Chromatin immunoprecipitation. Medical search

The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.

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

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.

Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.

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

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

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.

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

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.

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.

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.

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.

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

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.

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

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.

Established cell cultures that have the potential to propagate indefinitely.

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

A cell line derived from cultured tumor cells.

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.

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.

Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.

An 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.

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

Deacetylases that remove N-acetyl groups from amino side chains of the amino acids of HISTONES. The enzyme family can be divided into at least three structurally-defined subclasses. Class I and class II deacetylases utilize a zinc-dependent mechanism. The sirtuin histone deacetylases belong to class III and are NAD-dependent enzymes.

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.

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 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).

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 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.

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.

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.

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)

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.

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

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

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.

A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 2.7.7.6.

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

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.

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.

An enzyme that catalyzes the endonucleolytic cleavage to 3'-phosphomononucleotide and 3'-phospholigonucleotide end-products. It can cause hydrolysis of double- or single-stranded DNA or RNA. (From Enzyme Nomenclature, 1992) EC 3.1.31.1.

The 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 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.

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

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.

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.

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.

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

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

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.

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 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.

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

Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.

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

An enzyme that catalyzes the methylation of the epsilon-amino group of lysine residues in proteins to yield epsilon mono-, di-, and trimethyllysine. EC 2.1.1.43.

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.

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

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.

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

A heterotrimeric DNA-binding protein that binds to CCAAT motifs in the promoters of eukaryotic genes. It is composed of three subunits: A, B and C.

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

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.

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.

A positive regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.

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

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 negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.

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.

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.

Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL).

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.

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

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

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

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

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

DNA locations with the consensus sequence CANNTG. ENHANCER ELEMENTS may contain multiple copies of this element. E-boxes play a regulatory role in the control of transcription. They bind with basic helix-loop-helix (bHLH) type TRANSCRIPTION FACTORS. Binding specificity is determined by the specific bHLH heterodimer or homodimer combination and by the specific nucleotides at the 3rd and 4th position of the E-box sequence.

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.

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.

A family of zinc finger transcription factors that share homology with Kruppel protein, Drosophila. They contain a highly conserved seven amino acid spacer sequence in between their ZINC FINGER MOTIFS.

A continuous cell line of high contact-inhibition established from NIH Swiss mouse embryo cultures. The cells are useful for DNA transfection and transformation studies. (From ATCC [Internet]. Virginia: American Type Culture Collection; c2002 [cited 2002 Sept 26]. Available from http://www.atcc.org/)

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.

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.

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)

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

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.

A specificity protein transcription factor that regulates expression of a variety of genes including VASCULAR ENDOTHELIAL GROWTH FACTOR and CYCLIN-DEPENDENT KINASE INHIBITOR P27.

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

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.

A member of the p300-CBP transcription factor family that was initially identified as a binding partner for CAMP RESPONSE ELEMENT-BINDING PROTEIN. Mutations in CREB-binding protein are associated with RUBINSTEIN-TAYBI SYNDROME.

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 region of DNA which borders the 5' end of a transcription unit and where a variety of regulatory sequences are located.

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

The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.

All of the processes involved in increasing CELL NUMBER including CELL DIVISION.

One of the ESTROGEN RECEPTORS that has marked affinity for ESTRADIOL. Its expression and function differs from, and in some ways opposes, ESTROGEN RECEPTOR BETA.

A cell line generated from human embryonic kidney cells that were transformed with human adenovirus type 5.

Immunologic method used for detecting or quantifying immunoreactive substances. The substance is identified by first immobilizing it by blotting onto a membrane and then tagging it with labeled antibodies.

Cellular DNA-binding proteins encoded by the c-myc genes. They are normally involved in nucleic acid metabolism and in mediating the cellular response to growth factors. Elevated and deregulated (constitutive) expression of c-myc proteins can cause tumorigenesis.

The process by which a DNA molecule is duplicated.

Strains of mice in which certain GENES of their GENOMES have been disrupted, or "knocked-out". To produce knockouts, using RECOMBINANT DNA technology, the normal DNA sequence of the gene being studied is altered to prevent synthesis of a normal gene product. Cloned cells in which this DNA alteration is successful are then injected into mouse EMBRYOS to produce chimeric mice. The chimeric mice are then bred to yield a strain in which all the cells of the mouse contain the disrupted gene. Knockout mice are used as EXPERIMENTAL ANIMAL MODELS for diseases (DISEASE MODELS, ANIMAL) and to clarify the functions of the genes.

Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.

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)

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.

A family of DNA-binding transcription factors that contain a basic HELIX-LOOP-HELIX MOTIF.

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

Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO.

Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules.

In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.

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.

A subunit of NF-kappa B that is primarily responsible for its transactivation function. It contains a C-terminal transactivation domain and an N-terminal domain with homology to PROTO-ONCOGENE PROTEINS C-REL.

A CCAAT-enhancer-binding protein found in LIVER; INTESTINES; LUNG and ADIPOSE TISSUE. It is an important mediator of INTERLEUKIN-6 signaling.

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.

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.

Ubiquitous, inducible, nuclear transcriptional activator that binds to enhancer elements in many different cell types and is activated by pathogenic stimuli. The NF-kappa B complex is a heterodimer composed of two DNA-binding subunits: NF-kappa B1 and relA.

