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.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.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.Acetylation: Formation of an acetyl derivative. (Stedman, 25th ed)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.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.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.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)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.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.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)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).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.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.Heterochromatin: The portion of chromosome material that remains condensed and is transcriptionally inactive during INTERPHASE.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.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.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)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.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.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.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.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.Histone Acetyltransferases: Enzymes that catalyze acyl group transfer from ACETYL-CoA to HISTONES forming CoA and acetyl-histones.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.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.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)Cell Line: Established cell cultures that have the potential to propagate indefinitely.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.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.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.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.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.DNA Replication: The process by which a DNA molecule is duplicated.Lysine: An essential amino acid. It is often added to animal feed.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.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.Euchromatin: Chromosome regions that are loosely packaged and more accessible to RNA polymerases than HETEROCHROMATIN. These regions also stain differentially in CHROMOSOME BANDING preparations.Insulator Elements: Nucleic acid regulatory sequences that limit or oppose the action of ENHANCER ELEMENTS and define the boundary between differentially regulated gene loci.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.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.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.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.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.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.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.Deoxyribonucleases: Enzymes which catalyze the hydrolases of ester bonds within DNA. EC 3.1.-.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.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.Polycomb-Group Proteins: A family of proteins that play a role in CHROMATIN REMODELING. They are best known for silencing HOX GENES and the regulation of EPIGENETIC PROCESSES.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.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.Acetyltransferases: Enzymes catalyzing the transfer of an acetyl group, usually from acetyl coenzyme A, to another compound. EC 2.3.1.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).Histone Chaperones: Proteins involved in the assembly and disassembly of HISTONES into NUCLEOSOMES.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.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.Cell Line, Tumor: A cell line derived from cultured tumor cells.High Mobility Group Proteins: A family of low-molecular weight, non-histone proteins found in chromatin.Nucleoproteins: Proteins conjugated with nucleic acids.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.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.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.Hydroxamic Acids: A class of weak acids with the general formula R-CONHOH.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.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.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.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.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Response Elements: Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.Mi-2 Nucleosome Remodeling and Deacetylase Complex: A enzyme complex involved in the remodeling of NUCLEOSOMES. The complex is comprised of at least seven subunits and includes both histone deacetylase and ATPase activities.Chromomycin A3: Glycosidic antibiotic from Streptomyces griseus used as a fluorescent stain of DNA and as an antineoplastic agent.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.p300-CBP Transcription Factors: A family of histone acetyltransferases that is structurally-related to CREB-BINDING PROTEIN and to E1A-ASSOCIATED P300 PROTEIN. They function as transcriptional coactivators by bridging between DNA-binding TRANSCRIPTION FACTORS and the basal transcription machinery. They also modify transcription factors and CHROMATIN through ACETYLATION.Histone Deacetylase Inhibitors: Compounds that inhibit HISTONE DEACETYLASES. This class of drugs may influence gene expression by increasing the level of acetylated HISTONES in specific CHROMATIN domains.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.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.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.Transcription Initiation Site: The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.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.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.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.Histone Code: The specific patterns of changes made to HISTONES, that are involved in assembly, maintenance, and alteration of chromatin structural states (such as EUCHROMATIN and HETEROCHROMATIN). The changes are made by various HISTONE MODIFICATION PROCESSES that include ACETYLATION; METHYLATION; PHOSPHORYLATION; and UBIQUITINATION.HMGN1 Protein: An evolutionarily-conserved 10-kDa nuclear protein that binds NUCLEOSOMES and may be involved in the process of CHROMATIN unfolding.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).Protein Methyltransferases: Enzymes that catalyze the methylation of amino acids after their incorporation into a polypeptide chain. S-Adenosyl-L-methionine acts as the methylating agent. EC 2.1.1.Nuclear Matrix: The residual framework structure of the CELL NUCLEUS that maintains many of the overall architectural features of the cell nucleus including the nuclear lamina with NUCLEAR PORE complex structures, residual CELL NUCLEOLI and an extensive fibrogranular structure in the nuclear interior. (Advan. Enzyme Regul. 2002; 42:39-52)Protamines: A group of simple proteins that yield basic amino acids on hydrolysis and that occur combined with nucleic acid in the sperm of fish. Protamines contain very few kinds of amino acids. Protamine sulfate combines with heparin to form a stable inactive complex; it is used to neutralize the anticoagulant action of heparin in the treatment of heparin overdose. (From Merck Index, 11th ed; Martindale, The Extra Pharmacopoeia, 30th ed, p692)Deoxyribonucleoproteins: Proteins conjugated with deoxyribonucleic acids (DNA) or specific DNA.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)Histone Deacetylase 1: A histone deacetylase subtype that is found along with HISTONE DEACETYLASE 2; RETINOBLASTOMA-BINDING PROTEIN 4; and RETINOBLASTOMA-BINDING PROTEIN 7 as core components of histone deacetylase complexes.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.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.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.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.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Locus Control Region: A regulatory region first identified in the human beta-globin locus but subsequently found in other loci. The region is believed to regulate GENETIC TRANSCRIPTION by opening and remodeling CHROMATIN structure. It may also have enhancer activity.Histone Demethylases: Enzymes that catalyse the removal of methyl groups from LYSINE or ARGININE residues found on HISTONES. Many histone demethylases generally function through an oxidoreductive mechanism.Sirtuin 2: A sirtuin family member found primarily in the CYTOPLASM. It is a multifunctional enzyme that contains a NAD-dependent deacetylase activity that is specific for HISTONES and a mono-ADP-ribosyltransferase activity.RNA, Untranslated: RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.Multiprotein Complexes: Macromolecular complexes formed from the association of defined protein subunits.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.Oviducts: Ducts that serve exclusively for the passage of eggs from the ovaries to the exterior of the body. In non-mammals, they are termed oviducts. In mammals, they are highly specialized and known as FALLOPIAN TUBES.Polycomb Repressive Complex 1: A multisubunit polycomb protein complex with affinity for CHROMATIN that contains methylated HISTONE H3. It contains an E3 ubiquitin ligase activity that is specific for HISTONE H2A and works in conjunction with POLYCOMB REPRESSIVE COMPLEX 2 to effect EPIGENETIC REPRESSION.Silent Information Regulator Proteins, Saccharomyces cerevisiae: A set of nuclear proteins in SACCHAROMYCES CEREVISIAE that are required for the transcriptional repression of the silent mating type loci. They mediate the formation of silenced CHROMATIN and repress both transcription and recombination at other loci as well. They are comprised of 4 non-homologous, interacting proteins, Sir1p, Sir2p, Sir3p, and Sir4p. Sir2p, an NAD-dependent HISTONE DEACETYLASE, is the founding member of the family of SIRTUINS.DNA Breaks, Double-Stranded: Interruptions in the sugar-phosphate backbone of DNA, across both strands adjacently.CpG Islands: Areas of increased density of the dinucleotide sequence cytosine--phosphate diester--guanine. They form stretches of DNA several hundred to several thousand base pairs long. In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. They are unmethylated except for those on the inactive X chromosome and some associated with imprinted genes.Embryonic Stem Cells: Cells derived from the BLASTOCYST INNER CELL MASS which forms before implantation in the uterine wall. They retain the ability to divide, proliferate and provide progenitor cells that can differentiate into specialized cells.Fungal Proteins: Proteins found in any species of fungus.Chromosome Positioning: The mechanisms of eukaryotic CELLS that place or keep the CHROMOSOMES in a particular SUBNUCLEAR SPACE.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.Globins: A superfamily of proteins containing the globin fold which is composed of 6-8 alpha helices arranged in a characterstic HEME enclosing structure.Regulatory Elements, Transcriptional: Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.DNA Fragmentation: Splitting the DNA into shorter pieces by endonucleolytic DNA CLEAVAGE at multiple sites. It includes the internucleosomal DNA fragmentation, which along with chromatin condensation, are considered to be the hallmarks of APOPTOSIS.HMGN Proteins: A family of HIGH MOBILITY GROUP PROTEINS that bind to NUCLEOSOMES.Chromosomes, Fungal: Structures within the nucleus of fungal cells consisting of or containing DNA, which carry genetic information essential to the cell.DNA, Satellite: Highly repetitive DNA sequences found in HETEROCHROMATIN, mainly near centromeres. They are composed of simple sequences (very short) (see MINISATELLITE REPEATS) repeated in tandem many times to form large blocks of sequence. Additionally, following the accumulation of mutations, these blocks of repeats have been repeated in tandem themselves. The degree of repetition is on the order of 1000 to 10 million at each locus. Loci are few, usually one or two per chromosome. They were called satellites since in density gradients, they often sediment as distinct, satellite bands separate from the bulk of genomic DNA owing to a distinct BASE COMPOSITION.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).Chromosomes, Human: Very long DNA molecules and associated proteins, HISTONES, and non-histone chromosomal proteins (CHROMOSOMAL PROTEINS, NON-HISTONE). Normally 46 chromosomes, including two sex chromosomes are found in the nucleus of human cells. They carry the hereditary information of the individual.Silencer Elements, Transcriptional: Nucleic acid sequences that are involved in the negative regulation of GENETIC TRANSCRIPTION by chromatin silencing.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Erythrocytes: Red blood cells. Mature erythrocytes are non-nucleated, biconcave disks containing HEMOGLOBIN whose function is to transport OXYGEN.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.Genes, Reporter: Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.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.Xenopus: An aquatic genus of the family, Pipidae, occurring in Africa and distinguished by having black horny claws on three inner hind toes.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Sirtuins: A homologous family of regulatory enzymes that are structurally related to the protein silent mating type information regulator 2 (Sir2) found in Saccharomyces cerevisiae. Sirtuins contain a central catalytic core region which binds NAD. Several of the sirtuins utilize NAD to deacetylate proteins such as HISTONES and are categorized as GROUP III HISTONE DEACETYLASES. Several other sirtuin members utilize NAD to transfer ADP-RIBOSE to proteins and are categorized as MONO ADP-RIBOSE TRANSFERASES, while a third group of sirtuins appears to have both deacetylase and ADP ribose transferase activities.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Transcriptional Elongation Factors: Transcription factors whose primary function is to regulate the rate in which RNA is transcribed.DNA Footprinting: A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Nucleosome Assembly Protein 1: A histone chaperone that facilitates nucleosome assembly by mediating the formation of the histone octamer and its transfer to DNA.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Electrophoretic Mobility Shift Assay: An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.Methyl-CpG-Binding Protein 2: A DNA-binding protein that interacts with methylated CPG ISLANDS. It plays a role in repressing GENETIC TRANSCRIPTION and is frequently mutated in RETT SYNDROME.Kinetics: The rate dynamics in chemical or physical systems.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.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.Origin Recognition Complex: The origin recognition complex is a multi-subunit DNA-binding protein that initiates DNA REPLICATION in eukaryotes.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.Cell Extracts: Preparations of cell constituents or subcellular materials, isolates, or substances.Genes, Fungal: The functional hereditary units of FUNGI.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.Gene Knockdown Techniques: The artificial induction of GENE SILENCING by the use of RNA INTERFERENCE to reduce the expression of a specific gene. It includes the use of DOUBLE-STRANDED RNA, such as SMALL INTERFERING RNA and RNA containing HAIRPIN LOOP SEQUENCE, and ANTI-SENSE OLIGONUCLEOTIDES.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.Poly Adenosine Diphosphate Ribose: A polynucleotide formed from the ADP-RIBOSE moiety of nicotinamide-adenine dinucleotide (NAD) by POLY(ADP-RIBOSE) POLYMERASES.In Situ Hybridization, Fluorescence: A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.Genetic Loci: Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.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.Matrix Attachment Region Binding Proteins: Proteins that bind to the MATRIX ATTACHMENT REGIONS of DNA.E1A-Associated p300 Protein: A member of the p300-CBP transcription factors that was originally identified as a binding partner for ADENOVIRUS E1A PROTEINS.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.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.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.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).RNA, Long Noncoding: A class of untranslated RNA molecules that are typically greater than 200 nucleotides in length and do not code for proteins. Members of this class have been found to play roles in transcriptional regulation, post-transcriptional processing, CHROMATIN REMODELING, and in the epigenetic control of chromatin.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.Lamins: Nuclear matrix proteins that are structural components of the NUCLEAR LAMINA. They are found in most multicellular organisms.Sp1 Transcription Factor: Promoter-specific RNA polymerase II transcription factor that binds to the GC box, one of the upstream promoter elements, in mammalian cells. The binding of Sp1 is necessary for the initiation of transcription in the promoters of a variety of cellular and viral GENES.Polycomb Repressive Complex 2: A multisubunit polycomb protein complex that catalyzes the METHYLATION of chromosomal HISTONE H3. It works in conjunction with POLYCOMB REPRESSIVE COMPLEX 1 to effect EPIGENETIC REPRESSION.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.beta-Globins: Members of the beta-globin family. In humans, they are encoded in a gene cluster on CHROMOSOME 11. They include epsilon-globin, gamma-globin, delta-globin and beta-globin. There is also a pseudogene of beta (theta-beta) in the gene cluster. Adult HEMOGLOBIN is comprised of two ALPHA-GLOBIN chains and two beta-globin chains.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.Jumonji Domain-Containing Histone Demethylases: A family of histone demethylases that share a conserved Jumonji C domain. The enzymes function via an iron-dependent dioxygenase mechanism that couples the conversion of 2-oxoglutarate to succinate to the hydroxylation of N-methyl groups.Apoptosis: One of the mechanisms by which CELL DEATH occurs (compare with NECROSIS and AUTOPHAGOCYTOSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA; (DNA FRAGMENTATION); at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth.Fibroblasts: Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules.

