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.
Infections with nematodes of the order ASCARIDIDA.
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)
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.
Amino acids with uncharged R groups or side chains.
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.
A bone disorder involving ossification centers (EPIPHYSES) of the VERTEBRAL COLUMN.
Amino acids with uncharged R groups or side chains.
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
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.
A species of LENTIVIRUS, subgenus ovine-caprine lentiviruses (LENTIVIRUSES, OVINE-CAPRINE), closely related to VISNA-MAEDI VIRUS and causing acute encephalomyelitis; chronic arthritis; PNEUMONIA; MASTITIS; and GLOMERULONEPHRITIS in goats. It is transmitted mainly in the colostrum and milk.
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.
An enzyme that catalyzes the conversion of N-formyl-L-kynurenine and water to formate and L-kynurenine. It also acts on other aromatic formylamines. (Enzyme Nomenclature, 1992) EC
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 genus of SPONGES in the family Plakinidae, with the skeleton formed by small diactine (and some triactine) needle-like terminations.
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.
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.
Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors.
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.
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.
Particles of any solid substance, generally under 30 microns in size, often noted as PM30. There is special concern with PM1 which can get down to PULMONARY ALVEOLI and induce MACROPHAGE ACTIVATION and PHAGOCYTOSIS leading to FOREIGN BODY REACTION and LUNG DISEASES.
A member of the p300-CBP transcription factors that was originally identified as a binding partner for ADENOVIRUS E1A PROTEINS.
The portion of a retinal rod cell situated between the ROD INNER SEGMENT and the RETINAL PIGMENT EPITHELIUM. It contains a stack of photosensitive disk membranes laden with RHODOPSIN.
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.
Pollution prevention through the design of effective chemical products that have low or no toxicity and use of chemical processes that reduce or eliminate the use and generation of hazardous substances.
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)

3C technologies have enabled studies of the dynamics of high-order chromatin structures and long-range chromatin interactions (26-30). However, how these long-range interactions contribute to biological processes and human diseases is not well understood. Our research has focused on an enhancer containing the PCa risk-associated rs55958994 SNP, integrating higher-order chromatin structure data, gene expression profiling, and functional assays. Our results suggest that the rs55958994-containing enhancer regulates PCa progression through long-range interactions with multiple genes. Among these genes, ITGA5, CDH23, and CNTN1 were verified to be both regulated by the rs55958994-containing enhancer and associated with PCa progression; deletion of the enhancer region in PCa cells induced down-regulation of these target genes and led to defects in tumor initiation and migration and loss of CSCs.. Previous eQTL (expression quantitative trait locus) analyses suggested that rs55958994 is linked to KRT8 ...
DNA is wrapped around a histone octamer to form the basic unit of chromatin structure. During embryogenesis, dynamic changes of chromatin structure and chromatin modification occur after fertilization; subsequently, the epigenetic information is inherited through many rounds of the cell cycle. Thus, chromatin is essential for the determination of cell identity. Two strategies are used to modulate a chromatin environment: the covalent modification of histone tails and energy-dependent chromatin remodeling. The acetylation, methylation or phosphorylation of histone tails can have profound effects on chromatin structure and transcription (Jenuwein and Allis, 2001). Chromatin remodeling reactions are catalyzed by large protein complexes that use the energy of ATP hydrolysis to alter the structure or positioning of nucleosomes (Becker and Hörz, 2002; Clapier and Cairns, 2009). In addition to these events, histone variants play important roles in modulating chromatin structure (Henikoff and Ahmad, ...
Preparation of Chromatin Assembly Extracts from Preblastoderm Drosophila Embryos -- Analysis of Reconstituted Chromatin Using a Solid-Phase Approach -- In Vivo Chromatin Decondensation Assays: Molecular Genetic Analysis of Chromatin Unfolding Characteristics of Selected Proteins -- DNA Methyltransferase Probing of Chromatin Structure Within Populations and on Single Molecules -- Visualization of the Expression of HMGN Nucleosomal Binding Proteins in the Developing Mouse Embryo and in Adult Mouse Tissues -- Drug-Induced Premature Chromosome Condensation (PCC) Protocols: Cytogenetic Approaches in Mitotic Chromosome and Interphase Chromatin -- Analysis of DNA Topology in Yeast Chromatin -- Preparation and Analysis of Uniquely Positioned Mononucleosomes -- Monitoring DNA Breaks in Optically Highlighted Chromatin in Living Cells by Laser Scanning Confocal Microscopy -- Methods to Study Transcription-Coupled Repair in Chromatin -- Cytometric Analysis of DNA Damage: Phosphorylation of Histone H2AX as a ...
One of the longest standing problems in DNA repair is how cells relax chromatin in order to make DNA lesions accessible for global nucleotide excision repair (NER). Since chromatin has to be relaxed for efficient lesion detection, the key question is whether chromatin relaxation precedes lesion detection or vice versa. Chromatin accessibility factors have been proposed but not yet identified. Here we show that p53 acts as a chromatin accessibility factor, mediating UV-induced global chromatin relaxation. Using localized subnuclear UV irradiation, we demonstrate that chromatin relaxation is extended over the whole nucleus and that this process requires p53. We show that the sequence for initiation of global NER is as follows: transcription-associated lesion detection; p53-mediated global chromatin relaxation; and global lesion detection. The tumour suppressor p53 is crucial for genomic stability, a role partially explained by its pro-apoptotic capacity. We demonstrate here that p53 is also a ...
The THO complex is involved in transcription, genome stability, and messenger ribonucleoprotein (mRNP) formation, but its precise molecular function remains enigmatic. Under heat shock conditions, THO mutants accumulate large protein-DNA complexes that alter the chromatin density of target genes (heavy chromatin), defining a specific biochemical facet of THO function and a powerful tool of analysis. Here, we show that heavy chromatin distribution is dictated by gene boundaries and that the gene promoter is necessary and sufficient to convey THO sensitivity in these conditions. Single-molecule fluorescence insitu hybridization measurements show that heavy chromatin formation correlates with an unusually high firing pace of the promoter with more than 20 transcription events per minute. Heavy chromatin formation closely follows the modulation of promoter firing and strongly correlates with polymerase occupancy genome wide. We propose that the THO complex is required for tuning the dynamic of ...
Loss of function of CDKN2A/B, also known as INK4/ARF [encoding p16INK4A, p15INK4B, and p14ARF (mouse p19Arf)], confers susceptibility to cancers, whereas its up-regulation during organismal aging provokes cellular senescence and tissue degenerative disorders. To better understand the transcriptional regulation of p16INK4A, a CRISPR screen targeting open, noncoding chromatin regions adjacent to p16INK4A was performed in a human p16INK4A-P2A-mCherry reporter cell line. We identified a repressive element located in the 3′ region adjacent to the ARF promoter that controls p16INK4A expression via long-distance chromatin interactions. Coinfection of lentiviral dCas9-KRAB with selected single-guide RNAs against the repressive element abrogated the ARF/p16INK4A chromatin contacts, thus reactivating p16INK4A expression. Genetic CRISPR screening identified candidate transcription factors inhibiting p16INK4A regulation, including ZNF217, which was confirmed to bind the ARF/p16INK4A interaction loop. In ...
TY - JOUR. T1 - CAME. T2 - Identification of chromatin accessibility from nucleosome occupancy and methylome sequencing. AU - Piao, Yongjun. AU - Lee, Seong Keon. AU - Lee, Eun Joon. AU - Robertson, Keith D. AU - Shi, Huidong. AU - Ryu, Keun Ho. AU - Choi, Jeong Hyeon. PY - 2017/4/15. Y1 - 2017/4/15. N2 - Motivation: Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, Methyltransferase Accessibility Protocol for individual templates-Bisulfite Genome Sequencing (MAPit-BGS) and nucleosome occupancy and methylome sequencing (NOMe-seq) have been developed for simultaneously profiling chromatin accessibility and DNA methylation on single molecules. Therefore, there is a great demand in developing computational methods to identify chromatin ...
Here, we introduce the 3D Genome Browser, , which allows users to conveniently explore both their own and over 300 publicly available chromatin interaction data of different types. We design a new binary data format for Hi-C data that reduces the file size by at least a magnitude and allows users to visualize chromatin interactions over millions of base pairs within seconds. Our browser provides multiple methods linking distal cis-regulatory elements with their potential target genes. Users can seamlessly integrate thousands of other omics data to gain a comprehensive view of both regulatory landscape and 3D genome structure.
Two main chromatin assembly pathways ensure the proper transmission of chromatin organization and chromatin-based information throughout the cell cycle. A replication-dependent (RD) pathway that couples chromatin assembly to DNA synthesis and a replication-independent (RI) pathway. Whether these pathways contribute to the establishment of chromatin domains like heterochromatin or euchromatin by introducing modifications on histones or modulating chromatin structure remains unknown. Using Xenopus laevis egg extracts we monitored RD and RI chromatin assembly on single-stranded and double-stranded DNA templates. Even though RD assembly proceeded faster than RI assembly the histone content and saturation level with nucleosomes were similar. Despite these comparable topological features, the hydrodynamic behavior of both chromatin species in sucrose gradient centrifugation clearly differed. The RD assembled chromatin ran at lower sucrose concentrations than the RI created chromatin suggesting ...
Histones are responsible for packaging the genomes of almost all eukaryotes into fundamental repeating nucleosome units. The packaging must facilitate compaction into the cell nucleus but also enable dynamic access to the genome. A variety of mechanisms exist for targeting enzymes to undertake local opening of chromatin such as at active genes or for DNA repair. However, larger scale transitions in chromatin also occur where extended genome regions have altered chromatin organisation. This often involves abundant non-histone chromatin proteins that switch chromatin between states that are not well understood at the structural level. The contribution of highly basic non-histone chromatin proteins in vitro has been investigated using the HMGA2 protein implicated in human stem cell chromatin opening, and the Hematodinium DVNP protein which is suggested to replace histones as the dominant packaging protein in this dinoflagellate. These two proteins are compared to histone H1 which stabilises ...
1. Li X-Y, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD. The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol. 2011;12: R34. doi: 10.1186/gb-2011-12-4-r34 21473766. 2. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, et al. The accessible chromatin landscape of the human genome. Nature. 2012;489: 75-82. doi: 10.1038/nature11232 22955617. 3. Klemm SL, Shipony Z, Greenleaf WJ. Chromatin accessibility and the regulatory epigenome. Nat Rev Genet. 2019;20: 207-220. doi: 10.1038/s41576-018-0089-8 30675018. 4. Wu J, Huang B, Chen H, Yin Q, Liu Y, Xiang Y, et al. The landscape of accessible chromatin in mammalian preimplantation embryos. Nature. 2016;534: 652-657. doi: 10.1038/nature18606 27309802. 5. Clark SJ, Argelaguet R, Kapourani C-A, Stubbs TM, Lee HJ, Alda-Catalinas C, et al. scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in ...
The different chromatin features display distinct spatial patterns. It is thus worthwhile to explore the relationship between these patterns and the level of gene expression. Making use of RNA-seq data obtained from the different stages of C. elegans, we quantified the expression level of each gene. For each bin, we then calculated the correlation between the gene expression levels and the average signals of each chromatin feature of the bin. Figure 2b shows the spatial variation of these correlation coefficients around TSSs and TTSs. According to the correlation patterns, there are two main types of chromatin features: ones that are positively correlated with gene expression (such as H3K79me1, H3K79me2 and H3K79me3); and ones that are negatively correlated with gene expression (such as H3K9me2 and H3K9me3). While some features show largely uniform correlations across the 16-kb regions, some others are more variable across the regions. For example, H3K79me2 has a high correlation coefficient ...
Biomedical applications of high-throughput sequencing methods generate a vast amount of data in which numerous chromatin features are mapped along the genome. The results are frequently analysed by creating binary data sets that link the presence/absence of a given feature to specific genomic loci. However, the nucleosome occupancy or chromatin accessibility landscape is essentially continuous. It is currently a challenge in the field to cope with continuous distributions of deep sequencing chromatin readouts and to integrate the different types of discrete chromatin features to reveal linkages between them. Here we introduce the NucTools suite of Perl scripts as well as MATLAB- and R-based visualization programs for a nucleosome-centred downstream analysis of deep sequencing data. NucTools accounts for the continuous distribution of nucleosome occupancy. It allows calculations of nucleosome occupancy profiles averaged over several replicates, comparisons of nucleosome occupancy landscapes between
Chromatin fibers have been observed and measured in frozen hydrated sections of three types of cell (chicken erythrocytes and sperm of Patiria miniata and Thyone briareus) representing an approximately 20-bp range of nucleosomal repeat lengths. For sperm of the starfish P. miniata, it was possible to obtain images of chromatin fibers from cells that were swimming in seawater up to the moment of cryo-immobilization, thus providing a record of the native morphology of the chromatin of these cells. Glutaraldehyde fixation produced no significant changes in the ultrastructure or diameter of chromatin fibers, and fiber diameters observed in cryosections were similar to those recorded after low temperature embedding in Lowicryl K11M. Chromatin fiber diameters measured from cryosections of the three types of nuclei were similar, a striking contrast to the situation for chromatin isolated from these cell types, where a strong positive correlation between diameter and nucleosomal repeat length has been ...
Due to advances in molecular biology techniques, chromatin structure and function has re-emerged as a key research area in the investigation of gene regulation and expression. This indispensable new book provides the busy researcher with an overview of all the latest research in this important area. Topicality and breadth of coverage is assured by the contributions of an international group of over 30 leading scientists in this field. Contents list: Elements of chromatin structure: histones, nucleosomes, fibers; DNA structure: implications for chromatin structure and function; Replication and assembly; Promoter potentiation and activation: chromatin structure and transcriptional induction of heat shock genes; Initiation of expression: remodelling genes; Transcription on chromatin templates; Chromatin structure and epigenetic regulation in yeast; Epigenetic regulation in Drosophilia: a conspiracy of silence; Boundaries and domains; Epigenetic regulation in mammalian cells.Elgin, Sarah C. is the ...
There are variety of models and techniques to observe the presence of the 30nm fibers but it has been more observed that highly compacted chromatin fiber like 30nm fibers are not necessarily present for any gene regulation such as folding of DNA. Instead, 10 nm chromatin can be condensed enough into compacted domains through frequent bending and making 10nm fibers close to each other. In other words, it does not require to have 30nm fibers but is sufficient to have 10 nm chromatin fibers that is organized in genome to explain the complexities of nuclear organization and gene regulation. ...
Search and download thousands of Swedish university essays. Full text. Free. Essay: Moving Away from Proximal Ligation to Study Higher Order Chromatin Complexes at High Resolution.
Author(s): Chen, Song; Lake, Blue B; Zhang, Kun | Abstract: Single-cell RNA sequencing can reveal the transcriptional state of cells, yet provides little insight into the upstream regulatory landscape associated with open or accessible chromatin regions. Joint profiling of accessible chromatin and RNA within the same cells would permit direct matching of transcriptional regulation to its outputs. Here, we describe droplet-based single-nucleus chromatin accessibility and mRNA expression sequencing (SNARE-seq), a method that can link a cells transcriptome with its accessible chromatin for sequencing at scale. Specifically, accessible sites are captured by Tn5 transposase in permeabilized nuclei to permit, within many droplets in parallel, DNA barcode tagging together with the mRNA molecules from the same cells. To demonstrate the utility of SNARE-seq, we generated joint profiles of 5,081 and 10,309 cells from neonatal and adult mouse cerebral cortices, respectively. We reconstructed the transcriptome and
Chromatin compacts DNA to an extreme extend and allows eukaryotic genome fit the size of the nucleus. On the other hand, however, it must process the ability to untighten DNA and to permit the cellular machinery access to genome. Chromatin consists of nucleosomes in which a protein core is constituted by four canonical histones H2A, H2B, H3, H4 and wrapped around by 147 bp of DNA. Histone variants, and the chromatin remodelling machinery, can reorganize the compaction of chromatin and thus be important for epigenetic regulation of gene expression.. Histone variant H2A.Z is a universal mark of dynamic nucleosomes. H2A.Z is essential for growth, development and viability of a number of species including mammals. H2A.Z plays critical roles in multiple biological processes including gene transcription and replication, DNA repair, and genome integrity. The chromatin incorporation of H2A.Z is catalysed by SRCAP, an ATP-dependent, multi-component chromatin remodelling complex. The YL1 subunit of SRCAP ...
The epigenetics landscape of cells plays a key role in the establishment of cell-type specific gene expression programs characteristic of different cellular phenotypes. Different experimental procedures have been developed to obtain insights into the accessible chromatin landscape including DNase-seq, FAIRE-seq and ATAC-seq. However, current downstream computational tools fail to reliably determine regulatory region accessibility from the analysis of these experimental data. In particular, currently available peak calling algorithms are very sensitive to their parameter settings and show highly heterogeneous results, which hampers a trustworthy identification of accessible chromatin regions. Here, we present a novel method that predicts accessible and, more importantly, inaccessible gene-regulatory chromatin regions solely relying on transcriptomics data, which complements and improves the results of currently available computational methods for chromatin accessibility assays. We trained a hierarchical
The genetic information encoded by the DNA sequence, can be expressed in different ways. Genomic imprinting is an epigenetic phenomenon that results in monoallelic expression of imprinted genes in a parent of origin-dependent manner. Imprinted genes are frequently found in clusters and can share common regulatory elements. Most of the imprinted genes are regulated by Imprinting Control Regions (ICRs). H19/Igf2 region is a well known imprinted cluster, which is regulated by insulator function of ICR located upstream of the H19 gene. It has been proposed that the epigenetic control of the insulator function of H19 ICR involves organization of higher order chromatin interactions.. In this study we have investigated the role of post-translational modification in regulating insulator protein CTCF (CCCTC-binding factor). The results indicated novel links between poly(ADP-ribosyl)ation and CTCF, which are essential for regulating insulators function.. We also studied the higher order chromatin ...