Ubiquitously expressed basic HELIX-LOOP-HELIX MOTIF transcription factors. They bind CANNTG sequences in the promoters of a variety of GENES involved in carbohydrate and lipid metabolism.

A multiprotein complex composed of the products of c-jun and c-fos proto-oncogenes. These proteins must dimerize in order to bind to the AP-1 recognition site, also known as the TPA-responsive element (TRE). AP-1 controls both basal and inducible transcription of several genes.

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.

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.

Nucleic acid sequences involved in regulating the expression of genes.

An ERYTHROLEUKEMIA cell line derived from a CHRONIC MYELOID LEUKEMIA patient in BLAST CRISIS.

An E2F transcription factor that interacts directly with RETINOBLASTOMA PROTEIN and CYCLIN A and activates GENETIC TRANSCRIPTION required for CELL CYCLE entry and DNA synthesis. E2F1 is involved in DNA REPAIR and APOPTOSIS.

A protein that has been shown to function as a calcium-regulated transcription factor as well as a substrate for depolarization-activated CALCIUM-CALMODULIN-DEPENDENT PROTEIN KINASES. This protein functions to integrate both calcium and cAMP signals.

A human liver tumor cell line used to study a variety of liver-specific metabolic functions.

A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.

Macromolecular complexes formed from the association of defined protein subunits.

A histone deacetylase subtype that is found along with HISTONE DEACETYLASE 1; RETINOBLASTOMA-BINDING PROTEIN 4; and RETINOBLASTOMA-BINDING PROTEIN 7 as core components of histone deacetylase complexes.

A family of DNA binding proteins that regulate expression of a variety of GENES during CELL DIFFERENTIATION and APOPTOSIS. Family members contain a highly conserved carboxy-terminal basic HELIX-TURN-HELIX MOTIF involved in dimerization and sequence-specific DNA binding.

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

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.

Transport proteins that carry specific substances in the blood or across cell membranes.

The process of moving proteins from one cellular compartment (including extracellular) to another by various sorting and transport mechanisms such as gated transport, protein translocation, and vesicular transport.

Nuclear phosphoprotein encoded by the p53 gene (GENES, P53) whose normal function is to control CELL PROLIFERATION and APOPTOSIS. A mutant or absent p53 protein has been found in LEUKEMIA; OSTEOSARCOMA; LUNG CANCER; and COLORECTAL CANCER.

Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.

The sum of the weight of all the atoms in a molecule.

Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.

A pyrimidine analogue that inhibits DNA methyltransferase, impairing DNA methylation. It is also an antimetabolite of cytidine, incorporated primarily into RNA. Azacytidine has been used as an antineoplastic agent.

A forkhead transcription factor that is an essential activator of GLUCAGON gene expression.

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.

Elements of limited time intervals, contributing to particular results or situations.

A large superfamily of transcription factors that contain a region rich in BASIC AMINO ACID residues followed by a LEUCINE ZIPPER domain.

A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.

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.

Proteins that are normally involved in holding cellular growth in check. Deficiencies or abnormalities in these proteins may lead to unregulated cell growth and tumor development.

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

The series of cells in the red blood cell lineage at various stages of differentiation.

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 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.

Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.

A GATA transcription factor that is specifically expressed in hematopoietic lineages and plays an important role in the CELL DIFFERENTIATION of ERYTHROID CELLS and MEGAKARYOCYTES.

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.

Proteins whose abnormal expression (gain or loss) are associated with the development, growth, or progression of NEOPLASMS. Some neoplasm proteins are tumor antigens (ANTIGENS, NEOPLASM), i.e. they induce an immune reaction to their tumor. Many neoplasm proteins have been characterized and are used as tumor markers (BIOMARKERS, TUMOR) when they are detectable in cells and body fluids as monitors for the presence or growth of tumors. Abnormal expression of ONCOGENE PROTEINS is involved in neoplastic transformation, whereas the loss of expression of TUMOR SUPPRESSOR PROTEINS is involved with the loss of growth control and progression of the neoplasm.

A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.

Products of proto-oncogenes. Normally they do not have oncogenic or transforming properties, but are involved in the regulation or differentiation of cell growth. They often have protein kinase activity.

An ets proto-oncogene expressed primarily in adult LYMPHOID TISSUE; BRAIN; and VASCULAR ENDOTHELIAL CELLS.

Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.

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.

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 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.

Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.

Test for tissue antigen using either a direct method, by conjugation of antibody with fluorescent dye (FLUORESCENT ANTIBODY TECHNIQUE, DIRECT) or an indirect method, by formation of antigen-antibody complex which is then labeled with fluorescein-conjugated anti-immunoglobulin antibody (FLUORESCENT ANTIBODY TECHNIQUE, INDIRECT). The tissue is then examined by fluorescence microscopy.

A family of histone demethylases that share a conserved Jumonji C domain. The enzymes function via an iron-dependent dioxygenase mechanism that couples the conversion of 2-oxoglutarate to succinate to the hydroxylation of N-methyl groups.