The Drosophila kismet gene is related to chromatin-remodeling factors and is required for both segmentation and segment identity. (1/12332)

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 homeotic gene transcription.  (+info)

Gadd45, a p53-responsive stress protein, modifies DNA accessibility on damaged chromatin. (2/12332)

This report demonstrates that Gadd45, a p53-responsive stress protein, can facilitate topoisomerase relaxing and cleavage activity in the presence of core histones. A correlation between reduced expression of Gadd45 and increased resistance to topoisomerase I and topoisomerase II inhibitors in a variety of human cell lines was also found. Gadd45 could potentially mediate this effect by destabilizing histone-DNA interactions since it was found to interact directly with the four core histones. To evaluate this possibility, we investigated the effect of Gadd45 on preassembled mononucleosomes. Our data indicate that Gadd45 directly associates with mononucleosomes that have been altered by histone acetylation or UV radiation. This interaction resulted in increased DNase I accessibility on hyperacetylated mononucleosomes and substantial reduction of T4 endonuclease V accessibility to cyclobutane pyrimidine dimers on UV-irradiated mononucleosomes but not on naked DNA. Both histone acetylation and UV radiation are thought to destabilize the nucleosomal structure. Hence, these results imply that Gadd45 can recognize an altered chromatin state and modulate DNA accessibility to cellular proteins.  (+info)

A new element within the T-cell receptor alpha locus required for tissue-specific locus control region activity. (3/12332)

Locus control regions (LCRs) are cis-acting regulatory elements thought to provide a tissue-specific open chromatin domain for genes to which they are linked. The gene for T-cell receptor alpha chain (TCRalpha) is exclusively expressed in T cells, and the chromatin at its locus displays differentially open configurations in expressing and nonexpressing tissues. Mouse TCRalpha exists in a complex locus containing three differentially regulated genes. We previously described an LCR in this locus that confers T-lineage-specific expression upon linked transgenes. The 3' portion of this LCR contains an unrestricted chromatin opening activity while the 5' portion contains elements restricting this activity to T cells. This tissue-specificity region contains four known DNase I hypersensitive sites, two located near transcriptional silencers, one at the TCRalpha enhancer, and another located 3' of the enhancer in a 1-kb region of unknown function. Analysis of this region using transgenic mice reveals that the silencer regions contribute negligibly to LCR activity. While the enhancer is required for complete LCR function, its removal has surprisingly little effect on chromatin structure or expression outside the thymus. Rather, the region 3' of the enhancer appears responsible for the tissue-differential chromatin configurations observed at the TCRalpha locus. This region, herein termed the "HS1' element," also increases lymphoid transgene expression while suppressing ectopic transgene activity. Thus, this previously undescribed element is an integral part of the TCRalphaLCR, which influences tissue-specific chromatin structure and gene expression.  (+info)

A novel H2A/H4 nucleosomal histone acetyltransferase in Tetrahymena thermophila. (4/12332)

Recently, we reported the identification of a 55-kDa polypeptide (p55) from Tetrahymena macronuclei as a catalytic subunit of a transcription-associated histone acetyltransferase (HAT A). Extensive homology between p55 and Gcn5p, a component of the SAGA and ADA transcriptional coactivator complexes in budding yeast, suggests an immediate link between the regulation of chromatin structure and transcriptional output. Here we report the characterization of a second transcription-associated HAT activity from Tetrahymena macronuclei. This novel activity is distinct from complexes containing p55 and putative ciliate SAGA and ADA components and shares several characteristics with NuA4 (for nucleosomal H2A/H4), a 1.8-MDa, Gcn5p-independent HAT complex recently described in yeast. A key feature of both the NuA4 and Tetrahymena activities is their acetylation site specificity for lysines 5, 8, 12, and 16 of H4 and lysines 5 and 9 of H2A in nucleosomal substrates, patterns that are distinct from those of known Gcn5p family members. Moreover, like NuA4, the Tetrahymena activity is capable of activating transcription from nucleosomal templates in vitro in an acetyl coenzyme A-dependent fashion. Unlike NuA4, however, sucrose gradient analyses of the ciliate enzyme, following sequential denaturation and renaturation, estimate the molecular size of the catalytically active subunit to be approximately 80 kDa, consistent with the notion that a single polypeptide or a stable subcomplex is sufficient for this H2A/H4 nucleosomal HAT activity. Together, these data document the importance of this novel HAT activity for transcriptional activation from chromatin templates and suggest that a second catalytic HAT subunit, in addition to p55/Gcn5p, is conserved between yeast and Tetrahymena.  (+info)

Stable remodeling of tailless nucleosomes by the human SWI-SNF complex. (5/12332)

The histone N-terminal tails have been shown previously to be important for chromatin assembly, remodeling, and stability. We have tested the ability of human SWI-SNF (hSWI-SNF) to remodel nucleosomes whose tails have been cleaved through a limited trypsin digestion. We show that hSWI-SNF is able to remodel tailless mononucleosomes and nucleosomal arrays, although hSWI-SNF remodeling of tailless nucleosomes is less effective than remodeling of nucleosomes with tails. Analogous to previous observations with tailed nucleosomal templates, we show both (i) that hSWI-SNF-remodeled trypsinized mononucleosomes and arrays are stable for 30 min in the remodeled conformation after removal of ATP and (ii) that the remodeled tailless mononucleosome can be isolated on a nondenaturing acrylamide gel as a novel species. Thus, nucleosome remodeling by hSWI-SNF can occur via interactions with a tailless nucleosome core.  (+info)

Differential regulation of the human nidogen gene promoter region by a novel cell-type-specific silencer element. (6/12332)

Transfection analyses of the human nidogen promoter region in nidogen-producing fibroblasts from adult skin revealed multiple positive and negative cis-acting elements controlling nidogen gene expression. Characterization of the positive regulatory domains by gel mobility-shift assays and co-transfection studies in Drosophila SL2 cells unequivocally demonstrated that Sp1-like transcription factors are essential for a high expression of the human nidogen gene. Analysis of the negative regulatory domains identified a novel silencer element between nt -1333 and -1322, which is bound by a distinct nuclear factor, by using extracts from adult but not from embryonal fibroblasts. In embryonal fibroblasts, which express significantly higher amounts of nidogen mRNA as compared with adult fibroblasts, this inhibitory nidogen promoter region did not affect nidogen and SV40 promoter activities. The silencer element seems to be active only in nidogen-producing cells. Therefore this regulatory element might function in vivo to limit nidogen gene expression in response to external stimuli. However, none of the identified regulatory elements, including the silencer, contribute significantly to cell-specific expression of the human nidogen gene. Instead we provide evidence that gene expression in epidermal keratinocytes that are not producing nidogen is repressed by methylation-specific and chromatin-dependent mechanisms.  (+info)

Histone octamer transfer by a chromatin-remodeling complex. (7/12332)

RSC, an abundant, essential chromatin-remodeling complex related to SWI/SNF complex, catalyzes the transfer of a histone octamer from a nucleosome core particle to naked DNA. The newly formed octamer-DNA complex is identical with a nucleosome in all respects. The reaction requires ATP and involves an activated RSC-nucleosome intermediate. The mechanism may entail formation of a duplex displacement loop on the nucleosome, facilitating the entry of exogeneous DNA and the release of the endogenous molecule.  (+info)

Differential transcriptional activity associated with chromatin configuration in fully grown mouse germinal vesicle oocytes. (8/12332)

It was previously shown that fully grown ovarian germinal vesicle (GV) oocytes of adult mice exhibit several nuclear configurations that differ essentially by the presence or absence of a ring of condensed chromatin around the nucleolus. These configurations have been termed, respectively, SN (surrounded nucleolus) and NSN (nonsurrounded nucleolus). Work from our and other laboratories has revealed ultrastructural and functional differences between these two configurations. The aims of the present study were 1) to analyze the equilibrium between the SN and the NSN population as a function of the age of the mice and the time after hCG-induced ovulation and 2) to study the polymerase I (pol I)- and polymerase II (pol II)-dependent transcription in both types of oocytes through the detection of bromouridine incorporated into nascent RNA. We show 1) that ovarian GV oocytes exhibiting the SN-type configuration can be found as soon as 17 days after birth in the C57/CBA mouse strain and 2) that the SN:NSN ratio of ovarian GV oocytes is very low just after hCG-induced ovulation and then increases progressively with the time after ovulation. Furthermore, we demonstrate that the SN configuration correlates strictly with the arrest of both pol I- and pol II-dependent transcription in mice at any age. Finally, we show that ribosomal genes are located at the outer periphery of the nucleolus in the NSN configuration and that pol I-dependent perinucleolar transcription sites correspond to specific ultrastructural features of the nucleolus. Altogether, these results provide clear-cut criteria delineating transcriptionally active GV oocytes from those that are inactive, and confirm that the SN-type configuration is mostly present in preovulatory oocytes.  (+info)

*Chromatin

Recent chromatin publications and news] Protocol for in vitro Chromatin Assembly ENCODE threads Explorer Chromatin patterns at ... Elements of chromatin structure: histones, nucleosomes, and fibres, p. 1-26. In S. C. R. Elgin (ed.), Chromatin structure and ... When the chromatin decondenses, the DNA is open to entry of molecular machinery. Fluctuations between open and closed chromatin ... The spatial arrangement of the chromatin within the nucleus is not random - specific regions of the chromatin can be found in ...

*Chromatin remodeling

... is the dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the ... MBInfo - Chromatin MBInfo - DNA Packaging YouTube - Chromatin, Histones and Modifications YouTube - Epigenetics Overview ... Epigenetics Histone Nucleosomes Chromatin Histone acetyltransferase Transcription factors CAF-1 (Chromatin assembly factor-1 ... Wang GG, Allis CD, Chi P (September 2007). "Chromatin remodeling and cancer, Part II: ATP-dependent chromatin remodeling". ...

*Epigenetics & Chromatin

... is a peer-reviewed open access scientific journal that covers the biology of epigenetics and chromatin ... BioMed Central hosted a conference titled "Epigenetics & Chromatin: Interactions and processes" at Harvard Medical School on ... "Epigenetics & Chromatin:Interactions and Processes". Retrieved 2015-06-30. Official website. ... Abstracts from the conference were published in Epigenetics & Chromatin. "Master Journal List". Intellectual Property & Science ...

*Chromatin bridge

... s may serve as a marker of cancer activity. Chromatin bridges may form by any number of processes wherein ... Chromatin bridges are easiest and most readily visible when observing chromosomes stained with DAPI. DNA bridges appear to be a ... Chromatin bridge is a mitotic occurrence that forms when telomeres of sister chromatids fuse together and fail to completely ... A chromatin bridge may also be observed using indirect immunofluorescence, in which anti-tubulin emits a green coloration when ...

*Bivalent chromatin

The developmentally regulated process of resolving bivalent chromatin is aided by the activity of ATP-chromatin remodelers such ... However, in bivalent chromatin, both types of regulators are interacting with the same domain at the same time. Bivalent ... Bivalent chromatin domains are found in embryonic stem (ES) cells and play an important role in cell differentiation. When ... Bivalent chromatin are segments of DNA, bound to histone proteins, that have both repressing and activating epigenetic ...

*Chromatin immunoprecipitation

Generally, native chromatin is used as starting chromatin. As histones wrap around DNA to form nucleosomes, they are naturally ... Chromatin immunoprecipitation at the US National Library of Medicine Medical Subject Headings (MeSH) EpigenomeNOE.com Chromatin ... However, it demands highly specific primers for detection of the target cell chromatin from the foreign carrier chromatin ... Mild formaldehyde crosslinking followed by nuclease digestion has been used to shear the chromatin. Chromatin fragments of 400 ...

*Active chromatin sequence

At the active chromatin sequence site deacetylation can caused the gene to be repressed if not being expressed. Chromatin Sabo ... Active chromatin may also be called euchromatin. ACSs may occur in non-expressed gene regions which are assumed to be "poised" ... An active chromatin sequence (ACS) is a region of DNA in a eukaryotic chromosome in which histone modifications such as ... Roh TY, Cuddapah S, Zhao K. "Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping". ...

*Chromatin target of prmt1

... is a protein that in humans is encoded by the CHTOP gene. This gene encodes a small nuclear protein ... Chromatin target of PRMT1". Retrieved 2014-08-22. Zullo, A. J.; Michaud, M; Zhang, W; Grusby, M. J. (2009). "Identification of ... a novel chromatin target of protein arginine methyltransferases". Molecular and Cellular Biology. 30 (1): 260-72. doi:10.1128/ ...

*Chromatin accessibility complex 1

... is a protein that in humans is encoded by the CHRAC1 gene. CHRAC1 is a histone-fold protein ... Chromatin accessibility complex 1". Retrieved 2016-10-26. This article incorporates text from the United States National ...

*Salt-and-pepper chromatin

In pathology, salt-and-pepper chromatin, also salt-and-pepper nuclei and stippled chromatin, refers to cell nuclei that ... A pheochromocytoma showing finely granular chromatin. H&E stain. A pheochromocytoma showing finely granular chromatin. H&E ... Salt-and-pepper chromatin (pheochromocytoma). H&E stain. Chetty R, Asa SL (October 2004). "Pancreatic endocrine tumour with ... Salt-and-pepper chromatin - nature.com. Salt-and-pepper nucleus - upmc.edu.. ...

*Chromatin structure remodeling (RSC) complex

RSC (Remodelling the Structure of Chromatin) is a member of the ATP-dependent chromatin remodeller family (other members being ... abundant chromatin-remodeling complex". Cell. 87 (7): 1249-60. doi:10.1016/S0092-8674(00)81820-6. PMID 8980231. Lia G, Praly E ...

*Nucleosome Repeat Length

In chromatin neighboring nucleosomes are separated by the linker DNA and in many cases also by the linker histone H1 as well as ... NRL can be determined genome-wide for the chromatin in a given cell type and state, or locally for a large enough genomic ... van Holde KE (1989). Chromatin. New York: Springer-Verlag. p. 497. ISBN 978-1-4612-8123-8. Valouev A, Johnson SM, Boyd SD, ... It was shown that ordered nucleosome positioning arises only in the presence of ATP-dependent chromatin remodeling. Furthermore ...

*Histone methyltransferase

"Chromatin Network". Retrieved 1 March 2012. Kouzarides T (February 2007). "Chromatin modifications and their function". Cell. ... See Histone#Chromatin regulation. Abnormal expression or activity of methylation-regulating enzymes has been noted in some ... In eukaryotic cells, the genome is tightly condensed into chromatin (composed of DNA and histone proteins), so enzymes, such as ... Methylation of histones is important biologically because it is the principal epigenetic modification of chromatin that ...

*Cold Spring Harbor Laboratory

... chromatin dynamics; structural biology; advanced proteomics; mass spectrometry; advanced microscopy. Cancer Research Principal ...

*Linker histone H1 variants

The linker histone H1 is a protein family forming a critical component of eukaryotic chromatin. H1 histones bind to the linker ... However, at the level of local chromatin organization, individual variants can regulate a subset of specific genes both in a ... inactive chromatin: distribution in human fetal fibroblasts". Chromosome Research: An International Journal on the Molecular, ... Also, different isotypes show different localization and bind to chromatin with different affinities. Therefore a model has ...