TY - JOUR. T1 - Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns. AU - Srivastava, Divyanshi. AU - Mahony, Shaun. PY - 2019/1/1. Y1 - 2019/1/1. N2 - Transcription factors (TFs) selectively bind distinct sets of sites in different cell types. Such cell type-specific binding specificity is expected to result from interplay between the TFs intrinsic sequence preferences, cooperative interactions with other regulatory proteins, and cell type-specific chromatin landscapes. Cell type-specific TF binding events are highly correlated with patterns of chromatin accessibility and active histone modifications in the same cell type. However, since concurrent chromatin may itself be a consequence of TF binding, chromatin landscapes measured prior to TF activation provide more useful insights into how cell type-specific TF binding events became established in the first place. Here, we review the various sequence and chromatin ...
Abstract: To study the relation between chromatin structure and DNA function in detail it is necessary to have an in vitro procedure for assembling nucleosomes on a naked DNA template with properties similar to native chromatin. Such procedures exist for yeast and animal model systems but have not been developed for plants. The goal of this project was to lay the groundwork for developing a chromatin assembly extract from plants. Extracts from various plant materials were tested to determine their suitability for chromatin reconstitution. Tissues from plants are thought to have much higher levels of protease and nuclease activities than those of animals or yeast. Therefore, methods to determine the relative activity of proteases and nucleases had to be developed to determine if the template DNA, histones, and chromatin assembly proteins could survive the chromatin assembly reaction. Additionally, methods to streamline the isolation of maize nuclei and purification of histones were developed. ...
HI-TECH SOLUTIONS - Exporter, Importer, Manufacturer, Distributor & Supplier of Nuclear Chromatin Decondensation (N.C.D.) based in New Delhi, India
Employing a new algorithm for identifying differentially methylated regions (DMRs) from reduced representation bisulfite sequencing profiles, we identified 1972 hypermethylated and 3250 hypomethylated myogenic DMRs in a comparison of myoblasts (Mb) and myotubes (Mt) with 16 types of nonmuscle cell cultures. DMRs co-localized with a variety of chromatin structures, as deduced from ENCODE whole-genome profiles. Myogenic hypomethylation was highly associated with both weak and strong enhancer-type chromatin, while hypermethylation was infrequently associated with enhancer-type chromatin. Both myogenic hypermethylation and hypomethylation often overlapped weak transcription-type chromatin and Polycomb-repressed-type chromatin. For representative genes, we illustrate relationships between DNA methylation, the local chromatin state, DNaseI hypersensitivity, and gene expression. For example, MARVELD2 exhibited myogenic hypermethylation in transcription-type chromatin that overlapped a silenced promoter in Mb
TY - JOUR. T1 - The Hsp90 Molecular Chaperone Regulates the Transcription Factor Network Controlling Chromatin Accessibility. AU - Gvozdenov, Zlata. AU - Bendix, Lindsey D.. AU - Kolhe, Janhavi. AU - Freeman, Brian C.. PY - 2019/12/6. Y1 - 2019/12/6. N2 - Genomic events including gene regulation and chromatin status are controlled by transcription factors. Here we report that the Hsp90 molecular chaperone broadly regulates the transcription factor protein family. Our studies identified a biphasic use of Hsp90 in which early inactivation (15 min) of the chaperone triggered a wide reduction of DNA binding events along the genome with concurrent changes to chromatin structure. Long-term loss (6 h) of Hsp90 resulted in a decline of a divergent yet overlaying pool of transcription factors that produced a distinct chromatin pattern. Although both phases involve protein folding, the early point correlated with Hsp90 acting in a late folding step that is critical for DNA binding function, whereas ...
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Bysani M, Agren R, Davegårdh C, Volkov P, Rönn T, Unneberg P, Bacos K, Ling C Sci Rep 9 (1) - [2019-12-00; online 2019-05-23] Impaired insulin secretion from pancreatic islets is a hallmark of type 2 diabetes (T2D). Altered chromatin structure may contribute to the disease. We therefore studied the impact of T2D on open chromatin in human pancreatic islets. We used assay for transposase-accessible chromatin using sequencing (ATAC-seq) to profile open chromatin in islets from T2D and non-diabetic donors. We identified 57,105 and 53,284 ATAC-seq peaks representing open chromatin regions in islets of non-diabetic and diabetic donors, respectively. The majority of ATAC-seq peaks mapped near transcription start sites. Additionally, peaks were enriched in enhancer regions and in regions where islet-specific transcription factors (TFs), e.g. FOXA2, MAFB, NKX2.2, NKX6.1 and PDX1, bind. Islet ATAC-seq peaks overlap with 13 SNPs associated with T2D (e.g. rs7903146, rs2237897, rs757209, rs11708067 and ...
Chromatin is the template on which DNA-associated transactions take place in eukaryotic organisms. Nucleosomes consisting of the four histones H2A, H2B, H3 and H4 each organize 150bp of DNA and constitute a first layer of chromatin. The three-dimensional organization of chromatin as well as histone post-translational modifications (PTMs) regulate recruitment of chromatin-associated effector proteins (effectors). Heterochromatin protein 1 (HP1) is an effector associated with silenced genome regions. HP1 recognizes histone H3 trimethylated at lysine 9 (H3 K9me3) and can dimerize. This results in a protein with two binding domains allowing multivalent engagement of target chromatin. HP1 can further promote chromatin condensation and inter-fiber contacts. The effector p53 binding protein (53BP1) is a key regulator in the DNA damage repair pathway. It is known to target a trio of PTMs; H4 dimethylated at K20 (H4 K20me2), H2A(.X) ubiquitylated at K15 (H2A.X K15ub) and H2A.X phosphorylated at S139 ...
TY - JOUR. T1 - Transcription of isolated mouse liver chromatin. AU - Bacheler, Lee T.. AU - Smith, Kirby D.. PY - 1976. Y1 - 1976. N2 - Analysis of RNA transcription from isolated mouse liver chromatin has been undertaken by means of RN A-excess hybridizations with small amounts of radioactive DNA. This analysis indicates that mouse liver chromatin is a restricted template for the in vitro synthesis of RNA complements to repetitive DNA, but more RNA species are synthesized than are found in the RNA isolated from mouse liver nuclei. Extraction with 0.5 M NaCl destroys the template restriction of isolated chromatin. RNA synthesized in vitro from DNA or chromatin templates by Escherichia coli RNA polymerase, as well as in vivo mouse liver nuclear RNA, were each hybridized to 125I-labeled DNA of high, intermediate, or low reiteration frequency. Chromatin-primed and nuclear RNA saturate a smaller portion of each DNA fraction than does DNA-primed RNA. However, chromatin-primed RNA saturates more high ...
Principal Investigator: Oliver Bell. In metazoans, packaging of genomic DNA into the nucleosomal protein scaffold of chromatin provides an opportunity to tightly regulate accessibility and readout of the genetic information. In particular, chemical modifications of nucleosomes and DNA have emerged as important determinants of genome accessibility. However, the dynamic regulation of chromatin state and its contribution to epigenetic inheritance of gene expression has remained enigmatic and a key challenge in the field of chromatin biology.. We have developed a novel technology that allows for rapid addition and removal of chromatin regulatory activities to a gene locus in any murine cell type. The Chromatin in vivo Assay (CiA) employs small molecules, which simultaneously bind two distinct peptide domains to induce dimerization between a chromatin modifier and a DNA binding protein. The CiA approach provides high temporal control allowing us to study the kinetics and epigenetic memory of histone ...
Chromatin structure is influenced by multiples factors, such as pH, temperature, nature and concentration of counterions, post-translational modifications of histones and binding of structural non-histone proteins. RNA is also known to contribute to the regulation of chromatin structure as chromatin-induced gene silencing was shown to depend on the RNAi machinery in S. pombe, plants and Drosophila. Moreover, both in Drosophila and mammals, dosage compensation requires the contribution of specific non-coding RNAs. However, whether RNA itself plays a direct structural role in chromatin is not known. Here, we report results that indicate a general structural role for RNA in eukaryotic chromatin. RNA is found associated to purified chromatin prepared from chicken liver, or cultured Drosophila S2 cells, and treatment with RNase A alters the structural properties of chromatin. Our results indicate that chromatin-associated RNAs, which account for 2%-5% of total chromatin-associated nucleic acids, are polyA−
Author Summary Histones are the main protein components of chromatin. The N-terminal tails of histones stick out from the nucleosomes, the building blocks of chromatin, and are involved in the regulation of all DNA-dependent processes. Only Histone H2A has an additional C-terminal tail and currently very little is known about the function of this tail. The H2A C-terminus protrudes from the nucleosome and is located where the DNA enters and leaves the nucleosome. We show here that it can interact with the linker histone H1 that is important for higher order chromatin structure. We also find that this tail is involved in regulating nucleosome dynamics and mobility of H2A itself. The C-terminal H2A tail has also an important function in regulating the activity of chromatin remodelers, enzymes that can reposition nucleosomes. Furthermore we find that cells expressing C-terminally truncated H2A are more sensitive to stress, demonstrating that this tail is important for cellular homeostasis. Together our
The arrangement of compact chromatin of G0 lymphocytes was studied in three-dimensional reconstructions of the ensemble of the chromatin and of individual compact chromatin bodies. Rat spleen was seri
Background Chromatin organisation affects gene expression and regional mutation frequencies and contributes to carcinogenesis. Aberrant organisation of DNA has been correlated with cancer prognosis in analyses of the chromatin component of tumour cell nuclei using image texture analysis. As yet, the methodology has not been sufficiently validated to permit its clinical application. We aimed to define and validate a novel prognostic biomarker for the automatic detection of heterogeneous chromatin organisation. Methods Machine learning algorithms analysed the chromatin organisation in 461 000 images of tumour cell nuclei stained for DNA from 390 patients (discovery cohort) treated for stage I or II colorectal cancer at the Aker University Hospital (Oslo, Norway). The resulting marker of chromatin heterogeneity, termed Nucleotyping, was subsequently independently validated in six patient cohorts: 442 patients with stage I or II colorectal cancer in the Gloucester Colorectal Cancer Study (UK); 391 ...
Eukaryotic centromeres and telomeres are specialized chromosomal regions that share one common characteristic: their underlying DNA sequences are assembled into heritably repressed chromatin. Silent chromatin in budding and fission yeast is composed of fundamentally divergent proteins tat assemble very different chromatin structures. However, the ultimate behaviour of silent chromatin and the pathways that assemble it seem strikingly similar among Saccharomyces cerevisiae (S. cerevisiae), Schizosaccharomyces pombe (S. pombe) and other eukaryotes. Thus, studies in both yeasts have been instrumental in dissecting the mechanisms that establish and maintain silent chromatin in eukaryotes, contributing substantially to our understanding of epigenetic processes. In this review, we discuss current models for the generation of heterochromatic domains at centromeres and telomeres in the two yeast species.. ...
Scientists in Canada and the United States have used three-dimensional imaging techniques to settle a long-standing debate about how DNA and structural proteins are packaged into chromatin fibers. The researchers, whose findings are published in EMBO reports, reveal that the mouse genome consists of 10-nm chromatin fibers but did not find evidence for the wider 30-nm fibers that were previously thought to be important components of the DNA architecture.. DNA is an exceptionally long molecule that can reach several meters in length. This means it needs to be packaged into a highly compact state to fit within the limited space of the cell nucleus, said David Bazett-Jones, Senior Scientist at the Hospital for Sick Children, Toronto, and Professor at the University of Toronto, Canada. For the past few decades, scientists have favored structural models for chromatin organization where DNA is first wrapped around proteins in nucleosomes. In one possible model, the strand of repeating nucleosomes is ...
We describe an assay for transposase-accessible chromatin using sequencing (ATAC-seq), based on direct in vitro transposition of sequencing adaptors into native chromatin, as a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-s …
Posttranslational modifications play a key role in recruiting chromatin remodeling and modifying enzymes to specific regions of chromosomes to modulate chromatin structure. Alc1 (amplified in liver cancer 1), a member of the SNF2 ATPase superfamily with a carboxy-terminal macrodomain, is encoded by an oncogene implicated in the pathogenesis of hepatocellular carcinoma. Here we show that Alc1 interacts transiently with chromatin-associated proteins, including histones and the poly(ADP-ribose) polymerase Parp1. Alc1 ATPase and chromatin remodeling activities are strongly activated by Parp1 and its substrate NAD and require an intact macrodomain capable of binding poly(ADP-ribose). Alc1 is rapidly recruited to nucleosomes in vitro and to chromatin in cells when Parp1 catalyzes PAR synthesis. We propose that poly(ADP-ribosyl)ation of chromatin-associated Parp1 serves as a mechanism for targeting a SNF2 family remodeler to chromatin. ...
Chromatin is a complex polymer molecule in eukaryotic cells, primarily consisting of DNA and histones. Many works have shown that the 3D folding of chromatin structure plays an important role in DNA expression. The recently proposed Chro- mosome Conformation Capture technologies, especially the Hi-C assays, provide us an opportunity to study how the 3D structures of the chromatin are organized. Based on the data from Hi-C experiments, many chromatin 3D structure modeling methods have been proposed. However, there is limited ground truth to validate these methods and no robust chromatin structure alignment algorithms to evaluate the performance of these methods. In our work, we first made a thorough literature review of 25 publicly available population Hi-C-based chromatin 3D structure modeling methods. Furthermore, to evaluate and to compare the performance of these methods, we proposed a novel data simulation method, which combined the population Hi-C data and single-cell Hi-C data without ad ...
Beijing, China - Chromatin remodeling proteins (chromatin remodelers) are essential and powerful regulators for critical DNA-templated cellular processes, such as DNA replication, recombination, gene transcription/repression, and DNA damage repair. These molecular and genetic processes are important for a wide spectrum of cellular functions, including cell cycle, death, differentiation, pluripotency, and genome integrity. Recently, many scientific reports have shown that chromatin remodeling proteins could be promising new targets for the treatment of human malignancy.. This is a hot and exciting research topic for cancer researchers, and our article provides an updated understanding on the functions and mechanisms of chromatin remodelers in human cancers, says Dr. Chun Zhang, the principle investigator of the Department of Nuclear Medicine of Beijing Chao-Yang Hospital and Capital Medical University of China.. Chromatin remodeling is an energy-driven process in which chromatin remodelers use ...
The Chromatin, Replication and Chromosomal Stability Conference took place on June 20-21 in Stockholm, Sweden. In this article, I outline the broad scientific program of the meeting which reflected the wide diversity in epigenetics research. Distinct histone modifications are linked with specific chromatin structures and intranuclear positioning, thereby impacting replication timing and replication initiation, which in turn are related to gene expression and cell differentiation. Interference in any of these interconnected mechanisms can result in DNA breakage and lead to the activation of repair pathways. The DNA repair mechanisms again are influenced by the chromatin structure. In summary, the conference highlighted the functional implication of epigenetics in chromatin compaction, transcription regulation, replication control and DNA repair. The tight control of all these mechanisms defines the final cellular character.
In this report, we show that p53 is organized into two epigenetic domains with distinct chromatin structures, CpG methylation, histone compositions, and modifications, as well as associated regulatory factors. The open chromatin conformation, unmethylated CpG, and histone modifications associated the first domain are characteristic of an active chromatin, whereas the characteristics of the second domain, with full CpG methylation, nuclease resistance, and unacetylated histones, are reminiscent of inactive chromatin.. The promoter region has been known to be organized into a nucleosome-free structure (32), but whether this structure is due to the absence of histones or to a novel organization of the histone-DNA complex has not been investigated. The ChIP technique allows us to address this question, and we show that nuclease hypersensitivity and the absence of a nucleosomal DNA ladder in epigenetic domain I are associated with the depletion of the H2a/H2b dimer. Previous studies have shown that ...
TY - JOUR. T1 - ArchAlign. T2 - Coordinate-free chromatin alignment reveals novel architectures. AU - Lai, William K.M.. AU - Buck, Michael J.. PY - 2010/12/23. Y1 - 2010/12/23. N2 - To facilitate identification and characterization of genomic functional elements, we have developed a chromatin architecture alignment algorithm (ArchAlign). ArchAlign identifies shared chromatin structural patterns from high-resolution chromatin structural datasets derived from next-generation sequencing or tiled microarray approaches for user defined regions of interest. We validated ArchAlign using well characterized functional elements, and used it to explore the chromatin structural architecture at CTCF binding sites in the human genome. ArchAlign is freely available at AB - To facilitate identification and characterization of genomic functional elements, we have developed a chromatin architecture alignment algorithm (ArchAlign). ArchAlign identifies shared ...
