, INTEGRINS, which in turn attach through their extracellular domains to EXTRACELLULAR MATRIX PROTEINS.Ubiquitin-Protein Ligase Complexes: Complexes of enzymes that catalyze the covalent attachment of UBIQUITIN to other proteins by forming a peptide bond between the C-terminal GLYCINE of UBIQUITIN and the alpha-amino groups of LYSINE residues in the protein. The complexes play an important role in mediating the selective-degradation of short-lived and abnormal proteins. The complex of enzymes can be broken down into three components that involve activation of ubiquitin (UBIQUITIN-ACTIVATING ENZYMES), conjugation of ubiquitin to the ligase complex (UBIQUITIN-CONJUGATING ENZYMES), and ligation of ubiquitin to the substrate protein (UBIQUITIN-PROTEIN LIGASES).Capsid: The outer protein protective shell of a virus, which protects the viral nucleic acid.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Nocodazole: Nocodazole is an antineoplastic agent which exerts its effect by depolymerizing microtubules.RNA Interference: A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.Interphase: The interval between two successive CELL DIVISIONS during which the CHROMOSOMES are not individually distinguishable. It is composed of the G phases (G1 PHASE; G0 PHASE; G2 PHASE) and S PHASE (when DNA replication occurs).DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Microfilament Proteins: Monomeric subunits of primarily globular ACTIN and found in the cytoplasmic matrix of almost all cells. They are often associated with microtubules and may play a role in cytoskeletal function and/or mediate movement of the cell or the organelles within the cell.Lamins: Nuclear matrix proteins that are structural components of the NUCLEAR LAMINA. They are found in most multicellular organisms.N-Ethylmaleimide-Sensitive Proteins: ATPases that are members of the AAA protein superfamily (ATPase family Associated with various cellular Activities). The NSFs functions, acting in conjunction with SOLUBLE NSF ATTACHMENT PROTEINS (i.e. SNAPs, which have no relation to SNAP 25), are to dissociate SNARE complexes.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Green Fluorescent Proteins: Protein analogs and derivatives of the Aequorea victoria green fluorescent protein that emit light (FLUORESCENCE) when excited with ULTRAVIOLET RAYS. They are used in REPORTER GENES in doing GENETIC TECHNIQUES. Numerous mutants have been made to emit other colors or be sensitive to pH.Signal Transduction: The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).DNA, Single-Stranded: A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.Virion: The infective system of a virus, composed of the viral genome, a protein core, and a protein coat called a capsid, which may be naked or enclosed in a lipoprotein envelope called the peplos.Cell Line, Tumor: A cell line derived from cultured tumor cells.Protein Structure, Quaternary: The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).Histone-Lysine N-Methyltransferase: An enzyme that catalyzes the methylation of the epsilon-amino group of lysine residues in proteins to yield epsilon mono-, di-, and trimethyllysine. EC 2.1.1.43.RNA, Small Interfering: Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.DNA Helicases: Proteins that catalyze the unwinding of duplex DNA during replication by binding cooperatively to single-stranded regions of DNA or to short regions of duplex DNA that are undergoing transient opening. In addition DNA helicases are DNA-dependent ATPases that harness the free energy of ATP hydrolysis to translocate DNA strands.Transfection: The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Kinetochores: Large multiprotein complexes that bind the centromeres of the chromosomes to the microtubules of the mitotic spindle during metaphase in the cell cycle.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Nucleoproteins: Proteins conjugated with nucleic acids.Cytoskeletal Proteins: Major constituent of the cytoskeleton found in the cytoplasm of eukaryotic cells. They form a flexible framework for the cell, provide attachment points for organelles and formed bodies, and make communication between parts of the cell possible.Fluorescent Antibody Technique: Test for tissue antigen using either a direct method, by conjugation of antibody with fluorescent dye (FLUORESCENT ANTIBODY TECHNIQUE, DIRECT) or an indirect method, by formation of antigen-antibody complex which is then labeled with fluorescein-conjugated anti-immunoglobulin antibody (FLUORESCENT ANTIBODY TECHNIQUE, INDIRECT). The tissue is then examined by fluorescence microscopy.Spermatozoa: Mature male germ cells derived from SPERMATIDS. As spermatids move toward the lumen of the SEMINIFEROUS TUBULES, they undergo extensive structural changes including the loss of cytoplasm, condensation of CHROMATIN into the SPERM HEAD, formation of the ACROSOME cap, the SPERM MIDPIECE and the SPERM TAIL that provides motility.Capsid Proteins: Proteins that form the CAPSID of VIRUSES.Euchromatin: Chromosome regions that are loosely packaged and more accessible to RNA polymerases than HETEROCHROMATIN. These regions also stain differentially in CHROMOSOME BANDING preparations.Fluorescence Recovery After Photobleaching: A method used to study the lateral movement of MEMBRANE PROTEINS and LIPIDS. A small area of a cell membrane is bleached by laser light and the amount of time necessary for unbleached fluorescent marker-tagged proteins to diffuse back into the bleached site is a measurement of the cell membrane's fluidity. The diffusion coefficient of a protein or lipid in the membrane can be calculated from the data. (From Segen, Current Med Talk, 1995).Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Cytoplasm: The part of a cell that contains the CYTOSOL and small structures excluding the CELL NUCLEUS; MITOCHONDRIA; and large VACUOLES. (Glick, Glossary of Biochemistry and Molecular Biology, 1990)Cattle: Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.Lamin Type B: A subclass of ubiquitously-expressed lamins having an acidic isoelectric point. They are found to remain bound to nuclear membranes during mitosis.Cofilin 1: Cofilin 1 is a member of the cofilin family of proteins that is expressed in non-muscle CELLS. It has ACTIN depolymerization activity that is dependent on HYDROGEN-ION CONCENTRATION.Meiosis: A type of CELL NUCLEUS division, occurring during maturation of the GERM CELLS. Two successive cell nucleus divisions following a single chromosome duplication (S PHASE) result in daughter cells with half the number of CHROMOSOMES as the parent cells.Microtubule-Associated Proteins: High molecular weight proteins found in the MICROTUBULES of the cytoskeletal system. Under certain conditions they are required for TUBULIN assembly into the microtubules and stabilize the assembled microtubules.Nuclear Pore: An opening through the NUCLEAR ENVELOPE formed by the nuclear pore complex which transports nuclear proteins or RNA into or out of the CELL NUCLEUS and which, under some conditions, acts as an ion channel.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Immunoprecipitation: The aggregation of soluble ANTIGENS with ANTIBODIES, alone or with antibody binding factors such as ANTI-ANTIBODIES or STAPHYLOCOCCAL PROTEIN A, into complexes large enough to fall out of solution.Actin Depolymerizing Factors: A family of low MOLECULAR WEIGHT actin-binding proteins found throughout eukaryotes. They remodel the actin CYTOSKELETON by severing ACTIN FILAMENTS and increasing the rate of monomer dissociation.Cell Membrane: The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.Cell Nucleolus: Within most types of eukaryotic CELL NUCLEUS, a distinct region, not delimited by a membrane, in which some species of rRNA (RNA, RIBOSOMAL) are synthesized and assembled into ribonucleoprotein subunits of ribosomes. In the nucleolus rRNA is transcribed from a nucleolar organizer, i.e., a group of tandemly repeated chromosomal genes which encode rRNA and which are transcribed by RNA polymerase I. (Singleton & Sainsbury, Dictionary of Microbiology & Molecular Biology, 2d ed)Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Fibroblasts: Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules.Insulator Elements: Nucleic acid regulatory sequences that limit or oppose the action of ENHANCER ELEMENTS and define the boundary between differentially regulated gene loci.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Intermediate Filaments: Cytoplasmic filaments intermediate in diameter (about 10 nanometers) between the microfilaments and the microtubules. They may be composed of any of a number of different proteins and form a ring around the cell nucleus.Golgi Apparatus: A stack of flattened vesicles that functions in posttranslational processing and sorting of proteins, receiving them from the rough ENDOPLASMIC RETICULUM and directing them to secretory vesicles, LYSOSOMES, or the CELL MEMBRANE. The movement of proteins takes place by transfer vesicles that bud off from the rough endoplasmic reticulum or Golgi apparatus and fuse with the Golgi, lysosomes or cell membrane. (From Glick, Glossary of Biochemistry and Molecular Biology, 1990)Precipitin Tests: Serologic tests in which a positive reaction manifested by visible CHEMICAL PRECIPITATION occurs when a soluble ANTIGEN reacts with its precipitins, i.e., ANTIBODIES that can form a precipitate.Enhancer Elements, Genetic: Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.Bacterial Proteins: Proteins found in any species of bacterium.Vesicular Transport Proteins: A broad category of proteins involved in the formation, transport and dissolution of TRANSPORT VESICLES. They play a role in the intracellular transport of molecules contained within membrane vesicles. Vesicular transport proteins are distinguished from MEMBRANE TRANSPORT PROTEINS, which move molecules across membranes, by the mode in which the molecules are transported.Orthoreovirus, Mammalian: A species of ORTHOREOVIRUS infecting mammals (other than baboons). There are four serotypes. In humans they are generally benign but may sometimes cause upper respiratory tract illness or enteritis in infants and children. MAMMALIAN ORTHOREOVIRUS 3 is a very pathogenic virus in laboratory rodents.Polymers: Compounds formed by the joining of smaller, usually repeating, units linked by covalent bonds. These compounds often form large macromolecules (e.g., BIOPOLYMERS; PLASTICS).Adherens Junctions: Anchoring points where the CYTOSKELETON of neighboring cells are connected to each other. They are composed of specialized areas of the plasma membrane where bundles of the ACTIN CYTOSKELETON attach to the membrane through the transmembrane linkers, CADHERINS, which in turn attach through their extracellular domains to cadherins in the neighboring cell membranes. In sheets of cells, they form into adhesion belts (zonula adherens) that go all the way around a cell.Gene Expression Regulation, Developmental: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.Deoxyribonucleases: Enzymes which catalyze the hydrolases of ester bonds within DNA. EC 3.1.-.SNARE Proteins: A superfamily of small proteins which are involved in the MEMBRANE FUSION events, intracellular protein trafficking and secretory processes. They share a homologous SNARE motif. The SNARE proteins are divided into subfamilies: QA-SNARES; QB-SNARES; QC-SNARES; and R-SNARES. The formation of a SNARE complex (composed of one each of the four different types SNARE domains (Qa, Qb, Qc, and R)) mediates MEMBRANE FUSION. Following membrane fusion SNARE complexes are dissociated by the NSFs (N-ETHYLMALEIMIDE-SENSITIVE FACTORS), in conjunction with SOLUBLE NSF ATTACHMENT PROTEIN, i.e., SNAPs (no relation to SNAP 25.)Cricetinae: A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.Xenopus Proteins: Proteins obtained from various species of Xenopus. Included here are proteins from the African clawed frog (XENOPUS LAEVIS). Many of these proteins have been the subject of scientific investigations in the area of MORPHOGENESIS and development.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Telophase: The final phase of cell nucleus division following ANAPHASE, in which two daughter nuclei are formed, the CYTOPLASM completes division, and the CHROMOSOMES lose their distinctness and are transformed into CHROMATIN threads.Luminescent Proteins: Proteins which are involved in the phenomenon of light emission in living systems. Included are the "enzymatic" and "non-enzymatic" types of system with or without the presence of oxygen or co-factors.Soluble N-Ethylmaleimide-Sensitive Factor Attachment Proteins: SNARE binding proteins that facilitate the ATP hydrolysis-driven dissociation of the SNARE complex. They are required for the binding of N-ETHYLMALEIMIDE-SENSITIVE PROTEIN (NSF) to the SNARE complex which also stimulates the ATPASE activity of NSF. They are unrelated structurally to SNAP-25 PROTEIN.