Cellular DNA-binding proteins encoded by the c-jun genes (GENES, JUN). They are involved in growth-related transcriptional control. There appear to be three distinct functions: dimerization (with c-fos), DNA-binding, and transcriptional activation. Oncogenic transformation can take place by constitutive expression of c-jun.

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

A subclass of repressor proteins that do not directly bind DNA. Instead, co-repressors generally act via their interaction with DNA-BINDING PROTEINS such as a TRANSCRIPTIONAL SILENCING FACTORS or NUCLEAR RECEPTORS.

Microscopy of specimens stained with fluorescent dye (usually fluorescein isothiocyanate) or of naturally fluorescent materials, which emit light when exposed to ultraviolet or blue light. Immunofluorescence microscopy utilizes antibodies that are labeled with fluorescent dye.

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.

Intracellular receptors that can be found in the cytoplasm or in the nucleus. They bind to extracellular signaling molecules that migrate through or are transported across the CELL MEMBRANE. Many members of this class of receptors occur in the cytoplasm and are transported to the CELL NUCLEUS upon ligand-binding where they signal via DNA-binding and transcription regulation. Also included in this category are receptors found on INTRACELLULAR MEMBRANES that act via mechanisms similar to CELL SURFACE RECEPTORS.

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.

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

An early growth response transcription factor that has been implicated in regulation of CELL PROLIFERATION and APOPTOSIS.

Proteins prepared by recombinant DNA technology.

Different forms of a protein that may be produced from different GENES, or from the same gene by ALTERNATIVE SPLICING.

The entity of a developing mammal (MAMMALS), generally from the cleavage of a ZYGOTE to the end of embryonic differentiation of basic structures. For the human embryo, this represents the first two months of intrauterine development preceding the stages of the FETUS.

Techniques for removal by adsorption and subsequent elution of a specific antibody or antigen using an immunosorbent containing the homologous antigen or antibody.

A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.

A subfamily of nuclear receptors that regulate GENETIC TRANSCRIPTION of a diverse group of GENES involved in the synthesis of BLOOD COAGULATION FACTORS; and in GLUCOSE; CHOLESTEROL; and FATTY ACIDS metabolism.

Compounds or agents that combine with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction.

The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.

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.

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

A ubiquitously expressed zinc finger-containing protein that acts both as a repressor and activator of transcription. It interacts with key regulatory proteins such as TATA-BINDING PROTEIN; TFIIB; and ADENOVIRUS E1A PROTEINS.

Proteins found in any species of fungus.

A transcription factor that dimerizes with CORE BINDING FACTOR BETA SUBUNIT to form core binding factor. It contains a highly conserved DNA-binding domain known as the runt domain and is involved in genetic regulation of skeletal development and CELL DIFFERENTIATION.

A species of CERCOPITHECUS containing three subspecies: C. tantalus, C. pygerythrus, and C. sabeus. They are found in the forests and savannah of Africa. The African green monkey (C. pygerythrus) is the natural host of SIMIAN IMMUNODEFICIENCY VIRUS and is used in AIDS research.

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)

Gated transport mechanisms by which proteins or RNA are moved across the NUCLEAR MEMBRANE.

The specific patterns of changes made to HISTONES, that are involved in assembly, maintenance, and alteration of chromatin structural states (such as EUCHROMATIN and HETEROCHROMATIN). The changes are made by various HISTONE MODIFICATION PROCESSES that include ACETYLATION; METHYLATION; PHOSPHORYLATION; and UBIQUITINATION.

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.

Tumors or cancer of the human BREAST.

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.

Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.

CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)

Specific targeting and constitutive association of histone deacetylase complexes during transcriptional repression. (1/5197)

Specific recruitment of corepressor complexes containing histone deacetylases (HDAC) by transcription factors is believed to play an essential role in transcriptional repression. Recent studies indicate that repression by unliganded nuclear hormone receptors and by the Mad family of repressors requires distinct HDAC-containing corepressor complexes. In this work, we show that unliganded TR specifically recruits only the closely related N-CoR and SMRT-HDAC3 complexes, whereas the Mad1 recruits only the Sin3-HDAC1/2 complex. Significantly, both the Sin3 and Mi-2/NURD complexes also exhibit constitutive association with chromatin and contribute to chromatin deacetylation in a nontargeted fashion. These results suggest that HDAC complexes can contribute to gene repression by two distinct mechanisms as follows: (1) specific targeting by repressors and (2) constitutive association with chromatin. (+info)

Partially phosphorylated Pho4 activates transcription of a subset of phosphate-responsive genes. (2/5197)

A cell's ability to generate different responses to different levels of stimulus is an important component of an adaptive environmental response. Transcriptional responses are frequently controlled by transcription factors regulated by phosphorylation. We demonstrate that differential phosphorylation of the budding yeast transcription factor Pho4 contributes to differential gene expression. When yeast cells are grown in high-phosphate growth medium, Pho4 is phosphorylated on four critical residues by the cyclin-CDK complex Pho80-Pho85 and is inactivated. When yeast cells are starved for phosphate, Pho4 is dephosphorylated and fully active. In intermediate-phosphate conditions, a form of Pho4 preferentially phosphorylated on one of the four sites accumulates and activates transcription of a subset of phosphate-responsive genes. This Pho4 phosphoform binds differentially to phosphate-responsive promoters and helps to trigger differential gene expression. Our results demonstrate that three transcriptional outputs can be generated by a pathway whose regulation is controlled by one kinase, Pho80-Pho85, and one transcription factor, Pho4. Differential phosphorylation of Pho4 by Pho80-Pho85 produces phosphorylated forms of Pho4 that differ in their ability to activate transcription, contributing to multiple outputs. (+info)

Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. (3/5197)

Heritable, but reversible, changes in transposable element activity were first observed in maize by Barbara McClintock in the 1950s. More recently, transposon silencing has been associated with DNA methylation, histone H3 lysine-9 methylation (H3mK9), and RNA interference (RNAi). Using a genetic approach, we have investigated the role of these modifications in the epigenetic regulation and inheritance of six Arabidopsis transposons. Silencing of most of the transposons is relieved in DNA methyltransferase (met1), chromatin remodeling ATPase (ddm1), and histone modification (sil1) mutants. In contrast, only a small subset of the transposons require the H3mK9 methyltransferase KRYPTONITE, the RNAi gene ARGONAUTE1, and the CXG methyltransferase CHROMOMETHYLASE3. In crosses to wild-type plants, epigenetic inheritance of active transposons varied from mutant to mutant, indicating these genes differ in their ability to silence transposons. According to their pattern of transposon regulation, the mutants can be divided into two groups, which suggests that there are distinct, but interacting, complexes or pathways involved in transposon silencing. Furthermore, different transposons tend to be susceptible to different forms of epigenetic regulation. (+info)

Role of Saccharomyces single-stranded DNA-binding protein RPA in the strand invasion step of double-strand break repair. (4/5197)

The single-stranded DNA (ssDNA)-binding protein replication protein A (RPA) is essential for both DNA replication and recombination. Chromatin immunoprecipitation techniques were used to visualize the kinetics and extent of RPA binding following induction of a double-strand break (DSB) and during its repair by homologous recombination in yeast. RPA assembles at the HO endonuclease-cut MAT locus simultaneously with the appearance of the DSB, and binding spreads away from the DSB as 5' to 3' exonuclease activity creates more ssDNA. RPA binding precedes binding of the Rad51 recombination protein. The extent of RPA binding is greater when Rad51 is absent, supporting the idea that Rad51 displaces RPA from ssDNA. RPA plays an important role during RAD51-mediated strand invasion of the MAT ssDNA into the donor sequence HML. The replication-proficient but recombination-defective rfa1-t11 (K45E) mutation in the large subunit of RPA is normal in facilitating Rad51 filament formation on ssDNA, but is unable to achieve synapsis between MAT and HML. Thus, RPA appears to play a role in strand invasion as well as in facilitating Rad51 binding to ssDNA, possibly by stabilizing the displaced ssDNA. (+info)

ATF6 modulates SREBP2-mediated lipogenesis. (5/5197)

Activating transcription factor 6 (ATF6) and sterol regulatory element-binding proteins (SREBPs) are activated by proteolytic cleavage. The ensuing nuclear translocation of their N-termini (i.e., ATF6(N) and SREBP(N)) activates the respective target genes involved in unfolded protein response and lipogenesis. Here, we report that glucose deprivation activated ATF6 but suppressed the SREBP2-regulated transcription. Overexpression of ATF6(N) had similar inhibitory effects on SREBP2-targeted genes. The blockade of ATF6 cleavage by BiP/grp78 reversed this inhibitory effect. GST pull-down and immunoprecipitation assays revealed that ATF6(N) bound to SREBP2(N). Deletion analysis of the various functional domains of ATF6 indicated that the interaction was through its leucine-zipper domain. Chromatin immunoprecipitation assays revealed that ATF6(N) formed a complex with the SRE-bound SREBP2(N). The attenuated transcriptional activity of SREBP2 was due, in part, to the recruitment of HDAC1 to the ATF6-SREBP2 complex. As a functional consequence, the lipogenic effect of SREBP2(N) in liver cells was suppressed by ATF6(N). Our results provide a novel mechanism by which ATF6 antagonizes SREBP2 to regulate the homeostasis of lipid and glucose. (+info)

Formation, maintenance and consequences of the imprint at the mating-type locus in fission yeast. (6/5197)

Mating-type switching in the fission yeast Schizosaccharomyces pombe is initiated by a strand-specific imprint located at the mating-type (mat1) locus. We show that the imprint corresponds to a single-strand DNA break (SSB), which is site- but not sequence-specific. We identified three novel cis-acting elements, involved in the formation and stability of the SSB. One of these elements is essential for a replication fork pause next to mat1 and interacts in vivo with the Swi1 protein. Another element is essential for maintaining the SSB during cell cycle progression. These results suggest that the DNA break appears during the S-phase and is actively protected against repair. Consequently, during the following round of replication, a polar double-strand break is formed. We show that when the replication fork encounters the SSB, the leading-strand DNA polymerase is able to synthesize DNA to the edge of the SSB, creating a blunt-ended recombination intermediate. (+info)

MDR1 promoter hypermethylation in MCF-7 human breast cancer cells: changes in chromatin structure induced by treatment with 5-Aza-cytidine. (7/5197)