Transposable elements (TEs) are major structural components of eukaryotic genomes; however, mobilization of TEs generally has negative effects on the host genome. To counteract this threat, host cells have evolved genetic and epigenetic mechanisms that keep TEs silenced. One such mechanism involves the Piwi-piRNA complex, which represses TEs in animal gonads either by cleaving TE transcripts in the cytoplasm or by directing specific chromatin modifications at TE loci in the nucleus. Most Piwi-interacting RNAs (piRNAs) are derived from genomic piRNA clusters. There has been remarkable progress in our understanding of the mechanisms underlying piRNA biogenesis. However, little is known about how a specific locus in the genome is converted into a piRNA-producing site. In this review, we will discuss a possible link between chromatin boundaries and piRNA cluster formation.
Methyl-CpG-binding protein 2 (MeCP2) is generally considered to act as a transcriptional repressor, whereas recent studies suggest that MeCP2 is also involved in transcription activation. To gain insight into this dual function of MeCP2, we assessed the impact of MeCP2 on higher-order chromatin structure in living cells using mammalian cell systems harbouring a lactose operator and reporter gene-containing chromosomal domain to assess the effect of lactose repressor-tagged MeCP2 (and separate MeCP2 domains) binding in living cells. Our data reveal that targeted binding of MeCP2 elicits extensive chromatin unfolding. MeCP2-induced chromatin unfolding is triggered independently of the methyl-cytosine-binding domain. Interestingly, MeCP2 binding triggers the loss of HP1gamma at the chromosomal domain and an increased HP1gamma mobility, which is not observed for HP1alpha and HP1beta. Surprisingly, MeCP2-induced chromatin unfolding is not associated with transcriptional activation. Our study suggests ...
A primary challenge in the H3K27M field has been to resolve the contradictory observations indicating that PRC2 has a high affinity for H3K27M peptides, yet PRC2 and H3K27M are often mutually excluded from chromatin in H3K27M DIPG (4, 6, 9, 10). Our studies revealed that interaction of H3K27M with PRC2 is a dynamic process that cannot be captured by static, steady-state approaches. Namely, there is an initial phase after H3K27M is expressed and incorporated into chromatin, followed by PRC2 recruitment to H3K27M-containing chromatin, presumably due to its higher affinity toward H3K27M (Fig. 2C). However, in the next phase, PRC2 is released from H3K27M, as they do not colocalize at steady-state conditions in both isogenic 293 T-REx systems (e.g., this study, Figs. 2 and 3) and the H3K27M DIPG themselves (6). This dynamic model therefore accommodates both the finding of high H3K27M and PRC2 affinity in select assays and their failure to be stably colocalized on chromatin in cells. In line with the ...
Methylation of DNA is one of the earliest described epigenetic modifications. Hypermethylation is associated with gene silencing, while the inhibition of methylation is generally associated with reactivating silenced genes. The packaging of DNA in the nucleus into chromatin also plays a role in regulating gene expression. We sought to understand the crosstalk between changes in methylation status of the genome and changes in chromatin structure. 5-azacytidine (5-azaC), a potent DNA methytransferase inhibitor, has recently generated interest as a potential anti-cancer drug, possibly functioning by reactivating silenced tumor suppressor genes. We treated the hematologic cancer cell lines U-937 and T-HP1 with 5-aza for varying lengths of time. We then harvested DNA for methylation studies, RNA for gene expression studies and chromatin for nuclease accessibility studies. The chromatin accessibility was further measured at two different levels of resolution; the domain level (10s of kb) and ...
The assembly of eukaryotic genomes into chromatin is a highly complex and delicate task; the cell must efficiently package and condense the DNA into the eukaryotic nucleus while maintaining specific regions of accessible chromatin to enable important functions with chromatin substrates. While the chromatin structure must remain highly dynamic in order to accommodate changes in the expression of some genes, it also serves to stably maintain the functional states of other genes through epigenetic mechanisms (45, 51). Recently, genetic and biochemical analyses have identified a broad class of multisubunit chromatin remodeling complexes which are likely to play important roles both in the process of chromatin opening and in the maintenance of chromatin in a dynamic or flexible state (26, 48, 53). These complexes remodel or reorganize nucleosomes in a wide range of in vitro assays which test for altered accessibility of nucleosomal DNA.. Nucleosome remodeling complexes are modular entities. The ...
TY - JOUR. T1 - Effects of chromatin structure on the enzymatic and DNA binding functions of DNA methyltransferases DNMT1 and Dnmt3a in vitro. AU - Robertson, Andrea K.. AU - Geiman, Theresa M.. AU - Sankpal, Umesh Tanaji. AU - Hager, Gordon L.. AU - Robertson, Keith D.. PY - 2004/9/10. Y1 - 2004/9/10. N2 - DNA methylation is an epigenetic modification of the genome critical for numerous processes, including transcriptional repression and maintenance of chromatin structure. Recent studies have revealed connections between DNA methylation and other epigenetic modifications such as ATP-dependent chromatin remodeling. It remains unclear, however, exactly how chromatin and epigenetic chromatin modifications affect the biological properties of the DNA methyltransferases (DNMT1, DNMT3A, and DNMT3B). Using a highly purified system and the 5S rDNA gene as free DNA or assembled into a mononucleosome, we have compared the effects of chromatin structure on DNMT1 and Dnmt3a. The catalytic efficiency for ...
TY - JOUR. T1 - Modeling apoptotic chromatin condensation in normal cell nuclei. Requirement for intranuclear mobility and actin involvement. AU - Widlak, Piotr. AU - Palyvoda, Olena. AU - Kumala, Slawomir. AU - Garrard, William T.. N1 - Copyright: Copyright 2008 Elsevier B.V., All rights reserved.. PY - 2002/6/14. Y1 - 2002/6/14. N2 - Hallmarks of the terminal stages of apoptosis are genomic DNA fragmentation and chromatin condensation. Here, we have studied the mechanism of condensation both in vitro and in vivo. We found that DNA fragmentation per se of isolated nuclei from non-apoptotic cells induced chromatin condensation that closely resembles the morphology seen in apoptotic cells, independent of ATP utilization, at physiological ionic strengths. Interestingly, chromatin condensation was accompanied by release of nuclear actin, and both condensation and actin release could be blocked by reversibly pretreating nuclei with Ca2+, Cu2+, diamide, or low pH, procedures shown to stabilize ...
BACKGROUND: ATP-dependent chromatin remodelling complexes are responsible for establishing and maintaining the positions of nucleosomes. Chromatin remodellers are targeted to chromatin by transcription factors and non-coding RNA to remodel the chromatin into functional states. However, the influence of chromatin remodelling on shaping the functional epigenome is not well understood. Moreover, chromatin remodellers have not been extensively explored as a collective group across two-dimensional and three-dimensional epigenomic layers. RESULTS: Here, we have integrated the genome-wide binding profiles of eight chromatin remodellers together with DNA methylation, nucleosome positioning, histone modification and Hi-C chromosomal contacts to reveal that chromatin remodellers can be stratified into two functional groups. Group 1 (BRG1, SNF2H, CHD3 and CHD4) has a clear preference for binding at actively marked chromatin and Group 2 (BRM, INO80, SNF2L and CHD1) for repressively marked chromatin. We find
DNA repair in the eukaryotic cell disrupts local chromatin organization. To investigate whether the resetting of nucleosomal arrays can be linked to the repair process, we developed model systems, with both Xenopus egg extract and human cell extracts, to follow repair and chromatin assembly in parallel on circular DNA templates. Both systems were able to carry out nucleotide excision repair of DNA lesions. We observed that UV-dependent DNA synthesis occurs simultaneously with chromatin assembly, strongly indicating a mechanistic coupling between the two processes. A complementation assay established that chromatin assembly factor I (CAF1) is necessary for this repair associated chromatin formation.. ...
Even relatively minor errors in chromatin remodeling during spermiogenesis are associated with sperm DNA damage and infertility, yet little is known about the etiology. Mice with severe NPYq deletions are infertile due to severe sperm differentiation defects (Ward and Burgoyne, 2006; Yamauchi et al., 2009). We have recently observed that sperm from these mice presented abnormal chromatin packaging and DNA damage. Moreover, when these sperm were injected into the oocytes, a significant increase of oocyte arrest at pronuclei stage and of chromosome aberrations in the fertilized eggs were noted (Yamauchi et al., 2010). Here we provide evidence that the deficiency of NPYq encoded gene Sly is associated with sperm DNA damage and poor sperm chromatin condensation, and propose that SLY plays a role in spermatid-specific chromatin remodeling.. How can Sly/SLY be involved in sperm DNA damage phenotype? SLY protein has been shown to control the postmeiotic expression of ,100 genes, the majority of which ...
Covalent modifications of histones and histone variants have great influence on chromatin structure, which is involved in the transcriptional regulation of gene expression. Chromatin immunoprecipitation (ChIP) is a powerful tool for studying in vivo DNA-histone interactions. Strawberry is a model for Rosaceae and non-climacteric fruits, in which histone modifications have been implicated to affect fruit development and ripening. However, a validated ChIP method has not been reported in strawberry, probably due to its high levels of polysaccharides which affect the quality of prepared chromatin and the efficiency of immunoprecipitation. We describe a native chromatin immunoprecipitation (N-ChIP) protocol suitable for strawberry by optimizing the parameters for nuclei isolation, chromatin extraction, DNA fragmentation and validation analysis using quantitative real-time PCR (qRT-PCR). The qRT-PCR results show that both the active mark H3K36me3 and the silent mark H3K9me2 are efficiently immunoprecipitated
The chromatin remodeling complexes alter chromatin structures. They remodel nucleosomes in ATP-dependent manner and have essential roles in DNA damage repair, recombination, replication and transcriptional control. Increasing evidences indicate that subunits of chromatin remodelers are mutated and/or deregulated in a number of human cancers, and how they influence the cancer gene expression program during cancer initiation and progression is becomming clearer. Therefore, chromatin remodeling complexes arose as promising new targets for the treatment of human cancers. In this review, chromatin remodeling complexes, their epigenetic reader domains and available inhibitors are described. The insights into the misregulated chromatin remodelers pathways in human malignancies and the novel approach targeting deregulated chromatin remodelers to improve chemotherapy efficiency are discussed. ...
The activity of a single gene is influenced by the composition of the chromatin in which it is embedded. Nucleosome turnover, conformational dynamics, and covalent histone modifications each induce changes in the structure of chromatin and its affinity for regulatory proteins. The dynamics of histone modifications and the persistence of modification patterns for long periods are still largely unknown. In this study, we present a stochastic mathematical model that describes the molecular mechanisms of histone modification pattern formation along a single gene, with non-phenomenological, physical parameters. We find that diffusion and recruitment properties of histone modifying enzymes together with chromatin connectivity allow for a rich repertoire of stochastic histone modification dynamics and pattern formation. We demonstrate that histone modification patterns at a single gene can be established or removed within a few minutes through diffusion and weak recruitment mechanisms of histone modification
TY - JOUR. T1 - Alleviation of historic H1-mediated transcriptional repression and chromatin compaction by the acidic activation region in chromosomal protein HMG-14. AU - Ding, Hanfei. AU - Bustin, Michael. AU - Hansen, Ulla. PY - 1997/10/1. Y1 - 1997/10/1. N2 - Histone H1 promotes the generation of a condensed, transcriptionally inactive, higher-order chromatin structure. Consequently, historic H1 activity must be antagonized in order to convert chromatin to a transcriptionally competent, more extended structure. Using simian virus 40 minichromosomes as a model system, we now demonstrate that the nonhistoric chromosomal protein HMG-14, which is known to preferentially associate with active chromatin, completely alleviates historic H1-mediated inhibition of transcription by RNA polymerase II. HMG-14 also partially disrupts histone H1-dependent compaction of chromatin. Both the transcriptional enhancement and chromatin-unfolding activities of HMG-14 are mediated through its acidic, C-terminal ...
De novo chromatin assembly maintains histone density on the daughter strands in the wake of the replication fork. The heterotrimer chromatin assembly factor 1 (CAF-1) couples DNA replication to histone deposition in vitro, but is not essential for yeast cell proliferation. Depletion of CAF-1 in human cell lines demonstrated that CAF-1 was required for efficient progression through S-phase. Cells lacking CAF-1 accumulated in early and mid S-phase and replicated DNA slowly. The checkpoint kinase Chk1, but not Chk2, was phosphorylated in response to CAF-1 depletion, consistent with a DNA replication defect. CAF-1-depleted cell extracts completely lacked DNA replication-coupled chromatin assembly activity, suggesting that CAF-1 is required for efficient S-phase progression in human cells. These results indicate that, in contrast to yeast, human CAF-1 is necessary for coupling chromatin assembly with DNA replication.. ...
TY - JOUR. T1 - Analysis of chromatin structure by in vivo formaldehyde cross-linking. AU - Orlando, Valerio. AU - Strutt, Helen. AU - Paro, Renato. PY - 1997/2. Y1 - 1997/2. N2 - Recent advances leave no doubt that higher order chromatin structures play a fundamental role in many developmentally important mechanisms of gene regulation. In particular analyses in genetic model systems like yeast and Drosophila uncovered novel proteins that are involved in the regulation of chromatin structures. Many of these proteins do not bind directly to DNA but interact in large multimeric complexes. To identify the DNA elements regulated by these multiprotein complexes, alternative approaches to the standard methods of DNA-protein analysis had to be devised. Here we present a method that preserves the architecture of the higher order chromatin structures by crosslinking cells in vivo with formaldehyde. An immunoprecipitation strategy is then used to identify the DNA targets of chromosomal proteins of ...
Current models suggest that tissue-specific genes are arranged in discrete, independently controlled segments of chromatin referred to as regulatory domains. Transition from a closed to open chromatin structure may be an important step in the regulation of gene expression. To determine whether the human alpha-globin cluster, like the beta-globin cluster, lies within a discrete, erythroid-specific domain, we have examined the long-range genomic organization and chromatin structure around this region. The alpha genes lie adjacent to at least four widely expressed genes. The major alpha-globin regulatory element lies 40 kb away from the cluster within an intron of one of these genes. Therefore, unlike the beta cluster, cis-acting sequences controlling alpha gene expression are dispersed within a region of chromatin that is open in both erythroid and nonerythroid cells. This implies a difference in the hierarchical control of alpha- and beta-globin expression.
P-266. Study question: What is the impact of selecting spermatozoa with the highest chromatin integrity on ICSI outcomes? Summary answer: We selected spermatozoa with the highest progressive motility and chromatin integrity by microfluidic sperm selection (MFSS) and achieved superior implantation and delivery rates. What is known already: Sperm preparation methods aim at providing specimens for insemination with the highest progressive motility independent of phenotypic and genomic integrity. It has recently been recognized that a microfluidics device yielded spermatozoa with the highest progressive motility as well as superior chromatin integrity. Here we compared two sperm selection methods: density gradient centrifugation (DGC) and MFSS. Study design, size, duration: From October 2016 to January 2020, ejaculates that were processed by DGC and MFSS for ICSI treatment from 8 consenting men were screening for DNA fragmentation by TUNEL. In addition, ejaculates from 22 men were processed solely ...
A fraction of rat-liver chromatin that is transcriptionally active in vivo has been purified 6- to 7-fold over whole chromatin. This was accomplished by selectively shearing chromatin with DNase II followed by fractionating the released portion on the basis of its solubility properties in 2 mM MgCl2. The resulting soluble material comprises 11% of the total chromatin DNA and is impoverished in histone and enriched in nonhistone protein. Compared with unsheared chromatin, this minor fraction exhibits marked differences in chromosomal protein species. DNA renaturation studies indicate that this fraction is composed of a specific subset of whole genomal DNA sequences. Furthermore, DNA·RNA hybridization experiments suggest that almost 60% of the nonrepetitious DNA sequences of this minor fraction could code for cellular RNA. ...
DNase I hypersensitive site assay is perhaps the most widely used assay for detection of changes in chromatin structure. Studies of many spatially or temporally regulated genes, such as P-globin, have revealed the correlation of formation of DNase I hypersensitive sites with the status of transcription (22). This assay has also been used extensively in analyses of chromatin structure in injected Xenopus oocytes (24). Although the mechanism for the formation of DNase I hypersensitive sites is still not fully understood, the detection of DNase I hypersensitive sites are widely interpreted as results of chromatin remodeling induced by the binding of transcription factors.. 1. Inject 15-20 oocytes with DNA and with or without mRNA encoding TR/RXR (100 ng/ pL, 27.6 nL/oocyte) and treated with or without 50 nM T3. Incubate the oocytes overnight at 18°C incubator.. 2. Collect healthy oocytes and wash the oocytes once with 500 pL of MBSH buffer.. 3. To 15-20 oocytes, add 240 pL of DNase I buffer. ...
The Drosophila MSL complex mediates dosage compensation by increasing transcription of the single X chromosome in males approximately two-fold. This is accomplished through recognition of the X chromosome and subsequent acetylation of histone H4K16 on X-linked genes. Initial binding to the X is thought to occur at entry sites that contain a consensus sequence motif (MSL recognition element or MRE). However, this motif is only similar to 2 fold enriched on X, and only a fraction of the motifs on X are initially targeted. Here we ask whether chromatin context could distinguish between utilized and non-utilized copies of the motif, by comparing their relative enrichment for histone modifications and chromosomal proteins mapped in the modENCODE project. Through a comparative analysis of the chromatin features in male S2 cells (which contain MSL complex) and female Kc cells (which lack the complex), we find that the presence of active chromatin modifications, together with an elevated local GC ...