Chromatin condensation is confined to the loop and involves an all-or-none structural change. (1/2103)

Using differential scanning calorimetry in combination with pulsed field gel electrophoresis, we relate here the changes in the thermal profile of rat liver nuclei induced by very mild digestion of chromatin by endogenous nuclease with the chain length distribution of the DNA fragments. The enthalpy of the endotherm at 106 degrees C, which reflects the denaturation of the heterochromatic domains, decreases dramatically after the induction of a very small number of double-strand breaks per chromosome; the thermal transition disappears when the loops have undergone on average one DNA chain scission event. Quantitative analysis of the experimental data shows that the loop behaves like a topologically isolated domain. Also discussed is the process of heterochromatin formation, which occurs according to an all-or-none mechanism. In the presence of spermine, a strong condensation agent, only the loops that have undergone one break are able to refold, in confirmation of the extremely cooperative nature of the transition. Furthermore, our results suggest a relationship between the states that give rise to the endotherms at 90 degrees C and 106 degrees C and the morphologies referred to as class II and class III in a previous physicochemical study of the folding of chromatin fragments (Widom, 1986. J. Mol. Biol. 190:411-424) and support the view that the overall process of condensation follows a sequential (two-step) pathway.  (+info)

Proposed mechanism for sperm chromatin condensation/decondensation in the male rat. (2/2103)

Condensation of sperm chromatin occurs after spermatozoa have left the caput epididymis and are in transit to the cauda epididymis, during which time large numbers of disulfide bonds are formed. The formation of these disulfide bonds requires the repeated oxidation of the cofactor, NAD(P)H. To date, the means by which this oxidation is achieved has yet to be elucidated. Spermatozoa lose the bulk of their cytoplasm prior to leaving the testis; and, as a result, any shuttle systems for removing and transferring reducing equivalents into the mitochondria are unlikely to be operational. In an apparent preparation for the loss of cytoplasm, however, the following events occur during spermatogenesis. First, androgen-binding protein (ABP) is produced by the Sertoli cells of the testis; second, high affinity binding sites for ABP are inserted into the membrane surrounding the nucleus; and third, a nuclear location is acquired for the enzyme, 3alpha-hydroxysteroid dehydrogenase (3alpha-HSD). We propose that after the loss of cytoplasm, the nuclear region of spermatozoa is directly accessible to constituents contained in the lumen of the caput epididymis. As a consequence, luminal ABP attaches itself to the nuclear membrane via its binding sites, and is internalized. After internalization, ABP exerts its principle function, which is to bind to luminal 5alpha-dihydrotestosterone (5alpha-DHT), thereby ensuring its availability to the enzyme, 3alpha-HSD. In the conversion of 5alpha-DHT to 3alpha-androstanediol (3alpha-Diol), NAD(P)H is oxidized. Spermatozoa that reach the cauda epididymis have fully condensed chromatin. In addition, the nuclear region retains appreciable amounts of 5alpha-DHT and 3alpha-Diol, both bound to ABP. During fertilization, the bound 3alpha-Diol is converted back to 5alpha-DHT, reducing equivalents are transferred to NAD(P)+, and disulfide bonds are broken.IVF clinics report that spermatozoa with incompletely condensed chromatin have a low percentage of fertilization. If our proposed mechanism for chromatin condensation/decondensation is borne out by further research, IVF clinics might consider preincubating spermatozoa with 5alpha-DHT in order to increase the efficiency of fertilization.  (+info)

Expression of the Wdr9 gene and protein products during mouse development. (3/2103)

Human WDR9 has been mapped to chromosome 21, within one of the Down syndrome (DS) critical regions. Here, we study the expression pattern of the murine Wdr9 gene and its protein product. We show that Wdr9 is broadly expressed in the mouse embryo by means of in situ hybridization and immunohistochemistry. Wdr9 expression levels are dynamic during embryonic development as revealed by Northern blot analysis. We further show that WDR9 is a nuclear protein associated with BRG1, a SWI/SNF complex component. We also demonstrate that a polyglutamine-containing region of the protein functions as a transcriptional activation domain. We propose that WDR9 is a transcriptional regulator involved in chromatin remodeling through the action of two bromodomains and contacts to the SWI/SNF complex. These results may provide a molecular basis for the association of WDR9 with DS.  (+info)

Identification of SATB2 as the cleft palate gene on 2q32-q33. (4/2103)

Cytogenetic evidence, in the form of deletions and balanced translocations, points to the existence of a locus on 2q32-q33, for which haploinsufficiency results in isolated cleft palate (CPO). Here we show by high-resolution FISH mapping of two de novo CPO-associated translocations involving 2q32-q33 that one breakpoint interrupts the transcription unit of the gene encoding the DNA-binding protein SATB2 (formerly KIAA1034). The breakpoint in the other translocation is located 130 kb 3' to the SATB2 polyadenylation signal, within a conserved region of non-coding DNA. The SATB2 gene is transcribed in a telomeric to centromeric direction and lies in a gene-poor region of 2q32-q33; the nearest confirmed gene is 1.26 Mb centromeric to the SATB2 polyadenylation signal. SATB2-encoding transcripts are assembled from 11 exons that span 191 kb of genomic DNA. They encode a protein of 733 amino acids that has two CUT domains and a homeodomain and shows a remarkable degree of evolutionary conservation, with only three amino acid substitutions between mouse and human. This protein belongs to the same family as SATB1, a nuclear matrix-attachment region binding protein implicated in transcriptional control and control of chromatin remodelling. There are also sequence similarities to the Drosophila protein DVE. Whole mount in situ hybridization to mouse embryos shows site- and stage-specific expression of SATB2 in the developing palate. Despite the strong evidence supporting an important role for SATB2 in palate development, mutation analysis of 70 unrelated patients with CPO did not reveal any coding region variants.  (+info)

Chromatin assembly factor 1 is essential and couples chromatin assembly to DNA replication in vivo. (5/2103)

De novo chromatin assembly maintains histone density on the daughter strands in the wake of the replication fork. The heterotrimer chromatin assembly factor 1 (CAF-1) couples DNA replication to histone deposition in vitro, but is not essential for yeast cell proliferation. Depletion of CAF-1 in human cell lines demonstrated that CAF-1 was required for efficient progression through S-phase. Cells lacking CAF-1 accumulated in early and mid S-phase and replicated DNA slowly. The checkpoint kinase Chk1, but not Chk2, was phosphorylated in response to CAF-1 depletion, consistent with a DNA replication defect. CAF-1-depleted cell extracts completely lacked DNA replication-coupled chromatin assembly activity, suggesting that CAF-1 is required for efficient S-phase progression in human cells. These results indicate that, in contrast to yeast, human CAF-1 is necessary for coupling chromatin assembly with DNA replication.  (+info)

Fission yeast Tup1-like repressors repress chromatin remodeling at the fbp1+ promoter and the ade6-M26 recombination hotspot. (6/2103)

Chromatin remodeling plays crucial roles in the regulation of gene expression and recombination. Transcription of the fission yeast fbp1(+) gene and recombination at the meiotic recombination hotspot ade6-M26 (M26) are both regulated by cAMP responsive element (CRE)-like sequences and the CREB/ATF-type transcription factor Atf1*Pcr1. The Tup11 and Tup12 proteins, the fission yeast counterparts of the Saccharomyces cerevisiae Tup1 corepressor, are involved in glucose repression of the fbp1(+) transcription. We have analyzed roles of the Tup1-like corepressors in chromatin regulation around the fbp1(+) promoter and the M26 hotspot. We found that the chromatin structure around two regulatory elements for fbp1(+) was remodeled under derepressed conditions in concert with the robust activation of fbp1(+) transcription. Strains with tup11delta tup12delta double deletions grown in repressed conditions exhibited the chromatin state associated with wild-type cells grown in derepressed conditions. Interestingly, deletion of rst2(+), encoding a transcription factor controlled by the cAMP-dependent kinase, alleviated the tup11delta tup12delta defects in chromatin regulation but not in transcription repression. The chromatin at the M26 site in mitotic cultures of a tup11delta tup12delta mutant resembled that of wild-type meiotic cells. These observations suggest that these fission yeast Tup1-like corepressors repress chromatin remodeling at CRE-related sequences and that Rst2 antagonizes this function.  (+info)

Methylation at lysine 4 of histone H3 in ecdysone-dependent development of Drosophila. (7/2103)

Steroid hormones fulfil important functions in animal development. In Drosophila, ecdysone triggers moulting and metamorphosis through its effects on gene expression. Ecdysone works by binding to a nuclear receptor, EcR, which heterodimerizes with the retinoid X receptor homologue Ultraspiracle. Both partners are required for binding to ligand or DNA. Like most DNA-binding transcription factors, nuclear receptors activate or repress gene expression by recruiting co-regulators, some of which function as chromatin-modifying complexes. For example, p160 class coactivators associate with histone acetyltransferases and arginine histone methyltransferases. The Trithorax-related gene of Drosophila encodes the SET domain protein TRR. Here we report that TRR is a histone methyltransferases capable of trimethylating lysine 4 of histone H3 (H3-K4). trr acts upstream of hedgehog (hh) in progression of the morphogenetic furrow, and is required for retinal differentiation. Mutations in trr interact in eye development with EcR, and EcR and TRR can be co-immunoprecipitated on ecdysone treatment. TRR, EcR and trimethylated H3-K4 are detected at the ecdysone-inducible promoters of hh and BR-C in cultured cells, and H3-K4 trimethylation at these promoters is decreased in embryos lacking a functional copy of trr. We propose that TRR functions as a coactivator of EcR by altering the chromatin structure at ecdysone-responsive promoters.  (+info)

Retinoic acid receptor alpha fusion to PML affects its transcriptional and chromatin-remodeling properties. (8/2103)

PML-RAR is an oncogenic transcription factor forming in acute promyelocytic leukemias (APL) because of a chromosomal translocation. Without its ligand, retinoic acid (RA), PML-RAR functions as a constitutive transcriptional repressor, abnormally associating with the corepressor-histone deacetylase complex and blocking hematopoietic differentiation. In the presence of pharmacological concentrations of RA, PML-RAR activates transcription and stimulates differentiation. Even though it has been suggested that chromatin alteration is important for APL onset, the PML-RAR effect on chromatin of target promoters has not been investigated. Taking advantage of the Xenopus oocyte system, we compared the wild-type transcription factor RARalpha with PML-RAR as both transcriptional regulators and chromatin structure modifiers. Without RA, we found that PML-RAR is a more potent transcriptional repressor that does not require the cofactor RXR and produces a closed chromatin configuration. Surprisingly, repression by PML-RAR occurs through a further pathway that is independent of nucleosome deposition and histone deacetylation. In the presence of RA, PML-RAR is a less efficient transcriptional activator that is unable to modify the DNA nucleoprotein structure. We propose that PML-RAR, aside from its ability to recruit aberrant quantities of histone deacetylase complexes, has acquired additional repressive mechanisms and lost important activating functions; the comprehension of these mechanisms might reveal novel targets for antileukemic intervention.  (+info)