Resistance to the cytotoxic actions of antineoplastic drugs, whether intrinsic or acquired, remains a barrier to the establishment of curative chemotherapy regimens for advanced breast cancer. Over-expression of P-glycoprotein (P-gp), encoded by the MDR1 gene and known to mediate resistance to many antineoplastic drugs, may contribute to poor breast cancer treatment outcome. Nonetheless, the precise molecular mechanisms responsible for high or low level P-gp expression in breast cancer cells have not been established. We assessed the role of DNA hypermethylation near the MDR1 transcriptional regulatory region in MDR1 expression in MCF-7 breast cancer cells, which fail to express MDR1 mRNA, and MCF-7/ADR cells, known to express high MDR1 mRNA levels. When compared to MCF-7/ADR cells, MCF-7 cells manifested markedly diminished MDR1 transcription rates by nuclear run-off assay, but equivalent MDR1 promoter trans-activation activity in transient transfection experiments, indicating that cis factors were most likely responsible for the differences in MDR1 transcription between MCF-7/ADR cells and MCF-7 cells. Bisulfite genomic sequencing analyses revealed substantially less extensive MDR1 promoter methylation in MCF-7/ADR cells than in MCF-7 cells, suggesting that CpG dinucleotide methylation might contribute to the observed MDR1 transcription differences. Chromatin immunoprecipitation analyses indicated an inactive MDR1 chromatin conformation in MCF-7 cells, with a paucity of acetylated histones and the presence of 5-mC-binding proteins MeCP2 and MBD2, and an active MDR1 chromatin conformation in MCF-7/ADR cells, with an abundance of acetylated histones and the presence of the transcriptional trans-activator YB-1. Stable MCF-7 sublines which had been treated with the DNA methyltransferase inhibitor 5-azacytidine, exhibited a reduction in MDR1 promoter methylation and a complex MDR1 chromatin configuration, characterized by the simultaneous presence of transcriptional activators and repressors. In this state, MDR1 expression was markedly sensitive to treatment with the histone deacetylase inhibitor trichostatin A. (+info)

Spatial organization and dynamics of the association of Rec102 and Rec104 with meiotic chromosomes. (8/5197)

Meiotic double-strand breaks (DSBs) are formed by Spo11 in conjunction with at least nine other proteins whose roles are not well understood. We find that two of these proteins, Rec102 and Rec104, interact physically, are mutually dependent for proper subcellular localization, and share a requirement for Spo11 and Ski8 for their recruitment to meiotic chromosomes, suggesting that they work together as a functional unit. Rec102 associated extensively with chromatin loops during leptotene and zygotene and showed preferential binding in the vicinity at least of most DSB sites, consistent with a direct role in DSB formation. However, Rec102 was associated with both DSB-hot and DSB-cold regions, ruling out a simple model in which sites of DSB formation are dictated by where Rec102/104 complexes load. Both proteins persisted on chromatin until pachytene before abruptly disappearing, indicating that they remain on chromosomes well after DSB formation. These studies reveal unexpected behaviors for Rec102 and Rec104, and point to distinct roles and subcomplexes among the DSB proteins. (+info)

There are different types of Breast Neoplasms such as:

1. Fibroadenomas: These are benign tumors that are made up of glandular and fibrous tissues. They are usually small and round, with a smooth surface, and can be moved easily under the skin.

2. Cysts: These are fluid-filled sacs that can develop in both breast tissue and milk ducts. They are usually benign and can disappear on their own or be drained surgically.

3. Ductal Carcinoma In Situ (DCIS): This is a precancerous condition where abnormal cells grow inside the milk ducts. If left untreated, it can progress to invasive breast cancer.

4. Invasive Ductal Carcinoma (IDC): This is the most common type of breast cancer and starts in the milk ducts but grows out of them and invades surrounding tissue.

5. Invasive Lobular Carcinoma (ILC): It originates in the milk-producing glands (lobules) and grows out of them, invading nearby tissue.

Breast Neoplasms can cause various symptoms such as a lump or thickening in the breast or underarm area, skin changes like redness or dimpling, change in size or shape of one or both breasts, discharge from the nipple, and changes in the texture or color of the skin.

Treatment options for Breast Neoplasms may include surgery such as lumpectomy, mastectomy, or breast-conserving surgery, radiation therapy which uses high-energy beams to kill cancer cells, chemotherapy using drugs to kill cancer cells, targeted therapy which uses drugs or other substances to identify and attack cancer cells while minimizing harm to normal cells, hormone therapy, immunotherapy, and clinical trials.

It is important to note that not all Breast Neoplasms are cancerous; some are benign (non-cancerous) tumors that do not spread or grow.

Malignant prostatic neoplasms are cancerous tumors that can be aggressive and spread to other parts of the body (metastasize). The most common type of malignant prostatic neoplasm is adenocarcinoma of the prostate, which accounts for approximately 95% of all prostate cancers. Other types of malignant prostatic neoplasms include sarcomas and small cell carcinomas.

Prostatic neoplasms can be diagnosed through a variety of tests such as digital rectal examination (DRE), prostate-specific antigen (PSA) test, imaging studies (ultrasound, CT scan or MRI), and biopsy. Treatment options for prostatic neoplasms depend on the type, stage, and grade of the tumor, as well as the patient's age and overall health. Treatment options can include active surveillance, surgery (robotic-assisted laparoscopic prostatectomy or open prostatectomy), radiation therapy (external beam radiation therapy or brachytherapy), and hormone therapy.