Retroviral integration depends on the interaction between intasomes, host chromatin and cellular targeting cofactors as LEDGF/p75 or BET proteins. Previous studies indicated that the retroviral integrase, by itself, may play a role in the local integration site selection within nucleosomal target DNA. We focused our study on this local association by analyzing the intrinsic properties of various retroviral intasomes to functionally accommodate different chromatin structures in the lack of other cofactors. Using in vitro conditions allowing the efficient catalysis of full site integration without these cofactors, we show that distinct retroviral integrases are not equally affected by chromatin compactness. Indeed, while PFV and MLV integration reactions are favored into dense and stable nucleosomes, HIV-1 and ASV concerted integration reactions are preferred into poorly dense chromatin regions of our nucleosomal acceptor templates. Predicted nucleosome occupancy around integration sites identified in
The DNase I accessibility and chromatin organization of genes within the nucleus do correlate to their transcriptional activity. Here, we show that both serum starvation and overexpression of Tip5, a key regulator of ribosomal RNA gene (rDNA) repression, dictate DNase I accessibility, facilitate the association of rDNA with the nuclear matrix and thus regulate large-scale rDNA chromatin organization. Tip5 contains four AT-hooks and a TAM (Tip5/ARBP/MBD) domain, which were proposed to bind matrix-attachment regions (MARs) of the genome. Remarkably, the TAM domain of Tip5 functions as nucleolar localization and nuclear matrix targeting module, whereas AT-hooks do not mediate association with the nuclear matrix, but they are required for nucleolar targeting. These findings suggest a dual role for Tip5s AT-hooks and TAM domain, targeting the nucleolus and anchoring to the nuclear matrix, and suggest a function for Tip5 in the regulation of higher-order rDNA chromatin structure. ...
Thyroid hormone (T3) plays diverse roles in adult organ function and during vertebrate development. The most important stage of mammalian development affected by T3 is the perinatal period when plasma T3 level peaks. Amphibian metamorphosis resembles this mammalian postembryonic period and is absolutely dependent on T3. The ability to easily manipulate this process makes it an ideal model to study the molecular mechanisms governing T3 action during vertebrate development. T3 functions mostly by regulating gene expression through T3 receptors (TRs). Studies in vitro, in cell cultures and reconstituted frog oocyte transcription system have revealed that TRs can both activate and repress gene transcription in a T3-dependent manner and involve chromatin disruption and histone modifications. These changes are accompanied by the recruitment of diverse cofactor complexes. More recently, genetic studies in mouse and frog have provided strong evidence for a role of cofactor complexes in T3 signaling in vivo.
Thyroid hormone (T3) plays diverse roles in adult organ function and during vertebrate development. The most important stage of mammalian development affected by T3 is the perinatal period when plasma T3 level peaks. Amphibian metamorphosis resembles this mammalian postembryonic period and is absolutely dependent on T3. The ability to easily manipulate this process makes it an ideal model to study the molecular mechanisms governing T3 action during vertebrate development. T3 functions mostly by regulating gene expression through T3 receptors (TRs). Studies in vitro, in cell cultures and reconstituted frog oocyte transcription system have revealed that TRs can both activate and repress gene transcription in a T3-dependent manner and involve chromatin disruption and histone modifications. These changes are accompanied by the recruitment of diverse cofactor complexes. More recently, genetic studies in mouse and frog have provided strong evidence for a role of cofactor complexes in T3 signaling in vivo.
The acidic patch is a highly electronegative cleft on the histone H2A-H2B dimer in the nucleosome. It is a fundamental motif for protein binding and chromatin dynamics, but the cellular impact of targeting this potentially therapeutic site with exogenous molecules remains unclear. Here, we characterize a family of binuclear ruthenium compounds that selectively target the nucleosome acidic patch, generating intra-nucleosomal H2A-H2B cross-links as well as inter-nucleosomal cross-links. In contrast to cisplatin or the progenitor RAPTA-C anticancer drugs, the binuclear agents neither arrest specific cell cycle phases nor elicit DNA damage response, but rather induce an irreversible, anomalous state of condensed chromatin that ultimately results in apoptosis. In vitro, the compounds induce misfolding of chromatin fibre and block the binding of the regulator of chromatin condensation 1 (RCC1) acidic patch-binding protein. This family of chromatin-modifying molecules has potential for applications ...
ABSTRACT DNA in the eukaryotic nucleus is complexed with histone and non-histone proteins into chromatin. Nucleosomes, the basic repeating unit of chromatin, not only package DNA but are also intimately involved the regulation of gene expression. All DNA transactions including replication, transcription, recombination and repair take place in such a chromatin environment. Access to packaged nucleosomal DNA in vivo is mediated at least in part by protein complexes that modify or remodel chromatin. Buried sequences in nucleosomes can also transiently become accessible to DNA binding proteins during cycles of partial, reversible unwrapping of nucleosomal DNA from the histone octamer. We have investigated the ability of the human, bifunctional DNA glycosylase, endonuclease III (hNTH1), to initiate base excision repair (BER) of discretely positioned oxidative lesions in model nucleosomes. hNTH1 was able to process a thymine glycol (Tg) lesion almost as efficiently as naked DNA, when the minor groove of the
Recent genome-wide analyses of yeast and human chromatin revealed the widespread prevalence of DNase I hypersensitive sites (DNase I HSs) at gene regulatory regions with possible roles in eukaryotic gene regulation. The presence of DNase I HSs in plants has been described for only a few genes, and we analyzed the chromatin structure of an 80 kb genomic region containing 30 variably expressed genes by DNase I sensitivity assay at 500 bp resolution in Arabidopsis. Distinct DNase I HSs were found at the 5′ and/or 3′ ends of most genes irrespective of their expression levels. Further analysis of well-characterized genes showed that the DNase I HSs occurred near cis-regulatory elements in the promoters of these genes. Upon transcriptional activation of a heat-inducible gene, the DNase I HS was extended into the vicinity of a cis-element and adjacent TATA element in the promoter. Concomitant with this change in DNase I HS, histones were acetylated, removed from the promoter, and a transcription ...
T. kodakarensis MNase digestion. T. kodakarensis strain KOD1 [22] was cultivated under anaerobic conditions at 85 °C and an insoluble unfixed chromatin fraction prepared from cells at the late‐log/stationary‐phase transition [10]. Chromatin was digested with 1 unit/ml of MNase, or 0.1 units/ml of DNase I for 1 h at 37 °C in the presence of 10 μg/μl RNase A. De‐proteinized genomic DNA was digested with 0.03 units/ml of MNase [10].. S. cerevisiae MNase digestion. EUROSCARF wild‐type reference strain BY4742 was grown and chromatin digestion (pooled triplicate samples) performed as described [11], with chromatin in unfixed detergent‐permeabilised yeast spheroplasts incubated with 600 units/ml of MNase for 3 min at 37 °C. Illumina DNA sequencing. NEBNext DNA sample prep master mix set 1 was used for Illumina adaptor ligation. Adaptor ligates were size selected on polyacrylamide gels to preserve the size distribution of the fragments before sequencing in 100 nucleotide paired end mode ...
Since their discovery in the mid-1990s, nuclear actin-related proteins (ARPs) have gained attention for their roles as structural components of ATP-dependent chromatin-remodeling complexes. These remodelers can move nucleosomes along the DNA, evict them from chromatin, and exchange histone variants to alter chromatin states locally. Chromatin-remodeling facilitates DNA-templated processes such as transcription regulation, DNA replication, and repair. Consistent with a role for ARPs in shaping chromatin structure, recent genetic studies show that they affect developmental and cell-type specific transcriptional programming. Here, we focus on recent results that suggest a specific contribution of ARPs to long-range interactions in the nucleus, and review evidence indicating that some ARPs may act independently of chromatin-remodeling machines.. ...
It has been a puzzle how decondensed interphase chromosomes remain essentially unknotted. The natural expectation is that in the presence of type II DNA topoisomerases that permit passages of double-stranded DNA regions through each other, all chromosomes should reach the state of topological equilibrium. The topological equilibrium in highly crowded interphase chromosomes forming chromosome territories would result in formation of highly knotted chromatin fibres. However, Chromosome Conformation Capture (3C) methods revealed that the decay of contact probabilities with the genomic distance in interphase chromosomes is practically the same as in the crumpled globule state that is formed when long polymers condense without formation of any knots. To remove knots from highly crowded chromatin, one would need an active process that should not only provide the energy to move the system from the state of topological equilibrium but also guide topoisomerase-mediated passages in such a way th
B138 Background: Treatment of breast cancer cells with histone deacetylase (HDAC) inhibitors results in chromatin decondensation and the sensitization of cancer cells to DNA damaging agents such as topoisomerase II inhibitors. We previously reported that the HDAC inhibitors induced chromatin decondensation through the down-regulation of heterochromatin maintenance proteins such as heterochromatin protein 1 (HP1), structural maintenance of chromatin proteins (SMC) 1-5 and DNA methyltransferase 1 (DNMT1). Here we report the role of HDAC2 in the expression of heterochromatin maintenance proteins, chromatin decondensation and DNA damage induced by topoisomerase inhibition. Methods: HDAC2 was selectively depleted using siRNA transfection. HDAC2 depleted cells were evaluated by microarray and Western blot analysis for changes in HP1, DNMT1 and SMC mRNA and protein expression. Chromatin decondensation was evaluated by electron microscopy. DNA damage and cell death induced by the topoisomerase ...
Component of the gypsy chromatin insulator complex which is required for the function of the gypsy chromatin insulator and other endogenous chromatin insulators. Chromatin insulators are regulatory elements which establish independent domains of transcriptional activity within eukaryotic genomes. Insulators have two defining properties; they can block the communication between an enhancer and a promoter when placed between them and can also buffer transgenes from position effect variegation (PEV). Insulators are proposed to structure the chromatin fiber into independent domains of differing transcriptional potential by promoting the formation of distinct chromatin loops. This chromatin looping may involve the formation of insulator bodies, where homotypic interactions between individual subunits of the insulator complex could promote the clustering of widely spaced insulators at the nuclear periphery. Within the gypsy insulator complex, this protein may directly bind to insulator DNA at sites distinct
Gene expression is tightly regulated at the level of transcription through cooperation between cis-regulatory elements and trans-factors that bind to the regulatory elements. Together, these factors regulate the higher order chromatin structure which establishes domains that organize the genome and coordinate gene expression. However, the molecular mechanisms controlling transcription of individual loci within a topological domain (TAD) are not fully understood. The cystic fibrosis transmembrane conductance regulator (CFTR) gene provides a paradigm for investigating these mechanisms. CFTR occupies a TAD bordered by CTCF/cohesin binding sites within which are cell-type-selective cis-regulatory elements for the locus. We showed previously that intronic and extragenic enhancers, when occupied by specific transcription factors, are recruited to the CFTR promoter by a looping mechanism to drive gene expression. Here we use a combination of CRISPR/Cas9 editing of cis-regulatory elements and ...
We have shown for the first time that the function of CAF-1 is important for viability following double-strand DNA repair. Furthermore, CAF-1 functions genetically in both homologous recombination and NHEJ, and its function during double-strand DNA repair is dependent on the interaction between CAF-1 and PCNA. Given the biochemical role of CAF-1 in DNA synthesis-coupled chromatin assembly, we propose that CAF-1 mediates chromatin assembly during double-strand DNA repair in vivo.. We have observed sensitivity of CAF-1 mutants to a variety of double-strand DNA-damaging agents. A systematic analysis of the yeast deletion collection also isolated the cac2Δ as a mutant sensitive to MMS (Chang et al. 2002). Similarly, mutants of the genes encoding Arabidopsis CAF-1, fas1, and fas2 are sensitive to MMS (Takeda et al. 2004). Given the role of CAF-1 in chromatin assembly during NER of single-strand lesions and the sensitivity of CAF-1 mutants to UV irradiation (Gaillard et al. 1996; Kaufman et al. 1997; ...
TY - JOUR. T1 - Chromatin immunoprecipitation for studying transcriptional regulation in Xenopus oocytes and tadpoles.. AU - Stewart, David. AU - Tomita, Akihiro. AU - Shi, Yun Bo. AU - Wong, Jiemin. N1 - Copyright: This record is sourced from MEDLINE/PubMed, a database of the U.S. National Library of Medicine. PY - 2006. Y1 - 2006. N2 - Understanding the accurate temporal and spatial regulation of gene expression during development requires knowledge of the spectrum of transcription factors and cofactors involved and their functional interplay with chromatin. Chromatin immunoprecipitation (ChIP) has become a powerful technique that allows us to do so. A typical ChIP assay involves (1) treating cells or tissues with formaldehyde to rapidly crosslink chromatin-associated proteins to DNA, (2) shearing chromatin by sonication into small fragments, (3) immunoprecipitation of the proteins of interest, (4) reversal of crosslinking, and (5) quantitating the specific associated DNA sequences by PCR. ...
Project Synopsis:|br/||br/|Marketlines Company Mergers & Acquisitions (M&A), Partnerships & Alliances and Investments reports offer a comprehensive breakdown of the organic and inorganic growth activity undertaken by an organization to sustain its competitive advantage.|br/||br/|Project Description:|br/||br/|Marketlines Chromatin, Inc. Mergers & Acquisitions (M&A), Partnerships & Alliances and Investments report includes business description, detailed reports on mergers and acquisitions (M&A), divestments, capital raisings, venture capital investments, ownership and partnership transactions undertaken by Chromatin, Inc. since January 2007.|br/||br/|Scope:|br/||br/|- Provides intelligence on Chromatin, Inc.s M&A, strategic partnerships and alliances, capital raising and private equity transactions.|br/|- Detailed reports of various financial transactions undertaken by Chromatin, Inc. and its subsidiaries since 2007.|br/|- Information about key financial and legal advisors for Chromatin, Inc.s
Eukaryotic organisms package DNA into chromatin for compact storage in the cell nucleus, but this packaging process results in transcriptional repression of genes. Chromatin remodeling complexes have evolved to overcome the transcriptional repression caused by chromatin packaging of DNA into nucleosomes by histones. One example of a chromatin remodeling complex is the SWI/SNF complex in yeast which uses ATP to drive the chromatin apart and make DNA accessible to transcription factors. The yeast SWI2 protein was discovered as the catalytic subunit of the yeast SWI/SNF chromatin remodeling complex and is required for the complex to counteract the repressive nature of chromatin. BRG1 and BRM, SWI2 homologs, are part of human chromatin remodeling complexes and have been shown to play a redundant role in the regulation of certain cell cycle and cellular adhesion genes, as well as cellular pathways. Recent studies showing loss of BRG1 in human tumor cell lines and primary tissue samples, BRG1 ...
And demembranated X. laevis sperm,chromatin decondensation and nuclear membrane assembly had been observed. Demembranation was obtained in the identical manner as in the study described above. In each instances,micrococcal nuclease digestion was utilised to confirm nucleosome formation.plant D-3263 (hydrochloride) web cytoplasm and Animal chromatinBecause Xenopus sperm is deficient in H histones,exposure to micrococcal nuclease results in heterogeneous distribution of DNA fragment sizes. When Xenopus sperm nuclei had been incubated with Nicotiana ovule extracts,the chromatin proteins could be replaced by histones derived from Nicotiana ovules,resulting in remodeling on the chromatin structure. In both situations,nuclear remodeling and nucleosome assembly have been observed,suggesting that transcription variables andor cyclincdk complexes originating in the plant cytoplasm may well contribute towards the induction of nuclear reconstitution and chromatin formation. Having said that,complex ...
RNA Polymerase II (RNAP II) is recruited to core promoters by the pre-initiation complex (PIC) of general transcription factors. Within the PIC, transcription factor for RNA polymerase IIB (TFIIB) determines the start site of transcription. TFIIB binding has not been localized, genome-wide, in metazoans. Serial analysis of chromatin occupancy (SACO) is an unbiased methodology used to empirically identify transcription factor binding regions. In this report, we use TFIIB and SACO to localize TFIIB binding regions across the rat genome. A sample of the TFIIB SACO library was sequenced and 12,968 TFIIB genomic signature tags (GSTs) were assigned to the rat genome. GSTs are 20-22 base pair fragments that are derived from TFIIB bound chromatin. TFIIB localized to both non-protein coding and protein-coding loci. For 21% of the 1783 protein-coding genes in this sample of the SACO library, TFIIB binding mapped near the characterized 5 promoter that is upstream of the transcription start site (TSS). However,
The 3D structure of chromatin in the nucleus is important for gene expression and regulation. Chromosomal conformation capture techniques, such as Hi-C, generate large amounts of data showing interaction points on the genome but these are hard to interpret using standard tools. We have developed CSynth, a high performance 3D genome browser and real time chromatin restraint-based modeller to visualise dynamic and interactive models of chromatin capture data. CSynth does its calculations in the GPU hence is much faster than existing modelling software to infer and visualise the chromatin structure which also allow real-time interaction with the modelling parameters. It also allows straightforward comparison of interaction data and the results of third party 3D modelling outputs. In addition we include an option to view and manipulate these complicated structures using Virtual Reality (VR) allowing scientists to immerse themselves in the models for further understanding. This VR component has also proven
Oligodendrocyte precursor cells (OPCs) constitute the main proliferative cells in the adult brain, and deregulation of OPC proliferation-differentiation balance results in either glioma formation or defective adaptive (re)myelination. OPC differentiation requires significant genetic reprogramming implicating chromatin remodeling. Mounting evidence indicates that chromatin remodelers play important roles during normal development and their mutations are associated with neurodevelopmental defects, with CHD7 haploinsuficiency being the cause of CHARGE syndrome and CHD8 being one of the strongest Autism Spectrum Disorder (ASD) high-risk associated genes. Here, we report on uncharacterized functions of the chromatin remodelers Chd7 and Chd8 in OPCs. Their OPC-chromatin-binding profile combined with transcriptome and chromatin accessibility analyses of Chd7-deleted OPCs, demonstrates that Chd7 protects non-proliferative OPCs from apoptosis by chromatin-closing and transcriptional repression of p53.