Chromatin remodelling factor Isw1A complexed with DNA (deoxyribonucleic acid). Computer model showing the structure of yeast chromatin remodelling factor Isw1A , i. e. the imitation switch proteins 1 (del_ATPase, dark blue) and 3 (green) complexed with two DNA (yellow, magenta, cyan, orange). From yeast. - Stock Image C035/8413
The chromatin remodeling complexes alter chromatin structures. They remodel nucleosomes in ATP-dependent manner and have essential roles in DNA damage repair, recombination, replication and transcriptional control. Increasing evidences indicate that subunits of chromatin remodelers are mutated and/or deregulated in a number of human cancers, and how they influence the cancer gene expression program during cancer initiation and progression is becomming clearer. Therefore, chromatin remodeling complexes arose as promising new targets for the treatment of human cancers. In this review, chromatin remodeling complexes, their epigenetic reader domains and available inhibitors are described. The insights into the misregulated chromatin remodelers pathways in human malignancies and the novel approach targeting deregulated chromatin remodelers to improve chemotherapy efficiency are discussed. ...
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Since their discovery in the mid-1990s, nuclear actin-related proteins (ARPs) have gained attention for their roles as structural components of ATP-dependent chromatin-remodeling complexes. These remodelers can move nucleosomes along the DNA, evict them from chromatin, and exchange histone variants to alter chromatin states locally. Chromatin-remodeling facilitates DNA-templated processes such as transcription regulation, DNA replication, and repair. Consistent with a role for ARPs in shaping chromatin structure, recent genetic studies show that they affect developmental and cell-type specific transcriptional programming. Here, we focus on recent results that suggest a specific contribution of ARPs to long-range interactions in the nucleus, and review evidence indicating that some ARPs may act independently of chromatin-remodeling machines.. ...
Improved treatment for major depressive disorder (MDD) remains elusive because of the limited understanding of its underlying biological mechanisms. It is likely that stress-induced maladaptive transcriptional regulation in limbic neural circuits contributes to the development of MDD, possibly through epigenetic factors that regulate chromatin structure. We establish that persistent upregulation of the ACF (ATP-utilizing chromatin assembly and remodeling factor) ATP-dependent chromatin-remodeling complex, occurring in the nucleus accumbens of stress-susceptible mice and depressed humans, is necessary for stress-induced depressive-like behaviors. We found that altered ACF binding after chronic stress was correlated with altered nucleosome positioning, particularly around the transcription start sites of affected genes. These alterations in ACF binding and nucleosome positioning were associated with repressed expression of genes implicated in susceptibility to stress. Together, our findings ...
Crystallographic Studies of Large Complexes: From the Yeast Chromatin. Remodeling Factor ISW1a to the Entire Nucleosome-Traversing. Transcription Machinery. Kazuhiro Yamada, PhD. Senior Scientist/Over-assistant. Institute of Molecular Biology and Biophysics. ETH Zurich. Monday, October 1, 2012. 4 p.m. , Caspary Auditorium. Refreshments 3:45 p.m.. Recommended Readings:. Yen, K.; Vinayachandran, V.; Batta, K.; et al. 2012. Genome-wide Nucleosome Specificity and Directionality of Chromatin Remodelers. CELL 149(7):1461-1473 DOI: 10.1016/j.cell.2012.04.036. Richmond, Timothy J. 2012. Nucleosome recognition and spacing by chromatin remodelling factor ISW1a. BIOCHEMICAL SOCIETY TRANSACTIONS, 40: 347-350 DOI: 10.1042/BST20110748 Please request from Markus Library.. De Cian, A; Praly, E; Ding, F; et al. 2012. ATP-Independent Cooperative Binding of Yeast Isw1a to Bare and Nucleosomal DNA. PLOS ONE 7(2): e31845 DOI: 10.1371/journal.pone.0031845. Sharma, A.; Jenkins, K. R.; Heroux, A.; et al. 2011. Crystal ...
Regulation of gene expression includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA), and is informally termed gene regulation. Sophisticated programs of gene expression are widely observed in biology, for example to trigger developmental pathways, respond to environmental stimuli, or adapt to new food sources. Virtually any step of gene expression can be modulated, from transcriptional initiation, to RNA processing, and to the post-translational modification of a protein.. Gene regulation is essential for viruses, prokaryotes and eukaryotes as it increases the versatility and adaptability of an organism by allowing the cell to express protein when needed. Histone, DNA modifying enzymes and chromatin remodelling factors are major area to concentrate.. Relevant Conferences: Nucleic Acids Conferences , Biochemistry Conferences. 2ndInternational Conference on Transcriptomics, September 12-14, 2016 Philadelphia ...
One of the first ATP-dependent chromatin remodeling complexes was first identified and characterized more than a decade ago. Since then, the number of distinct ATP-dependent chromatin remodeling complexes and the variety of roles they play in nuclear processes have become dizzying. Some of the processes include transcription, replication, repair, recombination, and sister chromatid cohesion. The SWI/SNF-related ATP-dependent remodelers are divided into a number of subfamilies, all related by the SWI2/SNF2 ATPase at their catalytic core. In nearly every species where researchers have looked for them, one or more members of each subfamily have been identified. Here I have investigated the ATP-dependent chromatin remodeler ISWI. I have shown that Xenopus ISWI has a critical function in developing neural tissue. Whole mount in situ hybridization shows ISWI localized in neural tissue including the eye and developing neural tube. Injection of antisense ISWI RNA, morpholino oligonucleotides or ...
Adult stem cell function: Both regulators of intracellular signalling (e.g. Spry1) and chromatin remodelling factors are important for normal adult stem cell function. We are investigating the roles of these factors in adult stem cells in the muscle (in collaboration with Dr. Andrew Brack (Harvard) and brain. Supported by the BBSRC Researchers: Kieran Jones, Nemanja Saric ...
Several chromatin-remodelling proteins are implicated in the efficient repair of DNA damage in mammalian cells, including BRG1, CHD1L/ALC1, CHD4, INO80 and ISWI proteins ACF1 and SNF2H (Ahel et al., 2009; Kashiwaba et al., 2010; Lan et al., 2010; Larsen et al., 2010; Lee et al., 2010; Nakamura et al., 2011; Park et al., 2009; Park et al., 2006; Polo et al., 2010; Sánchez-Molina et al., 2011; Smeenk et al., 2010). Most of the chromatin-remodelling proteins are recruited to DNA breaks in a γH2AX-dependent manner and function to modulate chromatin structure and modifications in order to facilitate the access to either DNA or chromatin of factors involved in DNA damage signalling and repair. The function of chromatin remodellers in supporting DNA repair is often conserved from yeast to mammalian cells, indicating that chromatin reorganization during DNA repair is vital for maintenance of genome stability.. LSH has been extensively studied as a protein that promotes DNA methylation and silencing of ...
Mammalian SWI/SNF (mSWI/SNF) ATP-dependent chromatin remodeling complexes are large, multi-subunit molecular machines that play vital roles in regulating genomi...
El Centro Nacional de Biotecnología es un centro estratégico del Consejo Superior de Investigaciones Científicas con un objetivo mixto académico y de transferencia de tecnología en el área de la Biotecnología.
KOYAMA Hirofumi , NAGAO Taka-aki , INAI Tomomi , MIYAHARA Kohji , HAYASIDA Yasufumi , SHIRAHIGE Katsuhiko , TSUCHIYA Eiko Bioscience, Biotechnology, and Biochemistry 68(4), 909-919, 2004-04-23 J-STAGE References (45) ...
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Yes, its in the Teachings of the Buddha. Chapter 5 of the Abhidhamma Sangaha shows that there are 16 worlds for Rūpāvacara Brahmas and 4 worlds of Arūpāvacara Brahmas ...
Dietary nutrients interact with gene networks to orchestrate adaptive responses during metabolic stress. Here, we identify Baf60a as a diet-sensitive subunit of the SWI/SNF chromatin-remodeling complexes in the mouse liver that links the consumption of fat- and cholesterol-rich diet to elevated plasma cholesterol levels. Baf60a expression was elevated in the liver following feeding with a western diet. Hepatocyte-specific inactivation of Baf60a reduced bile acid production and cholesterol absorption, and attenuated diet-induced hypercholesterolemia and atherosclerosis in mice. Baf60a stimulates expression of genes involved in bile acid synthesis, modification, and transport through a CAR/Baf60a feedforward regulatory loop. Baf60a is required for the recruitment of the SWI/SNF chromatin-remodeling complexes to facilitate an activating epigenetic switch on target genes. These studies elucidate a regulatory pathway that mediates the hyperlipidemic and atherogenic effects of western diet ...
Excellgen Brahma-related Gene 1 protein, wild type, BRG1, SMARCA4 [RP-22] - Product Name Brahma-related Gene 1, BRG1, SMARCA4 Size 5,000 U Description The wild type human brahma-related gene 1 (Brg1) encodes a protein of 1,647 amino acids that contains a conserved domain of the SWI2/SNF2 family necessary for normal mitotic growth and transcription regulation (1-3). BRG1 is an essential component of the SWI/SNF chromatin remodeling complexes
One of the longest standing problems in DNA repair is how cells relax chromatin in order to make DNA lesions accessible for global nucleotide excision repair (NER). Since chromatin has to be relaxed for efficient lesion detection, the key question is whether chromatin relaxation precedes lesion detection or vice versa. Chromatin accessibility factors have been proposed but not yet identified. Here we show that p53 acts as a chromatin accessibility factor, mediating UV-induced global chromatin relaxation. Using localized subnuclear UV irradiation, we demonstrate that chromatin relaxation is extended over the whole nucleus and that this process requires p53. We show that the sequence for initiation of global NER is as follows: transcription-associated lesion detection; p53-mediated global chromatin relaxation; and global lesion detection. The tumour suppressor p53 is crucial for genomic stability, a role partially explained by its pro-apoptotic capacity. We demonstrate here that p53 is also a ...
Beijing, China - Chromatin remodeling proteins (chromatin remodelers) are essential and powerful regulators for critical DNA-templated cellular processes, such as DNA replication, recombination, gene transcription/repression, and DNA damage repair. These molecular and genetic processes are important for a wide spectrum of cellular functions, including cell cycle, death, differentiation, pluripotency, and genome integrity. Recently, many scientific reports have shown that chromatin remodeling proteins could be promising new targets for the treatment of human malignancy.. "This is a hot and exciting research topic for cancer researchers, and our article provides an updated understanding on the functions and mechanisms of chromatin remodelers in human cancers," says Dr. Chun Zhang, the principle investigator of the Department of Nuclear Medicine of Beijing Chao-Yang Hospital and Capital Medical University of China.. Chromatin remodeling is an energy-driven process in which chromatin remodelers use ...
Core component of the BAF (hSWI/SNF) complex. This ATP-dependent chromatin-remodeling complex plays important roles in cell proliferation and differentiation, in cellular antiviral activities and inhibition of tumor formation. The BAF complex is able to create a stable, altered form of chromatin that constrains fewer negative supercoils than normal. This change in supercoiling would be due to the conversion of up to one-half of the nucleosomes on polynucleosomal arrays into asymmetric structures, termed altosomes, each composed of 2 histones octamers. Stimulates in vitro the remodeling activity of SMARCA4/BRG1/BAF190A. Involved in activation of CSF1 promoter. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a postmitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The
ATP-dependent chromatin-remodeling complexes (remodelers) modulate gene transcription by regulating the accessibility of highly packaged genomic DNA. However, the molecular mechanisms involved at the nucleosomal level in this process remain controversial. Here, we monitor the real-time activity of single ySWI/SNF or RSC complexes on single, stretched nucleosomal templates under tensions above 1 pN forces. We find that these remodelers can translocate along DNA at rates of approximately 13 bp/s and generate forces up to approximately 12 pN, producing DNA loops of a broad range of sizes (20-1200 bp, average approximately 100 bp) in a nucleosome-dependent manner. This nucleosome-specific activity differs significantly from that on bare DNA observed under low tensions and suggests a nucleosome-remodeling mechanism through intranucleosomal DNA loop formation. Such loop formation may provide a molecular basis for the biological functions of remodelers.
