Chromatin. Medical search

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.

The mechanisms effecting establishment, maintenance, and modification of that specific physical conformation of CHROMATIN determining the transcriptional accessibility or inaccessibility of the DNA.

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.

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.

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.

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.

Formation of an acetyl derivative. (Stedman, 25th ed)

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.

The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.

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.

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)

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.

Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.

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)

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).

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.

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.

The portion of chromosome material that remains condensed and is transcriptionally inactive during INTERPHASE.

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.

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.

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)

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.

Interruption or suppression of the expression of a gene at transcriptional or translational levels.

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.

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.

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.

Enzymes that catalyze acyl group transfer from ACETYL-CoA to HISTONES forming CoA and acetyl-histones.

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.

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.

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)

Established cell cultures that have the potential to propagate indefinitely.

The parts of a macromolecule that directly participate in its specific combination with another molecule.

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.

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.

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.

Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.

The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.

The process by which a DNA molecule is duplicated.

An essential amino acid. It is often added to animal feed.

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.

Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.

Chromosome regions that are loosely packaged and more accessible to RNA polymerases than HETEROCHROMATIN. These regions also stain differentially in CHROMOSOME BANDING preparations.

Nucleic acid regulatory sequences that limit or oppose the action of ENHANCER ELEMENTS and define the boundary between differentially regulated gene loci.

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.

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.

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.

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.

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.

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.

Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.

Enzymes which catalyze the hydrolases of ester bonds within DNA. EC 3.1.-.

Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.

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.

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.

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.

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.

Enzymes catalyzing the transfer of an acetyl group, usually from acetyl coenzyme A, to another compound. EC 2.3.1.

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).

Proteins involved in the assembly and disassembly of HISTONES into NUCLEOSOMES.

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.

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.

A cell line derived from cultured tumor cells.

A family of low-molecular weight, non-histone proteins found in chromatin.

Proteins conjugated with nucleic acids.

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.

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.

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.

A class of weak acids with the general formula R-CONHOH.

A species of fruit fly much used in genetics because of the large size of its chromosomes.

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.

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.

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.

Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.

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.

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.

Glycosidic antibiotic from Streptomyces griseus used as a fluorescent stain of DNA and as an antineoplastic agent.

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.

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.

Compounds that inhibit HISTONE DEACETYLASES. This class of drugs may influence gene expression by increasing the level of acetylated HISTONES in specific CHROMATIN domains.

The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.

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 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.

The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.

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.

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.

Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.

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.

An evolutionarily-conserved 10-kDa nuclear protein that binds NUCLEOSOMES and may be involved in the process of CHROMATIN unfolding.

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).

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.

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)

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)

Proteins conjugated with deoxyribonucleic acids (DNA) or specific DNA.

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)

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.

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 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.

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.

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.

The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.

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.

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.

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 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.

Macromolecular complexes formed from the association of defined protein subunits.

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.

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.

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.

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.

Interruptions in the sugar-phosphate backbone of DNA, across both strands adjacently.

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.

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.

Proteins found in any species of fungus.

The mechanisms of eukaryotic CELLS that place or keep the CHROMOSOMES in a particular SUBNUCLEAR SPACE.

The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.

A superfamily of proteins containing the globin fold which is composed of 6-8 alpha helices arranged in a characterstic HEME enclosing structure.

Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.

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.

A family of HIGH MOBILITY GROUP PROTEINS that bind to NUCLEOSOMES.

Structures within the nucleus of fungal cells consisting of or containing DNA, which carry genetic information essential to the cell.

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.

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).

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.

Nucleic acid sequences that are involved in the negative regulation of GENETIC TRANSCRIPTION by chromatin silencing.

Nucleic acid sequences involved in regulating the expression of genes.

Red blood cells. Mature erythrocytes are non-nucleated, biconcave disks containing HEMOGLOBIN whose function is to transport OXYGEN.

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 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 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.

An aquatic genus of the family, Pipidae, occurring in Africa and distinguished by having black horny claws on three inner hind toes.

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.

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.

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)

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.

Transcription factors whose primary function is to regulate the rate in which RNA is transcribed.

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)

A histone chaperone that facilitates nucleosome assembly by mediating the formation of the histone octamer and its transfer to DNA.

A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

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.

The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.

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.

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.

The rate dynamics in chemical or physical systems.

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.

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.

The origin recognition complex is a multi-subunit DNA-binding protein that initiates DNA REPLICATION in eukaryotes.

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.

Preparations of cell constituents or subcellular materials, isolates, or substances.

The functional hereditary units of FUNGI.

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.

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.

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.

A polynucleotide formed from the ADP-RIBOSE moiety of nicotinamide-adenine dinucleotide (NAD) by POLY(ADP-RIBOSE) POLYMERASES.

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.

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.

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.

Proteins that bind to the MATRIX ATTACHMENT REGIONS of DNA.

A member of the p300-CBP transcription factors that was originally identified as a binding partner for ADENOVIRUS E1A PROTEINS.

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.

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.

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.

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).

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.

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.

Nuclear matrix proteins that are structural components of the NUCLEAR LAMINA. They are found in most multicellular organisms.

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.

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.

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.

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.

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.

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.

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.