It is becoming increasingly evident that the cellular response towards DNA damage is affected by the structure of the chromatin region surrounding the damage site [1], while at the same time the chromatin structure is affected by the damage response [2]. DNA double-strand breaks (DSBs) elicit a response in an Mbp-large chromatin region surrounding the break that involves alterations in several post-translational modifications (PTMs). Phosphorylation of histone variant H2AX at serine 139 (S139) to yield γ-H2AX is a hallmark step in the cellular response to DSB. The γ-H2AX chromatin domains, which can be visualized as ionizing radiation induced foci (IRIF), delineate regions where a large variety of signalling and repair proteins accumulate [3].. Immunofluorescence detection of PTMs demonstrated alterations in several modifications in the γ-H2AX domain following DSB induction that are associated with regulation of chromatin accessibility, recruitment of DNA damage response factors, and ...
In eukaryotic cells DNA is associated with histones and other proteins to form chromatin. The basic unit of chromatin is the nucleosome consisting of 140 bp of DNA wrapped around an octameric core of the four conserved histones H2A, H2B, H3 and H4.The relatively unstructured and highly charged N-terminal tail domains of histones, are central to the processes that modulate chromatin structure. A diverse and elaborate array of post-translational modifications that include acetylation, phosphorylation, methylation, ubiquitination and ADP-ribosylation, occur on the N-terminal tail domains of histones. Acetylation of lysine residues within these N-terminal domains by histone acetyl-transferases (HATs), is associated with transcriptional activation. This modification results in remodeling of the nucleosome structure into an open conformation more accessible to transcription complexes. In most species, histone H3 is primarily acetylated at lysines 9, 14, 18 and 23. Acetylation at lysine 9 appears to
Chromatin is the complex combination of DNA and proteins that makes up chromosomes.[1][2] It is found inside the nuclei of eukaryotic cells. Chromatin is divided into heterochromatin (condensed) and euchromatin (extended) forms.[3][4] Heterochromatin is composed mostly of satellite DNA tandem repeats. The active components of chromatin are DNA and histone proteins, although other proteins also occur.[5] The functions of chromatin are: ...
Abstract. NETosis, a form of cell death that manifests by the release of decondensed chromatin to the extracellular space, provides valuable insights into mechanisms and consequences of cellular demise. Because extracellular chromatin can immobilize microbes, the extended nucleohistone network was called a neutrophil extracellular trap (NET), and the process of chromatin release was proposed to serve an innate immune defense function. Extracellular chromatin NETs were initially observed in studies of neutrophils and are most prominent in these types of granulocytes. Subsequent studies showed that other granulocytes and, in a limited way, other cells of the innate immune response may also release nuclear chromatin following certain kinds of stimulation. Variations of NETosis were noted with cells that remain temporarily motile after the release of chromatin. Numerous stimuli for NETosis were discovered, including bacterial breakdown products, inflammatory stimuli, particulate matter, certain ...
Antisense transcription is widespread in genomes. Despite large differences in gene size and architecture, we find that yeast and human genes share a unique, antisense transcription-associated chromatin signature. We asked whether this signature is related to a biological function for antisense transcription. Using quantitative RNA-FISH, we observed changes in sense transcript distributions in nuclei and cytoplasm as antisense transcript levels were altered. To determine the mechanistic differences underlying these distributions, we developed a mathematical framework describing transcription from initiation to transcript degradation. At GAL1, high levels of antisense transcription alter sense transcription dynamics, reducing rates of transcript production and processing, while increasing transcript stability. This relationship with transcript stability is also observed as a genome-wide association. Establishing the antisense transcription-associated chromatin signature through disruption of the Set3C
ARONOW. Stepwise chromatin restructuring and unexpected rules for interaction of distributed cis-elements that form a locus control region in vivo. Catherine Ley-Ebert, Carolyn Florio, John Maier, Chris Cost and Bruce Aronow. Childrens Hospital Research Foundation and the University of Cincinnati, Cincinnati, Ohio, USA. We have performed a mutational analysis of the human adenosine deaminase (ADA) gene thymic locus control region in transgenic mice using CAT reporter genes. We examined in detail gene expression, chromatin structure based on low and high resolution MNase and DNAse hypersensitivity, restriction enzyme accessibility, and histone acetylation state analyses using chromatin immune precipitations. Mutations and perturbations of LCR cis-elements led to variably compromised LCR function and the formation of several common distinguishable chromatin structures.. Our results suggest that the ADA thymic LCR is formed by the interaction of distributed cis-elements that consist of a 200 97bp ...
This organism was chosen because it has epigenetically defined regional centromeres whose chromatin and protein compositions are similar to those of their human counterparts, to identify factors responsible for the replacement of histone H3 with CENP-A at centromeres.. In this report, the KAIST research group systematically analyzed the roles of the ATP-dependent chromatin-remodelers in the centromeric chromatin assembly of fission yeast as they serve as strong candidates for such factors ...
Chromatin, Chromatid, Chromsome Terminology - posted in General Biology Discussion: Some Questions to which I have found different/conflicting answers depending on what I have read or who I have talked to. Thanks in Advance. 1-Chromatin, chromosomes, and chromatid all consist of DNA AND some sort of proteins? 2-Is the following statement accurate: ALL types/forms of chromatin material and chromatids consist of chromosomes BUT not all types of chromosomes are chromatin or chromatids? 3-An...
... increasing chromatin compaction and repressing spurious transcription.[65][66][67] Increased chromatin compaction prevents ... Chromatin regulation[edit]. Histones undergo posttranslational modifications that alter their interaction with DNA and nuclear ... These minor histones usually carry out specific functions of the chromatin metabolism. For example, histone H3-like CENPA is ... Clarke HJ (1992). "Nuclear and chromatin composition of mammalian gametes and early embryos". Biochemistry and Cell Biology. 70 ...
Chromatin remodeling[edit]. Histone acetyltransferases serve many biological roles inside the cell. Chromatin is a combination ... Controlling the chromatin remodeling process within cancer cells may provide a novel drug target for cancer research.[30] ... For PCAF, these include the non-histone chromatin (high-mobility group (HMG)) proteins HMG-N2/HMG17 and HMG-I(Y), the ... p300/CBP have many non-histone substrates, including the non-histone chromatin proteins HMG1, HMG-N1/HMG14, and HMG-I(Y), the ...
... of proteins on Chromatin[edit]. The in vivo model mentioned above clearly explains 3-D and 1-D diffusion ... Bénichou O, Chevalier C, Meyer B, Voituriez R (January 2011). "Facilitated diffusion of proteins on chromatin". Phys. Rev. Lett ... After calculating the search time for a target protein, alternating between the 3-D and 1-D diffusion phases on the chromatin ... Just like prokaryotic cells, in eukaryotes, facilitated diffusion occurs in the nucleoplasm on chromatin filaments, accounted ...
Chromatin immunoprecipitation (ChIP) is a method used to determine the location of DNA binding sites on the genome for a ... Similar to chromatin immunoprecipitation (ChIP) outlined above, but rather than targeting DNA binding proteins as in ChIP, an ... Chromatin+immunoprecipitation at the US National Library of Medicine Medical Subject Headings (MeSH) ...
Single cell transposes-accessible chromatin sequencing maps chromatin accessibility across the genome. A transposase inserts ... Single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq)[edit]. Main article: ATAC-seq ... 4 Single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq) ... sequencing adapters directly into open regions of chromatin, allowing those regions to be amplified and sequenced.[39] ...
Main article: Chromatin. Darlington in his classic works on genetics[25][26] discussed hysteresis of the chromosomes, by which ...
Mutations in the TATA box region affects the binding of the TATA-binding protein (TBP) for transcription initiation, which may cause carriers to have a disease phenotype. Gastric cancer is correlated with TATA box polymorphism.[39] The TATA box has a binding site for the transcription factor of the PG2 gene. This gene produces PG2 serum, which is used as a biomarker for tumours in gastric cancer. Longer TATA box sequences correlates with higher levels of PG2 serum indicating gastric cancer conditions. Carriers with shorter TATA box sequences may produce lower levels of PG2 serum. Several neurodegenerative disorders are associated TATA box mutations.[40] Two disorders have been highlighted, spinocerebellar ataxia and Huntington's disease. In spinocerebellar ataxia, the disease phenotype is caused by expansion of the polyglutamine repeat in the TATA-binding protein (TBP). An accumulation of these polyglutamine-TBP cells will occur, as shown by protein aggregates in brain sections of patients, ...
... chromatin dynamics; structural biology; advanced proteomics; mass spectrometry; advanced microscopy. ...
An example of a repressor protein is the methionine repressor MetJ. MetJ interacts with DNA bases via a ribbon-helix-helix (RHH) motif.[2] MetJ is a homodimer consisting of two monomers, which each provides a beta ribbon and an alpha helix. Together, the beta ribbons of each monomer come together to form an antiparallel beta-sheet which binds to the DNA operator ("Met box") in its major groove. Once bound, the MetJ dimer interacts with another MetJ dimer bound to the complementary strand of the operator via its alpha helices. AdoMet binds to a pocket in MetJ that does not overlap the site of DNA binding. The Met box has the sequence AGACGTCT which is a palindrome (it shows dyad symmetry) allowing the same sequence to be recognised on either strand of the DNA. The junction between C and G in the middle of the Met box contains a pyrimidine-purine step that becomes positively supercoiled forming a kink in the phosphodiester backbone. This is how the protein checks for the recognition site as it ...
"Epigenetics & Chromatin. 12 (1): 40. doi:10.1186/s13072-019-0285-6. ISSN 1756-8935. PMC 6604379. PMID 31266517.. ... The hypothesis is that chromatin-DNA interactions are guided by combinations of histone modifications. While it is accepted ... Many of the histone tail modifications correlate very well to chromatin structure and both histone modification state and ... These recruited proteins then act to alter chromatin structure actively or to promote transcription. For details of gene ...
Histone acetylation alters chromatin structure. Shown in this illustration, the dynamic state of histone acetylation/ ... Winston F, Allis CD (July 1999). "The bromodomain: a chromatin-targeting module?". Nature Structural Biology. 6 (7): 601-4. doi ... Lysines on the amino terminal tails of histones have a tendency to weaken the chromatin's overall structure. Addition of an ... Suggested by the idea that the structure of chromatin can be modified to allow or deny access of transcription activators, ...
m6A and m4C methyltransferases are found primarily in prokaryotes (although recent evidence has suggested that m6A is abundant in eukaryotes[1]). m5C methyltransfereases are found in some lower eukaryotes, in most higher plants, and in animals beginning with the echinoderms. The m6A methyltransferases (N-6 adenine-specific DNA methylase) (A-Mtase) are enzymes that specifically methylate the amino group at the C-6 position of adenines in DNA. They are found in the three existing types of bacterial restriction-modification systems (in type I system the A-Mtase is the product of the hsdM gene, and in type III it is the product of the mod gene). These enzymes are responsible for the methylation of specific DNA sequences in order to prevent the host from digesting its own genome via its restriction enzymes. These methylases have the same sequence specificity as their corresponding restriction enzymes. These enzymes contain a conserved motif Asp/Asn-Pro-Pro-Tyr/Phe in their N-terminal section, this ...
Chromatin remodeling: from transcription to cancer.Cancer Genet. 2014 Sep;207(9):352-7. ... The mechanism behind this could be competition for the same polymerases, or chromatin modification. Divergent transcription ... Possible mechanisms behind this regulation include sequences in the promoter region, chromatin modification, and the spatial ... ENCODE threads Explorer RNA and chromatin modification patterns around promoters. Nature (journal) ...
Huntington's disease (HD) is an inherited neurodegenerative disorder, with symptoms emerging during an individual's mid-adulthood. The most noticeable symptoms of this progressive disease are cognitive and motor impairments, as well as behavioral alterations.[11] These impairments can develop into dementia, chorea, and eventually death. At the molecular level, HD results from a mutation in the huntingtin protein (Htt). More specifically, there is an abnormal repetition of a CAG sequence towards the 5'-end of the gene, which then leads to the development of a toxic polyglutamine (polyQ) stretch in the protein. The mutated Htt protein affects an individual's proper neural functions by inhibiting the action of REST/NRSF. REST/NRSF is an important silencer element that binds to regulatory regions to control the expression of certain proteins involved in neural functions. The mechanistic actions of huntingtin are still not fully understood, but a correlation between Htt and REST/NRSF exists in HD ...
... inactive chromatin, termed heterochromatin. This link between DNA methylation and chromatin structure is very important. In ... In yeast at least, H3K36me3 recruits enzymes such as histone deacetylases to condense chromatin and prevent the activation of ... Methylated DNA immunoprecipitation (MeDIP), analogous to chromatin immunoprecipitation, immunoprecipitation is used to isolate ... such as histone deacetylases and other chromatin remodeling proteins that can modify histones, thereby forming compact, ...
These pauses may be intrinsic to the RNA polymerase or due to chromatin structure.[citation needed] ...
Chromatin regulation[change , change source]. DNA on outside winding round histone on inside. View from top through helical ... For example, each human cell has about 1.8 meters of DNA, but wound on the histones it has about 90 millimeters of chromatin, ... Clarke HJ (1992). "Nuclear and chromatin composition of mammalian gametes and early embryos". Biochem. Cell Biol. 70 (10-11): ... They are the chief protein components of chromatin, the active component of chromosomes. ...
Chromatin structure inhibition is the process wherein the promoter is hidden by chromatin structure. Chromatin structure is ... Chromatin structure-oriented factors are more complex than for initiation control. Often the chromatin-altering factor becomes ... See: chromatin, histone, and nucleosome. *RNA Pol II catalysis improving factors. Improve the Vmax or Km of RNA Pol II, so ... See: chromatin, histone, and nucleosome. These methods of control can be combined in a modular method, allowing very high ...
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 4 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 ...
"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, ...
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 ...
Histones are proteins which are involved in the folding and compaction of the chromatin. There are several different types of ... 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 ... Razin A (September 1998). "CpG methylation, chromatin structure and gene silencing-a three-way connection". The EMBO Journal. ...
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 ...
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 ...
... and chromatin. This occurs through the synthesis of a new nuclear envelopes that forms around the chromatin which is gathered ... The nuclear envelope is broken down in this stage, long strands of chromatin condense to form shorter more visible strands ... Chromatin. 7 (1): 25. doi:10.1186/1756-8935-7-25. PMC 4247682. PMID 25435919. Hetzer MW (March 2010). "The nuclear envelope". ... at each pole and the reformation of the nucleolus as the chromosomes decidedness their chromatin back to the loose state it ...
Chromatin. 13 (1): 12. doi:10.1186/s13072-020-00334-y. ISSN 1756-8935. PMC 7059380. PMID 32138783. Wang, Qin; Dai, Tianyue; Sun ...
Jeanteur, Philippe (2008). Epigenetics and Chromatin. Springer. ISBN 9783540852360. Kaneko S, Li G, Son J, Xu CF, Margueron R, ... Heterochromatin is tightly packed chromatin which limits the accessibility of transcription machinery to the underlying DNA, ... Chromatin. 6 (1): 3. doi:10.1186/1756-8935-6-3. PMC 3606351. PMID 23448518. Martin C, Zhang Y (2005). "The diverse functions of ... due to PRC2/EZH2-EED-mediated H3K27 methylation and subsequent recruitment of PRC1 which facilitates condensation of chromatin ...
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 ...
ChromDB Contains 9,341 chromatin-associated proteins, including RNAi-associated proteins, for a broad range of organisms. ... CREMOFAC Contains 1725 redundant and 720 non-redundant chromatin-remodeling factor sequences in eukaryotes. The Krembil Family ... "ChromDB::Chromatin Database". Archived from the original on 2019-04-10. Retrieved 2010-01-29. Cremofac http://www.epigenomics. ...
The Relationship Between Chromatin Structure and DNA Damage in Mammalian Spermatozoa Kenneth Dominguez, Chris D. R. Arca, W. ... Sperm Chromatin Dispersion Test: Technical Aspects and Clinical Applications Jaime Gosálvez, Carmen López-Fernández, José Luís ... Assisted reproductive technologies Chromatin DNA DNA repair Histones Male gamete morphogenesis Male infertility Nucleoproteins ... Sperm Chromatin Structure Assay (SCSA®): 30 Years of Experience with the SCSA® ...