CHD8 (Chromodomain-Helicase-DNA binding protein 8) is a member of the chromodomain helicase DNA-binding (CHD) subfamily of enzymes, which also belongs to the SNF2 family of ATP-dependent chromatin remodelers ...
MS Thesis: EXPRESSION AND FUNCTION OF WILLIAMS SYNDROME TRANSCRIPTION FACTOR (WSTF) IN THE NEURAL DEVELOPMENT OF XENOPUS LAEVIS Imitation Switch (ISWI) is a member of the SWI2/SNF2 superfamily of ATP-dependent chromatin remodelers. Twenty different ISWI complexes have been identified so far in yeast, Drosophila, Xenopus and mammals. Three ISWI-containing complexes, WICH, ACF and CHRAC, have been characterized in Xenopus. Loss of ISWI function in Xenopus embryos results in severe defects in neural and eye development, including loss of retinal differentiation and formation of cataracts. We have begun to dissect the contributions of individual ISWI-dependent complexes to development, by using in situ hybridization and antisense morpholino knockdowns against subunits unique to different ISWI-containing complexes. Here I have investigated the WICH complex in Xenopus and have targeted the WSTF subunit. Whole mount in situ hybridization shows WSTF localized in the neural tissue including eye, brain, ...
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Estrogen receptor α (ER) is a member of the family of nuclear receptors and functions as a transcriptional factor to induce gene expression by binding to specific DNA sequences upon hormone treatment. It regulates cell growth, development and metabolic homeostasis in multi-cellular organisms. Estrogen-mediated transcription has been intensively studied genome-wide as well as on a small number of specific endogenous target promoters. However, the exact mechanism by which ER coordinates the activities of chromatin remodeling complexes and coactivators to facilitate initiation of transcription remains elusive. Here, we show the molecular mechanisms of the recruitment of the SWI/SNF chromatin remodeling complex by Fli-I, and recruitment of Tip60, a histone acetyltransferase.; Fli-I can bind directly to both ER and BAF53, an actin-related component of the SWI/SNF complex, suggesting that Fli-I may recruit SWI/SNF to ER target genes via interaction with BAF53. Depletion of endogenous Fli-I or BAF53 ...
Activation of HO in yeast involves recruitment of transcription factors in two waves. The first is triggered by inactivation of Cdk1 at the end of mitosis, which promotes import into the nucleus of the Swi5 transcription factor. Swi5 recruits the Swi/Snf chromatin-remodeling complex, which then facilitates recruitment of the SAGA histone acetylase, which in turn permits the binding of the SBF transcription factor. We show here that SBF then recruits the SRB/mediator complex and that this process occurs in the absence of Cdk1 activity. The second wave is triggered by reactivation of Cdk1, which leads to recruitment of PolII, TFIIB, and TFIIH. RNA polymerase is, therefore, recruited to HO in two steps and not as a holoenzyme. A similar sequence of events occurs at other SBF-regulated promoters, such as CLN1, CLN2, and PCL1.
ARID1A is a member of the SWI/SNF family, whose members have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodelling complex SWI/SNF, which is required for transcriptional activation of genes normally repressed by chromatin. It possesses at least two conserved domains that could be important for its function. First, it has an ARID domain, which is a DNA-binding domain that can specifically bind an AT-rich DNA sequence known to be recognized by a SWI/SNF complex at the beta-globin locus. Second, the C-terminus of the protein can stimulate glucocorticoid receptor-dependent transcriptional activation. It is thought that the protein encoded by this gene confers specificity to the SWI/SNF complex and may recruit the complex to its targets through either protein-DNA or protein-protein interactions. Two transcript variants encoding ...
Abstract: Gene-gene interactions shape complex phenotypes and modify the effects of mutations during development and disease. The effects of statistical gene-gene interactions on phenotypes have been used to assign genes to functional modules. However, directional, epistatic interactions, which reflect regulatory relationships between genes, have been challenging to map at large-scale. Here, we used combinatorial RNA interference and automated single-cell phenotyping to generate a large genetic interaction map for 21 phenotypic features of Drosophila cells. We devised a method that combines genetic interactions on multiple phenotypes to reveal directional relationships. This network reconstructed the sequence of protein activities in mitosis. Moreover, it revealed that the Ras pathway interacts with the SWI/SNF chromatin-remodelling complex, an interaction that we show is conserved in human cancer cells. Our study presents a powerful approach for reconstructing directional regulatory networks ...
Due to advances in molecular biology techniques, chromatin structure and function has re-emerged as a key research area in the investigation of gene regulation and expression. This indispensable new book provides the busy researcher with an overview of all the latest research in this important area. Topicality and breadth of coverage is assured by the contributions of an international group of over 30 leading scientists in this field. Contents list: Elements of chromatin structure: histones, nucleosomes, fibers; DNA structure: implications for chromatin structure and function; Replication and assembly; Promoter potentiation and activation: chromatin structure and transcriptional induction of heat shock genes; Initiation of expression: remodelling genes; Transcription on chromatin templates; Chromatin structure and epigenetic regulation in yeast; Epigenetic regulation in Drosophilia: a conspiracy of silence; Boundaries and domains; Epigenetic regulation in mammalian cells.Elgin, Sarah C. is the ...
FISH studies on several strongly transcribed chromosomal regions have shown a disposition for looping out from their respective chromosome territories (Mahy et al., 2002b; Volpi et al., 2000; Williams et al., 2002), suggesting a large-scale chromatin decondensation reminiscent of results obtained by targeting transcription factors to transgene arrays. In the first of these targeting studies chromatin decondensation was induced by the viral transcriptional VP16 acidic activation domain. Targeting was achieved within the context of large transgene arrays containing multiple-copy plasmid integrations; each plasmid carried direct repeats of 256 (Tumbar et al., 1999) or 96 (Tsukamoto et al., 2000) operator binding sites for fusion proteins between the lac or tet repressor and VP16. Despite the large opening activity observed, the biological relevance of these observations hinges on the actual physiological relevance of the experimental system. In particular, there are three obvious concerns.. First, ...
TY - JOUR. T1 - Chromatin remodeling complex interacts with ADD1/SREBP1c to mediate insulin-dependent regulation of gene expression. AU - Lee, Yun Sok. AU - Sohn, Dong Hyun. AU - Han, Daehee. AU - Lee, Han Woong. AU - Seong, Rho Hyun. AU - Kim, Jae Bum. PY - 2007/1/1. Y1 - 2007/1/1. N2 - Insulin plays a critical role in whole-body energy homeostasis by regulating lipid and glucose metabolism. In fat and liver tissues, ADD1/SREBP1c is a key transcription factor to mediate insulin-dependent regulation of gene expression. Although transcriptional and proteolytic activation of ADD1/SREBP1c has been studied intensively, the mechanism by which insulin regulates expression of its target genes with ADD1/SREBP1c at the chromatin level is unclear. Here, we reveal that SWI/SNF chromatin remodeling factors interact with the ADD1/SREBP1c and actively regulate insulin-dependent gene expression. Insulin enhanced recruitment of SWI/SNF chromatin remodeling factors to its target gene promoters with concomitant ...
Transcriptional regulation of inflammatory gene expression has been at the forefront of studies of innate immunity and is coordinately regulated by transcription factors, including NF-κB, and chromatin modifiers. The growing evidence for involvement of chromatin in the regulation of gene expression in innate immune cells, has uncovered an evolutionarily conserved role of microbial sensing and chromatin remodeling. Toll-like receptors and RIG-I-like receptors trigger these signaling pathways leading to transcriptional expression of a set of genes involved in inflammation. Tightly regulated control of this gene expression is a paramount, and often foremost, goal of most biological endeavors. In this review, we will discuss the recent progress about the molecular mechanisms governing control of pro-inflammatory gene expression by an evolutionarily conserved novel nuclear protein Akirin2 in macrophages and its emergence as an essential link between NF-κB and chromatin remodelers for transcriptional
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Enter the text here that is the new abstract information for your application. The organization of the nucleus and the regulated folding of the genome plays ess...
Chromatin is a complex polymer molecule in eukaryotic cells, primarily consisting of DNA and histones. Many works have shown that the 3D folding of chromatin structure plays an important role in DNA expression. The recently proposed Chro- mosome Conformation Capture technologies, especially the Hi-C assays, provide us an opportunity to study how the 3D structures of the chromatin are organized. Based on the data from Hi-C experiments, many chromatin 3D structure modeling methods have been proposed. However, there is limited ground truth to validate these methods and no robust chromatin structure alignment algorithms to evaluate the performance of these methods. In our work, we first made a thorough literature review of 25 publicly available population Hi-C-based chromatin 3D structure modeling methods. Furthermore, to evaluate and to compare the performance of these methods, we proposed a novel data simulation method, which combined the population Hi-C data and single-cell Hi-C data without ad ...
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This protocol describes the chromatin preparation from fresh or frozen tissues. The isolated chromatin can be used for chromatin immunoprecipitation assays using Diagenode&rsquo...
Single-cell chromatin accessibility sequencing from 13 mouse tissue types provides novel insights into regulatory dynamics and human disease states.
Chromatin remodelers can either organize or disrupt nucleosomal arrays, yet the mechanisms specifying these opposing actions are not clear. Here, we show that the outcome of nucleosome sliding by Chd1 changes dramatically ...
A number of years ago, inspired by the work of Dr. Bob Simpson [1], we developed a model system in yeast to study the events that occur when a gene is activated for transcription [2, 3]. This involves the purification from yeast cells of native plasmid ch
We recommend using an alternative version SMARCA4 Polyclonal Antibody Background SNF2beta;/BRG1 is a member of the SWI/SNF family of proteins and is part of the large ATP-dependent chromatin remodeling complex SNF/SWI, which...
c‐MYC and the SWI/SNF chromatin remodeling complex act as master regulators of transcription, and play a key role in human cancer. Although they are known to interact, the molecular details of their interaction are lacking. We have determined the structure of the RPT1 region of the INI1/hSNF5/BAF47/SMARCB1 subunit of the SWI/SNF complex that acts as a c‐MYC‐binding domain, and have localized the i ...
Learn more about the Chromatin Modification Pathway from related diseases, pathways, genes and PTMs with the Novus Bioinformatics Tool.
BRG1 is an essential component of the SWI/SNF chromatin remodeling complex and implicated in multiple functions through its interaction with different proteins, including the tumor suppressor protein pRb, serine-threonine kinase LKB1, and other transcrip
what is chromatin when it condesnses into chromosomes Chromatin is the same thing in metaphase than anyother point in the cell cycle, its DNA wrapp...
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Research staff Fredy Barneche CNRS Research Director - Tel. : +33 (0) 144 32 35 28 Anne-Flore Deton Research assistant - Tel. : +33 (0) 144 32