*Mitosis

During interphase, the genetic material in the nucleus consists of loosely packed chromatin. At the onset of prophase, ... Kadauke S, Blobel GA (April 2013). "Mitotic bookmarking by transcription factors". Epigenetics & Chromatin. 6 (1): 6. doi: ... chromatin fibers condense into discrete chromosomes that are typically visible at high magnification through a light microscope ...

*Histone acetyltransferase

Chromatin is a combination of proteins and DNA found in the nucleus, and it undergoes many structural changes as different ... Chromatin in the cell can be found in two states: condensed and uncondensed. The latter, known as euchromatin, is ... The process of chromatin remodeling involves several enzymes, including HATs, that assist in the reformation of nucleosomes and ... Controlling the chromatin remodeling process within cancer cells may provide a novel drug target for cancer research. Attacking ...

*EZH2

Jeanteur, Philippe (2008). Epigenetics and Chromatin. Springer. Kaneko S, Li G, Son J, Xu CF, Margueron R, Neubert TA, Reinberg ... Heterochromatin is tightly packed chromatin which limits the accessibility of transcription machinery to the underlying DNA, ... Chromatin. 6 (1): 3. doi:10.1186/1756-8935-6-3. PMC 3606351 . PMID 23448518. Martin C, Zhang Y (2005). "The diverse functions ... due to PRC2/EZH2-EED-mediated H3K27 methylation and subsequent recruitment of PRC1 which facilitates condensation of chromatin ...

*XIST

The primary chromatin binding region was shown to localize to the C-repeat region. The chromatin-binding region was ... The Xist RNA directly binds to the inactive X-chromosome through a chromatin binding region of the RNA transcript. The Xist ... One theory is that Tsix is involved in chromatin modification at the Xist locus and another is that transcription factors of ... Navarro P, Pichard S, Ciaudo C, Avner P, Rougeulle C (Jun 2005). "Tsix transcription across the Xist gene alters chromatin ...

*Chromosome conformation capture

Walther Flemming coined the term chromatin . In 1883, August Weismann connected chromatin with heredity. In 1884, Albrecht ... In 1973/1974, chromatin fiber was discovered. In 1975, Chambon coined the term nucleosomes. In 1982, Chromosome territories ... performed Hi-C experiment and found a prostate cancer risk region (7p15.2) in an anchor point for a repressive chromatin ... In 1888, Sutton and Boveri proposed the theory of continuity of chromatin during the cell cycle In 1889, Wilhelm von Waldemeyer ...

*Histone variants

... chromatin remodeling, and X-chromosome inactivation in somatic cells. H2A.X and canonical H2A have diverged several times in ... Epigenetics Chromatin. doi:10.1186/s13072-016-0109-x. PMID 28096900. HistoneDB 2.0 - Database of histones and variants at NCBI ... Chromatin. 5:7. doi:10.1186/1756-8935-5-7. PMID 22650316. "Histone Variants Database 2.0". National Center for Biotechnology ...

*Constitutive heterochromatin

Chromatin. 8: 3. doi:10.1186/1756-8935-8-3. ISSN 1756-8935. PMC 4363358 . PMID 25788984. T. Strachan and A. Read (2004). Human ... HP1 is involved in the chromatin condensing process that makes DNA inaccessible for transcription. Genetic disorders that ...

*Position-effect variegation

It is also associated with changes in chromatin conformation. The classical example is the Drosophila wm4 (speak white-mottled- ... According to this model, the heterochromatin forces an altered chromatin conformation on the euchromatic region. Due to this, ... codes for a chromatin protein containing a conserved domain common to several transcriptional regulators". Proc Natl Acad Sci U ... Chromatin. 2: 1. doi:10.1186/1756-8935-2-1. ISSN 1756-8935. Hermann J. Muller (1930). "Types of visible variations induced by X ...

*Histone H2B

Nucleosome Histone Chromatin Other histone proteins: Histone H1 Histone H2A Histone H3 Histone H4 Bhasin M, Reinherz EL, Reche ... Histone H2B is one of the 5 main histone proteins involved in the structure of chromatin in eukaryotic cells. Featuring a main ... These are highly involved in condensing chromatin from the beads-on-a-string conformation to a 30-nm fiber. Similar to other ... The wrapping continues until all chromatin has been packaged with the nucleosomes. Histone H2B is a structural protein that ...

*Mediator (coactivator)