... everything you need for studying or teaching Chromatin. ... Immediately download the Chromatin summary, chapter-by-chapter ... Chromatin Chromatin is a network of deoxyribonucleic acid (DNA) and nucleoproteins that constitutes a chromosome. Chromatin can ... Chromatin Chromatin is a network of deoxyribonucleic acid (DNA) and nucleoproteins that constitutes a chromosome. Chromatin can ...
... compact fibre called chromatin. An extreme example of the ordered folding and compaction that chromatin can undergo is seen ... during cell division, when the chromatin of each chromosome condenses and is divided between two daughter cells (see below Cell ... Other articles where Chromatin is discussed: cell: DNA packaging: …a dense, ... a dense, compact fibre called chromatin. An extreme example of the ordered folding and compaction that chromatin can undergo is ...
... because chromatin reconstituted with purified histones differs from chromatin assembled in vivo. Reconstituted chromatin lacks ... S1 A and B) (10, 11). PHO5 chromatin isolated in this way was indistinguishable from chromatin at the chromosomal locus on the ... Dependence of chromatin transcription on protein factors and acetyl-CoA. (A) Repressed PHO5 chromatin was transcribed as in Fig ... C) Effect of gcn5 bromoΔ SAGA on chromatin transcription. Repressed (pho4Δ) PHO5 chromatin was transcribed as in Fig. 1C with ...
Reflecting this singular role for chromatin, numerous approaches have evolved in the laboratory over the past three decades to ... Chromatin is of central importance to gene regulation in eukaryotes. ... Chromatin is of central importance to gene regulation in eukaryotes. Reflecting this singular role for chromatin, numerous ... Analysis of Chromatin Structure in Plant Cells Mala Singh, Amol Ranjan, Krishan Mohan Rai, Sunil Kumar Singh, Verandra Kumar, ...
Chromatin definition, the readily stainable substance of a cell nucleus, consisting of DNA, RNA, and various proteins, that ... chromatin. Historical Examples. of chromatin. *. While these changes are going on in the chromatin the Amphiaster forms. ... Origin of chromatin. First recorded in 1880-85; chromat- + -in2. Related formschro·ma·tin·ic, adjectivechro·ma·toid, adjective ... Word Origin and History for chromatin. n.. protoplasm in cell nuclei, 1882, from German, coined 1879 by German anatomist ...
A chromatin loop forms when an enhancer and a promoter, two widely separated elements in a DNA sequence, come into contact as ... A chromatin loop forms when an enhancer and a promoter, two widely separated elements in a DNA sequence, come into contact as ...
Protocols for reconstitution of chromatin on solid supports for analysis, preparation of positioned mononucleosomes, techniques ... this thorough volume is organized such that it begins with techniques related to the study of chromatin structure. ... Analysis of DNA Replication Associated Chromatin Decondensation: In Vivo Assay for Understanding Chromatin Remodeling ... Chromatin Protocols. Editors. * Srikumar P. Chellappan Series Title. Methods in Molecular Biology. Series Volume. 1288. ...
Chromatin rules.. Li Y1, Huang S1.. Author information. 1. 1 Department of Biochemistry and Molecular Biology, University of ... Binding of pioneer transcription factors remodels the repressive chromatin and leads to H3K4me1 poised enhancers. The H3K4me1 ... lineage/cell-specific enhancers are silent by repressive chromatin structure. ...
To investigate rDNA chromatin we have applied a technique called Chromatin Endogenous Cleavage (ChEC) (Schmid et al., 2004). In ... Most importantly the chromatin structure of the isolated material conserves important features of the chromatin in vivo (Figure ... Chromatin is defined as the entity composed of the DNA - encoding the genetic information - and associated proteins. Chromatin ... Below you find more details about our work on rDNA chromatin, PHO5 chromatin and the isolation of native chromosomal domains. ...
Chromatin definition, the readily stainable substance of a cell nucleus, consisting of DNA, RNA, and various proteins, that ... chromatin. *. During the resting stage this chromatin material may have the form of a thread, or may form a network of fibres ( ... chromaticity coordinates, chromaticity diagram, chromaticness, chromatics, chromatid, chromatin, chromatin body, chromatism, ... A brief account of a chromatin element resembling the accessory chromosome in Sagitta has been added for comparison. ...
Long strands of chromatin are usually bundled loosely within the nucleus.A single strand of chromatin is made up of a long ... The copies stay attached as the chromatin is packaged into chromatids. The 2 identical form a chromosome. ... involved in many aspects of how your body looks and how it works.The DNA in the nucleus is part of a material called chromatin ... What is chromatin and where is it found?. Chromatin is a combination of protein and DNA. Chromatin is found in the nucleus of ...
New live-cell imaging technique allows Northwestern University researchers to study chromatins dynamic processes, including ... Understanding chromatins cancer connection New nanoscale imaging technique allows researchers to study chromatin in live cells ... understanding-chromatins-cancer-connection.. html More in Technology & Engineering. * New UTSA study shows wearable technology ... "We know that chromatin is a major player in complex diseases," Backman said. "We just havent had the techniques to study it. ...
Definition of chromatin nucleolus. Provided by Stedmans medical dictionary and Includes medical terms and ...
This makes it possible for users to perform Chromatin immunoprecipitation (ChIP) assays using only 1000 cells per ... Chromatin immunoprecipitation. The Chromatrap® ChIP-seq Protein A kit (Cat no 500189) was used for ChIP in accordance with the ... Chromatin preparation. For the study the human endometrial carcinoma cell line Hec50 (Holinka et al., 1996) was utilized for ... Sometimes samples are small, cell types can be hard to come by or are difficult because they offer only a low chromatin yield. ...
... To mark the 2013 BioMed Central Epigenetics & Chromatin: Interactions and ... UpSETing chromatin during non-coding RNA production The packaging of eukaryotic DNA into nucleosomal arrays permits cells to ... Epigenetics & Chromatin: interactions and processes On 11 to 13 March 2013, BioMed Central will be hosting its inaugural ... The processes of chromatin disassembly and reassembly during DNA replication also h... ...
... and other approaches allow researchers to study chromatin structure and DNA-binding interactions to determine how they regulate ... At UMass, Randos lab is also performing comparative analyses of chromatin maps, with an eye to chromatin behavior. If you only ... so we can assess what we call chromatin gaps where there are sequence variants that act in cis to regulate the open chromatin ... whether at the chromatin level or at the DNA--binding level. "The technology completely revolutionized the whole chromatin ...
Thank you for your interest in participating in the 2020 Asilomar Chromatin, Chromosomes, & Epigenetics Conference (ACCEC)!. ... eventbrite registration link: ...
... point toward a novel function for tRNA genes and a common mechanism of compartmentalizing and organizing eukaryotic chromatin. ... Chromatin barriers restrict silenced chromatin domains from invading active domains. A recent study shows that a tRNA gene ... Chromatin barriers restrict silenced chromatin domains from invading active domains. A recent study shows that a tRNA gene ... the Unit on Chromatin and Transcription, National Institute of Child Health and Human Development, US National Institutes of ...
... of chromatin organization and then proceeds to describe the process of chromatin remodeling through a review of chromatin ... This Teaching Resource provides lecture notes and slides for a class covering chromatin remodeling mechanisms and is part of ... of chromatin organization and then proceeds to describe the process of chromatin remodeling through a review of chromatin ... of chromatin organization and then proceeds to describe the process of chromatin remodeling through a review of chromatin ...
Tag: Chromatin. The Sherpas: 7 biofuels feedstock developers clearing paths to the summit. October 9, 2012 , Jim Lane ... Chromatins Yield Machine: is instant gene-stacking a game-changer for energy crops?. [ 0 ] January 19, 2011 , admin ... Chromatin launches new SweetFuel sorghum hybrids at BioPro. [ 0 ] March 15, 2011 , admin ... Chromatin sorghum hybrids top trials for sugar yields. [ 0 ] February 16, 2011 , admin ...
Covers basic chromatin biology, imprinting at a genome-wide level, and epigenomics in disease biology and epidemiology, making ... The neurobiology of chromatin-associated mechanisms in the context of psychosis and mood spectrum disorders. 30. Genome-wide ... Part I. Basics of Chromatin Biology and Biochemistry:. 1. Introduction to epigenomics. 2. Epigenetics and its historical ... 3-D quantitative DNA methylation imaging for chromatin texture analysis in pharmacoepigenomics and toxicoepigenomics. Part IV. ...
Bipolar meiotic spindle formation without chromatin.. Brunet S1, Polanski Z, Verlhac MH, Kubiak JZ, Maro B. ... Non-specific chromatin is sufficient, however, to promote spindle assembly in Xenopus cell-free extracts that contain ... We found that a bipolar spindle can form in vivo in the absence of any chromatin due to the establishment of interactions ...
2014) Chromatin accessibility: A window into the genome. Epigenetics Chromatin 7(1):33. ... Here, we identify the small portion (,1%) of the maize genome residing in open chromatin. We demonstrate that open chromatin ... DNA methylation rates also closely mirror the chromatin accessibility landscape. Cytosine hypomethylation of open chromatin is ... Given that our results support intergenic functional variation explained almost exclusively by open chromatin, these chromatin ...
This up-to-date volume includes protocols that illustrate the broad use of chromatin immunoprecipitation (ChIP) and ChIP- ... Chromatin Immunoprecipitation. Methods and Protocols. Editors: Visa, Neus, Jordán-Pla, Antonio (Eds.) ... Chromatin Immunoprecipitation from Mouse Embryonic Tissue or Adherent Cells in Culture, Followed by Next-Generation Sequencing ... Includes cutting-edge techniques for the study of chromatin immunoprecipitation. *Provides step-by-step detail essential for ...
Modification of the chromatin landscape in fungal secondary metabolite clusters allows for a simple technological means to ... Chromatin-level regulation of biosynthetic gene clusters. *Jin Woo Bok1. na1, ... Chromatin-dependent regulation of secondary metabolite biosynthesis in fungi: is the picture complete? *Jérôme Collemare ... Deleting a Chromatin Remodeling Gene Increases the Diversity of Secondary Metabolites Produced by Colletotrichum higginsianum * ...
... These oversize outdoor citronella candles have insect-repelling mojo without the harsh aroma. The six ...
Transcription/Chromatin. Session: Structural Transitions in Chromatin - An Exploration of Mechanisms. • DNA Accessibility in ... The "Transcription/Chromatin" annual meeting theme will contain sessions titled: "Structural Transitions in Chromatin - An ... A session titled "Alternative Chromatin Structures" will illuminate the fact that nucleosome and chromatin structure is ... functions in the context of chromatin and is regulated by its multilayered structural organization. Likewise, chromatin ...
Thank you for your interest in spreading the word about Science.. NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.. ...
Recent chromatin publications and news] Protocol for in vitro Chromatin Assembly ENCODE threads Explorer Chromatin patterns at ... Elements of chromatin structure: histones, nucleosomes, and fibres, p. 1-26. In S. C. R. Elgin (ed.), Chromatin structure and ... When the chromatin decondenses, the DNA is open to entry of molecular machinery. Fluctuations between open and closed chromatin ... The precise structure of the chromatin fiber in the cell is not known in detail. This level of chromatin structure is thought ...
  • exists in the form of chromatin, which is made up of DNA bound to histones (simple alkaline proteins) and other nonhistone proteins. (
  • Transcription of chromatin requires an additional 20 proteins beyond those required for the transcription of naked DNA. (
  • Chromatin isolated from the chromosomal locus of the PHO5 gene of yeast in a transcriptionally repressed state was transcribed with 12 pure proteins (80 polypeptides): RNA polymerase II, six general transcription factors, TFIIS, the Pho4 gene activator protein, and the SAGA, SWI/SNF, and Mediator complexes. (
  • Reconstituted chromatin lacks the patterns of histone modification, histone variants, and nonhistone proteins shown to play important roles in transcription in vivo. (
  • Chromatin is defined as the entity composed of the DNA - encoding the genetic information - and associated proteins. (
  • A single strand of chromatin is made up of a long strand of DNA that is coiled around proteins. (
  • To help put this puzzle together, Backman has developed a new way to image chromatin, a complex of macromolecules -- including DNA, RNA, and proteins -- within living cells that house genetic information and determines which genes get expressed. (
  • Chromatin mapping and DNA-protein binding studies are being used to ask basic biological questions, including those about the behavior of nucleosomes - those beads on a string - and how proteins interact with DNA to regulate gene expression. (
  • Michelle D. Wang (Investigator, Howard Hughes Medical Institute, Cornell University) will discuss mechanical studies of nucleosome stability and structure and how DNA in nucleosomes may be accessed by motor proteins that are responsible for transcription-related chromatin remodeling. (
  • In general, there are three levels of chromatin organization: DNA wraps around histone proteins, forming nucleosomes and the so-called beads on a string structure (euchromatin). (
  • Epigenetic modification of the structural proteins in chromatin via methylation and acetylation also alters local chromatin structure and therefore gene expression. (
  • Histone proteins are the basic packers and arrangers of chromatin and can be modified by various post-translational modifications to alter chromatin packing (histone modification). (
  • Polycomb-group proteins play a role in regulating genes through modulation of chromatin structure. (
  • This message is to announce the creation of a new WWW resource deidicated to spreading information regarding the study of chromatin structure, with emphasis on the proteins that modify chromatin structure, and the effects that these modifications have on cell function. (
  • Our work focuses on the role of LLPS of nuclear proteins with chromatin as a possible mechanism for silencing genes through heterochromatin formation. (
  • The cover art of the February 4th issue of Biophysical Journal highlights LLPS of histone proteins and chromatin in the cell nucleus using a minimalist and abstract representation. (
  • One of the main interests of our lab is the role of LLPS of chromatin and nuclear proteins in genome organization and function. (
  • Chromatin immunoprecipitation (ChIP) is a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. (
  • Briefly, the conventional method is as follows: DNA and associated proteins on chromatin in living cells or tissues are crosslinked (this step is omitted in Native ChIP). (
  • citation needed] Cross-linked ChIP is mainly suited for mapping the DNA target of transcription factors or other chromatin-associated proteins, and uses reversibly cross-linked chromatin as starting material. (
  • The immunoprecipitated complexes (i.e., the bead-antibody-protein-target DNA sequence complex) are then collected and washed to remove non-specifically bound chromatin, the protein-DNA cross-link is reversed and proteins are removed by digestion with proteinase K. An epitope-tagged version of the protein of interest, or in vivo biotinylation can be used instead of antibodies to the native protein of interest. (
  • This LDXXLDAYM region (where X is any amino acid) is duplicated in the C terminus of chromatin target of PRMT1 protein (also known as Fop), which are chromatin-associated proteins that co-localise with facultative heterochromatin and are critical for oestrogen-dependent gene activation [ PMID: 19858291 ]. (
  • Chromatin is a dense, complex fibrous structure composed of associated proteins and molecules of deoxyribonucleic acid, or DNA, which contains the genetic material of an organism. (
  • New findings on the roles of chromatin, their interacting proteins and post-translational modifications, their numerous transcriptional properties and their role in development also will be addressed. (
  • Chromatin is the complex combination of DNA and proteins that makes up chromosomes . (
  • The active components of chromatin are DNA and histone proteins, although other proteins also occur. (
  • As the fundamental subunit of chromatin, nucleosomes form a chain of small ellipsoidal beads of histone proteins around which the DNA is circumscribed. (
  • These changes to the chromatin structure, called chromatin remodeling, may facilitate gene transcription by loosening the histone-DNA complex, allowing other proteins such as transcription factors access to the DNA. (
  • Chromatin remodeling is typically initiated by posttranslational modification of the amino acids that make up the histone proteins, as well as through methylation of neighboring DNA. (
  • This technology, developed by Ulrich Laemmi, a professor of molecular biology at the University of Geneva, involves DNA-binding molecules that act to change the structure of chromatin, the complex formed by DNA and the proteins to make chromosomes. (
  • Chromatin immunoprecipitation (ChIP) experiments examine histone modifications and genomic DNA sequences bound to specific regulatory proteins. (
  • The human genome is packaged into chromatin, which is composed of numerous proteins that help control gene expression, DNA replication and repair, and genome stability. (
  • The contributors describe how histone proteins, histone-modifying enzymes, chromatin remodelers, transcriptional regulatory complexes, enhancer-associated factors, and signaling proteins are dysregulated in cancer pathogenesis. (
  • Within the nucleus, genetic material is organized as chromatin, consisting of DNA and proteins. (
  • Chromatin/DNA binding proteins and their effects on chromatin structure and/or gene expression -Polycomb proteins -Rap1 (telomere silencing) -alpha2-MCM1 (repression of MAT locus) -CENP A/B/C (centromere structure/function) -XCAP-C/E, SMC1/2 (chromatin Condensation) -remodeling of chromatin by SWI/SNF proteins 10. (
  • Questions at the frontier of the field will be addressed - how is the activity of chromatin proteins regulated, what is the cross-talk between different chromatin states, how does folding of chromatin allow for long-range gene regulation, what is the role of RNA in directing chromatin structure? (
  • In this assay, chromatin bound proteins are crosslinked and the DNA is fragmented. (
  • [1] [2] The major components of chromatin are DNA and histone proteins, although many other chromosomal proteins have prominent roles too. (
  • Changes in chromatin structure are affected by chemical modifications of histone proteins such as methylation (DNA and proteins) and acetylation (proteins), and by non-histone, DNA-binding proteins. (
  • Histone proteins, the foundation blocks of chromatin, are modified by various post-translational modification to alter DNA packing. (
  • The nucleosome, the unit of coiling DNA in chromatin, has long been known to interfere with the initiation of transcription in vitro. (
  • Contrary to expectation, a nucleosome occluding the TATA box and transcription start sites did not impede transcription but rather, enhanced it: the level of chromatin transcription was at least sevenfold greater than that of naked DNA, and chromatin gave patterns of transcription start sites closely similar to those occurring in vivo, whereas naked DNA gave many aberrant transcripts. (