Developments in the analysis of the regulation of chromatin structure have provided much information on their relevance in the control of DNA replication and transcription, making it an important area of research.
Welcome to Virology’s second Essential Collection, on Chromatin and Viruses. This Collection expands on a recent review article...
The image depicts six broad categories of chromatin regulatory mechanisms, which are all known to be altered via mutations in the pathogenesis of human cancer.
iMedPub is a new approach to scientific publishing. As an open service to scientists, it is driven by researchers for researchers, while serving the interests of the general public chromatin | .
Answers from specialists on positive chromatin. First: One person in four tests positive. The vast majority of these people have no problems. The clinical picture is key, and how high the titer is may be helpful.
Literature and products to study chromatin modifying enzymes. Find out more about epigenetic writers and erasers and the tools used to study them.
... Klinisches W rterbuch von Otto Dornbl th. Definition und Bedeutung im historischen Lexikon der medizinischen Begriffe
chromatinic definition: Of or with respect to chromatin; Of or regarding the chromatin regarding the cell-nucleus.; (of material of a cell nucleus) readily coloured by stains; Of or with respect to chromatin;…
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Posttranslational modifications play a key role in recruiting chromatin remodeling and modifying enzymes to specific regions of chromosomes to modulate chromatin structure. Alc1 (amplified in liver cancer 1), a member of the SNF2 ATPase superfamily with a carboxy-terminal macrodomain, is encoded by an oncogene implicated in the pathogenesis of hepatocellular carcinoma. Here we show that Alc1 interacts transiently with chromatin-associated proteins, including histones and the poly(ADP-ribose) polymerase Parp1. Alc1 ATPase and chromatin remodeling activities are strongly activated by Parp1 and its substrate NAD and require an intact macrodomain capable of binding poly(ADP-ribose). Alc1 is rapidly recruited to nucleosomes in vitro and to chromatin in cells when Parp1 catalyzes PAR synthesis. We propose that poly(ADP-ribosyl)ation of chromatin-associated Parp1 serves as a mechanism for targeting a SNF2 family remodeler to chromatin. ...
Chromatin compacts DNA to an extreme extend and allows eukaryotic genome fit the size of the nucleus. On the other hand, however, it must process the ability to untighten DNA and to permit the cellular machinery access to genome. Chromatin consists of nucleosomes in which a protein core is constituted by four canonical histones H2A, H2B, H3, H4 and wrapped around by 147 bp of DNA. Histone variants, and the chromatin remodelling machinery, can reorganize the compaction of chromatin and thus be important for epigenetic regulation of gene expression.. Histone variant H2A.Z is a universal mark of dynamic nucleosomes. H2A.Z is essential for growth, development and viability of a number of species including mammals. H2A.Z plays critical roles in multiple biological processes including gene transcription and replication, DNA repair, and genome integrity. The chromatin incorporation of H2A.Z is catalysed by SRCAP, an ATP-dependent, multi-component chromatin remodelling complex. The YL1 subunit of SRCAP ...
TY - JOUR. T1 - CAME. T2 - Identification of chromatin accessibility from nucleosome occupancy and methylome sequencing. AU - Piao, Yongjun. AU - Lee, Seong Keon. AU - Lee, Eun Joon. AU - Robertson, Keith D. AU - Shi, Huidong. AU - Ryu, Keun Ho. AU - Choi, Jeong Hyeon. PY - 2017/4/15. Y1 - 2017/4/15. N2 - Motivation: Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, Methyltransferase Accessibility Protocol for individual templates-Bisulfite Genome Sequencing (MAPit-BGS) and nucleosome occupancy and methylome sequencing (NOMe-seq) have been developed for simultaneously profiling chromatin accessibility and DNA methylation on single molecules. Therefore, there is a great demand in developing computational methods to identify chromatin ...
This organism was chosen because it has epigenetically defined "regional centromeres" whose chromatin and protein compositions are similar to those of their human counterparts, to identify factors responsible for the replacement of histone H3 with CENP-A at centromeres.. In this report, the KAIST research group systematically analyzed the roles of the ATP-dependent chromatin-remodelers in the centromeric chromatin assembly of fission yeast as they serve as strong candidates for such factors ...
Figure 3. NoRC regulates telomeric heterochromatin. (A) TIP5 localizes at telomeres. Left: Z‐projection of a deconvolved image of a representative U2OS cell stained with α‐TIP5 antibody (red) followed by Q‐FISH with a telomere‐specific PNA probe (green). The same nucleus depicting colocalization of TIP5 with telomeres (white spots) is shown below. Middle: a representative U2OS cell immunostained with α‐TIP5 (red) and α‐TRF2 (green) antibodies is shown. Colocalization of TIP5 and TRF2 is depicted in yellow. Right: quantification of telomeres colocalizing with TIP5 in a representative experiment (N=4), each dot on the plot represents one cell (unpaired t‐test, P‐value ***,0.001, n=45). Red bars indicate mean values. Scale bars, 5 μm. (B) TIP5 is associated with telomeres. ChIPs in U2OS cells monitoring TIP5, TRF2 and Pol I at telomeres. Telomere DNA was assayed by dot hybridization with a telomere‐specific riboprobe. Data are normalized to input values. Error bars represent ...
The Drosophila kismet gene was identified in a screen for dominant suppressors of Polycomb, a repressor of homeotic genes. Here we show that kismet mutations suppress the Polycomb mutant phenotype by blocking the ectopic transcription of homeotic genes. Loss of zygotic kismet function causes homeotic transformations similar to those associated with loss-of-function mutations in the homeotic genes Sex combs reduced and Abdominal-B. kismet is also required for proper larval body segmentation. Loss of maternal kismet function causes segmentation defects similar to those caused by mutations in the pair-rule gene even-skipped. The kismet gene encodes several large nuclear proteins that are ubiquitously expressed along the anterior-posterior axis. The Kismet proteins contain a domain conserved in the trithorax group protein Brahma and related chromatin-remodeling factors, providing further evidence that alterations in chromatin structure are required to maintain the spatially restricted patterns of ...
We have shown for the first time that the function of CAF-1 is important for viability following double-strand DNA repair. Furthermore, CAF-1 functions genetically in both homologous recombination and NHEJ, and its function during double-strand DNA repair is dependent on the interaction between CAF-1 and PCNA. Given the biochemical role of CAF-1 in DNA synthesis-coupled chromatin assembly, we propose that CAF-1 mediates chromatin assembly during double-strand DNA repair in vivo.. We have observed sensitivity of CAF-1 mutants to a variety of double-strand DNA-damaging agents. A systematic analysis of the yeast deletion collection also isolated the cac2Δ as a mutant sensitive to MMS (Chang et al. 2002). Similarly, mutants of the genes encoding Arabidopsis CAF-1, fas1, and fas2 are sensitive to MMS (Takeda et al. 2004). Given the role of CAF-1 in chromatin assembly during NER of single-strand lesions and the sensitivity of CAF-1 mutants to UV irradiation (Gaillard et al. 1996; Kaufman et al. 1997; ...
INI1 (Integrase interactor 1), also known as SMARCB1, is the most studied subunit of chromatin remodelling complexes. Its role in colorectal tumorigenesis is not known. We examined SMARCB1/INI1 protein expression in 134 cases of colorectal cancer (CRC) and 60 matched normal mucosa by using tissue microarrays and western blot and categorized the results according to mismatch repair status (MMR), CpG island methylator phenotype, biomarkers of tumor differentiation CDX2, CK20, vimentin and p53. We validated results in two independent data sets and in cultured CRC cell lines. Herein, we show that negative SMARCB1/INI1 expression (11% of CRCs) associates with loss of CDX2, poor differentiation, liver metastasis and shorter patients survival regardless of the MMR status or tumor stage. Unexpectedly, even CRCs displaying diffuse nuclear INI1 staining (33%) show an adverse prognosis and vimentin over-expression, in comparison with the low expressing group (56%). The negative association of SMARCB1/INI1-lack of
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Oligodendrocyte precursor cells (OPCs) constitute the main proliferative cells in the adult brain, and deregulation of OPC proliferation-differentiation balance results in either glioma formation or defective adaptive (re)myelination. OPC differentiation requires significant genetic reprogramming implicating chromatin remodeling. Mounting evidence indicates that chromatin remodelers play important roles during normal development and their mutations are associated with neurodevelopmental defects, with CHD7 haploinsuficiency being the cause of CHARGE syndrome and CHD8 being one of the strongest Autism Spectrum Disorder (ASD) high-risk associated genes. Here, we report on uncharacterized functions of the chromatin remodelers Chd7 and Chd8 in OPCs. Their OPC-chromatin-binding profile combined with transcriptome and chromatin accessibility analyses of Chd7-deleted OPCs, demonstrates that Chd7 protects non-proliferative OPCs from apoptosis by chromatin-closing and transcriptional repression of p53.
A primary challenge in the H3K27M field has been to resolve the contradictory observations indicating that PRC2 has a high affinity for H3K27M peptides, yet PRC2 and H3K27M are often mutually excluded from chromatin in H3K27M DIPG (4, 6, 9, 10). Our studies revealed that interaction of H3K27M with PRC2 is a dynamic process that cannot be captured by static, steady-state approaches. Namely, there is an initial phase after H3K27M is expressed and incorporated into chromatin, followed by PRC2 recruitment to H3K27M-containing chromatin, presumably due to its higher affinity toward H3K27M (Fig. 2C). However, in the next phase, PRC2 is released from H3K27M, as they do not colocalize at steady-state conditions in both isogenic 293 T-REx systems (e.g., this study, Figs. 2 and 3) and the H3K27M DIPG themselves (6). This dynamic model therefore accommodates both the finding of high H3K27M and PRC2 affinity in select assays and their failure to be stably colocalized on chromatin in cells. In line with the ...
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Signaling cascades are essential in instructing cell proliferation and differentiation during animal development and are often manifested by turning on or shutting off the expression of a group of genes. The specificity of different signaling pathways is usually determined by activating specific transcription factors that bind to the enhancers of their target genes. However, in eukaryotic cells the full transcription of a particular target gene is also dependent on the recruitment of chromatin remodelers and histone modifiers, in addition to transcription factors, in order to ensure a local chromatin environment that is permissive for the access of a complete set of regulatory proteins. Although CAF-1 was initially identified as a histone chaperone for DNA synthesis-coupled chromatin assembly (Smith and Stillman, 1989; Das et al., 2009), it is becoming increasingly evident that CAF-1 has functions in the regulation of other cellular and developmental processes, such as heterochromatin formation ...
Metazoans regulate biological functions in a number of ways, including via gene expression. Epigenetics is the term for regulation of gene expression, other than via changes in the DNA sequence. Modification of DNA or histones by methylation, acetylation, phosphorylation, and ubiquitination affects gene expression and function. Enzymes that chemically modify genomic DNA and histones, as well as epigenetic chromatin remodeling factors, regulate chromatin accessibility and therefore gene expression. Some chromatin remodeling factors contain a chromatin organization modifier domain, or chromodomain, responsible for ATP hydrolysis-dependent chromatin reorganization. Other protein families regulating chromatin structure include bromodomain proteins, plant homeodomain proteins, and the inhibitor of growth family. During the process of stem cell differentiation into terminally differentiated cells, altered expression of chromatin modification enzyme and chromatin remodeling factor genes changes histone ...