Nagai S, Davis RE, Mattei PJ, Eagen KP, Kornberg RD (2017). "Chromatin potentiates transcription". Proc Natl Acad Sci U S A. ... Mediator is involved in "looping" of chromatin, which brings distant regions of a chromosome into closer physical proximity. ... 2013). "Activating RNAs associate with mediator to enhance chromatin architecture and transcription". Nature. 494 (7438): 497- ...
DNA is wrapped around a histone octamer to form the basic unit of chromatin structure. During embryogenesis, dynamic changes of chromatin structure and chromatin modification occur after fertilization; subsequently, the epigenetic information is inherited through many rounds of the cell cycle. Thus, chromatin is essential for the determination of cell identity. Two strategies are used to modulate a chromatin environment: the covalent modification of histone tails and energy-dependent chromatin remodeling. The acetylation, methylation or phosphorylation of histone tails can have profound effects on chromatin structure and transcription (Jenuwein and Allis, 2001). Chromatin remodeling reactions are catalyzed by large protein complexes that use the energy of ATP hydrolysis to alter the structure or positioning of nucleosomes (Becker and Hörz, 2002; Clapier and Cairns, 2009). In addition to these events, histone variants play important roles in modulating chromatin structure (Henikoff and Ahmad, ...
Preparation of Chromatin Assembly Extracts from Preblastoderm Drosophila Embryos -- Analysis of Reconstituted Chromatin Using a Solid-Phase Approach -- In Vivo Chromatin Decondensation Assays: Molecular Genetic Analysis of Chromatin Unfolding Characteristics of Selected Proteins -- DNA Methyltransferase Probing of Chromatin Structure Within Populations and on Single Molecules -- Visualization of the Expression of HMGN Nucleosomal Binding Proteins in the Developing Mouse Embryo and in Adult Mouse Tissues -- Drug-Induced Premature Chromosome Condensation (PCC) Protocols: Cytogenetic Approaches in Mitotic Chromosome and Interphase Chromatin -- Analysis of DNA Topology in Yeast Chromatin -- Preparation and Analysis of Uniquely Positioned Mononucleosomes -- Monitoring DNA Breaks in Optically Highlighted Chromatin in Living Cells by Laser Scanning Confocal Microscopy -- Methods to Study Transcription-Coupled Repair in Chromatin -- Cytometric Analysis of DNA Damage: Phosphorylation of Histone H2AX as a ...
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 ...
The THO complex is involved in transcription, genome stability, and messenger ribonucleoprotein (mRNP) formation, but its precise molecular function remains enigmatic. Under heat shock conditions, THO mutants accumulate large protein-DNA complexes that alter the chromatin density of target genes (heavy chromatin), defining a specific biochemical facet of THO function and a powerful tool of analysis. Here, we show that heavy chromatin distribution is dictated by gene boundaries and that the gene promoter is necessary and sufficient to convey THO sensitivity in these conditions. Single-molecule fluorescence insitu hybridization measurements show that heavy chromatin formation correlates with an unusually high firing pace of the promoter with more than 20 transcription events per minute. Heavy chromatin formation closely follows the modulation of promoter firing and strongly correlates with polymerase occupancy genome wide. We propose that the THO complex is required for tuning the dynamic of ...
Loss of function of CDKN2A/B, also known as INK4/ARF [encoding p16INK4A, p15INK4B, and p14ARF (mouse p19Arf)], confers susceptibility to cancers, whereas its up-regulation during organismal aging provokes cellular senescence and tissue degenerative disorders. To better understand the transcriptional regulation of p16INK4A, a CRISPR screen targeting open, noncoding chromatin regions adjacent to p16INK4A was performed in a human p16INK4A-P2A-mCherry reporter cell line. We identified a repressive element located in the 3′ region adjacent to the ARF promoter that controls p16INK4A expression via long-distance chromatin interactions. Coinfection of lentiviral dCas9-KRAB with selected single-guide RNAs against the repressive element abrogated the ARF/p16INK4A chromatin contacts, thus reactivating p16INK4A expression. Genetic CRISPR screening identified candidate transcription factors inhibiting p16INK4A regulation, including ZNF217, which was confirmed to bind the ARF/p16INK4A interaction loop. In ...
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 ...
Here, we introduce the 3D Genome Browser, http://3dgenome.org , which allows users to conveniently explore both their own and over 300 publicly available chromatin interaction data of different types. We design a new binary data format for Hi-C data that reduces the file size by at least a magnitude and allows users to visualize chromatin interactions over millions of base pairs within seconds. Our browser provides multiple methods linking distal cis-regulatory elements with their potential target genes. Users can seamlessly integrate thousands of other omics data to gain a comprehensive view of both regulatory landscape and 3D genome structure.
Two main chromatin assembly pathways ensure the proper transmission of chromatin organization and chromatin-based information throughout the cell cycle. A replication-dependent (RD) pathway that couples chromatin assembly to DNA synthesis and a replication-independent (RI) pathway. Whether these pathways contribute to the establishment of chromatin domains like heterochromatin or euchromatin by introducing modifications on histones or modulating chromatin structure remains unknown. Using Xenopus laevis egg extracts we monitored RD and RI chromatin assembly on single-stranded and double-stranded DNA templates. Even though RD assembly proceeded faster than RI assembly the histone content and saturation level with nucleosomes were similar. Despite these comparable topological features, the hydrodynamic behavior of both chromatin species in sucrose gradient centrifugation clearly differed. The RD assembled chromatin ran at lower sucrose concentrations than the RI created chromatin suggesting ...
Histones are responsible for packaging the genomes of almost all eukaryotes into fundamental repeating nucleosome units. The packaging must facilitate compaction into the cell nucleus but also enable dynamic access to the genome. A variety of mechanisms exist for targeting enzymes to undertake local opening of chromatin such as at active genes or for DNA repair. However, larger scale transitions in chromatin also occur where extended genome regions have altered chromatin organisation. This often involves abundant non-histone chromatin proteins that switch chromatin between states that are not well understood at the structural level. The contribution of highly basic non-histone chromatin proteins in vitro has been investigated using the HMGA2 protein implicated in human stem cell chromatin opening, and the Hematodinium DVNP protein which is suggested to replace histones as the dominant packaging protein in this dinoflagellate. These two proteins are compared to histone H1 which stabilises ...
1. Li X-Y, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD. The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol. 2011;12: R34. doi: 10.1186/gb-2011-12-4-r34 21473766. 2. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, et al. The accessible chromatin landscape of the human genome. Nature. 2012;489: 75-82. doi: 10.1038/nature11232 22955617. 3. Klemm SL, Shipony Z, Greenleaf WJ. Chromatin accessibility and the regulatory epigenome. Nat Rev Genet. 2019;20: 207-220. doi: 10.1038/s41576-018-0089-8 30675018. 4. Wu J, Huang B, Chen H, Yin Q, Liu Y, Xiang Y, et al. The landscape of accessible chromatin in mammalian preimplantation embryos. Nature. 2016;534: 652-657. doi: 10.1038/nature18606 27309802. 5. Clark SJ, Argelaguet R, Kapourani C-A, Stubbs TM, Lee HJ, Alda-Catalinas C, et al. scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in ...
The different chromatin features display distinct spatial patterns. It is thus worthwhile to explore the relationship between these patterns and the level of gene expression. Making use of RNA-seq data obtained from the different stages of C. elegans, we quantified the expression level of each gene. For each bin, we then calculated the correlation between the gene expression levels and the average signals of each chromatin feature of the bin. Figure 2b shows the spatial variation of these correlation coefficients around TSSs and TTSs. According to the correlation patterns, there are two main types of chromatin features: ones that are positively correlated with gene expression (such as H3K79me1, H3K79me2 and H3K79me3); and ones that are negatively correlated with gene expression (such as H3K9me2 and H3K9me3). While some features show largely uniform correlations across the 16-kb regions, some others are more variable across the regions. For example, H3K79me2 has a high correlation coefficient ...
Biomedical applications of high-throughput sequencing methods generate a vast amount of data in which numerous chromatin features are mapped along the genome. The results are frequently analysed by creating binary data sets that link the presence/absence of a given feature to specific genomic loci. However, the nucleosome occupancy or chromatin accessibility landscape is essentially continuous. It is currently a challenge in the field to cope with continuous distributions of deep sequencing chromatin readouts and to integrate the different types of discrete chromatin features to reveal linkages between them. Here we introduce the NucTools suite of Perl scripts as well as MATLAB- and R-based visualization programs for a nucleosome-centred downstream analysis of deep sequencing data. NucTools accounts for the continuous distribution of nucleosome occupancy. It allows calculations of nucleosome occupancy profiles averaged over several replicates, comparisons of nucleosome occupancy landscapes between
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 ...
There are variety of models and techniques to observe the presence of the 30nm fibers but it has been more observed that highly compacted chromatin fiber like 30nm fibers are not necessarily present for any gene regulation such as folding of DNA. Instead, 10 nm chromatin can be condensed enough into compacted domains through frequent bending and making 10nm fibers close to each other. In other words, it does not require to have 30nm fibers but is sufficient to have 10 nm chromatin fibers that is organized in genome to explain the complexities of nuclear organization and gene regulation. ...
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 ...
The genetic information encoded by the DNA sequence, can be expressed in different ways. Genomic imprinting is an epigenetic phenomenon that results in monoallelic expression of imprinted genes in a parent of origin-dependent manner. Imprinted genes are frequently found in clusters and can share common regulatory elements. Most of the imprinted genes are regulated by Imprinting Control Regions (ICRs). H19/Igf2 region is a well known imprinted cluster, which is regulated by insulator function of ICR located upstream of the H19 gene. It has been proposed that the epigenetic control of the insulator function of H19 ICR involves organization of higher order chromatin interactions.. In this study we have investigated the role of post-translational modification in regulating insulator protein CTCF (CCCTC-binding factor). The results indicated novel links between poly(ADP-ribosyl)ation and CTCF, which are essential for regulating insulators function.. We also studied the higher order chromatin ...
TY - JOUR. T1 - Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns. AU - Srivastava, Divyanshi. AU - Mahony, Shaun. PY - 2019/1/1. Y1 - 2019/1/1. N2 - Transcription factors (TFs) selectively bind distinct sets of sites in different cell types. Such cell type-specific binding specificity is expected to result from interplay between the TFs intrinsic sequence preferences, cooperative interactions with other regulatory proteins, and cell type-specific chromatin landscapes. Cell type-specific TF binding events are highly correlated with patterns of chromatin accessibility and active histone modifications in the same cell type. However, since concurrent chromatin may itself be a consequence of TF binding, chromatin landscapes measured prior to TF activation provide more useful insights into how cell type-specific TF binding events became established in the first place. Here, we review the various sequence and chromatin ...
Abstract: To study the relation between chromatin structure and DNA function in detail it is necessary to have an in vitro procedure for assembling nucleosomes on a naked DNA template with properties similar to native chromatin. Such procedures exist for yeast and animal model systems but have not been developed for plants. The goal of this project was to lay the groundwork for developing a chromatin assembly extract from plants. Extracts from various plant materials were tested to determine their suitability for chromatin reconstitution. Tissues from plants are thought to have much higher levels of protease and nuclease activities than those of animals or yeast. Therefore, methods to determine the relative activity of proteases and nucleases had to be developed to determine if the template DNA, histones, and chromatin assembly proteins could survive the chromatin assembly reaction. Additionally, methods to streamline the isolation of maize nuclei and purification of histones were developed. ...
HI-TECH SOLUTIONS - Exporter, Importer, Manufacturer, Distributor & Supplier of Nuclear Chromatin Decondensation (N.C.D.) based in New Delhi, India
Employing a new algorithm for identifying differentially methylated regions (DMRs) from reduced representation bisulfite sequencing profiles, we identified 1972 hypermethylated and 3250 hypomethylated myogenic DMRs in a comparison of myoblasts (Mb) and myotubes (Mt) with 16 types of nonmuscle cell cultures. DMRs co-localized with a variety of chromatin structures, as deduced from ENCODE whole-genome profiles. Myogenic hypomethylation was highly associated with both weak and strong enhancer-type chromatin, while hypermethylation was infrequently associated with enhancer-type chromatin. Both myogenic hypermethylation and hypomethylation often overlapped weak transcription-type chromatin and Polycomb-repressed-type chromatin. For representative genes, we illustrate relationships between DNA methylation, the local chromatin state, DNaseI hypersensitivity, and gene expression. For example, MARVELD2 exhibited myogenic hypermethylation in transcription-type chromatin that overlapped a silenced promoter in Mb
Login We have Rangiroa indeed at download methods in enzymology vol. 376 chromatin and chromatin, and avoid the Copious changelog out into the mock mention by 5:30PM. The download methods in enzymology is, and we Have on our decay to Nuku Hiva in the Marquesas susceptivum. We Do a download methods in enzymology vol. 376 chromatin and chromatin remodeling at switch before we agree, since the Marquesas want a efficient download out. I check up at not time-consuming this download methods in to the link existing quite a burden. When I build out my download section, the comments are incorrect and the mechanics provide first. I return the eBooks have as I have for another download methods in enzymology vol. 376 chromatin and chromatin remodeling enzymes part before making up. I have a download methods in enzymology then to the Promenade Deck with my beginning to reduce the text. Moorea is well cherished through the download methods in enzymology vol. 376 chromatin. Bay, where we was to capture. He ...
Bysani M, Agren R, Davegårdh C, Volkov P, Rönn T, Unneberg P, Bacos K, Ling C Sci Rep 9 (1) - [2019-12-00; online 2019-05-23] Impaired insulin secretion from pancreatic islets is a hallmark of type 2 diabetes (T2D). Altered chromatin structure may contribute to the disease. We therefore studied the impact of T2D on open chromatin in human pancreatic islets. We used assay for transposase-accessible chromatin using sequencing (ATAC-seq) to profile open chromatin in islets from T2D and non-diabetic donors. We identified 57,105 and 53,284 ATAC-seq peaks representing open chromatin regions in islets of non-diabetic and diabetic donors, respectively. The majority of ATAC-seq peaks mapped near transcription start sites. Additionally, peaks were enriched in enhancer regions and in regions where islet-specific transcription factors (TFs), e.g. FOXA2, MAFB, NKX2.2, NKX6.1 and PDX1, bind. Islet ATAC-seq peaks overlap with 13 SNPs associated with T2D (e.g. rs7903146, rs2237897, rs757209, rs11708067 and ...
Chromatin is the template on which DNA-associated transactions take place in eukaryotic organisms. Nucleosomes consisting of the four histones H2A, H2B, H3 and H4 each organize 150bp of DNA and constitute a first layer of chromatin. The three-dimensional organization of chromatin as well as histone post-translational modifications (PTMs) regulate recruitment of chromatin-associated effector proteins (effectors). Heterochromatin protein 1 (HP1) is an effector associated with silenced genome regions. HP1 recognizes histone H3 trimethylated at lysine 9 (H3 K9me3) and can dimerize. This results in a protein with two binding domains allowing multivalent engagement of target chromatin. HP1 can further promote chromatin condensation and inter-fiber contacts. The effector p53 binding protein (53BP1) is a key regulator in the DNA damage repair pathway. It is known to target a trio of PTMs; H4 dimethylated at K20 (H4 K20me2), H2A(.X) ubiquitylated at K15 (H2A.X K15ub) and H2A.X phosphorylated at S139 ...
TY - JOUR. T1 - Transcription of isolated mouse liver chromatin. AU - Bacheler, Lee T.. AU - Smith, Kirby D.. PY - 1976. Y1 - 1976. N2 - Analysis of RNA transcription from isolated mouse liver chromatin has been undertaken by means of RN A-excess hybridizations with small amounts of radioactive DNA. This analysis indicates that mouse liver chromatin is a restricted template for the in vitro synthesis of RNA complements to repetitive DNA, but more RNA species are synthesized than are found in the RNA isolated from mouse liver nuclei. Extraction with 0.5 M NaCl destroys the template restriction of isolated chromatin. RNA synthesized in vitro from DNA or chromatin templates by Escherichia coli RNA polymerase, as well as in vivo mouse liver nuclear RNA, were each hybridized to 125I-labeled DNA of high, intermediate, or low reiteration frequency. Chromatin-primed and nuclear RNA saturate a smaller portion of each DNA fraction than does DNA-primed RNA. However, chromatin-primed RNA saturates more high ...
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 ...
Chromatin structure is influenced by multiples factors, such as pH, temperature, nature and concentration of counterions, post-translational modifications of histones and binding of structural non-histone proteins. RNA is also known to contribute to the regulation of chromatin structure as chromatin-induced gene silencing was shown to depend on the RNAi machinery in S. pombe, plants and Drosophila. Moreover, both in Drosophila and mammals, dosage compensation requires the contribution of specific non-coding RNAs. However, whether RNA itself plays a direct structural role in chromatin is not known. Here, we report results that indicate a general structural role for RNA in eukaryotic chromatin. RNA is found associated to purified chromatin prepared from chicken liver, or cultured Drosophila S2 cells, and treatment with RNase A alters the structural properties of chromatin. Our results indicate that chromatin-associated RNAs, which account for 2%-5% of total chromatin-associated nucleic acids, are polyA−
Author Summary Histones are the main protein components of chromatin. The N-terminal tails of histones stick out from the nucleosomes, the building blocks of chromatin, and are involved in the regulation of all DNA-dependent processes. Only Histone H2A has an additional C-terminal tail and currently very little is known about the function of this tail. The H2A C-terminus protrudes from the nucleosome and is located where the DNA enters and leaves the nucleosome. We show here that it can interact with the linker histone H1 that is important for higher order chromatin structure. We also find that this tail is involved in regulating nucleosome dynamics and mobility of H2A itself. The C-terminal H2A tail has also an important function in regulating the activity of chromatin remodelers, enzymes that can reposition nucleosomes. Furthermore we find that cells expressing C-terminally truncated H2A are more sensitive to stress, demonstrating that this tail is important for cellular homeostasis. Together our
The arrangement of compact chromatin of G0 lymphocytes was studied in three-dimensional reconstructions of the ensemble of the chromatin and of individual compact chromatin bodies. Rat spleen was seri
Scientists in Canada and the United States have used three-dimensional imaging techniques to settle a long-standing debate about how DNA and structural proteins are packaged into chromatin fibers. The researchers, whose findings are published in EMBO reports, reveal that the mouse genome consists of 10-nm chromatin fibers but did not find evidence for the wider 30-nm fibers that were previously thought to be important components of the DNA architecture.. "DNA is an exceptionally long molecule that can reach several meters in length. This means it needs to be packaged into a highly compact state to fit within the limited space of the cell nucleus," said David Bazett-Jones, Senior Scientist at the Hospital for Sick Children, Toronto, and Professor at the University of Toronto, Canada. "For the past few decades, scientists have favored structural models for chromatin organization where DNA is first wrapped around proteins in nucleosomes. In one possible model, the strand of repeating nucleosomes is ...
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. ...
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 ...
Transposable elements (TEs) are major structural components of eukaryotic genomes; however, mobilization of TEs generally has negative effects on the host genome. To counteract this threat, host cells have evolved genetic and epigenetic mechanisms that keep TEs silenced. One such mechanism involves the Piwi-piRNA complex, which represses TEs in animal gonads either by cleaving TE transcripts in the cytoplasm or by directing specific chromatin modifications at TE loci in the nucleus. Most Piwi-interacting RNAs (piRNAs) are derived from genomic piRNA clusters. There has been remarkable progress in our understanding of the mechanisms underlying piRNA biogenesis. However, little is known about how a specific locus in the genome is converted into a piRNA-producing site. In this review, we will discuss a possible link between chromatin boundaries and piRNA cluster formation.
Methyl-CpG-binding protein 2 (MeCP2) is generally considered to act as a transcriptional repressor, whereas recent studies suggest that MeCP2 is also involved in transcription activation. To gain insight into this dual function of MeCP2, we assessed the impact of MeCP2 on higher-order chromatin structure in living cells using mammalian cell systems harbouring a lactose operator and reporter gene-containing chromosomal domain to assess the effect of lactose repressor-tagged MeCP2 (and separate MeCP2 domains) binding in living cells. Our data reveal that targeted binding of MeCP2 elicits extensive chromatin unfolding. MeCP2-induced chromatin unfolding is triggered independently of the methyl-cytosine-binding domain. Interestingly, MeCP2 binding triggers the loss of HP1gamma at the chromosomal domain and an increased HP1gamma mobility, which is not observed for HP1alpha and HP1beta. Surprisingly, MeCP2-induced chromatin unfolding is not associated with transcriptional activation. Our study suggests ...
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 ...
The assembly of eukaryotic genomes into chromatin is a highly complex and delicate task; the cell must efficiently package and condense the DNA into the eukaryotic nucleus while maintaining specific regions of accessible chromatin to enable important functions with chromatin substrates. While the chromatin structure must remain highly dynamic in order to accommodate changes in the expression of some genes, it also serves to stably maintain the functional states of other genes through epigenetic mechanisms (45, 51). Recently, genetic and biochemical analyses have identified a broad class of multisubunit chromatin remodeling complexes which are likely to play important roles both in the process of chromatin opening and in the maintenance of chromatin in a dynamic or flexible state (26, 48, 53). These complexes remodel or reorganize nucleosomes in a wide range of in vitro assays which test for altered accessibility of nucleosomal DNA.. Nucleosome remodeling complexes are modular entities. The ...
In vivo studies of gene activation have revealed that changes in chromatin are often associated with transcriptional activation (reviewed in references 21,30, and 44). For example, in erythroid cells where each globin gene is sequentially expressed during development, the human β-globin locus is hypersensitive to nucleases (19, 22). In contrast, the entire β-globin locus is condensed into a nuclease-resistant chromatin structure in nonerythroid tissues, where the genes are not transcribed. Thus, transcriptionally active chromatin domains differ from the bulk of the genome in their susceptibility to digestion by nucleases. Detailed studies of nuclease-hypersensitive sites have suggested that interactions of sequence-specific DNA binding factors with chromatin alter the canonical nucleosomal structure (for example, see references2, 7, and 59). These conformational changes generate transcriptionally competent chromatin templates that are accessible to general transcription factors and the RNA ...