  • Methods of investigating chromatin remodeling, whether in changes in nucleosome structure or position with respect to the incorporated DNA or in histone modifications, have progressed rapidly over the recent years. (
  • A session titled "Structural Transitions in Chromatin - An Exploration of Mechanisms" will highlight cutting-edge technologies devoted to studying the complexity of chromatin structure beyond the nucleosome. (
  • A session titled "Alternative Chromatin Structures" will illuminate the fact that nucleosome and chromatin structure is affected by many factors that contribute to the transcription processes. (
  • Main articles: Nucleosome, Chromatosome and Histone The basic repeat element of chromatin is the nucleosome, interconnected by sections of linker DNA, a far shorter arrangement than pure DNA in solution. (
  • Then the chromatin is sheared by micrococcal nuclease digestion, which cuts DNA at the length of the linker, leaving nucleosomes intact and providing DNA fragments of one nucleosome (200bp) to five nucleosomes (1000bp) in length.Thereafter, methods similar to XChIP are used for clearing the cell debris, immunoprecipitating the protein of interest, removing protein from the immunoprecipated complex, and purifying and analyzing the complex-associated DNA. (
  • The basic unit of chromatin, the nucleosome core particle (NCP), controls how DNA in eukaryotic cells is compacted, replicated and read. (
  • The solvent-exposed upper and lower faces of the nucleosome form an undulating surface with distinct electrochemical features used for chromatin protein recognition. (
  • The basic structural unit of chromatin is the nucleosome . (
  • H1 histone plays a role in linking the nucleosome structures together to condense chromatin. (
  • Relatively little is known about how remodeling factors change nucleosome structure and how different factors work together to promote chromatin remodeling. (
  • Essential role of chromatin assembly factor-1-mediated rapid nucleosome assembly for DNA replication and cell division in vertebrate cells. (
  • The chromatin is organized as nucleosome filaments but does not form a 30 nm fiber. (
  • Techniques for genome/chromatin analysis -Fluorescent Insitu Analysis -psoralen, polyamine crosslinking -In vivo nucleosome foot printing -Dnase I/Micrococcal Nuclease sensitivity -VM26 Topoisomerase II site mapping 9. (
  • The meeting will highlight how chromatin structures, ranging from the nucleosome - the "building block" of chromatin - up to the dynamic three-dimensional spatial organization of chromatin, are regulated and how they control genome functions. (
  • A 30 nm condensed chromatin fiber consisting of nucleosome arrays in their most compact form. (
  • However, with a limited number of well-studied large, complex genomes, many general principles relating chromatin structure to genome regulation remain unknown. (
  • Factors that relieve inhibition by histones have been identified by transcribing chromatin reconstituted with purified histones and genetic analysis. (
  • Although informative, these studies are incomplete, because chromatin reconstituted with purified histones differs from chromatin assembled in vivo. (
  • In the old 'beads-on-a-string' electron micrograph of chromatin, it does not look like it has such a heady complex of transcription factors, enhancers, and higher order histones. (
  • The University of Massachusetts Medical School's Oliver Rando is working to understand the interplay of chromatin organization and replication - what happens to the histones during replication? (
  • The primary protein components of chromatin are histones, which bind to DNA and function as "anchors" around which the strands are wound. (
  • The artwork shows chromatin consisting of the nuclear core particle (comprised of two copies of the four core histones) with DNA wrapped around the particle. (
  • It is essential that 5 mM Na butyrate is present in all solutions throughout chromatin isolation when using antibodies to acetylated histones to prevent deacetylation. (
  • Post-translational modifications of histones play an important role in regulating chromatin dynamics and function. (
  • Histones and Nucleosomes and chromatin structure/function -H1 repression of transcription -Post translational modification of histones acetylation (H4, H3), phosphorylation (H1, H3) and ubiquitination (H2A, H2B) -Histone variants (ex. (
  • PHO5 chromatin in the transcriptionally repressed state was excised from yeast chromosomes in circular form by recombination and purified by affinity chromatography as described ( Fig. S1 A and B ) ( 10 , 11 ). (
  • Thank you for your interest in participating in the 2020 Asilomar Chromatin, Chromosomes, & Epigenetics Conference (ACCEC)! (
  • the characteristic shapes of chromosomes visible during this stage are the result of DNA being coiled into highly condensed chromatin. (
  • For example, spermatozoa and avian red blood cells have more tightly packed chromatin than most eukaryotic cells, and trypanosomatid protozoa do not condense their chromatin into visible chromosomes at all. (
  • When Does Chromatin Condense to Form Chromosomes? (
  • Chromatin condenses to form chromosomes during prophase of mitosis, and during prophase I and prophase II of meiosis. (
  • The chromatin is condensed 10,000 times into chromosomes to fit inside the nucleus of a cell, where cellular division occurs. (
  • What Is the Relationship Between Chromatin and Chromosomes? (
  • Chromatin is a strand of DNA wrapped around a protein, and is a building block of all chromosomes. (
  • Sex chromatin is derived from one of the two X chromosomes in the female which replicates its deoxyribonucleic acid much later than the other and is thus positively heteropyknotic. (
  • To mark the 2013 BioMed Central Epigenetics & Chromatin: Interactions and processes conference,Epigenetics & Chromatin has launched a new thematic series of publications aimed to discuss how the dynamic processes of epigenetic and chromatin components come together to regulate cellular processes. (
  • On 11 to 13 March 2013, BioMed Central will be hosting its inaugural conference, Epigenetics & Chromatin: Interactions and Processes, at Harvard Medical School, Boston, MA, USA. (
  • Epigenetics & Chromatin has now la. (
  • The Epigenetics and Stem Cell Biology Laboratory (ESCBL) within the Division of Intramural Research (DIR) of the National Institute of Environmental Health Sciences (NIEHS), part of the National Institutes of Health (NIH), is recruiting a tenure-track Investigator in the areas of transcription, epigenetics, or chromatin biology. (
  • Scientists within the ESCBL investigate the fundamental mechanisms by which epigenetics influences chromatin architecture, transcription, and gene expression. (
  • The successful candidate is expected to lead an innovative, independent research program exploring epigenetics, chromatin architecture or transcription that enhances our understanding the effects of the environment on human health. (
  • The field of epigenetics involves the study of chromatin-based phenomena and heritable changes in gene expression not resulting from changes in gene structure or sequence. (
  • Active Motif is committed to the development of high-quality products for researchers in this important field of research through the development of high-quality products centered on chromatin biology and epigenetics. (
  • Several epigenetic mechanisms introduce variation to chromatin structure, including covalent histone modifications, histone variant composition, DNA methylation, and Noncoding RNA. (
  • One such modification, methylation, is involved in the regulation of the epigenetic program of a cell, determining chromatin structure, and regulating transcription. (
  • Both components can be modified, e.g. by methylation, which controls how tightly chromatin is packed, and thus how accessible particular DNA regions are. (
  • Chromatin Chromatin is a network of deoxyribonucleic acid (DNA) and nucleoproteins that constitutes a chromosome. (
  • An extreme example of the ordered folding and compaction that chromatin can undergo is seen during cell division, when the chromatin of each chromosome condenses and is divided between two daughter cells ( see below Cell division and growth). (
  • A brief account of a chromatin element resembling the accessory chromosome in Sagitta has been added for comparison. (
  • In Illinois, Chromatin announced the successful first demonstration that genes can be assembled, stacked, and expressed in sugarcane using the company's mini-chromosome technology. (
  • Data available already demonstrate that genetic, molecular and developmental analysis of these genes provides an avenue to the identification of regulatory and structural chromatin components, and hence to fundamental aspects of chromosome structure and function. (
  • While prior publications have indirectly shown that chromatin does not form the 30 nm fiber in vivo, according to Dudko, the current study may be the most convincing evidence yet that the 30 nm fiber is not a native mammalian chromosome structure. (
  • While chromosome conformation capture techniques provide a wealth of information about the spatial organization of chromatin in a cell, the methods are challenging to perform and the results are difficult to interpret. (
  • Our chromosome conformation capture technology simplifies your chromatin folding studies and allows you to determine DNA contact frequencies and chromosome conformation. (
  • Our emerging view of chromatin structure has already provided unexpected insights into human genome evolution, describing the impact of such constraints on the evolution of chromosome architecture, on gene function and on patterns of mutation and selection. (
  • It leads to condensation of the inactive X chromosome into the heterochromatic sex chromatin. (
  • The organization of chromatin correlates both with the formation of tumors and their invasiveness. (
  • Mitosis is accompanied by dramatic changes in chromatin organization and nuclear architecture. (
  • The lecture begins with a discussion of chromatin organization and then proceeds to describe the process of chromatin remodeling through a review of chromatin remodeling complexes and methods used to study their function. (
  • Their distinction has become blurred, and we have realized that eukaryotic transcription, in all its complexity, functions in the context of chromatin and is regulated by its multilayered structural organization. (
  • The authors used a rigorous approach of careful mathematical modeling and experiments to show how chromatin loops may form in vivo," said Frank Alber , who studies the 3-D organization of genomes at the University of Southern California in Los Angeles, but was not involved in the work. (
  • This review highlights critical host factors that influence chromatin structure and organization and that also impact HIV integration, transcriptional regulation and latency. (
  • Chambeyron S and Bickmore WA (2004) Chromatin decondensation and nuclear re‐organization of the Hoxb locus upon induction of transcription. (
  • Chromatin determines the physical shape and organization of DNA within the nucleus. (
  • We have, therefore, investigated chromatin assembled in vivo as a template for transcription in vitro. (
  • That section is followed by protocols to analyze DNA and histone modifications, while the third section includes methods to study DNA replication and repair, in the context of chromatin. (
  • For additional information, see Histone modifications in chromatin regulation and RNA polymerase control by chromatin structure. (
  • Higher‐order chromatin structure and histone modifications. (
  • We use high-throughput approaches to capture chromatin modifications (bisulfite-seq, ChIP-seq, etc.) together with assays for chromatin accessibility to study how chromatin is organized. (
  • Together, we aim to establish links between chromatin and its modifications with genomic variability, and thus to provide fundamental insights into chromatin modifications and genome evolution. (
  • Chromatin Immunoprecipitation is a powerful tool to study protein:DNA complexes and can be used to map transcription factor binding sites or to study epigenetic modifications. (
  • Chromatin controls the access of protein factors to the DNA and is thus an important determinant for many essential processes, such as transcription, replication, and DNA-repair. (
  • The processes of chromatin disassembly and reassembly during DNA replication also h. (
  • All cellular processes involving the nuclear DNA, including transcription, recombination, and replication, must contend with local chromatin states. (
  • For example, histone acetylation results in loosening and increased accessibility of chromatin for replication and transcription. (
  • Chromatin assembly factor 1 subunit A (CAF1 subunit A or subunit p150) is a core component of the CAF-1 complex, a complex thought to mediate chromatin assembly in DNA replication and DNA repair [ PMID: 17065558 ]. (
  • Chromatin influences Human Immunodeficiency Virus (HIV) integration and replication. (
  • Dear Bionet readers, I am posting this note to ask for comments and suggestions for a new news group on genome/chromatin structure and function: tentatively called bionet.genome.structure The importance of chromatin/genomes structure for the processes of replication, transcription and recombination is becoming more and more apparent. (
  • Chromatin context can affects the expression and replication timing of a gene domain. (
  • Chromatin structure and DNA replication -ORC1 protein of yeast 15. (
  • The functions of chromatin are to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis , and to serve as a mechanism to control expression and DNA replication. (
  • Acetylation results in the loosening of chromatin and lends itself to replication and transcription. (
  • The eukaryotic genome is accommodated by the structure of chromatin. (
  • The choice of the RNA Pol II dependent PHO5 gene and the ribosomal DNA locus, containing genes transcribed by RNA Pol I and III enables comparative analysis of chromatin transcribed by the three different eukaryotic RNA polymerases. (
  • These results, similar to previous observations in Saccharomyces cerevisiae , point toward a novel function for tRNA genes and a common mechanism of compartmentalizing and organizing eukaryotic chromatin. (
  • Chromatin is a complex of DNA, protein and RNA found in eukaryotic cells. (
  • The Shen laboratory is answering basic questions concerning the regulation and maintenance of the eukaryotic genome, which is organized into chromatin. (
  • DNA is compacted, folded and organized within chromatin in the nuclei of eukaryotic cells. (
  • ChIP-seq, or chromatin immunoprecipitation and sequencing, is a technique that allows researchers to understand transcriptional regulation via mapping of protein-DNA interactions and epigenetic markers on a genome-wide scale. (
  • The DNA-protein complexes (chromatin-protein) are then sheared into ~500 bp DNA fragments by sonication or nuclease digestion. (
  • Friend of Prmt1, a novel chromatin target of protein arginine methyltransferases. (
  • ATP-dependent chromatin remodeling, which is carried out by large protein complexes of the SWI/SNF family, is recognized as a major mode of chromatin modification. (
  • Chromatin is a macromolecular complex of a DNA macromolecule and protein macromolecules (and RNA). (
  • The formed protein/DNA complex is called chromatin. (
  • Chromatin immunoprecipitation (ChIP) is a powerful research technique used to identify and analyze protein-DNA interactions within the genome in vivo . (
  • Reese BE, Bachman KE, Baylin SB, Rountree MR. The methyl-CpG binding protein MBD1 interacts with the p150 subunit of chromatin assembly factor 1. (
  • We offer a variety of products for chromatin immunoprecipitation, including protein A and G reagents, antibodies, and PCR and qPCR reagents. (
  • All three were binding sites for the mammalian chromatin organizing protein CTCF. (
  • Chromatin immunoprecipitation (ChIP) can be used as a tool to study protein:DNA complexes and identify protein-binding sites in the DNA. (
  • If the chromatin is over-sheared, it risks damaging the epitope bound by the protein or may prevent qPCR primers from recognizing the DNA fragments. (
  • If there is too much antibody, it can lead to non-specific binding whereas too little antibody will not be able to bind all of the chromatin-bound protein resulting in misrepresentation of the antibody enrichment. (
  • Reflecting this singular role for chromatin, numerous approaches have evolved in the laboratory over the past three decades to study chromatin structure and its alterations. (
  • Updated and revised, this thorough volume is organized such that it begins with techniques related to the study of chromatin structure. (
  • Authoritative and up-to-date, Chromatin Protocols, Third Edition aims to help researchers in facilitating in-depth molecular analysis of various aspects of chromatin structure and function. (
  • In pluripotent stem cells or multipotent stem/progenitor cells, lineage/cell-specific enhancers are silent by repressive chromatin structure. (
  • Chromatin is highly dynamic changing in structure and composition according to the functional state of genomic loci. (
  • We are working on the analysis of chromatin structure and function with a special focus on chromatin alterations associated with the process of transcription. (
  • Likewise, chromatin structure is responsive to complicated manipulations by the cellular machinery that make the DNA more or less accessible for the transcriptional apparatus. (
  • But according to Job Dekker, a Howard Hughes Medical Institute investigator at the University of Massachusetts Medical School, a corner has been turned: Researchers have advanced from simply cataloging chromatin structure to actually manipulating it. (
  • The overall structure of the chromatin network further depends on the stage of the cell cycle. (
  • The local structure of chromatin during interphase depends on the specific genes present in the DNA. (
  • The structure of chromatin networks is currently poorly understood and remains an active area of research in molecular biology. (
  • Z-DNA is thought to play a specific role in chromatin structure and transcription because of the properties of the junction between B- and Z-DNA. (
  • jrbone at voice: 713-792-2549 Roth Lab Homepage-- Chromatin Structure & Function Page-- 'The truths of organic nature are of a charming and awesome beauty. (
  • In position-effect variegation (PEV) therefore, gene inactivation results from a change in chromatin structure. (
  • By manipulating DNA sequences that guide genome-folding, researchers confirm an existing model of chromatin structure inside the nucleus. (
  • Compared to its sequence, relatively little is known about the structure of the human genome, which enables more than two meters of chromatin to fit inside the nucleus. (
  • First, the researchers observed that, in vivo, chromatin tends to be highly flexible at the kilobase scale, conflicting with a previously hypothesized higher order structure called the 30 nanometer (nm) fiber. (
  • Combining chromatin conformation capture with long-read nanopore sequencing, Pore-C provides long-range contact information, shedding light on higher-order structure. (
  • investigated chromatin structure in human cells with Pore-C, using this technique to additionally gain a greater understanding of complex cancer genomic rearrangements and improve assembly scaffolding. (
  • In S.C.R. Elgin (ed) Chromatin structure and gene expression. (
  • Since the structure of chromatin influences whether DNA can "unzip" and express genes, Laemmi's DNA-binding molecules is designed to influence gene expression directly, and treat diseases caused by over-or-under expression of certain genes. (