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)

... 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 ... When chromatin is condensed, the nucleus becomes more rigid. When chromatin is decondensed, the nucleus becomes more elastic ...

https://en.wikipedia.org/wiki/Chromatin

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 ...

https://en.wikipedia.org/wiki/Chromatin_immunoprecipitation

... 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 ...

https://en.wikipedia.org/wiki/Chromatin_bridge

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 ...

https://en.wikipedia.org/wiki/Bivalent_chromatin

"Epigenetics & Chromatin". Epigenetics & Chromatin. Retrieved 2020-10-29. "Epigenetics & Chromatin". Epigenetics & Chromatin. ... "Epigenetics & Chromatin". Epigenetics & Chromatin. Retrieved 2020-10-29. "Epigenetics & Chromatin". Epigenetics & Chromatin. ... "Epigenetics & Chromatin". Epigenetics & Chromatin. Retrieved 2020-10-29. "Epigenetics & Chromatin". Journal Citation Reports ... "Archive of "Epigenetics & Chromatin"". www.ncbi.nlm.nih.gov. Retrieved 2020-11-05. "Epigenetics & Chromatin". Socolar. ...

https://en.wikipedia.org/wiki/Epigenetics_&_Chromatin

A chromatin variant corresponds to a section of the genome that differs in chromatin states across cell types/states within an ... Chromatin variants range in sizes. The smallest chromatin variants cover a few hundred DNA base pairs, such as seen at ... The largest chromatin variants capture a few thousand DNA base pairs, such as seen at Large Organized Chromatin Lysine domains ... Chromatin variants are found across the genome, inclusive of repetitive and non-repetitive DNA sequence. ...

https://en.wikipedia.org/wiki/Chromatin_variant

... 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". ...

https://en.wikipedia.org/wiki/Chromatin_remodeling

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 (2005). "Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping ...

https://en.wikipedia.org/wiki/Active_chromatin_sequence

Hoek M, Stillman B (October 2003). "Chromatin assembly factor 1 is essential and couples chromatin assembly to DNA replication ... Chromatin assembly factor-1 (CAF-1) is a protein complex - including Chaf1a (p150), Chaf1b (p60), and p48 subunits in humans, ... However, loss of function in p48 would alter how well the complex is able to chaperone chromatin, but would not stop it as a ... Volk, Andrew; Crispino, John D. (August 2015). "The role of the chromatin assembly complex (CAF-1) and its p60 subunit (CHAF1b ...

https://en.wikipedia.org/wiki/Chromatin_assembly_factor_1

... (SCSA) is a diagnostic approach that detects sperm abnormality with a large extent of DNA ... "Sperm Chromatin Structure Assay (SCSA) , Center for Women's Health , OHSU". www.ohsu.edu. Retrieved 2021-03-31. Evenson, Donald ... The small AO molecules penetrate through the sperm chromatin in access to double-stranded DNA and single-stranded DNA in intact ... Evenson, D.P. (1999-04-01). "Utility of the sperm chromatin structure assay as a diagnostic and prognostic tool in the human ...

https://en.wikipedia.org/wiki/Sperm_Chromatin_Structure_Assay

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

https://en.wikipedia.org/wiki/Chromatin_target_of_prmt1

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

https://en.wikipedia.org/wiki/Chromatin_accessibility_complex_1

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. Salt-and-pepper chromatin (pheochromocytoma). H&E stain. ... Neuroendocrine tumour of the lung with salt-and-pepper chromatin. H&E stain. Neuroendocrine tumour of the small intestine with ... Salt-and-pepper chromatin - nature.com. Salt-and-pepper nucleus - upmc.edu. (Pathology). ...

https://en.wikipedia.org/wiki/Salt-and-pepper_chromatin

There are four subfamilies of chromatin remodelers: SWI/SNF, INO80, ISW1, and CHD. The RSC complex is a 15-subunit chromatin ... RSC (Remodeling the Structure of Chromatin) is a member of the ATP-dependent chromatin remodeler family. The activity of the ... While there are many similarities between these two chromatin remodeling complexes, they remodel different parts of chromatin. ... After this chromatin remodeling complex was discovered, the RSC complex was found when its components, Snf2 and Swi2p, were ...

https://en.wikipedia.org/wiki/Chromatin_structure_remodeling_(RSC)_complex

... (also called "open chromatin") is a lightly packed form of chromatin (DNA, RNA, and protein) that is enriched in ... Chromatin. Atlas of plant and animal histology". mmegias.webs.uvigo.es. Retrieved 2021-12-02. Enukashvily NI (January 2013). " ... Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin - Tedesco M, ... October 2021). "Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin". ...

https://en.wikipedia.org/wiki/Euchromatin

Their work on the nucle-osome core particle, the fun-da-mental repeat-ing unit of chro-matin, resul-ted ul-ti-mately in its ... They have since de-term-ined the organ-iz-a-tion of nucle-osomes in the chro-matin fiber. He was the postdoctoral supervisor of ... Richmond's work provides a basis for integrating decades of biochemical, physical, and genetic studies of chromatin. His focus ... 2003 (over 1450 citations) Dorigo, Benedetta; Schalch, Thomas; Bystricky, Kerstin; Richmond, Timothy J. (2003). "Chromatin ...

https://en.wikipedia.org/wiki/Timothy_J._Richmond

Histone code Nucleosome Chromatin Other histone proteins: Histone H1 Histone H2A Histone H3 Histone H4 Bhasin M, Reinherz EL, ... 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 ...

https://en.wikipedia.org/wiki/Histone_H2B

"Chromatin Network". Retrieved 1 March 2012. Kouzarides T (February 2007). "Chromatin modifications and their function". Cell. ... The genomic DNA of eukaryotes associates with histones to form chromatin. The level of chromatin compaction depends heavily on ... See Histone#Chromatin regulation. Abnormal expression or activity of methylation-regulating enzymes has been noted in some ... Histone methylation is a principal epigenetic modification of chromatin that determines gene expression, genomic stability, ...

https://en.wikipedia.org/wiki/Histone_methyltransferase

... chromatin dynamics; structural biology; advanced proteomics; mass spectrometry; advanced microscopy.[citation needed] Cancer ...

https://en.wikipedia.org/wiki/Cold_Spring_Harbor_Laboratory

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. 8 (5): 405-424. doi:10.1023/A:1009262819961 ... Also, different isotypes show different localization and bind to chromatin with different affinities. Therefore a model has ...

https://en.wikipedia.org/wiki/Linker_histone_H1_variants

Histones are proteins which are involved in the folding and compaction of the chromatin. There are several different types of ... 2021). "Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer". Gut. 71 (5 ... In general, DNA methylation attracts proteins which fold that section of the chromatin and repress the related genes. The ... This persistent hyperglycemic environment is leads to DNA methylation as well because the chemistry within chromatin in the ...