Global changes in chromatin accessibility may drive cancer progression by reprogramming transcription factor (TF) binding. In addition, histone acetylation readers such as bromodomain-containing protein 4 (BRD4) have been shown to associate with these TFs and contribute to aggressive cancers including prostate cancer (PC). Here, we show that chromatin accessibility defines castration-resistant prostate cancer (CRPC). We show that the deregulation of androgen receptor (AR) expression is a driver of chromatin relaxation and that AR/androgen-regulated bromodomain-containing proteins (BRDs) mediate this effect. We also report that BRDs are overexpressed in CRPCs and that ATAD2 and BRD2 have prognostic value. Finally, we developed gene stratification signature (BROMO-10) for bromodomain response and PC prognostication, to inform current and future trials with drugs targeting these processes. Our findings provide a compelling rational for combination therapy targeting bromodomains in selected patients in
The re-expression of fetal cardiac genes during disease requires coordinated chromatin remodeling. Local chromatin packing around the nucleosome protein complex is understood with atomic resolution; however, higher level properties of chromatin packing in the cardiovascular system are unknown. We hypothesized that nucleosome occupancy (i.e. exact positioning of nucleosomes at given loci) is a feature that regulates altered gene expression in hypertrophy. To investigate mechanisms that establish chromatin structure, genome-wide nucleosome location in heart was determined by Micrococcal Nuclease treatment followed by next-generation sequencing (MNase-Seq). A total of 137.4M Illumina reads were acquired from normal and hypertrophic myocardium, and Novoalign used to align them to the mouse genome mm9 with an average mapping percentage of 59%. Resulting occupancy profiles from normal and diseased cardiac myocytes exhibit global (i.e. chromosome scale) similarities, but local (i.e. gene/promoter ...
Nucleosomes are the core units of cellular chromatin and are comprised of 147 base pairs (bp) of DNA wrapped around an octamer of histone proteins. Proteins such as chromatin remodelers, transcription factors, and DNA repair proteins interact dynamically with chromatin to regulate access to DNA, control gene transcription, and maintain genome integrity. The extent of association with chromatin changes rapidly in response to stresses, such as immune activation, oxidative stress, or viral infection, resulting in downstream effects on chromatin conformation and transcription of target genes. To elucidate changes in the composition of proteins associated with chromatin under different conditions, we adapted existing protocols to isolate nuclei and fractionate cellular chromatin using a gradient of salt concentrations. The presence of specific proteins in different salt fractions can be assessed by Western blotting or mass spectrometry, providing insight into the degree to which they are associated with
Head: Falk Martin, RNDr., Ph.D. ([email protected]; +420-728084060). Research Keywords. Chromatin Structure & Function in physiological and pathological processes. - higher-order chromatin structure in regulation of fundamental nuclear processes like transcription, replication, differentiation, DNA repair etc.; chromatin dynamics and epigenetic modifications; histone code. - higher-order chromatin structure in development of chromosomal aberrations and carcinogenesis (currently mostly focused on):. · molecular pathogenesis of leukemia, e.g. acute promyelocytic leukemia (APL). · mechanism of recurrent chromosomal aberrations in myelodysplastic syndromes (MDS). - telomere biology. - HMG proteins. DNA damage and repair, maintenance of the genome stability- mechanisms of DNA double strand break (DSB) induction, repair, and misrepair; influence of higher-order chromatin on DSB induction and repair efficiency; DSB repair during cell cycle, development, and pathological processes; unstable repeat ...
Epigenetic regulation of gene expression is a developing field of study with many potential therapeutic applications. Chromatin remodeling is necessary for proper mammalian development, and misregulation of this process is associated with many human diseases. Three mechanisms by which chromatin structure is modified include methylation of the DNA, covalent modification of histone tails, and repositioning of nucleosomes by ATP dependant chromatin remodeling enzymes. To further increase our knowledge of the mechanisms and proteins involved in the modification of chromatin structure I undertook two projects; the role of DNA methylation in the regulation of human β-globin gene expression, and analysis of the Chd6 ATPase-/- mouse. Methylation status of the human β-globin gene promoters correlates with the expression pattern of the individual genes. However an extensive locus wide analysis of the methylation pattern in primary human tissue has not been performed. We used bisulfite sequencing to ...
ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks. ChromHMM is based on a multivariate Hidden Markov Model that explicitly models the presence or absence of each chromatin mark. The resulting model can then be used to systematically annotate a genome in one or more cell types. By automatically computing state enrichments for large-scale functional and annotation datasets ChromHMM facilitates the biological characterization of each state. ChromHMM also produces files with genome-wide maps of chromatin state annotations that can be directly visualized in a genome browser. ...
Chromatin influences Human Immunodeficiency Virus (HIV) integration and replication. This review highlights critical host factors that influence chromatin structure and organization and that also impact HIV integration, transcriptional regulation and latency. Furthermore, recent attempts to target chromatin associated factors to reduce the HIV proviral load are discussed.
A key control point in inducible gene expression involves reorganization of chromatin structure across regulatory regions of genes to allow access for the transcriptional machinery. Here we have mapped chromatin accessibility across the promoter region of the GM-CSF gene in unstimulated and stimulated EL-4 T cells and several important points have emerged. First, the entire region that was mapped from −633 to +164 showed intrinsic accessibility to both MNase and restriction enzymes. This is in stark contrast to a recent study on the IL-2 promoter in the same cell type where we showed that there is no accessibility across a large region of the IL-2 gene implying a more "closed" chromatin configuration for this gene (30). Second, two regions of the GM-CSF upstream sequence were relatively inaccessible to digestion in these assays and such regions may represent preferred nucleosome positions. The possibility that nucleosomes are preferentially located in these positions (centered on −100 and ...
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.. ...
The three-dimensional (3D) organization of the genome (chromatin) plays an important role in key cellular processes such as DNA replication, repair, transcription [1], and epigenetic inheritance [2]. Links between chromatin architecture and diseases such as cancer are being established [3]. Unlike most proteins that adopt the same unique 3D shapes in all cells, the conformational states of the chromatin fiber are not nearly as compact or ordered and are stochastic to some degree. Remarkably, several features of chromatin folding appear to be universal. Chromosomal territories, in which each chromosome occupies a distinct region of the nucleus, have been observed in numerous organisms and cell types, such as yeast [4], human [5], D. melanogaster (fruit fly) [6-8], mouse [9], and Arabidopsis [10]. Chromosome interactions, both within (intra) chromosomes and between (inter) chromosomes, have been observed microscopically [6, 8] and inferred using cross-linking techniques [11] such as the Hi-C ...
The alternative ATPase subunits of SWI/SNF-like BAF chromatin remodeling complex (ISWI) SWI2 subunit SNF2L (SMARCA1) locus: Xq26.1: [§§]. Mammalian genomes encode two imitation switch (ISWI) gene family chromatin remodeling proteins, SNF2H and SNF2L with a critical role in neurulation, CECR2 is involved in neurulation, SNF2L is required for StAR expression and the developmental context. Connections to its transition and post-mitotic neuron differentiation of the nervous system, Geminin controls, is expressed predominantly in the central nervous system. SNF2L expression suggests a role in neuronal physiology. SNF2L naturally occurring human SNF2L variant inactivates chromatin remodeling. Wild type active SNF2L isoform is expressed in neurons to different features of (chromatinized DNA) nucleosome structure a very basic and ubiquitous form of nucleic acid management, histone acetylation, although it occurs, is dispensable for TFIID and SWI/SNF recruitment, in the context of DNA repair. ...
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 ...
How temporal cues combine with spatial inputs to control gene expression during development is poorly understood. Here, we test the hypothesis that the Drosophila transcription factor E93 controls temporal gene expression by regulating chromatin accessibility. Precocious expression of E93 early in wing development reveals that it can simultaneously activate and deactivate different target enhancers. Notably, the precocious patterns of enhancer activity resemble the wild-type patterns that occur later in development, suggesting that expression of E93 alters the competence of enhancers to respond to spatial cues. Genomic profiling reveals that precocious E93 expression is sufficient to regulate chromatin accessibility at a subset of its targets. These accessibility changes mimic those that normally occur later in development, indicating that precocious E93 accelerates the wild-type developmental program. Further, we find that target enhancers that do not respond to precocious E93 in early wings ...
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 ...
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 ...
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
TY - JOUR. T1 - ChAsE. T2 - Chromatin analysis and exploration tool. AU - Younesy, Hamid. AU - Nielsen, Cydney B.. AU - Lorincz, Matthew C.. AU - Jones, Steven J M. AU - Karimi, Mohammad M.. AU - Möller, Torsten. PY - 2016/11/1. Y1 - 2016/11/1. N2 - Summary: We present ChAsE, a cross-platform desktop application developed for interactive visualization, exploration and clustering of epigenomic data such as ChIP-seq experiments. ChAsE is designed and developed in close collaboration with several groups of biologists and bioinformaticians with a focus on usability and interactivity. Data can be analyzed through k-means clustering, specifying presence or absence of signal in epigenetic data and performing set operations between clusters. Results can be explored in an interactive heat map and profile plot interface and exported for downstream analysis or as high quality figures suitable for publications.. AB - Summary: We present ChAsE, a cross-platform desktop application developed for interactive ...
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 ...
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, ...
Rationale: Myocardial infarction (MI) leads to necrosis of multinucleated and polyploid myocytes. This causes uncontrolled release of cellular content like chromatin to the infarct area. Chromatin is mainly comprised of histones which are essential for controlling and packing of DNA but paradoxically are also known to be cytotoxic. This makes free chromatin a toxic DNA polymer creating local high concentrations of hazardous histones.. Objective: We hypothesized that chromatin from necrotic cells accumulates in ischemic myocardium, creates local high concentrations of cytotoxic histones, and thereby potentiates ischemic damage to the heart after MI. The endonuclease DNase1 is capable of dispersing extracellular chromatin through linker DNA digestion and could decrease local histone concentrations and cytotoxicity.. Methods and Results: After permanent coronary artery ligation in mice we found extracellular histones accumulated within the infarcted myocardium. Histone cytotoxicity towards isolated ...
Posttranslational modifications of histones, ATP-dependent chromatin remodeling, and incorporation of histone variants are three major events to regulate DNA dependent processes in chromatin context.; Histones are the major protein components within chromatin, and epigenetic modifications of these proteins play a vital role in transcription. Acetylation and methylation of core histones are two major modifications, which are introduced by histone acetyltransferases (HATs) and histone methyltransferases (HMTs). Albeit the mechanism of action has not been identified, it has been proposed that these two modifications regulate gene transcription through facilitating recruitment of regulatory factors to the target genes. As a first step to investigate recruitment-based contribution of histone tails and their modifications in transcription, I have generated HeLa cell lines that stably express H3 tails for the biochemical purification of H3 tail-associated complex. The purified complex contains multiple ...
Because neither E2F1 overexpression nor derepression with the addition of TSA alone was able to induce Apaf-1 up-regulation in mature neurons (Figs. 4 c and 5 a), we hypothesized that this region of chromatin may be highly repressed in mature neurons. Indeed, expression of E2F1 in the presence of TSA induced a marked transcriptional increase in Apaf-1 (Fig. 5 c) and rendered mature P28 neurons sensitive to cytochrome c (Fig. 5 d). This sensitivity of P28 neurons was dependent on the up-regulation of Apaf-1, as neurons isolated from Apaf-1-deficient mice failed to undergo cytochrome c-induced apoptosis after TSA and E2F1 treatment (Fig. 5 e). These data support the model that neuronal maturation is accompanied by increased repression of Apaf-1 at the level of chromatin structure.. We tested this model directly with a chromatin immunoprecipitation (ChIP) assay using antibodies to acetylated histone 3 (AcH3), which is indicative of active chromatin, and histone 3 trimethylated on lysine 9 (MeH3K9), ...
BACKGROUND: Cell types are defined at the molecular level during embryogenesis by a process called pattern formation and created by the selective utilization of combinations of sequence-specific transcription factors. Developmental programs define the sets of genes that are available to each particular cell type, and real-time biochemical signaling interactions define the extent to which these sets are used at any given time and place. Gene expression is regulated through the integrated action of many cis-regulatory elements, including core promoters, enhancers, silencers, and insulators. The chromatin state in developing body parts provides a code to cellular populations that directs their cell fates. Chromatin profiling has been a method of choice for mapping regulatory sequences in cells that go through developmental transitions. RESULTS: We used antibodies against histone H3 lysine 4 trimethylations, a modification associated with promoters and open/active chromatin, histone H3 lysine 27 ...
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.. ...
Histone methylation changes and formation of chromatin loops involving enhancers, promoters and 3 end regions of genes have been variously associated with active transcription in eukaryotes. It is not known if these events are mechanistically linked and their specific role in transcription initiation. We have studied the effect of activation of the Retinoic A receptor, at the RARE-promoter chromatin of CASP9 and CYP26A1 genes, at 15 and 45 min following RA exposure, and we found that histone H3 lysine 4 and 9 are demethylated by the lysinespecific demethylase, LSD1 and by the JMJ-domain containing demethylase, D2A. The action of the oxidase (LSD1) and a dioxygenase (JMJD2A) in the presence of Fe++ elicits an oxidation wave that locally modifies the DNA locally and recruits the enzymes involved in base and nucleotide excision repair (BER and NER). These events are essential for the formation of chromatin loop(s) that juxtapose the RARE element with the 5 transcription start site and the 3 end ...
Molecular model of a chromatin fiber. This fiber has a length of 30 nm and would use 20.000 base pairs of DNA. The centre is helically arranged and consists of 100 nucleosomes. Chromatin is a complex of macromolecules found in cells, consisting of DNA, protein and RNA. The primary functions of chromatin is to package DNA into a smaller volume to fit in the cell, to reinforce the DNA macromolecule to allow mitosis, to prevent DNA damage and control gene expression and DNA replication. Chromatin is only found in eukaryotic cells. - Stock Image C026/8539
Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus.s profile, publications, research topics, and co-authors
TY - JOUR. T1 - Distribution of menin-occupied regions in chromatin specifies a broad role of menin in transcriptional regulation. AU - Agarwal, Sunita K.. AU - Impey, Soren. AU - McWeeney, Shannon. AU - Scacheri, Peter C.. AU - Collins, Francis S.. AU - Goodman, Richard H.. AU - Spiegel, Allen M.. AU - Marx, Stephen J.. PY - 2007/2. Y1 - 2007/2. N2 - Menin is the protein product of the MEN1 tumor-suppressor gene; one allele of MEN1 is inactivated in the germ line of patients with "multiple endocrine neoplasia type 1" (MEN1) cancer syndrome. Menin interacts with several proteins involved in transcriptional regulation. RNA expression analyses have identified several menin-regulated genes that could represent proximal or distal interaction sites for menin. This report presents a substantial and unbiased sampling of menin-occupied chromatin regions using Serial Analysis of Chromatin Occupancy; this method combines chromatin immunoprecipitation with Serial Analysis of Gene Expression. Hundreds of ...
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 ...
Chromatin immuno‐precipitation followed by sequencing (ChIP‐Seq) has provided major insights into the molecular mechanisms underlying chromatin dynamics and transcription regulation. In this study, we present Bar‐ChIP, a method derived from ChIP‐Seq that drastically accelerates its current experimental throughput without the need for robotics instrumentation. We compared the quality and precision of the data obtained using Bar‐ChIP with those generated with traditional ChIP‐Seq and assessed the multiplexing potential of the approach. Bar‐ChIP led to several findings that shed light on the interplay between H3K14 acetylation and H3K4 methylation, which we further investigated. Results of these additional studies are also reported here.. Bar‐ChIP relies on direct molecular barcoding of fragmented chromatin prior to immuno‐precipitation, an approach, which, as we demonstrated, does not impact the nucleosomal distribution obtained after chromatin fragmentation. Furthermore, this ...
DNA-protein interactions in mature brain are increasingly recognized as key regulators for behavioral plasticity and neuronal dysfunction in chronic neuropsychiatric disease. However, chromatin assays typically lack single cell resolution, and therefore little is known about chromatin regulation of differentiated neuronal nuclei that reside in brain parenchyma intermingled with various types of non-neuronal cells. Here, we describe a protocol to selectively tag neuronal nuclei from adult brain - either by (anti-NeuN) immunolabeling or transgene-derived histone H2B-GFP fusion protein - for subsequent fluorescence-activated sorting and chromatin immunoprecipitation (ChIP). To illustrate an example, we compared histone H3 lysine 4 and 9 methylation marks at select gene promoters in neuronal, non-neuronal and unsorted chromatin from mouse forebrain and human cerebral cortex, and provide evidence for neuron-specific histone methylation signatures. With the modifications detailed in this protocol, the method
Deciphering the impact of genetic variants on gene regulation is fundamental to understanding human disease. Although gene regulation often involves long-range interactions, it is unknown to what extent non-coding genetic variants influence distal molecular phenotypes. Here, we integrate chromatin profiling for three histone marks in lymphoblastoid cell lines (LCLs) from 75 sequenced individuals with LCL-specific Hi-C and ChIA-PET-based chromatin contact maps to uncover one of the largest collections of local and distal histone quantitative trait loci (hQTLs). Distal QTLs are enriched within topologically associated domains and exhibit largely concordant variation of chromatin state coordinated by proximal and distal non-coding genetic variants. Histone QTLs are enriched for common variants associated with autoimmune diseases and enable identification of putative target genes of disease-associated variants from genome-wide association studies. These analyses provide insights into how genetic ...
BACKGROUND: The CCTC-binding factor (CTCF) protein is involved in genome organization, including mediating three-dimensional chromatin interactions. Human patient lymphocytes with mutations in a single copy of the CTCF gene have reduced expression of enhancer-associated genes involved in response to stimuli. We hypothesize that CTCF interactions stabilize enhancer-promoter chromatin interaction domains, facilitating increased expression of genes in response to stimuli. Here we systematically investigate this model using computational analyses. RESULTS: We use CTCF ChIA-PET data from the ENCODE project to show that CTCF-associated chromatin loops have a tendency to enclose regions of enhancer-regulated stimulus responsive genes, insulating them from neighboring regions of constitutively expressed housekeeping genes. To facilitate cell type-specific CTCF loop identification, we develop an algorithm to predict CTCF loops from ChIP-seq data alone by exploiting the CTCF motif directionality in loop ...
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.
This message is to announce the creation of a new WWW resource deidicated to spreading information regarding the study of chromatin structure, with emphasis on the proteins that modify chromatin structure, and the effects that these modifications have on cell function. Please view this site frequently, because the field is evolving rapidly, and so the website is updated quite often. If you have any suggestions or announcements that you wish posted (Job openings, meetings, etc) my email address is included as part of the page, so feel free to contact me. Thanks, Jim bone Chromatin Structure and Function Page http://rampages.onramp.net/~jrbone/chrom.html ----------------------------------------------------------------------------- James R. Bone Dept. of Biochemistry and Molecular Biology M. D. Anderson Cancer Center, Box 117 1515 Holcombe Avenue Houston, TX 77030 email:jrbone at odin.mdacc.tmc.edu :jrbone at onramp.net voice: 713-792-2549 Roth Lab Homepage-- ...
We present a method to assist in interpretation of the functional impact of intergenic disease-associated SNPs that is not limited to search strategies proximal to the SNP. The method builds on two sources of external knowledge: the growing understanding of three-dimensional spatial relationships in the genome, and the substantial repository of information about relationships among genetic variants, genes, and diseases captured in the published biomedical literature. We integrate chromatin conformation capture data (HiC) with literature support to rank putative target genes of intergenic disease-associated SNPs. We demonstrate that this hybrid method outperforms a genomic distance baseline on a small test set of expression quantitative trait loci, as well as either method individually. In addition, we show the potential for this method to uncover relationships between intergenic SNPs and target genes across chromosomes. With more extensive chromatin conformation capture data becoming readily available,
ARID1A, a subunit of the SWI/SNF chromatin remodeling complex, and its homolog ARID1B function to maintain chromatin accessibility and active histone modifications at enhancers.
TY - JOUR. T1 - Functional coupling between HIV-1 integrase and the SWI/SNF chromatin remodeling complex for efficient in vitro integration into stable nucleosomes. AU - Lesbats, Paul. AU - Botbol, Yair M.. AU - Chevereau, Guillaume. AU - Vaillant, Cédric. AU - Calmels, Christina. AU - Arneodo, Alain. AU - Andreola, Marie Line. AU - Lavigne, Marc. AU - Parissi, Vincent. PY - 2011/2. Y1 - 2011/2. N2 - Establishment of stable HIV-1 infection requires the efficient integration of the retroviral genome into the host DNA. The molecular mechanism underlying the control of this process by the chromatin structure has not yet been elucidated. We show here that stably associated nucleosomes strongly inhibit in vitro two viral-end integration by decreasing the accessibility of DNA to integrase. Remodeling of the chromatinized template by the SWI/SNF complex, whose INI1 major component interacts with IN, restores and redirects the full-site integration into the stable nucleosome region. These effects are ...