In summary, Prostatic Neoplasms are tumors that occur in the prostate gland, which can be benign or malignant. The most common types of malignant prostatic neoplasms are adenocarcinoma of the prostate, and other types include sarcomas and small cell carcinomas. Diagnosis is done through a variety of tests, and treatment options depend on the type, stage, and grade of the tumor, as well as the patient's age and overall health.

There are several risk factors for developing HCC, including:

* Cirrhosis, which can be caused by heavy alcohol consumption, viral hepatitis (such as hepatitis B and C), or fatty liver disease
* Family history of liver disease
* Chronic obstructive pulmonary disease (COPD)
* Diabetes
* Obesity

HCC can be challenging to diagnose, as the symptoms are non-specific and can be similar to those of other conditions. However, some common symptoms of HCC include:

* Yellowing of the skin and eyes (jaundice)
* Fatigue
* Loss of appetite
* Abdominal pain or discomfort
* Weight loss

If HCC is suspected, a doctor may perform several tests to confirm the diagnosis, including:

* Imaging tests, such as ultrasound, CT scan, or MRI, to look for tumors in the liver
* Blood tests to check for liver function and detect certain substances that are produced by the liver
* Biopsy, which involves removing a small sample of tissue from the liver to examine under a microscope

Once HCC is diagnosed, treatment options will depend on several factors, including the stage and location of the cancer, the patient's overall health, and their personal preferences. Treatment options may include:

* Surgery to remove the tumor or parts of the liver
* Ablation, which involves destroying the cancer cells using heat or cold
* Chemoembolization, which involves injecting chemotherapy drugs into the hepatic artery to reach the cancer cells
* Targeted therapy, which uses drugs or other substances to target specific molecules that are involved in the growth and spread of the cancer

Overall, the prognosis for HCC is poor, with a 5-year survival rate of approximately 20%. However, early detection and treatment can improve outcomes. It is important for individuals at high risk for HCC to be monitored regularly by a healthcare provider, and to seek medical attention if they experience any symptoms.

Explanation: Neoplastic cell transformation is a complex process that involves multiple steps and can occur as a result of genetic mutations, environmental factors, or a combination of both. The process typically begins with a series of subtle changes in the DNA of individual cells, which can lead to the loss of normal cellular functions and the acquisition of abnormal growth and reproduction patterns.

Over time, these transformed cells can accumulate further mutations that allow them to survive and proliferate despite adverse conditions. As the transformed cells continue to divide and grow, they can eventually form a tumor, which is a mass of abnormal cells that can invade and damage surrounding tissues.

In some cases, cancer cells can also break away from the primary tumor and travel through the bloodstream or lymphatic system to other parts of the body, where they can establish new tumors. This process, known as metastasis, is a major cause of death in many types of cancer.

It's worth noting that not all transformed cells will become cancerous. Some forms of cellular transformation, such as those that occur during embryonic development or tissue regeneration, are normal and necessary for the proper functioning of the body. However, when these transformations occur in adult tissues, they can be a sign of cancer.

See also: Cancer, Tumor

Word count: 190

There are several types of genomic instability, including:

1. Chromosomal instability (CIN): This refers to changes in the number or structure of chromosomes, such as aneuploidy (having an abnormal number of chromosomes) or translocations (the movement of genetic material between chromosomes).
2. Point mutations: These are changes in a single base pair in the DNA sequence.
3. Insertions and deletions: These are changes in the number of base pairs in the DNA sequence, resulting in the insertion or deletion of one or more base pairs.
4. Genomic rearrangements: These are changes in the structure of the genome, such as chromosomal breaks and reunions, or the movement of genetic material between chromosomes.

Genomic instability can arise from a variety of sources, including environmental factors, errors during DNA replication and repair, and genetic mutations. It is often associated with cancer, as cancer cells have high levels of genomic instability, which can lead to the development of resistance to chemotherapy and radiation therapy.

Research into genomic instability has led to a greater understanding of the mechanisms underlying cancer and other diseases, and has also spurred the development of new therapeutic strategies, such as targeted therapies and immunotherapies.

In summary, genomic instability is a key feature of cancer cells and is associated with various diseases, including cancer, neurodegenerative disorders, and aging. It can arise from a variety of sources and is the subject of ongoing research in the field of molecular biology.

Liver neoplasms, also known as liver tumors or hepatic tumors, are abnormal growths of tissue in the liver. These growths can be benign (non-cancerous) or malignant (cancerous). Malignant liver tumors can be primary, meaning they originate in the liver, or metastatic, meaning they spread to the liver from another part of the body.