Principal Investigator: Oliver Bell. In metazoans, packaging of genomic DNA into the nucleosomal protein scaffold of chromatin provides an opportunity to tightly regulate accessibility and readout of the genetic information. In particular, chemical modifications of nucleosomes and DNA have emerged as important determinants of genome accessibility. However, the dynamic regulation of chromatin state and its contribution to epigenetic inheritance of gene expression has remained enigmatic and a key challenge in the field of chromatin biology.. We have developed a novel technology that allows for rapid addition and removal of chromatin regulatory activities to a gene locus in any murine cell type. The Chromatin in vivo Assay (CiA) employs small molecules, which simultaneously bind two distinct peptide domains to induce dimerization between a chromatin modifier and a DNA binding protein. The CiA approach provides high temporal control allowing us to study the kinetics and epigenetic memory of histone ...
Meeting Description: The workshop will discuss the structural and dynamic aspects of chromatin and how they are regulated by other factors such as histone chaperones, chromatin factors, and chromatin remodelers. The talks will cover topics including nucleosome structure, nucleosome remodeling, covalent modification of histones, histone exchange, and histone variants. The workshop will also discuss various biophysical tools used to study chromatin including X-ray crystallography, NMR, single molecule, and computation. ...
SWI/SNF-type chromatin remodelers, such as BRAHMA (BRM), and H3K27 demethylases both have active roles in regulating gene expression at the chromatin level1-5, but how they are recruited to specific genomic sites remains largely unknown. Here we show that RELATIVE OF EARLY FLOWERING 6 (REF6), a plant-unique H3K27 demethylase6, targets genomic loci containing a CTCTGYTY motif via its zinc-finger (ZnF) domains and facilitates the recruitment of BRM. Genome-wide analyses showed that REF6 colocalizes with BRM at many genomic sites with the CTCTGYTY motif. Loss of REF6 results in decreased BRM occupancy at BRM-REF6 co-targets. Furthermore, REF6 directly binds to the CTCTGYTY motif in vitro, and deletion of the motif from a target gene renders it inaccessible to REF6 in vivo. Finally, we show that, when its ZnF domains are deleted, REF6 loses its genomic targeting ability. Thus, our work identifies a new genomic targeting mechanism for an H3K27 demethylase and demonstrates its key role in recruiting ...
The compact structure of the eukaryotic genome dictates the accessibility to genes, and therefore adds an additional layer of regulation for gene expression. A specialized class of proteins called chromatin remodelers facilitates this process in the cell. The imitation switch (ISWI) subfamily of chromatin remodelers is a well studied class of proteins affecting gene expression. Its member ISW2 was recently shown to behave differently from other chromatin remodeling proteins. For instance, the ISW2 complex has been shown to be stimulated by ~5-6 fold in its ATPase activity when bound to a nucleosome rather than to a DNA molecule. Nucleosome remodeling by ISW2 has even been shown to depend on the N-terminal tail of histone H4 and therefore, the octamer of a nucleosome might be playing a significant role in nucleosome remodeling by the ISW2 complex. The aim in this investigation was to delineate the protein-protein interactions that the ISW2 complex establishes with the octamer upon binding to a
Ovarian cancer is the fifth leading cause of cancer-related deaths in women. There are about 20,000 new cases per year and only 46% of those women survive five years. Despite aggressive treatments of surgical resection followed by highly toxic chemotherapies and radiation, ovarian cancer outcomes have remained dismal due to lack of early detection and lack of availability of targeted treatments. Recent research has revealed that ovarian cancer subtypes have diverse genetic backgrounds and suggest a need to develop specialized therapeutic strategies for specific subtypes. Several ovarian cancer subtypes have high mutation frequencies in SWI/SNF (switch/sucrose non-fermentable) complex members. The SWI/SNF complex was first discovered in yeast for its involvement in mating type switching and sugar metabolism. The SWI/SNF complex is a chromatin remodeler whose job is to properly space and place nucleosomes, the protein spools for DNA, throughout the genome. Proper placement of these nucleosome ...
How is SWI/SNF Related, Matrix-Associated, Actin-Dependent, Regulator of Chromatin abbreviated? SMARC stands for SWI/SNF Related, Matrix-Associated, Actin-Dependent, Regulator of Chromatin. SMARC is defined as SWI/SNF Related, Matrix-Associated, Actin-Dependent, Regulator of Chromatin somewhat frequently.
If you have a question about this talk, please contact Zoubin Ghahramani.. Chromatin state segmentation-the division of a genome into regions of similar combinatorial patterns of DNA or histone modifications, as measured through high-throughput sequencing-is a common problem in genomics research. Recent large-scale projects have generated enormous amounts of chromatin state information, without corresponding advances in techniques for analyzing with these large, complex datasets.. In this talk, I will first outline the problem of chromatin state segmentation and discuss current approaches. I will then review the non-parametric Bayesian "sticky" HDP -HMM model for time-series segmentation, and introduce a variational mean-field algorithm for inference in the sticky HDP -HMM with an application to chromatin state segmentation.. This talk is part of the Machine Learning @ CUED series.. ...
Chromatin describes the complex of DNA and proteins that packs DNA into condensed structures. But this is not its only function: by packing the DNA it prevents possible transcription and therefore is a powerful mechanism for control of gene expression. Especially since the chromatin state can be passed on to progenies allowing for a fixed gene expression over multiple proliferations. Experiments in Drosophila could show that dependent on the position of gene on the chromosome and therefore its chromatin packing state different reproducible cell proliferation patterns emerged. The resulting different eye patterns lead to the hypothesis that the chromatin packaging state of a gene can govern the pattern phenotype of the corresponding tissue. Therefore chromatin engineering yields the possibility to further understand and manipulate cell patterns in mammalian cells. The basis for this project is a mammalian cell line that switches between two possible states reported by fluorescent proteins by ...
A major focus of the current study was to use more natural arrays to investigate chromatin decondensation upon transcription induction. It is widely believed that chromatin is extensively compacted within nuclei, but that transcriptionally active regions decondense to the level of DNA wrapped around nucleosomes, namely a 10-nm fiber. To investigate chromatin organization in a transcriptionally active region, the authors constructed their arrays from bacterial artificial chromosomes (BACs) that contained known inducible mammalian genes. Consistent with several previous studies (Tumbar et al., 1999; Müller et al., 2001, 2004; Janicki et al., 2004), induction of transcription in these arrays caused them to decondense into a series of colinear spots (Fig. 1 B). By measuring the distance between these spots, the authors discovered that the degree of decondensation is not large: on average, the array decondenses to a level that is ∼96-fold more compacted than a 10-nm fiber.. A distinguishing ...
The mechanisms underlying the neurodevelopmental deficits associated with CHARGE syndrome, which include cerebellar hypoplasia, developmental delay, coordination problems, and autistic features, have not been identified. CHARGE syndrome has been associated with mutations in the gene encoding the ATP-dependent chromatin remodeler CHD7. CHD7 is expressed in neural stem and progenitor cells, but its role in neurogenesis during brain development remains unknown. Here we have shown that deletion of ...
The interplay of active and repressive histone modifications is assumed to have a key role in the regulation of gene expression. In contrast to this generally accepted view, we show that the transcription of genes temporally regulated during fly and worm development occurs in the absence of canonically active histone modifications. Conversely, strong chromatin marking is related to transcriptional and post-transcriptional stability, an association that we also observe in mammals. Our results support a model in which chromatin marking is associated with the stable production of RNA, whereas unmarked chromatin would permit rapid gene activation and deactivation during development. In the latter case, regulation by transcription factors would have a comparatively more important regulatory role than chromatin marks.. ...
How does chromatin structure determine the fate of transcripts? How do transcripts direct changes in chromatin? Our lab is investigating the role of chromatin and RNA in controlling transcriptional and post-transcriptional gene regulatory processes. We are focusing on gaining mechanistic insights into how small non-coding RNAs induce changes in chromatin and transcription in animals. We are also aiming to identify the role of chromatin on post-transcriptional gene regulatory processes. We use an interdisciplinary approach combining biochemistry, genetics, cell, molecular and computational biology and functional genomics as key tools to tackle these exciting questions.. ...
Chromosome conformation capture (3C) has revolutionized the ways in which the conformation of chromatin and its relationship to other molecular functions can be studied. 3C-based techniques are used to determine the spatial arrangement of chromosomes in organisms ranging from bacteria to humans. In particular, they can be applied to the study of chromosome folding and organization in model organisms with small genomes and for which powerful genetic tools exist, such as budding yeast. Studies in yeast allow the mechanisms that establish or maintain chromatin structure to be analyzed at very high resolution with relatively low cost, and further our understanding of these fundamental processes in higher eukaryotes as well. Here we provide an overview of chromatin structure and introduce methods for performing 3C, with a focus on studies in budding yeast. Variations of the basic 3C approach (e.g., 3C-PCR, 5C, and Hi-C) can be used according to the scope and goals of a given experiment.
Taken together, these studies will reveal how the transcriptional machinery competes with chromatin assembly to regulate transcription, not only during genome activation but potentially also during differentiation and reprogramming.. 2. The role of chromatin structure and nuclear architecture in genome activation. Chromatin regulates the accessibility of the genome for DNA binding proteins. Changes in chromatin structure and nuclear organization are thus critical to understanding how regions of the genome become transcriptionally competent. We have previously shown that dramatic changes in chromatin structure accompany the onset of zygotic gene expression (Vastenhouw et al., Nature 2010 PMID: 20336069; Zhang et al., GR 2014 PMID: 24285721). Thus, the onset of transcription during genome activation provides a powerful system to study the relationship between chromatin structure and transcriptional activity.. We have recently found that transcriptional activity and accumulation of the produced RNA ...
Thaete and colleagues (14) showed association of both SS18 and SS18-SSX with the DNA-dependent ATPase BRM, the catalytic subunit of SWI/SNF chromatin remodeling complexes. Subsequently, Kato and colleagues (15) showed that SS18 is a stable and integral component of SWI/SNF complexes using coimmunoprecipitation and mass spectroscopy in nuclear extracts of HeLa cells.. Middeljans and colleagues (16) extended these results by showing that the fusion oncoprotein is similarly incorporated into stable SWI/SNF complexes. All commonly observed subunits were recovered in reciprocal purifications between tandem affinity purification-tagged SS18-SSX1 and other subunits, indicating minimal perturbation of the core complex when the fusion oncogene is stably expressed in HEK293 cells. Kadoch and Crabtree (17) observed high-affinity binding of both SS18 and SS18-SSX to the core subunits of SWI/SNF, and immunodepletion of nuclear extracts showed undetectable levels outside of this association. In contrast with ...
DNA calls for the return of the nuclear envelope (NE) after mitosis, according to Ulbert et al. (page 469). The abundance of DNA may thus be one reason why the NE reforms so quickly.. NE reformation occurs so quickly that breaking down the process in vivo has so far been impossible. Many scientists instead use in vitro reconstitution assays, which indicate that chromatin decondensation (as occurs at the end of mitosis) initiates the recruitment of vesicle populations to chromatin. In the new work, the authors aimed to identify membrane and chromatin components that mediate this recruitment and thus NE assembly.. The main component of chromatin is, of course, DNA. The group found that excess naked DNA prevented in vitro NE reformation by titrating vesicles away from chromatin at early stages. DNA alone was a more potent inhibitor than chromatin, although chromatin proteins might also contribute, particularly later on as the envelope matures.. DNA does not bind pure liposomes, so the authors next ...