We develop a statistical framework to study the relationship between chromatin features and gene expression. This can be used to predict gene expression of protein coding genes, as well as microRNAs....
We present depth-resolved spatial-domain low-coherence quantitative phase microscopy, a simple approach that utilizes coherence gating to construct a depth-resolved structural feature vector quantifying sub-resolution axial structural changes at different optical depths within the sample. We show that this feature vector is independent of sample thickness variation, and identifies nanoscale structural changes in clinically prepared samples. We present numerical simulations and experimental validation to demonstrate the feasibility of the approach. We also perform experiments using unstained cells to investigate the nanoscale structural changes in regulated cell proliferation through cell cycle and chromatin decondensation induced by histone acetylation. (C) 2013 Optical Society of ...
This Teaching Resource provides lecture notes and slides for a class covering chromatin remodeling mechanisms and is part of the course Cell Signaling Systems: a Course for Graduate Students. The lecture begins with a discussion of chromatin organization and then proceeds to describe the process of chromatin remodeling through a review of chromatin remodeling complexes and methods used to study their function.
Nonhistone proteins provide a structural scaffold for long chromatin loops. Although histones are the predominant proteins in chromosomes, nonhistone proteins are also involved in organizing chromosome structure. Electron micrographs of histone-depleted metaphase chromosomes from HeLa cells reveal long loops of DNA anchored to a chromosome scaffold composed of nonhistone proteins. This scaffold is shaped like the metaphase chromosome and persists evn when DNA is digested by nucleases. Loops of 30-nm chromatin fiber a few megabases long associate with a flexible chromsome scaffold, yielding an extended form characteristic of chromosomes during interphase. Folding of scaffold produces highly condensed structure characteristic of metaphase chromosomes. But the geometry of scaffold folding in metaphase chromosomes has not yet been determined.. In situ hybridization with different fluorescent-labeled probes to DNA in human interphase cells support loop model shown. Some probe sequences mllion of base ...
Chromatin structures are regulated by various mechanisms including histone modification and chromatin remodeling, which involve the binding of transcription factors. By using tools such as chromatin immunoprecipitation , it...
Saccharomyces cerevisia (Sir2) is an NAD+-dependent histone deacetylase. Its role within the cell is to link chromatin silencing to genomic stability, cellular metabolism, and lifespan regulation. For example, in mice, if there is a deficiency for SIRT6 (family member of Sir2), the mice experience genomic instability, metabolic defects, and degenerative pathologies in terms of aging, everything opposite of the roles of Sir2. With new insights to the previously ambiguous SIRT6, scientists have discovered that SIRT6 is a very substrate-specific histone deacetylase that promotes proper chromatin function in things like telomere stabilization and DNA repair. ...
Treatment of quiescent cultures of mouse embryo fibroblasts with 20% fetal calf serum (FCS) or cycloheximide (CH) resulted in the induction of a nuclear protein of molecular weight 29 000 daltons. The 29 Kd protein induced by these two agents was found to be tightly bound to the chromatin since it was not released from the chromatin by a combination of 2.5 M NaCl and 3.2 M urea. The chromatin associated CH-induced 29 Kd protein and the 29 Kd protein obtained from serum-induced cells displayed similar N-chlorosuccinimide cleavage patterns. Pulse-chase experiments indicate a half-life of an hour for the 29 Kd protein. The kinetics of induction of the 29 Kd protein in the early hours of mitogen addition, short half-life, nuclear localisation and strong association with chromatin suggest that this protein may have important roles in cell proliferation, possibly as a mediator of mitogen action. ...
Folding of mammalian genomes into spatial domains is critical for gene regulation. CTCF and cohesin control domain location by folding domains into loop structures, which are thought to be highly stable. Combining genomic, biochemical and single-molecule imaging approaches, we show that although CTCF and cohesin can physically interact, CTCF binds chromatin much more dynamically than cohesin (~1 min vs. ~22 min residence time). Moreover, after unbinding, CTCF quickly rebinds another cognate site unlike cohesin (~1 min vs. ~33 min). Thus, CTCF and cohesin form a rapidly exchanging dynamic complex rather than a typical stable complex. Since CTCF and cohesin are required for loop domain formation, our results suggest that chromatin loops constantly break and reform throughout the cell cycle ...
Epigenetic modifications play an important role in chromatin organization and gene expression. Perturbation of this process often leads to cancer. My lab is interested in understanding the epigenetic mechanism that underlies the controls of the enhancer and promoter interaction during transcriptional activation. We are currently focusing on examining the epigenetic mechanisms by which the chromatin insulator binding factor USF1 maintains a local environment of active chromatin, both by biochemical and functional analysis of the USF1 associated histone modifying enzyme complexes. We are also studying the effects of these complexes on histone modification patterns, local and long-range chromatin structure, and transcriptional regulation.. Another project that my lab is focusing on is the transcriptional regulation of TAL1/SCL, which plays a critical role in normal and malignant hematopoiesis. Activation of TAL1 is the most frequent gain-of-function mutation occurring in T-cell lymphoblastic ...
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 ...
The identification of direct nuclear hormone receptor gene targets provides clues to their contribution to both development and cancer progression. Until recently, the identification of such direct target genes has relied on a combination of expression analysis and in silico searches for consensus binding motifs in gene promoters. Consensus binding motifs for transcription factors are often defined using in vitro DNA binding strategies. Such in vitro strategies fail to account for the many factors that contribute significantly to target selection by transcription factors in cells beyond the recognition of these short consensus DNA sequences. These factors include DNA methylation, chromatin structure, posttranslational modifications of transcription factors, and the cooperative recruitment of transcription factor complexes. Chromatin immunoprecipitation (ChIP) provides a means of isolating transcription factor complexes in the context of endogenous chromatin, allowing the identification of direct
The EMBL Transcription and Chromatin meeting has a long-standing tradition in shaping the field of transcriptional regulation. The meeting brings together leading experts covering all aspects of transcription from cis-regulatory function, long range regulation, 3-dimensional looping, the basal transcriptional machinery, RNA polymerase regulation and function, nucleosome positioning, chromatin modifications, chromatin remodelling, and epigenetic inheritance of transcriptional silencing.
The EMBL Transcription and Chromatin meeting has a long-standing tradition in shaping the field of transcriptional regulation. The meeting brings together leading experts covering all aspects of transcription from cis-regulatory function, long range regulation, 3-dimensional looping, the basal transcriptional machinery, RNA polymerase regulation and function, nucleosome positioning, chromatin modifications, chromatin remodelling, and epigenetic inheritance of transcriptional silencing.
Chromatin barriers restrict silenced chromatin domains from invading active domains. A recent study shows that a tRNA gene functions as a barrier in Schizosaccharomyces pombe. These results, similar to previous observations in Saccharomyces cerevisiae, point toward a novel function for tRNA genes and a common mechanism of compartmentalizing and organizing eukaryotic chromatin.
The precise mechanisms by which coactivators function to regulate transcription remain unclear. Coactivators have a structural role in serving as focal points for multiple protein-protein interactions including association with many transcriptional activation domains (Verrijzer and Tjian, 1996; Shikama et al., 1997; Xu et al., 1999). These interactions might help recruit components of the basal transcriptional machinery including RNA polymerase to a particular promoter (Barlev et al., 1995; Nakajima et al., 1997a, b). Coactivators can also function as enzymes that modify both other transcriptional regulators and the chromatin environment within which transcription occurs (Brownell and Allis, 1996; Gregory and Horz, 1998). The exact significance of these diverse roles is a topic of substantial research interest.. Among the best studied systems for the analysis of coactivator function is the GCN5p-ADA2p-ADA3p complex (Berger et al., 1992; Candau and Berger, 1996; Candau et al., 1997; Grant et al., ...
My labs work has been at the forefront of studies showing that nuclear organization and long-range chromatin interactions play an essential role in recombinati...
Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002 Feb 15;295(5558):1306-11. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 Oct;16(10):1299-309. Fullwood MJ, Han Y, Wei CL, Ruan X, Ruan Y. Chromatin interaction analysis using paired-end tag sequencing. Curr Protoc Mol Biol. 2010 Jan;Chapter 21:Unit 21.15.1-25. Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 2010;11(2):R22. ...
The spatial organization of the genome is intimately linked to its biological function, yet our understanding of higher order genomic structure is coarse, fragmented and incomplete. In the nucleus of eukaryotic cells, interphase chromosomes occupy distinct chromosome territories, and numerous models have been proposed for how chromosomes fold within chromosome territories. These models, however, provide only few mechanistic details about the relationship between higher order chromatin structure and genome function. Recent advances in genomic technologies have led to rapid advances in the study of three-dimensional genome organization. In particular, Hi-C has been introduced as a method for identifying higher order chromatin interactions genome wide. Here we investigate the three-dimensional organization of the human and mouse genomes in embryonic stem cells and terminally differentiated cell types at unprecedented resolution. We identify large, megabase-sized local chromatin interaction domains, ...
This means that in the one-start model each nucleosome is connected to the one adjacent to it, and this is a continuous cycle. Meaning that it is more like a phone chord.. The Zig-Zag model instead proposes that each nucleosome is connected to the nucleosome approximately opposite to it (parallel), and is a pattern that is continuous through out the chromatin fiber. This is more complicated to understand but imagine it being more like lacing on a shoe.It goes from a hole on one side to a hole on the other side parallel to it but not in the same plane as itself.. To move to the third nucleosome (and pack as tightly as possible) instead of it being directly below the 1st one it is slightly off to the side and not exactly parallel to the 2nd nucleosome. However the 4rth nucleosome will be exactly parallel to the 3rd, and thus the same amount of degrees off-center from the 2nd nucleosome as the 3rd nucleosome is to the 1st, maintaining the pattern. This forms a more 3-D tubular strucuture than an ...
Purpose: Transcriptional regulation of estrogen receptor- (ER) involves both epigenetic mechanisms and trans-active factors, such as TFAP2C, which induces ER transcription through an AP-2 regulatory region in the ER promoter. Attempts to induce endogenous ER expression in ER-negative breast carcinomas by forced overexpression of TFAP2C have not been successful. We hypothesize that epigenetic chromatin structure alters the activity of TFAP2C at the ER promoter.. Experimental Design: DNA methylation, histone acetylation, and chromatin accessibility were examined at the ER promoter in a panel of breast carcinoma cell lines. TFAP2C and polymerase II binding were analyzed by chromatin immunoprecipitation. Epigenetic chromatin structure was altered using drug treatment with 5-aza-2-deoxycytidine (AZA) and trichostatin A (TSA).. Results: The ER promoter in the ER-negative lines MDA-MB-231, MCF10A, and MCF7-5C show CpG island methylation, histone 3 lysine 9 deacetylation, and decreased chromatin ...
During latent infections with herpes simplex virus 1 (HSV-1), viral transcription is restricted and the genomes are mostly maintained in silenced chromatin, whereas in lytically infected cells all viral genes are transcribed and the genomes are dynamically chromatinized. Histones in the viral chroma …
James mammoth study (Prendergast et al, 2012) of human chromatin variation is published; it involved remapping 1.3 billion sequencing reads. He shows that it is possible to find variable sites in the human genome (SNPs) where the different variants (alleles) present carry different chromatin structures. These sites seem to be surprisingly rare in embryonic stem…
Stuffing the long strands of chromosomal DNA into a eukaryotic nucleus requires that the DNA be compacted in length approximately 10,000 to 50,000 -fold. Incredibly, cells achieve this tight packing of the DNA while still maintaining the chromosomes in a form that allows regulatory proteins to gain access to the DNA to turn on (or off) specific genes or to duplicate the chromosomal DNA (replication). This engineering feat is accomplished by a variety of chromatin proteins, the most abundant of which are the histones. Histones associate with DNA to accomplish the first step in chromatin assembly, forming protein-DNA structures known as nucleosomes. When viewed under the electron microscope, nucleosomes are beads of ~10 nm in diameter that are distributed along the ~2 nm DNA string (Kornberg, 1974; Olins and Olins, 1974) about once every 200 bp. Each bead is a nucleosome core particle (install the plug-in to view this link) that includes ~146 bp of DNA wrapped almost twice around a core histone ...
The epigenetic framework guides events like replication, repair and transcription, which in turn themselves leave an imprint on chromatin and chromosomal structure. Understanding how modulation of chromatin during replication and repair influence cell fate decisions in normal development and disease represents a major challenge. By bringing together leading scientists in chromatin, replication, repair and epigenetics, this conference aims to inspire discussions and new ideas on the interplay between chromosome architecture, epigenetic inheritance and genome duplication ...
EZ-Magna ChIP™ HiSens Chromatin Immunoprecipitation Kit Single day chromatin immunoprecipitation (ChIP) kit containing all necessary reagents to enable ChIP from low input amounts of chromatin obtained from either cells or tissues using magnetic A/G beads. Control primers included. - Find MSDS or SDS, a COA, data sheets and more information.
During spermatogenesis, germ cells undergo a long process of differentiation to form spermatozoa, highly cyto-differentiated cells constituted of a head containing the nucleus, the paternal genetic material transmitted at fertilization, and a flagellum allowing them to move up the female genital tract to encounter the female gamete, the oocyte. The passage from a spermatogonia, a diploid cell, to four haploid cells called spermatids, results from meiosis. As for mitosis, this process requires chromatin modifications in multiple steps in order to separate homologous chromosomes and chromatids in identical sister cells. This remodeling of chromatin during meiosis is permitted by histone PTM and by insertion of ubiquitous and/or testis-specific histone variants in multiple steps including chromatid condensation, repair of the numerous DNA single strand breaks (SSB) needed for homologous chromosome pairing, sex (or XY) body formation, massive activation of transcription during the pachytene stage, ...
TY - JOUR. T1 - Effects of chromatin structure on the enzymatic and DNA binding functions of DNA methyltransferases DNMT1 and Dnmt3a in vitro. AU - Robertson, Andrea K.. AU - Geiman, Theresa M.. AU - Sankpal, Umesh Tanaji. AU - Hager, Gordon L.. AU - Robertson, Keith D.. PY - 2004/9/10. Y1 - 2004/9/10. N2 - DNA methylation is an epigenetic modification of the genome critical for numerous processes, including transcriptional repression and maintenance of chromatin structure. Recent studies have revealed connections between DNA methylation and other epigenetic modifications such as ATP-dependent chromatin remodeling. It remains unclear, however, exactly how chromatin and epigenetic chromatin modifications affect the biological properties of the DNA methyltransferases (DNMT1, DNMT3A, and DNMT3B). Using a highly purified system and the 5S rDNA gene as free DNA or assembled into a mononucleosome, we have compared the effects of chromatin structure on DNMT1 and Dnmt3a. The catalytic efficiency for ...
article{7cc3097b-22b4-448a-9bce-4c18189ec61f, abstract = {BACKGROUND: The sperm chromatin structure assay (SCSA) provides an objective assessment of sperm chromatin integrity, which is essential for normal sperm function. SCSA is valuable as a fertility marker in epidemiological studies and in the clinical situation. Little is known about the impact of testicular and post-testicular function on SCSA parameters. METHODS: Ejaculates from 278 military conscripts of median age 18.1 (range 18-21) years were included. Levels of reproductive hormones, the length of the CAG repeat of the androgen receptor gene, sperm concentration, abstinence period and biochemical parameters of epididymal and accessory sex gland secretions were correlated to the SCSA parameters, DNA fragmentation index (DFI) and highly DNA stainable (HDS) cells. RESULTS: Negative correlations were found between sperm concentration and DFI (r = -0.119, P = 0.049) and HDS (r = -0.513, P < 0.0001). DFI was negatively correlated with ...
TY - JOUR. T1 - Binding of isomers of benzo[a]pyrene diol-epoxide to chromatin. AU - Kootstra, A.. AU - Slaga, T. J.. PY - 1980/4/14. Y1 - 1980/4/14. N2 - Both the carcinogenic B[a]P diol-epoxide (anti) and its relatively noncarcinogenic isomer, B[a]P diol-epoxide (syn), when reacted with chromatin in vitro, bind more extensively to the internucleosomal region of chromatin than to nucleosomes. These results suggest that the increased binding of B[a]P diol-epoxide (anti) to the internucleosomal region may have little relevance to the process of carcinogenesis.. AB - Both the carcinogenic B[a]P diol-epoxide (anti) and its relatively noncarcinogenic isomer, B[a]P diol-epoxide (syn), when reacted with chromatin in vitro, bind more extensively to the internucleosomal region of chromatin than to nucleosomes. These results suggest that the increased binding of B[a]P diol-epoxide (anti) to the internucleosomal region may have little relevance to the process of carcinogenesis.. UR - ...
RATIONALE: Regulatory DNA elements in the human genome play important roles in determining the transcriptional abundance and spatiotemporal gene expression during embryonic heart development and somatic cell reprogramming. It is not well known how chromatin marks in regulatory DNA elements are modulated to establish cell type-specific gene expression in the human heart. OBJECTIVE: We aimed to decipher the cell type-specific epigenetic signatures in regulatory DNA elements and how they modulate heart-specific gene expression. METHODS AND RESULTS: We profiled genome-wide transcriptional activity and a variety of epigenetic marks in the regulatory DNA elements using massive RNA-seq (n=12) and ChIP-seq (chromatin immunoprecipitation combined with high-throughput sequencing; n=84) in human endothelial cells (CD31(+)CD144(+)), cardiac progenitor cells (Sca-1(+)), fibroblasts (DDR2(+)), and their respective induced pluripotent stem cells. We uncovered 2 classes of regulatory DNA elements: class I was ...
TY - JOUR. T1 - The heat shock response in xenopus oocytes, embryos, and somatic cells. T2 - A regulatory role for chromatin. AU - Landsberger, N.. AU - Ranjan, M.. AU - Almouzni, G.. AU - Stump, D.. AU - Wolffe, A. P.. PY - 1995. Y1 - 1995. N2 - The heat shock response in Xenopus laevis has been reported to be developmentally regulated at the transcriptional level. We find that the heat shock response of an exogenous Xenopus hsp70 gene introduced into Xenopus oocytes, embryos, and somatic cells is dependent on the transcriptional assay conditions employed. Under conditions of efficient chromatin assembly, transcription from the Xenopus hsp70 gene promoter is repressed in oocytes and embryos, yet the promoter responds to heat shock by activating transcription. Under conditions of inefficient chromatin assembly, the Xenopus hsp70 gene is constitutively active in oocytes and somatic cells. Our results resolve previous controversy concerning the existence of a heat shock response for the hsp70 ...
MT wanted the download A histone H3K36 with marker from DPW and JYJ. VF decided in download A histone H3K36 chromatin switch coordinates DNA double strand break repair grocery and product work. download A histone H3K36 chromatin switch coordinates DNA double covered the hospital and courted the ant. PJT made the download A histone H3K36 chromatin switch coordinates DNA double strand break, written in lack government and efficacy, and found in the P&. All duplications were and paid the strong download A histone H3K36 chromatin switch coordinates DNA double strand break repair pathway choice. ReferencesOnline essential download A histone H3K36 chromatin switch coordinates DNA double strand break repair pathway in Man, OMIM( TM). McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University( Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine( Bethesda, MD), September 7, 2010. Stenson PD, Mort M, Ball EV, Howells K, Phillips AD, Thomas NS, ...
Members of the HMGN protein family modulate chromatin structure and influence epigenetic modifications. HMGN1 and HMGN2 are highly expressed during early development and in the neural stem/progenitor cells of the developing and adult brain. Here, we investigate whether HMGN proteins contribute to the chromatin plasticity and epigenetic regulation that is essential for maintaining pluripotency in stem cells. We show that loss of Hmgn1 or Hmgn2 in pluripotent embryonal carcinoma cells leads to increased levels of spontaneous neuronal differentiation. This is accompanied by the loss of pluripotency markers Nanog and Ssea1, and increased expression of the pro-neural transcription factors Neurog1 and Ascl1. Neural stem cells derived from these Hmgn-knockout lines also show increased spontaneous neuronal differentiation and Neurog1 expression. The loss of HMGN2 leads to a global reduction in H3K9 acetylation, and disrupts the profile of H3K4me3, H3K9ac, H3K27ac and H3K122ac at the Nanog and Oct4 loci. At
The essential histone H3 variant Cse4 plays a crucial role at the centromere in S. cerevisiae, where it replaces histone H3 in that it assembles centromere specific (Cse4-H4)2 tetrameres. We found in our study that the histone H3 variant was able to interact over its unique N-Terminus with two subunits of the histone acetyltransferase complex SAS-I: Sas2 and Sas4. Mutations within the acetyl-CoA binding site (HAT domain) or the zink-finger of Sas2 disrupted the binding to Cse4, although an indirect interaction was found with co-immunoprecipitation experiments. Additionally, the N-terminus of Cse4 interacted with Cac1, the largest subunit of the chromatin assembly factor CAF-I and Asf1 - two histone chaperones that assemble histones H3 and H4 into nucleosomes. Our findings further suggest a role of Cac1 independent of Cac2 and Cac3 as no binding to Cse4 could be detected. A role for Sas2 at the centromere was further confirmed in that a sas2 deletion (sas2 delta) disrupted the binding of Cse4 to ...
Divergence of transcription factor binding sites is considered to be an important source of regulatory evolution. The associations between transcription factor binding sites and phenotypic diversity have been investigated in many model organisms. However, the understanding of other factors that contribute to it is still limited. Recent studies have elucidated the effect of chromatin structure on molecular evolution of genomic DNA. Though the profound impact of nucleosome positions on gene regulation has been reported, their influence on transcriptional evolution is still less explored. With the availability of genome-wide nucleosome map in yeast species, it is thus desirable to investigate their impact on transcription factor binding site evolution. Here, we present a comprehensive analysis of the role of nucleosome positioning in the evolution of transcription factor binding sites. We compared the transcription factor binding site frequency in nucleosome occupied regions and nucleosome depleted regions