https://en.wikipedia.org/wiki/Epigenetic_therapy

The complexes formed by the looping of the DNA are known as chromatin. The basic structural unit of chromatin is the nucleosome ... Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of ... This led to chromatin states which define genomic regions by grouping the interactions of different proteins and/or histone ... Chromatin states are also useful in identifying regulatory elements that have no defined sequence, such as enhancers. This ...

https://en.wikipedia.org/wiki/H4K8ac

During interphase, the genetic material in the nucleus consists of loosely packed chromatin. At the onset of prophase, ... A, normal mitosis; B, chromatin bridge; C, multipolar mitosis; D, ring mitosis; E, dispersed mitosis; F, asymmetrical mitosis; ... Kadauke S, Blobel GA (April 2013). "Mitotic bookmarking by transcription factors". Epigenetics & Chromatin. 6 (1): 6. doi: ... non-attached condensed chromatin in the area of the mitotic figure) indicates high risk human papillomavirus infection-related ...

https://en.wikipedia.org/wiki/Mitosis

... and chromatin. This occurs through the synthesis of a new nuclear envelope that forms around the chromatin gathered at each ... The nuclear envelope is broken down in this stage, long strands of chromatin condense to form shorter more visible strands ... The nucleolus reforms as the chromatin reverts back to the loose state it possessed during interphase. The division of the ... Chromatin. 7 (1): 25. doi:10.1186/1756-8935-7-25. PMC 4247682. PMID 25435919. Hetzer MW (March 2010). "The nuclear envelope". ...

https://en.wikipedia.org/wiki/Cell_division

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 ...

https://en.wikipedia.org/wiki/Histone_acetyltransferase

Chromatin. 13 (1): 12. doi:10.1186/s13072-020-00334-y. ISSN 1756-8935. PMC 7059380. PMID 32138783. Wang, Qin; Dai, Tianyue; Sun ...

https://en.wikipedia.org/wiki/I-motif_DNA

Jeanteur P (2008). Epigenetics and Chromatin. Springer. ISBN 9783540852360. Kaneko S, Li G, Son J, Xu CF, Margueron R, Neubert ... 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 (November 2005). "The diverse ... due to PRC2/EZH2-EED-mediated H3K27 methylation and subsequent recruitment of PRC1 which facilitates condensation of chromatin ...

https://en.wikipedia.org/wiki/EZH2

Talbert, P.; Meers, M.P.; Henikoff, S. (2019). "Old cogs, new tricks: the evolution of gene expression in a chromatin context ... Chromatin. 10 (55): 55. doi:10.1186/s13072-017-0162-0. PMC 5704553. PMID 29179736. Erives, A.; Levine, M. (2004). "Coordinate ...

https://en.wikipedia.org/wiki/Albert_Erives

"Chromatin Immuprecipitation". www.bio.brandeis.edu. Krogan NJ, Dover J, Wood A, Schneider J, Heidt J, Boateng MA, Dean K, Ryan ... 2013). "Genome-wide chromatin state transitions associated with developmental and environmental cues". Cell. 152 (3): 642-654. ... It is thought that they achieve this through alterations in chromatin structure, such as histone modification and DNA ... To a large extent, differences in transcription factor binding are determined by the chromatin accessibility of their binding ...

https://en.wikipedia.org/wiki/Cellular_differentiation

ChromDB Contains 9,341 chromatin-associated proteins, including RNAi-associated proteins, for a broad range of organisms. ... "ChromDB::Chromatin Database". Archived from the original on 2019-04-10. Retrieved 2010-01-29. Cremofac "Home". epigenomics.ca. ... CREMOFAC Contains 1725 redundant and 720 non-redundant chromatin-remodeling factor sequences in eukaryotes. The Krembil Family ...

https://en.wikipedia.org/wiki/Computational_epigenetics

Chromatin & Gene Expression Group. Chromatin & Gene Expression Group - October, 2018. Front Row: Jackson Hoffman, Nicholas ...

https://www.niehs.nih.gov/research/atniehs/labs/escbl/pi/cge/gallery/index.cfm

NLMs networks, gene regulation, and chromatin research focuses on diverse aspects of gene regulation, such as chromatin ... Conducting research on chromatin structure, epigenetics, and gene expression/regulation. *Investigating nucleosomal binding ...

https://www.nlm.nih.gov/research/focus/Networks.html

... single-cell profiling of chromatin states. sciMAP-ATAC produces data of equivalent quality to non-spatial sci-ATAC and retains ... where we produce spatial trajectories and integrate our data with non-spatial single-nucleus RNA and other chromatin ... single-cell combinatorial indexing on Microbiopsies Assigned to Positions for the Assay for Transposase Accessible Chromatin, ... Chromatin accessibility analysis. The filtered bam file was used for chromatin accessibility peak calling for each of the five ...

https://www.nature.com/articles/s41467-021-21515-7?error=cookies_not_supported&code=215a18f3-b1d5-4fba-855a-9aa01ddff247

Cardiff researcher finds chromatin in volcano. 24 July 2013 An international collaboration including researchers from Osaka, ...

https://www.cardiff.ac.uk/news/view/77021-cardiff-researcher-finds-chromatin-in-volcano

Detailed analyses of cohesins movements indicate how this protein complex hauls chromatin fibers to package DNA into loops. ... Detailed analyses of cohesins movements indicate how this protein complex hauls chromatin fibers to package DNA into loops. ... Detailed analyses of cohesins movements indicate how this protein complex hauls chromatin fibers to package DNA into loops. ... By manipulating DNA sequences that guide genome-folding, researchers confirm an existing model of chromatin structure inside ...

https://www.the-scientist.com/tag/chromatin-dynamics

Dopamine modification on chromatin linked to addiction. At a Glance. *Researchers found that dopamine can modify the structure ... In chromatin, DNA (yellow) is wound around histone proteins (blue). Chemical changes to histones can affect the way the genes ... Chemical modifications of chromatin-the structure that DNA and proteins called histones are packed into to form chromosomes-can ...