There are several types of liver neoplasms, including:

1. Hepatocellular carcinoma (HCC): This is the most common type of primary liver cancer and arises from the main cells of the liver (hepatocytes). HCC is often associated with cirrhosis and can be caused by viral hepatitis or alcohol abuse.
2. Cholangiocarcinoma: This type of cancer arises from the cells lining the bile ducts within the liver (cholangiocytes). Cholangiocarcinoma is rare and often diagnosed at an advanced stage.
3. Hemangiosarcoma: This is a rare type of cancer that originates in the blood vessels of the liver. It is most commonly seen in dogs but can also occur in humans.
4. Fibromas: These are benign tumors that arise from the connective tissue of the liver (fibrocytes). Fibromas are usually small and do not spread to other parts of the body.
5. Adenomas: These are benign tumors that arise from the glandular cells of the liver (hepatocytes). Adenomas are usually small and do not spread to other parts of the body.

The symptoms of liver neoplasms vary depending on their size, location, and whether they are benign or malignant. Common symptoms include abdominal pain, fatigue, weight loss, and jaundice (yellowing of the skin and eyes). Diagnosis is typically made through a combination of imaging tests such as CT scans, MRI scans, and ultrasound, and a biopsy to confirm the presence of cancer cells.

Treatment options for liver neoplasms depend on the type, size, location, and stage of the tumor, as well as the patient's overall health. Surgery may be an option for some patients with small, localized tumors, while others may require chemotherapy or radiation therapy to shrink the tumor before surgery can be performed. In some cases, liver transplantation may be necessary.

Prognosis for liver neoplasms varies depending on the type and stage of the cancer. In general, early detection and treatment improve the prognosis, while advanced-stage disease is associated with a poorer prognosis.

1. Tumor size and location: Larger tumors that have spread to nearby tissues or organs are generally considered more invasive than smaller tumors that are confined to the original site.
2. Cellular growth patterns: The way in which cancer cells grow and divide can also contribute to the overall invasiveness of a neoplasm. For example, cells that grow in a disorganized or chaotic manner may be more likely to invade surrounding tissues.
3. Mitotic index: The mitotic index is a measure of how quickly the cancer cells are dividing. A higher mitotic index is generally associated with more aggressive and invasive cancers.
4. Necrosis: Necrosis, or the death of cells, can be an indication of the level of invasiveness of a neoplasm. The presence of significant necrosis in a tumor is often a sign that the cancer has invaded surrounding tissues and organs.
5. Lymphovascular invasion: Cancer cells that have invaded lymphatic vessels or blood vessels are considered more invasive than those that have not.
6. Perineural invasion: Cancer cells that have invaded nerve fibers are also considered more invasive.
7. Histological grade: The histological grade of a neoplasm is a measure of how abnormal the cancer cells look under a microscope. Higher-grade cancers are generally considered more aggressive and invasive than lower-grade cancers.
8. Immunohistochemical markers: Certain immunohistochemical markers, such as Ki-67, can be used to evaluate the proliferative activity of cancer cells. Higher levels of these markers are generally associated with more aggressive and invasive cancers.

Overall, the degree of neoplasm invasiveness is an important factor in determining the likelihood of the cancer spreading to other parts of the body (metastasizing) and in determining the appropriate treatment strategy for the patient.

1) They share similarities with humans: Many animal species share similar biological and physiological characteristics with humans, making them useful for studying human diseases. For example, mice and rats are often used to study diseases such as diabetes, heart disease, and cancer because they have similar metabolic and cardiovascular systems to humans.

2) They can be genetically manipulated: Animal disease models can be genetically engineered to develop specific diseases or to model human genetic disorders. This allows researchers to study the progression of the disease and test potential treatments in a controlled environment.

3) They can be used to test drugs and therapies: Before new drugs or therapies are tested in humans, they are often first tested in animal models of disease. This allows researchers to assess the safety and efficacy of the treatment before moving on to human clinical trials.

4) They can provide insights into disease mechanisms: Studying disease models in animals can provide valuable insights into the underlying mechanisms of a particular disease. This information can then be used to develop new treatments or improve existing ones.

5) Reduces the need for human testing: Using animal disease models reduces the need for human testing, which can be time-consuming, expensive, and ethically challenging. However, it is important to note that animal models are not perfect substitutes for human subjects, and results obtained from animal studies may not always translate to humans.

6) They can be used to study infectious diseases: Animal disease models can be used to study infectious diseases such as HIV, TB, and malaria. These models allow researchers to understand how the disease is transmitted, how it progresses, and how it responds to treatment.

7) They can be used to study complex diseases: Animal disease models can be used to study complex diseases such as cancer, diabetes, and heart disease. These models allow researchers to understand the underlying mechanisms of the disease and test potential treatments.

8) They are cost-effective: Animal disease models are often less expensive than human clinical trials, making them a cost-effective way to conduct research.

9) They can be used to study drug delivery: Animal disease models can be used to study drug delivery and pharmacokinetics, which is important for developing new drugs and drug delivery systems.

10) They can be used to study aging: Animal disease models can be used to study the aging process and age-related diseases such as Alzheimer's and Parkinson's. This allows researchers to understand how aging contributes to disease and develop potential treatments.

Neuroblastoma is caused by a genetic mutation that affects the development and growth of nerve cells. The cancerous cells are often sensitive to chemotherapy, but they can be difficult to remove surgically because they are deeply embedded in the nervous system.