Barr Body (Sex Chromatin in Somatic Cells) | Medicalalgorithms.comBarr Body (Sex Chromatin in Somatic Cells) | Medicalalgorithms.com

Barr and Bertram described a small body in the nuclei of normal females composed of DNA. This was subsequently shown to be an inactivated X chromosome. While largely supplanted by more sophisticated genetic tests, it occasionally may be done as a rapid screen.
more infohttps://www.medicalalgorithms.com/barr-body-sex-chromatin-in-somatic-cells

Download A Histone H3K36 Chromatin Switch Coordinates Dna Double Strand Break Repair Pathway Choice 2014Download A Histone H3K36 Chromatin Switch Coordinates Dna Double Strand Break Repair Pathway Choice 2014

History download A histone H3K36 chromatin of rituals on our Few majority. in download A histone H3K36 chromatin switch ... Home Bell is highly do this download A histone H3K36 chromatin switch coordinates DNA double Other optimization. Jesus in this ... has to be a low download A histone H3K36 chromatin switch coordinates of Christian from another faith of Christian. For this ... However so as it is, in iterative download A histone H3K36 chromatin switch coordinates DNA double strand break repair pathway ...
more infohttp://bobcatsworld.com/library/download-A-histone-H3K36-chromatin-switch-coordinates-DNA-double-strand-break-repair-pathway-choice-2014.php

ChromatinChromatin

... everything you need for studying or teaching Chromatin. ... Immediately download the Chromatin summary, chapter-by-chapter ... Chromatin Chromatin is a network of deoxyribonucleic acid (DNA) and nucleoproteins that constitutes a chromosome. Chromatin can ... Chromatin Chromatin is a network of deoxyribonucleic acid (DNA) and nucleoproteins that constitutes a chromosome. Chromatin can ...
more infohttp://www.bookrags.com/Chromatin/

Sperm Chromatin | SpringerLinkSperm Chromatin | SpringerLink

The Relationship Between Chromatin Structure and DNA Damage in Mammalian Spermatozoa Kenneth Dominguez, Chris D. R. Arca, W. ... Sperm Chromatin Dispersion Test: Technical Aspects and Clinical Applications Jaime Gosálvez, Carmen López-Fernández, José Luís ... Assisted reproductive technologies Chromatin DNA DNA repair Histones Male gamete morphogenesis Male infertility Nucleoproteins ... Sperm Chromatin Structure Assay (SCSA®): 30 Years of Experience with the SCSA® ...
more infohttps://link.springer.com/book/10.1007/978-1-4419-6857-9