Duke University, Department of Pharmacology and Cancer Biology. David MacAlpine uses genomic approaches to study how the start sites of DNA replication are selected and regulated in the context of the local chromatin environment to maintain genomic stability and to ensure the accurate inheritance of genetic and epigenetic information. In the past two years he has published papers in Cell, Nature, PNAS, Genome Res (2X), EMBO J, Genes Dev (2X), MCB (2X) and NAR.. ...
Wysocka J, Swigut T, Xiao H, Milne TA, Kwon SY, Landry J, Kauer M, Tackett AJ, Chait BT, Badenhorst P, Wu C, Allis CD. A PHD finger of NURF couples histone H3 l
... , Authors: Dessen P. Published in: Atlas Genet Cytogenet Oncol Haematol.
A full understanding of how the BAF complex exactly influences the fate of neuronal stem cells has been hindered by the absence of mutant models completely lacking BAF complexes. Here the scientists have been able to create knockout mutants lacking the entire BAF complex.. The result: The subunits BAF150 und BAF170 are central key factors, acting as scaffolding proteins for the interaction with the up to 15 subunits of the functional complex. These subunits serve as regulators of stability and functionality of the BAF complex, as indicated by a massive impairment of the murine forebrain development in BAF155/BAF170 deletion mutants.. Together with a dramatic reduction in active euchromatin, the loss of functional BAF-complexes resulted in a comprehensive decrease of gene expression events. Simultaneously, the scientists observed a global increase in repressive heterochromatin marks. The authors conclude: BAF complexes rather influence repression mechanism in neuronal cells indirectly than ...
"The role of nucleoplasmin in chromatin assembly and disassembly". Philosophical Transactions of the Royal Society B. 339 (1289 ... Ito T, Tyler JK, Bulger M, Kobayashi R, Kadonaga JT (1996). "ATP-facilitated chromatin assembly with a nucleoplasmin-like ...
"The Role of Nucleoplasmin in Chromatin Assembly and Disassembly". Philosophical Transactions: Biological Sciences. The Royal ... nucleosome assembly, genome stability, ribosome biogenesis, DNA duplication and transcriptional regulation. During the assembly ... Philpott, Anna; Leno, Gregory H. (1992). "Nucleoplasmin remodels sperm chromatin in Xenopus egg extracts". Cell. 69 (5): 759- ... "Nucleoplasmin-Mediated Decondensation of Mytilus Sperm Chromatin. Identification and Partial Characterization of a ...
... chromatin assembly and disassembly MeSH G04.335.487.350 --- phagocytosis MeSH G04.335.487.350.091 --- autophagy MeSH G04.335. ... virus assembly MeSH G04.185.515.880.960 --- virus shedding MeSH G04.185.515.910 --- virulence MeSH G04.185.672.360 --- eye ...
... chromatin assembly and disassembly MeSH G05.195.830 --- sos response (genetics) MeSH G05.200.760 --- dna replication timing ... chromatin assembly and disassembly MeSH G05.315.125 --- dosage compensation, genetic MeSH G05.315.125.970 --- x chromosome ...
"The JmjC domain protein Epe1 prevents unregulated assembly and disassembly of heterochromatin". EMBO J. 26: 4670. 2007. PMID ... "Plasticity of fission yeast CENP-A chromatin driven by relative levels of histone H3 and H4". PLoS Genet. 3: e121. 2007. PMID ... "Raf1 Is a DCAF for the Rik1 DDB1-like protein and has separable roles in siRNA generation and chromatin modification". PLoS ... insight into how transcription and resulting non-coding RNA might influence the assembly of specialised CENP-A chromatin and ...
NPC assembly is a very rapid process yet defined intermediate states occur which leads to the idea that this assembly occurs in ... This disassembly of the NPC peripheral groups is largely thought to be phosphate driven, as several of these nucleoporins are ... One possibility is that as a protein complex it binds to the chromatin. It is then inserted into the double membrane close to ... This prepore would form when several Nup complexes come together and bind to the chromatin. This would have the double membrane ...
Lerner L, Henriksen MA, Zhang X, Darnell JE (October 2003). "STAT3-dependent enhanceosome assembly and disassembly: synergy ... Wallberg AE, Neely KE, Hassan AH, Gustafsson JA, Workman JL, Wright AP (March 2000). "Recruitment of the SWI-SNF chromatin ... "BAF60a mediates critical interactions between nuclear receptors and the BRG1 chromatin-remodeling complex for transactivation ... states of hsp70 and hsp90 during sequential steps in the process of glucocorticoid receptor.hsp90 heterocomplex assembly". J. ...
"Assembly and disassembly of nucleosome core particles containing histone variants by human nucleosome assembly protein I". ... Chadwick BP, Willard HF (January 2001). "A novel chromatin protein, distantly related to histone H2A, is largely excluded from ... El Kharroubi A, Piras G, Zensen R, Martin MA (May 1998). "Transcriptional activation of the integrated chromatin-associated ... The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes ...
Motility and Shape Regulation of assembly and disassembly of filament systems Motor function, regulation and diversity D. ... Chromatin and Chromosomes Karyotypes Translocations, inversions, deletions and duplications Aneuploidy and polyploidy Structure ... Assembly, Organization and Dynamics Small molecules Macromolecules (e.g., nucleic acids, polysaccharides, proteins and complex ... Viruses Genome replication and regulation Virus assembly Virus-host interactions H. Methods Restriction maps and PCR Nucleic ...
Assembly and disassembly. An image of a newt lung cell stained with fluorescent dyes during metaphase. The mitotic spindle can ... During most of the cell cycle these are organized in a DNA-protein complex known as chromatin, and during cell division the ... In most cells, the disassembly of the nuclear envelope marks the end of the prophase of mitosis. However, this disassembly of ... The best-known of these is the nucleolus, which is mainly involved in the assembly of ribosomes. After being produced in the ...
... for it is clear that it plays no essential part in the nuclear membrane assembly around chromatin. The presence of lamins in ... These different disassembly events are initiated by the cyclin B/Cdk1 protein kinase complex (MPF). Once this complex is ... Chromatin that interacts with lamina forms lamina-assosiated domains (LADs). The average length of human LADs is 0.1-10 MBp. ... It has been shown that lamin polypeptides have an affinity for binding chromatin through their α-helical (rod like) domains at ...
In most cells, the disassembly of the nuclear envelope marks the end of the prophase of mitosis. However, this disassembly of ... Inhibition of lamin assembly itself is an inducer of apoptosis. The nuclear envelope acts as a barrier that prevents both DNA ... During most of the cell cycle these are organized in a DNA-protein complex known as chromatin, and during cell division the ... The best-known of these is the nucleolus, which is mainly involved in the assembly of ribosomes. After being produced in the ...
Keller DM, Lu H (2003). "p53 serine 392 phosphorylation increases after UV through induction of the assembly of the CK2.hSPT16. ... LeRoy G, Orphanides G, Lane WS, Reinberg D (1998). "Requirement of RSF and FACT for transcription of chromatin templates in ... interacts specifically with histones H2A/H2B to effect nucleosome disassembly and transcription elongation. FACT is composed of ... Orphanides G, Wu WH, Lane WS, Hampsey M, Reinberg D (1999). "The chromatin-specific transcription elongation factor FACT ...
Chromatin greatly impedes transcription in eukaryotes. Assembly of large multi-protein preinitiation complex is required for ... it causes disassembly of elongation factors and/or an assembly of termination factors that cause conformational changes of the ... The eukaryotic genome is organized into a compact chromatin structure that allows only regulated access to DNA. The chromatin ... Pausing can influence chromatin structure at promoters to facilitate gene activity and lead to rapid or synchronous ...
M-Cdk's also phosphorylate elements of the nuclear lamina (the framework that supports the envelope) leading to the dis-assembly ... a mesh of intermediate filaments which stabilizes the nuclear membrane as well as being involved in chromatin function and ... "Inner/Outer Nuclear Membrane Fusion in Nuclear Pore Assembly". Molecular Biology of the Cell. 21 (23): 4197-4211. doi:10.1091/ ...
This allows chromatin to separate from the nuclear lamina in order to be condensed. As apoptosis continues, cell structures ... During mitosis, lamins are phosphorylated by Mitosis-Promoting Factor (MPF), which drives the disassembly of the lamina and the ... Stuurman, Nico; Heins, Susanne; Aebi, Ueli (1998-01-01). "Nuclear Lamins: Their Structure, Assembly, and Interactions". Journal ... This allows chromatin to condense and the DNA to be replicated. After chromosome segregation, dephosphorylation of nuclear ...
2005). "Assembly and disassembly of nucleosome core particles containing histone variants by human nucleosome assembly protein ... 2002). "Dual roles of p300 in chromatin assembly and transcriptional activation in cooperation with nucleosome assembly protein ... Nucleosome assembly protein 1-like 1 is a protein that in humans is encoded by the NAP1L1 gene. This gene encodes a member of ... "Entrez Gene: NAP1L1 nucleosome assembly protein 1-like 1". Kato S, Sekine S, Oh SW, et al. (1995). "Construction of a human ...
Keller DM, Lu H (2003). "p53 serine 392 phosphorylation increases after UV through induction of the assembly of the CK2.hSPT16. ... LeRoy G, Orphanides G, Lane WS, Reinberg D (1998). "Requirement of RSF and FACT for transcription of chromatin templates in ... FACT interacts specifically with histones H2A/H2B to effect nucleosome disassembly and transcription elongation. FACT and ... The protein encoded by this gene is a subunit of a heterodimer that, along with SUPT16H, forms chromatin transcriptional ...
Part of the assembly process includes a compaction step, in which ULF tighten and assume a smaller diameter. The reasons for ... Vimentin heads are able to alter nuclear architecture and chromatin distribution, and the liberation of heads by HIV-1 protease ... During mitosis, lamins are phosphorylated by MPF, which drives the disassembly of the lamina and the nuclear envelope. Nestin ... Limited co-assembly in vitro to form heteropolymers with type III vimentin and type IV alpha-internexin". J. Biol. Chem. 274 ( ...
The chromosomes uncoil back into chromatin. Cytokinesis, the pinching of the cell membrane in animal cells or the formation of ... At this stage, the synapsis (pairing/coming together) of homologous chromosomes takes place, facilitated by assembly of central ... and is marked by decondensation and lengthening of the chromosomes and the disassembly of the spindle. Nuclear envelopes reform ...
Kleiger, G., Saha, A., Lewis, S., Kuhlman, B., and Deshaies, R.J. (2009). Rapid E2-E3 assembly and disassembly enable ... This was followed by identifying novel functions for p97, including removal of proteins from chromatin as part of the DNA ... Deshaies, R.J., Sanders, S., Feldheim, D., and Schekman, R. (1991). Assembly of yeast Sec proteins involved in translocation ... Cand1 promotes assembly of new SCF complexes through dynamic exchange of F box proteins. Cell 153, 206-215 ...
Once the ring has been constructed the structure is maintained by a continual assembly and disassembly that, aided by the Arp2/ ... Actin takes part in the regulation of chromatin structure interact with both the RNA polymerase I, II and III In Pol I ... This new situation favors the dynamics of assembly and disassembly. The most notable of these proteins are gelsolin and cofilin ... and provide trafficking routes through the cytoplasm to aid signal transduction Rapid assembly and disassembly of actin network ...
The protein gelsolin, which is a key regulator in the assembly and disassembly of actin. It has six subdomains, S1-S6, each of ... Transcription - Actin is involved in chromatin reorganization,[80][107][115][116] transcription initiation and interaction with ... This new situation favors the dynamics of assembly and disassembly. The most notable of these proteins are gelsolin and cofilin ... Once the ring has been constructed the structure is maintained by a continual assembly and disassembly that, aided by the Arp2/ ...