https://www.nih.gov/news-events/nih-research-matters/dopamine-modification-chromatin-linked-addiction

Chromatin. A complex of ,!g,DNA and basic proteins (as histone) in ,!g,eukaryotic cells that is condensed into ,!g,chromosomes ... There are two types: heterochromatic which is densely coiled chromatin that appears as nodules in or along chromosomes and ... Euchromatic is the less coiled and genetically active portion of chromatin that is largely composed of genes. ...

https://counterbalance.org/biogloss/chrmtn-body.html?client=ctns2

Recent studies have suggested that ADNP functions as an important chromatin regulator. However, how ADNP-regulated chromatin ... ADNP Controls Gene Expression Through Local Chromatin Architecture by Association With BRG1 and CHD4 Front Cell Dev Biol. 2020 ... Here we show that ADNP interacts with two chromatin remodelers, BRG1 and CHD4. ADNP is required for proper establishment of ... Thus, our work revealed a key role of ADNP in the establishment of local chromatin landscape and structure of developmental ...

https://pubmed.ncbi.nlm.nih.gov/32714933/

Genome Instability and Chromatin Remodeling Section Weidong Wang, PhD, Chief The Genome Instability and Chromatin Remodeling ... Home Research & Funding Labs at NIA Laboratory of Genetics & Genomics Genome Instability and Chromatin Remodeling Section ... Chromatin-remodeling complexes that regulate transcription, replication and repair.. Findings and Publications Yan Z, Delannoy ... several chromatin-remodeling complexes (BAF, PBAF, NURD), and Top3b-TDRD3 topoisomerase complex. Given that Top3b is the first ...

https://www.nia.nih.gov/research/labs/lgg/genome-instability-and-chromatin-remodeling-section

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... and repressed chromatin (heterochromatin). The functional organization of chromatin is important for regulation of ... 2021). We are currently addressing the question of how LSH molecular function alters chromatin structure and maintains genomic ... nucleosome occupancy and DNA methylation and are crucial for organization of the genome into active chromatin (euchromatin) ... and repressed chromatin (heterochromatin). The functional organization of chromatin is important for regulation of ...

https://ccr.cancer.gov/careers/post-doctoral-fellow-chromatin-epigenetics/26025

Chromatin responses to DNA damage / Xuetong Shen. Author: Shen, Xuetong. National Institutes of Health (U.S.). DNA Repair ... Transcription Factor E2F1 Acts as a Chromatin Accessibility Factor for DNA Repair ...

https://videocast.nih.gov/watch=7881

However, they impact chromatin dynamics and should be reflected in particular in the motion of a single locus. We present here ... Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions. Author(s). Amitai, Assaf; ... Is it possible to extract tethering forces applied on chromatin from the statistics of a single locus trajectories imaged in ... "Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions." Edited by Alexandre V Morozov. ...

https://dspace.mit.edu/handle/1721.1/99728

... is a multifunctional epigenetic reader playing a role in transcriptional regulation and chromatin structure, which was linked ... MeCP2 and Chromatin Compartmentalization Annika Schmidt et al. Cells. 2020. . Free PMC article Show details Display options ... MeCP2 and Chromatin Compartmentalization Annika Schmidt 1 , Hui Zhang 1 , M Cristina Cardoso 1 ... Idris M, Coussement L, Alves MM, De Meyer T, Melotte V. Idris M, et al. Epigenetics Chromatin. 2023 Aug 3;16(1):31. doi: ...

https://pubmed.ncbi.nlm.nih.gov/32260176

Chromatin Immunoprecipitation Sequencing. A technique for identifying the BINDING SITES on nucleic acid sequences that are ... Therapeutic Techniques and Equipment CategoryInvestigative TechniquesGenetic TechniquesChromatin ImmunoprecipitationChromatin ... and Equipment CategoryInvestigative TechniquesImmunologic TechniquesImmunoprecipitationChromatin ImmunoprecipitationChromatin ... and Equipment CategoryInvestigative TechniquesGenetic TechniquesSequence AnalysisHigh-Throughput Nucleotide SequencingChromatin ...

https://www.ncbi.nlm.nih.gov/mesh?term=2031081[uid]

... suggesting inhibition of chromatin assembly. Defective chromatin assembly causes dysregulation of gene expression and genomic ... Our preliminary results further show that formaldehyde reduces the total amount of histone in the chromatin fraction and the ... In Aim 2, we will determine the impact of aberrant chromatin assembly on formaldehyde-induced changes in gene expression, ... In Aim 3, we will investigate whether formaldehyde exposure compromises chromatin assembly in vivo. The proposed concept that a ...

https://tools.niehs.nih.gov/portfolio/index.cfm?do=portfolio.grantDetail&grant_number=R01ES033160

... or a weaker architectural role in chromatin loop formation. TAD borders directly impact on chromatin dynamics by restricting ... We discuss how sub-TAD chromatin dynamics, constrained into a recently described statistical helix conformation, can produce ... organization of the eukaryote genomes and discusses the relationship to chromatin loop formation. CTCF protein appears as a ... Recent investigations on 3D chromatin folding revealed that the eukaryote genomes are both highly compartmentalized and ...

https://www.mdpi.com/2073-4425/6/3/734/htm

The packaging of chromatin into the nucleus of a eukaryotic cell requires an extraordinary degree of compaction and physical ... The packaging of chromatin into the nucleus of a eukaryotic cell requires an extraordinary degree of compaction and physical ... In this review, we focus on these aspects of chromatin organization and discuss novel approaches such as live cell imaging and ... tools likely to give significant insights into our understanding of the very dynamic nature of chromatin and chromatin ...

https://www.jic.ac.uk/research-impact/publications/insights-into-chromatin-structure-and-dynamics-in-plants/