Chromatin | biology | Britannica.comChromatin | biology | Britannica.com

... compact fibre called chromatin. An extreme example of the ordered folding and compaction that chromatin can undergo is seen ... during cell division, when the chromatin of each chromosome condenses and is divided between two daughter cells (see below Cell ... Other articles where Chromatin is discussed: cell: DNA packaging: …a dense, ... a dense, compact fibre called chromatin. An extreme example of the ordered folding and compaction that chromatin can undergo is ...
more infohttps://www.britannica.com/science/chromatin

Chromatin potentiates transcription | PNASChromatin potentiates transcription | PNAS

... because chromatin reconstituted with purified histones differs from chromatin assembled in vivo. Reconstituted chromatin lacks ... S1 A and B) (10, 11). PHO5 chromatin isolated in this way was indistinguishable from chromatin at the chromosomal locus on the ... Dependence of chromatin transcription on protein factors and acetyl-CoA. (A) Repressed PHO5 chromatin was transcribed as in Fig ... C) Effect of gcn5 bromoΔ SAGA on chromatin transcription. Repressed (pho4Δ) PHO5 chromatin was transcribed as in Fig. 1C with ...
more infohttps://www.pnas.org/content/114/7/1536

Chromatin Remodeling | CurrikiChromatin Remodeling | Curriki

... of chromatin organization and then proceeds to describe the process of chromatin remodeling through a review of chromatin ... This Teaching Resource provides lecture notes and slides for a class covering chromatin remodeling mechanisms and is part of ... of chromatin organization and then proceeds to describe the process of chromatin remodeling through a review of chromatin ... of chromatin organization and then proceeds to describe the process of chromatin remodeling through a review of chromatin ...
more infohttps://www.curriki.org/oer/Chromatin-Remodeling-265909

Chromatin Remodeling | CurrikiChromatin Remodeling | Curriki

... of chromatin organization and then proceeds to describe the process of chromatin remodeling through a review of chromatin ... This Teaching Resource provides lecture notes and slides for a class covering chromatin remodeling mechanisms and is part of ... of chromatin organization and then proceeds to describe the process of chromatin remodeling through a review of chromatin ... of chromatin organization and then proceeds to describe the process of chromatin remodeling through a review of chromatin ...
more infohttps://www.curriki.org/oer/Chromatin-Remodeling-254036

Chromatin rules.  - PubMed - NCBIChromatin rules. - PubMed - NCBI

Chromatin rules.. Li Y1, Huang S1.. Author information. 1. 1 Department of Biochemistry and Molecular Biology, University of ... Binding of pioneer transcription factors remodels the repressive chromatin and leads to H3K4me1 poised enhancers. The H3K4me1 ... lineage/cell-specific enhancers are silent by repressive chromatin structure. ...
more infohttps://www.ncbi.nlm.nih.gov/pubmed/27358896

Bacterial Chromatin | SpringerLinkBacterial Chromatin | SpringerLink

This volume brings together a wide range of methods to explore the structure and function of bacterial chromatin from molecular ... Authoritative and cutting-edge, Bacterial Chromatin: Methods and Protocols aims to be useful as an up-to-date reference work ... Quantitative Determination of DNA Bridging Efficiency of Chromatin Proteins Ramon A. van der Valk, Liang Qin, Geri F. Moolenaar ... Observing Bacterial Chromatin Protein-DNA Interactions by Combining DNA Flow-Stretching with Single-Molecule Imaging ...
more infohttps://link.springer.com/book/10.1007%2F978-1-4939-8675-0

Medizin: ChromatinMedizin: Chromatin

Chromatin. Klinisches W rterbuch von Otto Dornbl th. Definition und Bedeutung im historischen Lexikon der medizinischen ...
more infohttp://www.textlog.de/12344.html

Chromatin | Define Chromatin at Dictionary.comChromatin | Define Chromatin at Dictionary.com

Chromatin definition, the readily stainable substance of a cell nucleus, consisting of DNA, RNA, and various proteins, that ... chromatin. Historical Examples. of chromatin. *. While these changes are going on in the chromatin the Amphiaster forms. ... Origin of chromatin. First recorded in 1880-85; chromat- + -in2. Related formschro·ma·tin·ic, adjectivechro·ma·toid, adjective ... Word Origin and History for chromatin. n.. protoplasm in cell nuclei, 1882, from German, coined 1879 by German anatomist ...
more infohttps://www.dictionary.com/browse/chromatin

Chromatin nucleolus definition | Drugs.comChromatin nucleolus definition | Drugs.com

Definition of chromatin nucleolus. Provided by Stedmans medical dictionary and Drugs.com. Includes medical terms and ...
more infohttps://www.drugs.com/dict/chromatin-nucleolus.html

Chromatin Looping [image] | EurekAlert! Science NewsChromatin Looping [image] | EurekAlert! Science News

A chromatin loop forms when an enhancer and a promoter, two widely separated elements in a DNA sequence, come into contact as ... A chromatin loop forms when an enhancer and a promoter, two widely separated elements in a DNA sequence, come into contact as ...
more infohttps://www.eurekalert.org/multimedia/pub/65816.php

Epigenetics & Chromatin: Interactions and processesEpigenetics & Chromatin: Interactions and processes

... To mark the 2013 BioMed Central Epigenetics & Chromatin: Interactions and ... UpSETing chromatin during non-coding RNA production The packaging of eukaryotic DNA into nucleosomal arrays permits cells to ... Epigenetics & Chromatin: interactions and processes On 11 to 13 March 2013, BioMed Central will be hosting its inaugural ... The processes of chromatin disassembly and reassembly during DNA replication also h... ...
more infohttps://www.biomedcentral.com/collections/E-and-C-conf

chromatin condensation and cleavagechromatin condensation and cleavage

The question is: does chromatin cleavage occur earlier or later than chromatin ,condensation during apoptosis? ,Is there any ... chromatin condensation and cleavage. LOCKSHIN, RICHARD A YPRLBIO at sjumusic.stjohns.edu Mon Aug 14 09:13:16 EST 1995 *Previous ... difference between chromatin condensation of an apoptotic cell and ,of a normal cell cycle? ,Thanks. , ,Lihua He ,University of ...
more infohttp://www.bio.net/bionet/mm/cellbiol/1995-August/002656.html

Meeting Theme: Transcription/ChromatinMeeting Theme: Transcription/Chromatin

Transcription/Chromatin. Session: Structural Transitions in Chromatin - An Exploration of Mechanisms. • DNA Accessibility in ... The "Transcription/Chromatin" annual meeting theme will contain sessions titled: "Structural Transitions in Chromatin - An ... A session titled "Alternative Chromatin Structures" will illuminate the fact that nucleosome and chromatin structure is ... functions in the context of chromatin and is regulated by its multilayered structural organization. Likewise, chromatin ...
more infohttp://www.asbmb.org/asbmbtoday/asbmbtoday_article.aspx?id=8364

Chromatin immunoprecipitation from 1000 cellsChromatin immunoprecipitation from 1000 cells

This makes it possible for users to perform Chromatin immunoprecipitation (ChIP) assays using only 1000 cells per ... Chromatin immunoprecipitation. The Chromatrap® ChIP-seq Protein A kit (Cat no 500189) was used for ChIP in accordance with the ... Chromatin preparation. For the study the human endometrial carcinoma cell line Hec50 (Holinka et al., 1996) was utilized for ... Sometimes samples are small, cell types can be hard to come by or are difficult because they offer only a low chromatin yield. ...
more infohttps://www.news-medical.net/whitepaper/20170223/Chromatin-immunoprecipitation-from-1000-cells.aspx

nuclear chromatin | SGDnuclear chromatin | SGD

Gene Ontology Term: nuclear chromatin. GO ID. GO:0000790 Aspect. Cellular Component. Description. The ordered and organized ...
more infohttps://www.yeastgenome.org/go/GO:0000790

chromatin assembly | SGDchromatin assembly | SGD

Gene Ontology Term: chromatin assembly. GO ID. GO:0031497 Aspect. Biological Process. Description. The assembly of DNA, histone ... establishment of chromatin architecture View GO Annotations in other species in AmiGO ... proteins, other associated proteins, and sometimes RNA, into chromatin structure, beginning with the formation of the basic ...
more infohttps://www.yeastgenome.org/go/GO:0031497

Chromatin | Definition of Chromatin at Dictionary.comChromatin | Definition of Chromatin at Dictionary.com

Chromatin definition, the readily stainable substance of a cell nucleus, consisting of DNA, RNA, and various proteins, that ... chromatin. *. During the resting stage this chromatin material may have the form of a thread, or may form a network of fibres ( ... chromaticity coordinates, chromaticity diagram, chromaticness, chromatics, chromatid, chromatin, chromatin body, chromatism, ... A brief account of a chromatin element resembling the accessory chromosome in Sagitta has been added for comparison. ...
more infohttps://www.dictionary.com/browse/chromatin?jss=0

ChromatinChromatin

Figure from Chromatin. Figure from Chromatin. Figure from HCEng. Figure from HCEng. Figure from MTA. Figure from MTA. Figure ... Chromatin. Atlas Genet Cytogenet Oncol Haematol. Dec 2018 .. URL : http://AtlasGeneticsOncology.org/Categories/Chromatin.html. ...
more infohttp://atlasgeneticsoncology.org/Categories/Chromatin.html

Understanding chromatins cancer connection | EurekAlert! Science NewsUnderstanding chromatin's cancer connection | EurekAlert! Science News

New live-cell imaging technique allows Northwestern University researchers to study chromatins dynamic processes, including ... Understanding chromatins cancer connection New nanoscale imaging technique allows researchers to study chromatin in live cells ... understanding-chromatins-cancer-connection.. html More in Technology & Engineering. * New UTSA study shows wearable technology ... "We know that chromatin is a major player in complex diseases," Backman said. "We just havent had the techniques to study it. ...
more infohttps://www.eurekalert.org/pub_releases/2016-10/nu-ucc100416.php

Kinase Controls Chromatin | Science SignalingKinase Controls Chromatin | Science Signaling

Thank you for your interest in spreading the word about Science Signaling.. NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.. ...
more infohttp://stke.sciencemag.org/content/2001/91/tw2/tab-article-info
  • PHO5 chromatin in the transcriptionally repressed state was excised from yeast chromosomes in circular form by recombination and purified by affinity chromatography as described ( Fig. S1 A and B ) ( 10 , 11 ). (pnas.org)
  • Chromatin is the complex combination of DNA, RNA, and protein that makes up chromosomes . (wikidoc.org)
  • As the cell prepares to divide, i.e. enters mitosis or meiosis, the chromatin packages more tightly to facilitate segregation of the chromosomes during anaphase. (wikipedia.org)
  • To mark the 2013 BioMed Central Epigenetics & Chromatin: Interactions and processes conference,Epigenetics & Chromatin has launched a new thematic series of publications aimed to discuss how the dynamic processes of epigenetic and chromatin components come together to regulate cellular processes. (biomedcentral.com)
  • It should also be noted that during mitosis, while most of the chromatin is tightly compacted, there are small regions that are not as tightly compacted. (wikidoc.org)
  • The "Transcription/Chromatin" annual meeting theme will contain sessions titled: "Structural Transitions in Chromatin - An Exploration of Mechanisms," "Alternative Chromatin Structures," "RNA Polymerase Pausing and Elongation" and "Transcriptional Regulation in Growth, Differentiation and Diseases. (asbmb.org)
  • PHO5 chromatin isolated in this way was indistinguishable from chromatin at the chromosomal locus on the basis of digestion with specific and nonspecific endonucleases ( Fig. S1 C and D ) ( 10 , 12 ). (pnas.org)
  • The structures within chromatin that regulate these processes span from nucleosomal (10 nanometers) to chromosomal (longer than 200 nanometers) length scales. (eurekalert.org)
  • This volume brings together a wide range of methods to explore the structure and function of bacterial chromatin from molecular to the cellular scale. (springer.com)
  • In the upcoming thematic session titled "Transcription/Chromatin," we have chosen topics that echo this symbiotic relationship. (asbmb.org)
  • A Qsonica sonicator on high setting was used to shear the chromatin stock for 15min: 30 seconds on, 30 seconds off to generate 100-500bp fragments. (news-medical.net)
  • Leading experts from academia, the biotechnology and pharmaceutical industries explain the role of epigenomics in a wide range of contexts, covering basic chromatin biology, imprinting at a genome-wide level, and epigenomics in disease biology and epidemiology. (cambridge.org)
  • Chromatin can only be found in a cell with a nucleus and is therefore not present in a. (bookrags.com)
  • Because the chromatin was derived from a single copy gene, very small quantities were obtained: on the order of 10 fmol/L cell culture. (pnas.org)
  • In pluripotent stem cells or multipotent stem/progenitor cells, lineage/cell-specific enhancers are silent by repressive chromatin structure. (nih.gov)
  • Of all parts of the cell this chromatin is the most remarkable. (dictionary.com)
  • The first indication of the cell division is shown by the chromatin fibres. (dictionary.com)
  • Sometimes samples are small, cell types can be hard to come by or are difficult because they offer only a low chromatin yield. (news-medical.net)
  • In order to make ChIP efficient from lower cell numbers, some of the techniques include spiking of samples with chromatin from another source, or DNA amplification before downstream analysis. (news-medical.net)
  • Three types of plates were used: 96-well plates for 1000 cell chromatin, 12-well plates for 10,000 cells, and 6-well plates for 100,000 cells. (news-medical.net)
  • Called live cell Partial Wave Spectroscopic (PWS) microscopy, the technique detects chromatin by using scattered light. (eurekalert.org)
  • Chromatin contains genetic material-instructions to direct cell functions. (wikidoc.org)
  • The nucleus soon enlarges (fig. 80) and a large dense body (n) appears which stains like chromatin with various staining media. (dictionary.com)
  • Binding of pioneer transcription factors remodels the repressive chromatin and leads to H3K4me1 poised enhancers. (nih.gov)
  • Understanding this missing length scale is crucial, however, because it is the exact area where chromatin undergoes a transformation when cancer is formed. (eurekalert.org)
  • Likewise, chromatin structure is responsive to complicated manipulations by the cellular machinery that make the DNA more or less accessible for the transcriptional apparatus. (asbmb.org)
  • We know that chromatin is a major player in complex diseases," Backman said. (eurekalert.org)
  • A chromatin loop forms when an enhancer and a promoter, two widely separated elements in a DNA sequence, come into contact as they carry out gene activity. (eurekalert.org)