... image analysis software was developed that is capable of extracting high resolution maps of cytoskeletal assembly/disassembly ... J. 81(1):66-78 doi:10.1016/S0006-3495(01)75680-9 Gasser, S.M. (2002) Visualizing chromatin dynamics in interphase nuclei. ... 1998) Fluorescent speckle microscopy: Visualizing the movement, assembly, and turnover of macromolecular assemblies in living ... 1998) Fluorescent speckle microscopy: Visualizing the movement, assembly, and turnover of macromolecular assemblies in living ...
... II Transcription: the process of transcript elongation facilitated by disassembly of nucleosomes. ... The ω subunit facilitates assembly of RNAP and stabilizes assembled RNAP.[26] ... "RNA polymerase V transcription guides ARGONAUTE4 to chromatin". Nature Genetics. 41 (5): 630-4. doi:10.1038/ng.365. PMC ... regulation of preinitiation complex assembly". Trends in Biochemical Sciences. 16: 402-408. doi:10.1016/0968-0004(91)90164-Q. ...
They create non-enzymatic DNA-protein crosslinks through non-specific crosslinking of chromatin-interacting proteins to DNA. ...
The formation or destruction of chromatin structures.. Synonyms. chromatin assembly/disassembly View GO Annotations in other ... Gene Ontology Term: chromatin assembly or disassembly. GO ID. GO:0006333 Aspect. Biological Process. Description. ...
The Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products across databases. You can use this browser to view terms, definitions, and term relationships in a hierarchical display. Links to summary annotated gene data at MGI are provided in Term Detail reports.
... and modification of that specific physical conformation of CHROMATIN determining the transcriptional accessibility or ...
R-BTA-3301854. Nuclear Pore Complex (NPC) Disassembly. R-BTA-4551638. SUMOylation of chromatin organization proteins. R-BTA- ... R-BTA-191859. snRNP Assembly. R-BTA-3108214. SUMOylation of DNA damage response and repair proteins. R-BTA-3301854. Nuclear ... Pore Complex (NPC) Disassembly. R-BTA-4551638. SUMOylation of chromatin organization proteins. R-BTA-4570464. SUMOylation of ... R-BTA-191859. snRNP Assembly. R-BTA-3108214. SUMOylation of DNA damage response and repair proteins. ...
Maintains telomeric chromatin, which is involved in silencing the expression of genes located at the telomere. Required for ... chromatin assembly or disassembly Source: SGDInferred from direct assayi*. "Dicentric chromosome stretching during anaphase ... nuclear chromatin Source: SGDTraceable author statementi*. "Relocalization of telomeric Ku and SIR proteins in response to DNA ... chromatin silencing at telomere Source: SGDInferred from mutant phenotypei*. "Components of the Ku-dependent non-homologous end ...
Chromatin assembly and disassembly are essent See details National Institutes of Health. 7/16/2009. ... Trans-NIH Recovery Act Research Support The packaging of the eukaryotic genome together with histone proteins into chromatin ...
chromatin assembly or disassembly Source: MGI ,p>Inferred from Direct Assay,/p> ,p>Used to indicate a direct assay for the ...
... a chromatin remodeling complex that mobilizes nucleosomes and reconfigures irregular chromatin to a regular nucleosomal array ... and is involved in the maintenance of chromatin structures during DNA replication processes. Essential component of the NoRC ( ... Complexes containing SMARCA5 are capable of forming ordered nucleosome arrays on chromatin; this may require intact histone H4 ... chromatin assembly or disassembly Source: MGI ,p>Inferred from Direct Assay,/p> ,p>Used to indicate a direct assay for the ...
Chromatin Assembly and Disassembly. Dr. Jessica Tyler, MD Anderson Cancer Center, Houston ... Epigenetics & Chromatin: Interactions and Processes 2013. Epigenetics & Chromatin: Interactions and Processes 2013. BioMed ... The session on chromatin interactions could not have started with a better introduction than that given by Dr. Job Dekker ( ... This fusion of TAL DNA binding protein to LSD1 (lysine specific demethylase) was used to locally modify the chromatin state to ...
chromatin assembly or disassembly. IEA. --. GO:0006338. chromatin remodeling. IEA. --. GO:0006351. transcription, DNA-templated ... a chromatin remodeling complex that mobilizes nucleosomes and reconfigures irregular chromatin to a regular nucleosomal array ... a chromatin remodeling complex that mobilizes nucleosomes and reconfigures irregular chromatin to a regular nucleosomal array ... The WSTF-SNF2h chromatin remodeling complex interacts with several nuclear proteins in transcription. (PMID: 16603771) Cavellán ...
Chromatin maintains nuclear mechanical stability and shape in coordination with lamins and the cy... ... Chromatin Assembly And Disassembly. The mechanisms effecting establishment, maintenance, and modification of that specific ... Sex Chromatin. In the interphase nucleus, a condensed mass of chromatin representing an inactivated X chromosome. Each X ... Chromatin mechanics underlies this link, as alterations to chromatin and its physical properties can disrupt or rescue nuclear ...
... spaces nucleosomes to promote formation of silent chromatin. Two copies of its ATPase subunit SNF2h bind opposite sides of a ... Chromatin Assembly and Disassembly* * Chromosomal Proteins, Non-Histone / chemistry * Chromosomal Proteins, Non-Histone / ... The ATP-dependent chromatin assembly factor (ACF) spaces nucleosomes to promote formation of silent chromatin. Two copies of ... A nucleotide-driven switch regulates flanking DNA length sensing by a dimeric chromatin remodeler Mol Cell. 2015 Mar 5;57(5): ...
Chromatin Assembly and Disassembly / genetics* * Chromatin Assembly and Disassembly / physiology * Gene Expression Regulation ... on inflammatory genes via a process involving recruitment of transcriptional coactivator proteins and changes in chromatin ...
Nucleosome assembly factor; involved in chromatin assembly, disassembly; required for recovery after DSB repair; role in H3K56 ... Histone binding protein; involved in DNA replication-dependent and independent nucleosome assembly, nucleosome disassembly, ... histone acetylation, chromatin silencing, and gene expression; localizes to the nucleus. View computational annotations ...
Aizer A, Brody Y, Ler L W, Sonenberg N, Singer R H, Shav-Tal Y (2008). The dynamics of mammalian P body transport, assembly, ... and disassembly in vivo. Mol Biol Cell, 19(10): 4154-4166PubMedPubMedCentralCrossRefGoogle Scholar ... Hübner M R, Spector D L (2010). Chromatin dynamics. Annu Rev Biophys, 39(1): 471-489PubMedPubMedCentralCrossRefGoogle Scholar ... chromatin structure and dynamics FROS FISH TALE CRISPR/Cas9 single-guide RNA Suntag super-resolution imaging ...
Phosphorylates the chromatin assembly factors ASF1A AND ASF1B. Phosphorylation of ASF1A prevents its proteasome-mediated ... thereby enhancing chromatin assembly (By similarity). Negative regulator of amino acid starvation-induced autophagy (By ... Serine/threonine-protein kinase involved in the process of chromatin assembly and probably also DNA replication, transcription ... regulation of chromatin assembly or disassembly Source: UniProtKB. *spermatogenesis Source: UniProtKB-KW ...
Chromatin Assembly and Disassembly; Exocytosis; Membrane Fusion; Munc18 Proteins; Optical Tweezers; Protein Folding; SNARE ...
Chromatin Assembly and Disassembly. *SNARE Proteins. *Synaptotagmins. *Munc18 Proteins. *Optical Tweezers. Dr. Zhang obtained a ... Using optical tweezers, he found that representative chromatin remodeling factors contain DNA translocases and first measured ... showed how specific lipid bindings can act as molecular glue to hold oligomeric assemblies of membrane proteins. ...
Chromatin Assembly and Disassembly / genetics * Cohort Studies * Disease Progression * Female * Gene Frequency ... Mutation of chromatin remodeling genes alters gene regulation, but the overall effect of these alterations may also be modified ... may have implications not only for prognosis but also for understanding the role of chromatin remodeling gene mutations in ...
chromatin assembly/disassembly Protein Function :. InterPro :. HSP40/DnaJ pept-bd , J dom sf , DnaJ C , DnaJ domain [+] , DnaJ ...
"The role of nucleoplasmin in chromatin assembly and disassembly". Philosophical Transactions of the Royal Society B. 339 (1289 ... Ito T, Tyler JK, Bulger M, Kobayashi R, Kadonaga JT (1996). "ATP-facilitated chromatin assembly with a nucleoplasmin-like ...
"The Role of Nucleoplasmin in Chromatin Assembly and Disassembly". Philosophical Transactions: Biological Sciences. The Royal ... nucleosome assembly, genome stability, ribosome biogenesis, DNA duplication and transcriptional regulation. During the assembly ... Philpott, Anna; Leno, Gregory H. (1992). "Nucleoplasmin remodels sperm chromatin in Xenopus egg extracts". Cell. 69 (5): 759- ... "Nucleoplasmin-Mediated Decondensation of Mytilus Sperm Chromatin. Identification and Partial Characterization of a ...
Two high-throughput (HT) experimental technologies, gene expression microarrays and Chromatin Immuno-Precipitation on Chip ( ... chromatin assembly or disassembly. 1.6E-03. 4.7E-03. amino acid biosynthesis (5) ... Two transcriptional modules involved in the biological processes of chromatin cohesion and DNA repair and G2/M cell cycle ... Clusters associated with the biological processes of synapsis/recombination and spore wall assembly were clearly discerned in ...
Chromatin Assembly and Disassembly Flow Cytometry Gene Expression Regulation, Fungal Nonsense Mediated mRNA Decay RNA ... Analysis of the reporter in 4967 nonessential yeast genes revealed striking phenotypic overlaps between chromatin remodeling, ...
Categories: Chromatin Assembly and Disassembly Image Types: Photo, Illustrations, Video, Color, Black&White, PublicDomain, ...
  • The CPC plays a major role in restricting spindle assembly to the vicinity of chromosomes in oocytes and eggs and is a major focus of our studies. (cancer.gov)
  • Our collaborative projects range from developing new atomic force microscopy applications to enable fluorescent single molecule recognition within native chromatin, analyzing the structure of human artificial chromosomes, to mapping chromatin domains at fragile regions in human chromosomes. (nih.gov)
  • The movement of enhancers and promoters in and out of higher-order chromatin structures within the nucleus are associated with changes in expression and histone modifications.However, the factors responsible for mediating these changes and determining enhancer:promoter specificity are still not completely known.In this review, we summarize what is known about the patterns of epigenetic and chromatin features characteristic of elements involved in long-range interactions. (nih.gov)
  • The movement of enhancers and promoters in and out of higher-order chromatin structures within the nucleus are associated with changes in expression and histone modifications. (nih.gov)
  • abstract = "Chromatin coregulators are important factors in tumorigenesis and cancer progression. (elsevier.com)
  • Moreover, BGP-15 alone inhibited the activity of histone deacetylases (HDACs), thereby increasing chromatin accessibility at multiple genomic loci including the stress-inducible HSPA1A. (springer.com)
  • a) An active chromatin hub (ACH) is a structure that allows enhancers and promoters to come into close spatial proximity with each other (40). (nih.gov)
  • We reveal hierarchical assembly of a transcriptionally active chromatin hub containing the ASE and RAG promoters, with Rag2 recruitment and expression dependent on assembly of a functional ASE- Rag1 framework. (rupress.org)
  • It is widely accepted that the kinetochore is built on CENP-A-marked centromeric chromatin in a hierarchical order from inner to outer kinetochore. (rupress.org)
  • Clb1, 2, 3 and 4) in complex with Cdk1 leads to spindle assembly and sister chromatid alignment. (wikipedia.org)
  • Thus, the combination of gender and mutation of a specific gene, such as BAP1, may have implications not only for prognosis but also for understanding the role of chromatin remodeling gene mutations in kidney cancer progression. (nih.gov)
  • Essential role of chromatin remodeling protein Bptf in early mouse embryos and embryonic stem cells. (nih.gov)
  • Nucleoplasmin-Mediated Decondensation of Mytilus Sperm Chromatin. (wikipedia.org)
  • The addition of demembranated sperm chromatin to LSE results in nuclei formation where DNA is replicated in a semiconservative fashion once per cell cycle. (jove.com)
  • Here, we describe protocols (1) to prepare cell-free egg extracts (LSE), (2) to treat Xenopus sperm chromatin with two different DNA damaging approaches (MMS and UV), (3) to prepare the DNA damage-mimicking structure AT70, and (4) to trigger the ATR/Chk1-mediated DNA damage checkpoint in LSE with damaged sperm chromatin or a DNA damage-mimicking structure. (jove.com)
  • In particular, Xenopus egg extracts allow for the study of de novo kinetochore assembly in a physiological context. (cancer.gov)