  • Some viruses, especially the herpesviruses, also manipulate their chromatin structure to help establish and maintain a latent infection. (
  • The physical structure of the genome, chromatin structure and nuclear organisation, is important for many aspects of genome function. (
  • Chromatin structure can also influence the evolution of the genome. (
  • Many aspects of chromatin structure are detectably conserved among mammals. (
  • There is an interplay between chromatin structure and the patterns of divergence seen in the underlying DNA sequence. (
  • This interplay can be seen at the level of individual genes and their regulatory elements, but also at the level of multimegabase domains of higher order chromatin structure. (
  • Conservation of higher‐order chromatin structure. (
  • 2007) Chromatin structure regulates gene conversion. (
  • Pleiotropic xenobiotics can trigger dynamic alterations in mammalian chromatin structure and function but many of these are likely non-adverse and simply reflect short-term changes in DNA transactions underlying normal homeostatic, adaptive and protective cellular responses. (
  • In recent years, it has become clear that the deregulation of chromatin structure plays an important role in numerous cancers. (
  • Genome/Chromatin structure and function (new news group info! (
  • Such interelationship between gene function and changes in chromatin structure have been demonstrated through an evolution of techniques from Dnase I sensitivity mapping to fluorescent in situ hybridization (FISH. (
  • 1. Genome/chromatin accessibility and recombination -recombination hotspots (mieotic and mitotic) -fragile sites -imprinting and recombination rates -ectopic gene targeting and chromatin structure 3. (
  • Biologically important mutants and knockouts that affect genome/chromatin structure -ex. (
  • The 2016 Gordon Conference on Chromatin Structure and Function will present leading-edge research on chromatin and its role in regulating gene expression, genome function and cell states. (
  • There will be a focus on new methods for engineering and re-engineering chromatin states to determine the relationships between chromatin structure and function, and on analysis at the level of single molecules and single cells. (
  • This conference has a long history of attracting the very top researchers in the area of chromatin structure and function, and is an important forum for fostering new ideas, interactions and collaborations. (
  • We review progress that has been made in applying this technology for the study of chromatin structure and discuss its prospects for the in situ analysis of nuclear architecture and chromatin function. (
  • During spermiogenesis , the spermatid 's chromatin is remodelled into a more spaced packaged, widened, almost crystal-like structure. (
  • The structure of chromatin during interphase is optimised to allow easy access of transcription and DNA repair factors to the DNA while compacting the DNA into the nucleus . (
  • Chromatin undergoes various forms of change in its structure. (
  • A recent study showed that there is a bivalent structure present in the chromatin: methylated lysine residues at location 4 and 27 on histone 3. (
  • Unlike any other title on the topic, Sperm Chromatin: Biological and Clinical Applications in Male Infertility and Assisted Reproduction is an invaluable addition to the literature and will serve as an indispensable resource for basic scientists with an interest in sperm biology and for urologists, gynecologists, reproductive endocrinologists, and embryologists working in the field of infertility. (
  • Newer technologies - beginning with chromatin immuno-precipitation about 20 years ago, right up to next-gen sequencing - have kept the chromatin biology and DNA-binding fields spinning. (
  • The technology completely revolutionized the whole chromatin biology field in general," says Jorge Ferrer of the Hospital Clínic de Barcelona. (
  • Leading experts from academia, the biotechnology and pharmaceutical industries explain the role of epigenomics in a wide range of contexts, covering basic chromatin biology, imprinting at a genome-wide level, and epigenomics in disease biology and epidemiology. (
  • Authoritative and practical, Chromatin Immunoprecipitation: Methods and Protocols features techniques, including bioinformatic analysis of ChIP data, will be of interest to a very broad research community in the fields of biochemistry, molecular biology, microbiology, and biomedicine. (
  • In this review, the authors highlight recent advances in the architectural understanding of chromatin biology elucidated by EM. (
  • Last but not least, protocols for studying chromatin and its relation with transcriptional regulation are presented in a fourth section. (
  • Furthermore, we concentrate our efforts on two genomic loci for which a robust chromatin transition had been observed when they switch their transcriptional state. (
  • The final goal of our studies is to derive a complete molecular description of chromatin in different transcriptional states. (
  • These two transcriptional states reside in distinct chromatin structures ( Figure 2 ). (
  • The "Transcription/Chromatin" annual meeting theme will contain sessions titled: "Structural Transitions in Chromatin - An Exploration of Mechanisms," "Alternative Chromatin Structures," "RNA Polymerase Pausing and Elongation" and "Transcriptional Regulation in Growth, Differentiation and Diseases. (
  • Lysine trimethylation can either lead to increased transcriptional activity (trimethylation of histone H3 lysine 4) or transcriptional repression and chromatin compaction (trimethylation of histone H3 lysine 9 or 27). (
  • On the contrary, increase in metastatic ability is accompanied by changes in chromatin pattern as assessed by textural features. (
  • Protocols for reconstitution of chromatin on solid supports for analysis, preparation of positioned mononucleosomes, techniques to study premature chromatin condensation and the use of comparative genomic hybridization to assess genomic aberration are included as well. (
  • Novel techniques for imaging chromatin using atomic force microscopy and the isolation of specific genomic regions using engineered DNA binding molecules generated by CRISPR are then examined. (
  • Chromatin conformation capture (3C) techniques reveal genomic interactions in three dimensions. (
  • Genomic functions take place in chromatin, not in naked DNA. (
  • In many eukaryotes, tightly packed chromatin, the so-called heterochromatin, occurs at repeat-rich genomic regions and is thought to suppress gene expression and limit genetic variability of these regions. (
  • So far, knowledge on mechanisms governing genomic variability is limited, as is the role of chromatin in this processes. (
  • Chromatin fragments of 400 - 500bp have proven to be suitable for ChIP assays as they cover two to three nucleosomes. (
  • In Chromatin Remodeling: Methods and Protocols , expert researchers contribute chapters which include methods for investigating chromatin remodeling in vitro and in vivo, in yeast, plants, and mammalian cells, and at local and global levels. (
  • This Teaching Resource provides lecture notes and slides for a class covering chromatin remodeling mechanisms and is part of the course "Cell Signaling Systems: a Course for Graduate Students. (
  • Our research focuses on understanding how chromatin is remodeled to accommodate various nuclear functions, such as transcription and DNA repair, and how defects in chromatin remodeling might lead to cancer. (
  • Chromatin is modified via two major modes, mechanisms that involve ATP-dependent chromatin remodeling and mechanisms that involve histone modification. (
  • Our current research focuses on a novel and evolutionarily conserved class of ATP-dependent chromatin remodeling complexes called the INO80 class. (
  • Alternatively, chromatin remodeling where the histone assumes a more closed confirmation blocks transcription factor access to the DNA, resulting in loss of gene expression. (
  • The SNP boosts TMEM106b expression by promoting binding of the chromatin remodeling factor CTCF. (
  • Not only is the technique label-free, allowing researchers to study chromatin within unharmed, living cells, but it does so with high-throughput and at very low cost. (
  • Some are using population-based sequencing approaches, while others are exploiting the power of microscopy to study chromatin architecture on a cell-by-cell basis. (
  • We demonstrate that open chromatin predicts molecular phenotypes such as gene expression and recombination. (
  • To understand nuclear processes it is necessary to gain insight in the molecular nature of chromatin and the mechanisms involved in its establishment, maintenance and alteration. (
  • The image depicts six broad categories of chromatin regulatory mechanisms, which are all known to be altered via mutations in the pathogenesis of human cancer. (
  • Nevertheless, viruses have evolved to utilize the host mechanisms that transcribe and replicate cellular DNA assembled in chromatin. (
  • Written and edited by experts in the field, this collection from Cold Spring Harbor Perspectives in Medicine examines the chromatin components that are commonly mutated, what is understood about the mechanisms that lead to hematological malignancies and solid tumors, and prospects for the therapeutic modulation of chromatin. (
  • This makes it possible for users to perform Chromatin immunoprecipitation (ChIP) assays using only 1000 cells per immunoprecipitation. (
  • Chromatin structural assays can efficiently integrate information across diverse regulatory elements, revealing the functional noncoding genome. (
  • These factors include ATP-dependent chromatin remodelers ( 3 , 4 ), histone-modifying enzymes ( 5 ⇓ - 7 ), FACT ( 8 ), and TFIIS ( 9 ). (
  • 1%) of the maize genome residing in open chromatin. (
  • In the first phase we will use biochemical approaches to identify ncRNAs involved in the regulation of chromatin and transcription. (
  • Cellular processes mediated through nuclear DNA must contend with chromatin. (
  • In general, chromatin accessibility may be assayed through in situ digestion of the nuclear DNA with a non-sequence-specific nuclease, followed by quantification of the resulting DNA fragments ( 5 ). (
  • Nuclear DNA content and chromatin pattern of rat rhabdomyosarcoma. (
  • These data suggest that, in rat rhabdomyosarcoma cell sublines, metastatic ability could be associated with nuclear morphological changes at the level of chromatin texture. (
  • Here we discuss the use of magnetic tweezers for the study of nuclear architecture and the mechanical properties of chromatin in living cells. (
  • Chromatin is isolated and antibodies to the antigen of interest are used to determine whether the target binds to a specific DNA sequence or to map the distribution across the genome (microarray or DNA sequencing). (
  • Sigma's Imprint brand of antibodies are validated in ChIP application and lot tested each time for successful chromatin immunoprecipitation experiment. (
  • Binding of pioneer transcription factors remodels the repressive chromatin and leads to H3K4me1 poised enhancers. (
  • Evidence over many years has revealed that transcription factors and chromatin regulators are associated with a variety of non-coding (nc)RNAs, but their function remains largely unknown. (
  • In order to make ChIP efficient from lower cell numbers, some of the techniques include spiking of samples with chromatin from another source, or DNA amplification before downstream analysis. (
  • To do that, researchers are using ChIP-seq, among other methods, to develop chromatin maps, which they can then use in comparative studies. (
  • This up-to-date volume includes protocols that illustrate the broad use of chromatin immunoprecipitation (ChIP) and ChIP-related methods in a variety of biological research areas. (
  • There are mainly two types of ChIP, primarily differing in the starting chromatin preparation. (
  • The first uses reversibly cross-linked chromatin sheared by sonication called cross-linked ChIP (XChIP). (
  • Native ChIP (NChIP) uses native chromatin sheared by micrococcal nuclease digestion. (
  • Whatever your preferred method of chromatin preparation we have a ChIP kit suited to your needs. (
  • The Imprint ChIP Kit provides a complete solution for Chromatin Immunoprecipitation including columns and reagents for DNA purification and an integrated protocol for ChIP DNA amplification with our GenomePlex ® Whole Genome Amplification Kit ( WGA2 ). (
  • According to chromatin immunoprecipitation sequencing (CHIP-Seq) maps from ENCODE, these three SNP sites bound CTCF in neuronal, glial, and lymphoblast cell lines. (
  • A successful ChIP experiment is dependent on high quality chromatin. (
  • As genome-wide chromatin architecture maps become widely available, the field is shifting focus from mapping to understanding the dynamics of such structures in development, the cell cycle, and on short time scales in single cells. (
  • We developed a novel approach, DCS (Displacement Correlation Spectroscopy) based on time-resolved image correlation analysis to map chromatin dynamics simultaneously across the whole nucleus in cultured human cells. (
  • Baylor's Erez Lieberman Aiden , Suhas Rao , and their colleagues recently created the first relatively high-resolution, 3-D map of the human genome , which included almost 10,000 chromatin loops. (
  • To uncover these interrelations and to generate an interpretable summary of the massive datasets of the ENCODE Project, we apply unsupervised learning methodologies, converting dozens of chromatin datasets into discrete annotation maps of regulatory regions and other chromatin elements across the human genome. (
  • 2004) Chromatin architecture of the human genome: gene‐rich domains are enriched in open chromatin fibers. (
  • Oxford Nanopore provides the complete solution for investigating chromatin conformation: Pore-C is an end-to-end workflow, from sample preparation to analysis. (
  • The consequences in terms of chromatin accessibility and compaction depend both on the modified amino acid and the type of modification. (
  • In this study, we use a differential nuclease sensitivity assay based on micrococcal nuclease (MNase) digestion to discover open chromatin regions in the maize genome. (
  • High concentrations of micrococcal nuclease may over-digest the chromatin, leading to sub-nucleosomal particles. (
  • Both histone acetylation and trimethylation of H3K4 (H3K4me3) were important for chromatin transcription. (
  • Fine-scale characterization of the chromatin structural landscape requires an assay that can distinguish accessible (open) from condensed chromatin at the nucleosomal to subnucleosomal scales. (
  • Chromatin undergoes various structural changes during a cell cycle. (
  • The data also allow resolution of entire megabase-sized structural variants (SVs), and an understanding of their association with chromatin conformation (see case study below). (
  • Complementary structural techniques such as NMR, SAXS and EM have been developed to visualize chromatin components, with some advantages over X-ray crystallography. (
  • Chromatin exists in many configurations and undergoes dynamic structural changes. (
  • Chromatin can only be found in a cell with a nucleus and is therefore not present in a. (
  • The nucleus soon enlarges (fig. 80) and a large dense body (n) appears which stains like chromatin with various staining media. (
  • Long strands of chromatin are usually bundled loosely within the nucleus. (
  • An irregular aggregation of chromatin in the nucleus of a cell not undergoing mitosis. (
  • Chromatin has several functions, the main one being to condense the six feet of DNA in every cell down to fit inside the nucleus. (
  • Viral DNA genomes entering the nucleus of host cells encounter the cellular chromatin environment. (
  • If the viral genomes are not assembled into chromatin when they enter the nucleus, they are faced with attempts by the host cell to restrict expression of the foreign DNA by assembly and modification of chromatin on the viral genomes so as to silence the viral DNA. (
  • To date, humans and several model systems with small genomes have had their chromatin landscapes well-characterized ( 1 ⇓ ⇓ - 4 ). (
  • As well as investigating chromatin architecture, the long reads obtained from the Pore-C workflow enable users to scaffold genome assemblies and correct genomes. (
  • 2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. (
  • We found that a bipolar spindle can form in vivo in the absence of any chromatin due to the establishment of interactions between microtubule asters that are progressively stabilized by an increase in the number of microtubules involved, demonstrating that spindle formation is an intrinsic property of the microtubule network. (
  • Here we use a polymer model of chromatin fiber to investigate whether, and to what extent, looping interactions between elements in the vicinity of an enhancer-promoter pair can influence their contact frequency. (
  • Our equilibrium polymer simulations show that a chromatin loop, formed by elements flanking either an enhancer or a promoter, suppresses enhancer-promoter interactions, working as an insulator. (
  • Today is the first day for late abstract submission for the 2011 Chromatin Meeting . (
  • Understanding this missing length scale is crucial, however, because it is the exact area where chromatin undergoes a transformation when cancer is formed. (
  • A Qsonica sonicator on high setting was used to shear the chromatin stock for 15min: 30 seconds on, 30 seconds off to generate 100-500bp fragments. (
  • Mild formaldehyde crosslinking followed by nuclease digestion has been used to shear the chromatin. (
  • Presentations will encompass a wide variety of technical approaches - from Angstrom level description of chromatin components to visualization of micron-scale structures by light microscopy, and the use of quantitative proteomics and computational modeling. (
  • These methods rediscover and summarize diverse aspects of chromatin architecture, elucidate the interplay between chromatin activity and RNA transcription, and reveal that a large proportion of the genome lies in a quiescent state, even across multiple cell types. (
  • The structures within chromatin that regulate these processes span from nucleosomal (10 nanometers) to chromosomal (longer than 200 nanometers) length scales. (
  • When the chromatin becomes tightly packed, the replicated chromosomal DNA, called sister chromatids, are connected at the centromere. (
  • Written by leading, internationally renowned clinicians and basic scientists with expertise in sperm DNA, Sperm Chromatin: Biological and Clinical Applications in Male Infertility and Assisted Reproduction provides readers with a thoughtful and comprehensive review of the biological and clinical significance of sperm DNA damage. (
  • The work covers the fundamental principles of sperm chromatin architecture and function, the proposed modes of DNA damage and repair, the tests of sperm DNA damage, the clinical aspects of DNA damage and the impact of DNA damage on reproductive outcome. (
  • This condensed version of Zini and Agarwal's Sperm Chromatin: Biological and Clinical Applications in Male Infertility and Assisted Reproduction offers select, clinical chapters for a handy, resource about this cutting-edge topic in reproductive medicine. (
  • Generally, native chromatin is used as starting chromatin. (
  • Nevertheless, the molecular nature of the different chromatin states remains still largely unknown. (
  • Comparison of time required for protocol completion from fixation through purification using different Chromatin Immunoprecipitation kits. (
  • Lastly, we use the regulatory annotations to revisit previously uncharacterized disease-associated loci, resulting in focused, testable hypotheses through the lens of the chromatin landscape. (