The Mediator kinase module bound and phosphorylated key components of the chromatin remodeling complex switch/sucrose non- ... CDK8 and CDK19 regulate intestinal differentiation and homeostasis via the chromatin remodeling complex SWI/SNF. ... CDK8 and CDK19 regulate intestinal differentiation and homeostasis via the chromatin remodeling complex SWI/SNF. ... coordinated by the interaction between the chromatin remodeling complex SWI/SNF and Mediator kinase. ...

https://www.jci.org/articles/view/158593/figure/2

UHRF1 chromatin reader domains contribute to DNA hypermethylation in colorectal cancer cells. To dissect the role of UHRF1, the ... Chromatin reader domains of DNMT-targeting protein, UHRF1, are responsible for cancerous DNA hypermethylation. Tue, 08/20/2019 ... Using colorectal cancer cells, the team found that chromatin reader domains of UHRF1 maintain cancerous DNA hypermethylation. ... Home » Antibody News » Chromatin reader domains of DNMT-targeting protein, UHRF1, are responsible for cancerous DNA ...

https://www.novusbio.com/antibody-news/chromatin-reader-domains-of-dnmt-targeting-protein-uhrf1-are-responsible-for-cancerous-dna-hypermethylation

We revised our look, but we still have all the same great content! Cant find something you need? Please contact [email protected].. ...

http://commonfund.nih.gov/science-news/new-techniques-revealing-varied-shapes-chromatin

An emerging class of enhancer-like lncRNAs may link chromosome structure to chromatin state and establish active chromatin ... An emerging class of enhancer-like lncRNAs may link chromosome structure to chromatin state and establish active chromatin ... Eukaryotic genomes are packaged into chromatin, where diverse histone modifications can demarcate chromatin domains that ... Eukaryotic genomes are packaged into chromatin, where diverse histone modifications can demarcate chromatin domains that ...

https://www.cirm.ca.gov/node/11000/

Our objectives now are to better understand the role of chromatin, enhancers and long non-coding RNAs in the onset and ... Splicing-associated chromatin signatures: a combinatorial and position-dependent role for histone marks in splicing definition. ... The regulation of alternative splicing is a multilayer process in which chromatin (in blue), long non-coding RNAs (in purple) ... Unexpectedly, in the past 20 years, chromatin and epigenetic modifications have been shown to play an important role in the ...

https://www.igh.cnrs.fr/en/research/departments/genome-dynamics/composante-epigenetique-de-lepissage-alternatif

Real Time Chromatin Dynamics and Function (U01 Clinical Trial Not Allowed) RFA-RM-20-003. RMOD ... These include: 1) better means of studying chromatin dynamics in live cells and in complex tissues, which will likely imply a ... A description of how the proposed work will dramatically impact our ability to study and understand aspects of chromatin ... Applications that focus on technologies that do not allow the continuous monitoring of chromatin structure and dynamics in live ...

http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-20-003.html

These findings show that SARS-CoV-2 acutely rewires host chromatin, facilitating future studies of the long-term epigenomic ... Some viruses restructure host chromatin, influencing gene expression, with implications for disease outcome. Whether this ... finding widespread host chromatin restructuring that features widespread compartment A weakening, A-B mixing, reduced intra-TAD ...

https://www.iasp-pain.org/publications/pain-research-forum/papers-of-the-week/paper/sars-cov-2-restructures-host-chromatin-architecture/

Order High-Mobility Group Non-Histone Chromatin Protein Proteins from many different species. Find the right product on ... High-Mobility Group Non-Histone Chromatin Protein Proteins by Origin. Find High-Mobility Group Non-Histone Chromatin Protein ... High-Mobility Group Non-Histone Chromatin Protein Proteins by Source. Find High-Mobility Group Non-Histone Chromatin Protein ... High-Mobility Group Non-Histone Chromatin Protein Proteins by Protein Type. Find High-Mobility Group Non-Histone Chromatin ...

https://www.antibodies-online.com/hi/high-mobility-group-non-histone-chromatin-protein-62891/high-mobility-group-non-histone-chromatin-protein-proteins-46169/

Our research tackles important questions regarding the coupling between 3D structure and functions of chromatin. Our objective ... our research addresses generic or specific biological questions on chromatin and gene regulation by developing physical and ... is to provide some universal principles driving chromatin folding and regulation, while contextualizing our approaches to ... Filed under: chromatin, epigenetics, Approches quantitatives de lexpression et de la dynamique des génomes, 3D chromosome ...

http://www.ens-lyon.fr/LBMC/equipes/biologie-physique-de-la-chromatine

Animals, Cell Division, Chromatin, Chromatin Assembly and Disassembly, DNA Replication, Epigenesis, Genetic, Epigenomics, ... Chromatin replication and epigenome maintenance. Research output: Contribution to journal › Review › peer-review ... Chromatin and nuclear structure influence where and when DNA replication initiates, whereas the replication process itself ... During cell division the entire genome must be accurately replicated and the chromatin landscape reproduced on new DNA. ...

https://www.cpr.ku.dk/staff/?pure=en%2Fpublications%2Fchromatin-replication-and-epigenome-maintenance

Chromatin structures are dynamically changed by nucleosome binding proteins . (bvsalud.org)

NLM's networks, gene regulation, and chromatin research focuses on diverse aspects of gene regulation, such as chromatin organization, DNA conformation, DNA-protein interaction, DNA regulatory elements, and gene regulatory networks. (nih.gov)
Epigenetic modifications comprise histone modifications, histone variants, nucleosome occupancy and DNA methylation and are crucial for organization of the genome into active chromatin (euchromatin) and repressed chromatin (heterochromatin). (cancer.gov)
The functional organization of chromatin is important for regulation of transcription, cellular differentiation, and genome maintenance. (cancer.gov)
This review presents the most recent advances in topological domains' organization of the eukaryote genomes and discusses the relationship to chromatin loop formation. (mdpi.com)
CTCF protein appears as a central factor of these two organization levels having either a strong insulating role at TAD borders, or a weaker architectural role in chromatin loop formation. (mdpi.com)
The packaging of chromatin into the nucleus of a eukaryotic cell requires an extraordinary degree of compaction and physical organization. (jic.ac.uk)
In this review, we focus on these aspects of chromatin organization and discuss novel approaches such as live cell imaging and photobleaching as important tools likely to give significant insights into our understanding of the very dynamic nature of chromatin and chromatin regulatory processes. (jic.ac.uk)
Stability and function of eukaryotic genomes are closely linked to chromatin structure and organization. (ku.dk)
Research has revealed a hierarchical organization into chromosomal territories, compartments, domains, and eventually chromatin loops that serve to bring transcriptional enhancers in proximity of their target promoters. (fmi.ch)
It has become increasingly apparent that proper control of gene expression requires complex organization of DNA at the level of chromatin. (nih.gov)
Chromatin insulators are DNA-protein complexes that influence gene expression by establishing chromatin domains subject to distinct transcriptional controls, likely through alteration of their spatial organization. (nih.gov)

However, they impact chromatin dynamics and should be reflected in particular in the motion of a single locus. (mit.edu)
TAD borders directly impact on chromatin dynamics by restricting contacts within specific genomic portions thus confining chromatin loop formation within TADs. (mdpi.com)

With their new method performed in mouse embryonic stem cells, the researchers could confirm the existence of key structural features of chromosomes, notably TADs and chromatin loops. (fmi.ch)

Eukaryotic genomes are packaged into chromatin, where diverse histone modifications can demarcate chromatin domains that facilitate or block gene expression. (ca.gov)
Chromatin is the fundamental structure of genomic DNA in eukaryotic cells . (bvsalud.org)

ATAC-Seq is based on transposase-mediated insertion of sequencing primers into open chromatin regions. (activemotif.com)
Why study Open Chromatin? (activemotif.com)
Figure 1: Active Motif's ATAC-Seq assay reliably detects regions of open chromatin. (activemotif.com)
DNAse-Seq, which has long been the gold standard for generating genome-wide profiles of open chromatin, is shown above in blue. (activemotif.com)
The underlying DNA sequence of differentially open chromatin regions can be analyzed to identify the most enriched transcription factor binding sites. (activemotif.com)
The open chromatin profiles are similar to DNAse-Seq profiles generated by the ENCODE consortium. (activemotif.com)

The Genome Instability and Chromatin Remodeling Section (GICRS), led by Weidong Wang, focuses on three main projects: (1) multiprotein complexes in DNA damage response and genome maintenance, (2) a dual-activity topoisomerase complex and its roles in DNA transcription, mRNA metabolism, coronavirus RNA replication, neurodevelopment and mental disorders, and (3) chromatin remodeling complexes and gene regulation. (nih.gov)
The GICRS has successfully identified components of the Fanconi anemia core complex, Bloom syndrome complex, ATRX-syndrome complex, FANCM-MHF DNA remodeling complex, RNF8-FAAP20 ubiquitin cascade, several chromatin-remodeling complexes (BAF, PBAF, NURD), and Top3b-TDRD3 topoisomerase complex. (nih.gov)
Chromatin-remodeling complexes that regulate transcription, replication and repair. (nih.gov)
In particular, we have shown that non-coding RNAs and histone modifications can communicate with the splicing machinery via recruitment of chromatin/splicing-adaptor complexes. (cnrs.fr)
Drosophila harbors the largest diversity of known chromatin insulator complexes. (nih.gov)

ADNP is required for proper establishment of chromatin accessibility, nucleosome configuration, and bivalent histone modifications of developmental genes. (nih.gov)
Bivalent chromatin is characterized by the simultaneous presence of H3K4me3 and H3K27me3, histone modifications generally associated with transcriptionally active and repressed chromatin, respectively. (nih.gov)
Histone modifications and histone variants are also involved in regulating chromatin and nucleosome structures. (bvsalud.org)

While BRD4 association with chromatin is known to de-compact it and activate transcription of key proto-oncogenes, the mechanism involved is currently unknown. (nih.gov)
Consistent with its role in localized chromatin de-compaction, BRD4 HAT activity regulates transcription at these gene loci as well. (nih.gov)
BRD4 HAT activity thus plays a key role in chromatin remodeling and transcription. (nih.gov)
Change in gene expression associated with pancreatic cancer could be attributed to the variation in histone posttranslational modifications leading to subsequent remodeling of the chromatin template during transcription. (nih.gov)

HiChIP contact analysis shows that global chromatin interactions are dramatically increased during FXR activation. (biorxiv.org)
We demonstrate that chromatin conformation, including genome-wide interactions, TADs, intra-chromosomal and inter-chromosomal Foxa2-anchored loops, drastically changes upon addition of FXR agonist. (biorxiv.org)
chromosomal interactions are detected as ligation products after chromatin crosslinking with formaldehyde, which 'glues' proteins and DNA together in an irreversible manner. (fmi.ch)

Chemical modifications of chromatin-the structure that DNA and proteins called histones are packed into to form chromosomes-can affect gene expression. (nih.gov)
Unexpectedly, in the past 20 years, chromatin and epigenetic modifications have been shown to play an important role in the regulation of alternative splicing. (cnrs.fr)

There are two types: heterochromatic which is densely coiled chromatin that appears as nodules in or along chromosomes and contains relatively few genes. (counterbalance.org)
Chromatin fragments interact with many partners such as the nuclear membrane, other chromosomes or nuclear bodies, but the resulting forces cannot be directly measured in vivo. (mit.edu)
The researchers went even further to characterize and sort cells based on: their complex patterns of gene expression, the presence or absence of chemical (or epigenetic) marks on their DNA, the way their chromosomes are packaged into chromatin , and their electrical properties. (nih.gov)
A filamentary assembly of DNA and a protein structure base, primarily histone, chromatin is the form in which genes appear on chromosomes. (nih.gov)

Euchromatic is the less coiled and genetically active portion of chromatin that is largely composed of genes. (counterbalance.org)
Thus, our work revealed a key role of ADNP in the establishment of local chromatin landscape and structure of developmental genes by association with BRG1 and CHD4. (nih.gov)
Here, we show that bivalent chromatin does not poise genes for rapid activation but protects promoters from de novo DNA methylation. (nih.gov)

This raises the question of whether structures such as TADs and chromatin loops detected by 3C methods actually exist in living cells. (fmi.ch)

Methyl-CpG binding protein 2 (MeCP2) is a multifunctional epigenetic reader playing a role in transcriptional regulation and chromatin structure, which was linked to Rett syndrome in humans. (nih.gov)
Thus, these studies reveal a transcriptional mechanism of intestinal cell specification, coordinated by the interaction between the chromatin remodeling complex SWI/SNF and Mediator kinase. (jci.org)

By manipulating DNA sequences that guide genome-folding, researchers confirm an existing model of chromatin structure inside the nucleus. (the-scientist.com)
higher order chromatin structure. (nih.gov)
2021). We are currently addressing the question of how LSH molecular function alters chromatin structure and maintains genomic stability and cellular differentiation. (cancer.gov)
An emerging class of enhancer-like lncRNAs may link chromosome structure to chromatin state and establish active chromatin domains. (ca.gov)
changes in the chromatin structure of a gene were considered to be the passive consequence of the binding of these factors. (nih.gov)
However, it is now clear that chromatin structure is an integral part of the process of gene regulation. (nih.gov)
Our research tackles important questions regarding the coupling between 3D structure and functions of chromatin. (ens-lyon.fr)
Chromatin and nuclear structure influence where and when DNA replication initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. (ku.dk)
Micrococcal nuclease digestion showed an altered chromatin structure in hPaf1/PD2-KD cells. (nih.gov)
Crick's notes for a seminar presentation on September 23, 1976 at the Salk Institute for Biological Studies on the structure of chromatin. (nih.gov)
Crick had been interested in chromatin since he conducted studies of its structure with Alexander Rich in the mid-1950s. (nih.gov)
Chromatin structure related to oncogenesis. (bvsalud.org)
In this review article, we discuss the current progress toward understanding the relationship between chromatin structure and cancer development. (bvsalud.org)

We have previously shown that pioneer factor Foxa2 opens chromatin for binding of nuclear receptors FXR and LXRα during acute ligand activation. (biorxiv.org)
Overall, our results suggest that hPaf1/PD2 in association with MLL1 regulates methylation of H3K4 residues, as well as interacts and regulates nuclear shuttling of chromatin remodeling protein CHD1, facilitating its function in pancreatic cancer cells. (nih.gov)
Undifferentiated tumours with histologic grade III, nuclear grade I, no lymphocytic infiltrate and involvement of overlying skin, nipple and areola were more often associated with low sex chromatin incidence. (who.int)

The regulation of alternative splicing is a multilayer process in which chromatin (in blue), long non-coding RNAs (in purple) and RNA binding factors (in orange) work in an integrated way to establish the final splicing outcome. (cnrs.fr)
In close connection with experimental biology, our research addresses generic or specific biological questions on chromatin and gene regulation by developing physical and computational models. (ens-lyon.fr)
Our objective is to provide some universal principles driving chromatin folding and regulation, while contextualizing our approaches to fundamental, specific problems of 3D genomics. (ens-lyon.fr)

Taking advantage of available genome-wide ChIP-seq and RNA-seq data from the ENCODE and ROADMAP Epigenomics project, we are now identifying the chromatin signatures that differentially mark included and excluded exons, to study what these events have in common in order to depict novel regulatory mechanisms of alternative splicing and improve the current prediction tools by adding to the splicing code the information embedded at the chromatin level. (cnrs.fr)
This assay provides genome-wide profiles of open and accessible regions of chromatin that are indicative of active regulatory regions. (activemotif.com)

To conclude, the confined trajectories we observed in vivo reflect local interaction on chromatin. (mit.edu)

Is it possible to extract tethering forces applied on chromatin from the statistics of a single locus trajectories imaged in vivo? (mit.edu)
BRD4 HAT activity and H3K122 acetylation is responsible for nucleosome eviction and opening of the chromatin, as evidenced by the ability of BRD4, but not BRD4 HAT mutants, to evict nucleosomes both in vitro and in vivo. (nih.gov)

Recent investigations on 3D chromatin folding revealed that the eukaryote genomes are both highly compartmentalized and extremely dynamic. (mdpi.com)

The nucleosome , the primary unit of chromatin , consists of DNA and histone proteins , and is important for the maintenance of genomic DNA . (bvsalud.org)

Histone mutations are present in many types of cancers , suggesting that chromatin and/or nucleosome structures could be closely related to cancer development. (bvsalud.org)

Detailed analyses of cohesin's movements indicate how this protein complex hauls chromatin fibers to package DNA into loops. (the-scientist.com)
Find High-Mobility Group Non-Histone Chromatin Protein Proteins for a variety of species such as anti-Candida albicans High-Mobility Group Non-Histone Chromatin Protein, anti-Emericella nidulans High-Mobility Group Non-Histone Chromatin Protein, anti-Schizosaccharomyces pombe High-Mobility Group Non-Histone Chromatin Protein. (antibodies-online.com)
Find High-Mobility Group Non-Histone Chromatin Protein Proteins validated for a specific application such as ELISA. (antibodies-online.com)
Also, a reduction in hPaf1 level resulted in reduced MLL1 expression and a corresponding decrease in the level of CHD1 (Chromohelicase DNA-binding protein 1), an ATPase dependent chromatin remodeling enzyme that specifically binds to H3K4 di and trimethyl marks. (nih.gov)

Here, we present single-cell combinatorial indexing on Microbiopsies Assigned to Positions for the Assay for Transposase Accessible Chromatin, or sciMAP-ATAC, as a method for highly scalable, spatially resolved, single-cell profiling of chromatin states. (nature.com)
Figure 2: Active Motif's ATAC-Seq assay distinguishes sample groups by identifying chromatin regions that are differentially open. (activemotif.com)

Genome Survey of Chromatin-Modifying Enzymes in Threespine Stickleback: A Crucial Epigenetic Toolkit for Adaptation? (portlandpress.com)

The National Cancer Institute (NCI) is seeking an outstanding, internationally recognized, and visionary leader in the field of chromatin biology to direct an internationally recognized research program in the current Laboratory of Receptor Biology and Gene Expression (LRBGE) in the NCI Center for Cancer Research (CCR). (nih.gov)

Ligand-treated livers exhibit extensive redistribution of topological associated domains (TAD and substantial increase in Foxa2-anchored loops, suggesting Foxa2 is involved in dynamic chromatin conformational changes. (biorxiv.org)

Human RNA polymerase II-association factor 1 (hPaf1/PD2) regulates histone methylation and chromatin remodeling in pancreatic cancer. (nih.gov)

Required for DNA-binding by the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. (antibodies-online.com)

Splicing-associated chromatin signatures: a combinatorial and position-dependent role for histone marks in splicing definition. (cnrs.fr)

Inhibiting its interaction with chromatin has been a successful therapeutic strategy against many cancers including acute myeloid leukemia, Burkitt's lymphoma, breast, colon and lung cancer. (nih.gov)

Our objectives now are to better understand the role of chromatin, enhancers and long non-coding RNAs in the onset and maintenance of a cell-specific splicing program, using as an inducible cell reprogramming model system the epithelial-to-mesenchymal transition (EMT), a process involved in early development and cancer metastasis. (cnrs.fr)

Here we show that ADNP interacts with two chromatin remodelers, BRG1 and CHD4. (nih.gov)

We apply sciMAP-ATAC to assess cortical lamination in the adult mouse primary somatosensory cortex and in the human primary visual cortex, where we produce spatial trajectories and integrate our data with non-spatial single-nucleus RNA and other chromatin accessibility single-cell datasets. (nature.com)

However, how ADNP-regulated chromatin mechanisms control gene expression and stem cell fate commitment remains unclear. (nih.gov)
Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. (ku.dk)

Our group is looking for a postdoctoral candidate who has an interest in the relationship between chromatin and its role in human disease. (cancer.gov)

Active chromatin and noncoding RNAs: an intimate relationship. (ca.gov)
Home › About CIRM › Our Publications › Grantee publications › Active chromatin and noncoding RNAs: an intimate relationship. (ca.gov)
While silent chromatin has been associated with long noncoding RNAs (lncRNAs) for some time, new studies suggest that noncoding RNAs also modulate the active chromatin state. (ca.gov)

Moreover, recent studies have shown that loss of insulator activity in IDH1 mutant gliomas and T cell acute lymphoblastic leukemias leads to disruption of boundaries between chromatin domains and subsequent oncogene activation. (nih.gov)

We hypothesized that Foxa2 also enables chromatin conformational changes during ligand activation. (biorxiv.org)

Using colorectal cancer cells, the team found that chromatin reader domains of UHRF1 maintain cancerous DNA hypermethylation. (novusbio.com)

The Mediator kinase module bound and phosphorylated key components of the chromatin remodeling complex switch/sucrose non-fermentable (SWI/SNF) in intestinal epithelial cells. (jci.org)
Here we characterized the 3D genome and epigenome of human cells after SARS-CoV-2 infection, finding widespread host chromatin restructuring that features widespread compartment A weakening, A-B mixing, reduced intra-TAD contacts and decreased H3K27ac euchromatin modification levels. (iasp-pain.org)

This protocol describes a procedure for generating and purifying wild type and mutant versions of the human INO80 chromatin remodeling complex. (jove.com)

Anatomy25

Organisms5

Chemicals and Drugs75

Analytical, Diagnostic and Therapeutic Techniques and Equipment17

Phenomena and Processes67

Information Science3

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

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

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

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

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

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

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

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

Chromatin

Chromatin Assembly and Disassembly

Histones

Chromatin Immunoprecipitation

Nucleosomes

Chromosomal Proteins, Non-Histone

Acetylation

Micrococcal Nuclease

Transcription, Genetic

Promoter Regions, Genetic

Cell Nucleus

Chromatin Assembly Factor-1

Transcription Factors

Sex Chromatin

DNA

DNA-Binding Proteins

Nuclear Proteins

Heterochromatin

Epigenesis, Genetic

Protein Binding

Methylation

Deoxyribonuclease I

Gene Silencing

Gene Expression Regulation

Histone Deacetylases

Repressor Proteins

Histone Acetyltransferases

Saccharomyces cerevisiae Proteins

HeLa Cells

Chromosomes

Cell Line

Binding Sites

Saccharomyces cerevisiae

Molecular Sequence Data

Histone-Lysine N-Methyltransferase

DNA Methylation

Base Sequence

DNA Replication

Lysine

Cell Cycle Proteins

Transcriptional Activation

Euchromatin

Insulator Elements

RNA Polymerase II

Centromere

Mitosis

Drosophila Proteins

Mutation

Chickens

Enhancer Elements, Genetic

Deoxyribonucleases

Gene Expression Regulation, Fungal

DNA Damage

Polycomb-Group Proteins

DNA Helicases

Spermatozoa

Acetyltransferases

Interphase

Histone Chaperones

Models, Genetic

Protein Structure, Tertiary

Cell Line, Tumor

High Mobility Group Proteins

Nucleoproteins

Models, Biological

Cell Cycle

DNA Repair

Hydroxamic Acids

Drosophila melanogaster

Adenosine Triphosphatases

Drosophila

Gene Expression Regulation, Developmental

Trans-Activators

Response Elements

Mi-2 Nucleosome Remodeling and Deacetylase Complex

Chromomycin A3

Amino Acid Sequence

p300-CBP Transcription Factors

Histone Deacetylase Inhibitors

Nucleic Acid Conformation