There are several different types of neuroblastoma, including:

1. Infantile neuroblastoma: This type of neuroblastoma occurs in children under the age of one and is often more aggressive than other types of the cancer.
2. Juvenile neuroblastoma: This type of neuroblastoma occurs in children between the ages of one and five and tends to be less aggressive than infantile neuroblastoma.
3. Adult neuroblastoma: This type of neuroblastoma occurs in adults and is rare.
4. Metastatic neuroblastoma: This type of neuroblastoma has spread to other parts of the body, such as the bones or liver.

Symptoms of neuroblastoma can vary depending on the location and size of the tumor, but they may include:

* Abdominal pain
* Fever
* Loss of appetite
* Weight loss
* Fatigue
* Bone pain
* Swelling in the abdomen or neck
* Constipation
* Increased heart rate

Diagnosis of neuroblastoma typically involves a combination of imaging tests, such as CT scans and MRI scans, and biopsies to confirm the presence of cancerous cells. Treatment for neuroblastoma usually involves a combination of chemotherapy, surgery, and radiation therapy. The prognosis for neuroblastoma varies depending on the type of cancer, the age of the child, and the stage of the disease. In general, the younger the child and the more aggressive the treatment, the better the prognosis.

Neoplasm refers to an abnormal growth of cells that can be benign (non-cancerous) or malignant (cancerous). Neoplasms can occur in any part of the body and can affect various organs and tissues. The term "neoplasm" is often used interchangeably with "tumor," but while all tumors are neoplasms, not all neoplasms are tumors.

Types of Neoplasms

There are many different types of neoplasms, including:

1. Carcinomas: These are malignant tumors that arise in the epithelial cells lining organs and glands. Examples include breast cancer, lung cancer, and colon cancer.
2. Sarcomas: These are malignant tumors that arise in connective tissue, such as bone, cartilage, and fat. Examples include osteosarcoma (bone cancer) and soft tissue sarcoma.
3. Lymphomas: These are cancers of the immune system, specifically affecting the lymph nodes and other lymphoid tissues. Examples include Hodgkin lymphoma and non-Hodgkin lymphoma.
4. Leukemias: These are cancers of the blood and bone marrow that affect the white blood cells. Examples include acute myeloid leukemia (AML) and chronic lymphocytic leukemia (CLL).
5. Melanomas: These are malignant tumors that arise in the pigment-producing cells called melanocytes. Examples include skin melanoma and eye melanoma.

Causes and Risk Factors of Neoplasms

The exact causes of neoplasms are not fully understood, but there are several known risk factors that can increase the likelihood of developing a neoplasm. These include:

1. Genetic predisposition: Some people may be born with genetic mutations that increase their risk of developing certain types of neoplasms.
2. Environmental factors: Exposure to certain environmental toxins, such as radiation and certain chemicals, can increase the risk of developing a neoplasm.
3. Infection: Some neoplasms are caused by viruses or bacteria. For example, human papillomavirus (HPV) is a common cause of cervical cancer.
4. Lifestyle factors: Factors such as smoking, excessive alcohol consumption, and a poor diet can increase the risk of developing certain types of neoplasms.
5. Family history: A person's risk of developing a neoplasm may be higher if they have a family history of the condition.

Signs and Symptoms of Neoplasms

The signs and symptoms of neoplasms can vary depending on the type of cancer and where it is located in the body. Some common signs and symptoms include:

1. Unusual lumps or swelling
2. Pain
3. Fatigue
4. Weight loss
5. Change in bowel or bladder habits
6. Unexplained bleeding
7. Coughing up blood
8. Hoarseness or a persistent cough
9. Changes in appetite or digestion
10. Skin changes, such as a new mole or a change in the size or color of an existing mole.

Diagnosis and Treatment of Neoplasms

The diagnosis of a neoplasm usually involves a combination of physical examination, imaging tests (such as X-rays, CT scans, or MRI scans), and biopsy. A biopsy involves removing a small sample of tissue from the suspected tumor and examining it under a microscope for cancer cells.

The treatment of neoplasms depends on the type, size, location, and stage of the cancer, as well as the patient's overall health. Some common treatments include:

1. Surgery: Removing the tumor and surrounding tissue can be an effective way to treat many types of cancer.
2. Chemotherapy: Using drugs to kill cancer cells can be effective for some types of cancer, especially if the cancer has spread to other parts of the body.
3. Radiation therapy: Using high-energy radiation to kill cancer cells can be effective for some types of cancer, especially if the cancer is located in a specific area of the body.
4. Immunotherapy: Boosting the body's immune system to fight cancer can be an effective treatment for some types of cancer.
5. Targeted therapy: Using drugs or other substances to target specific molecules on cancer cells can be an effective treatment for some types of cancer.

Prevention of Neoplasms

While it is not always possible to prevent neoplasms, there are several steps that can reduce the risk of developing cancer. These include:

1. Avoiding exposure to known carcinogens (such as tobacco smoke and radiation)
2. Maintaining a healthy diet and lifestyle
3. Getting regular exercise
4. Not smoking or using tobacco products
5. Limiting alcohol consumption
6. Getting vaccinated against certain viruses that are associated with cancer (such as human papillomavirus, or HPV)
7. Participating in screening programs for early detection of cancer (such as mammograms for breast cancer and colonoscopies for colon cancer)
8. Avoiding excessive exposure to sunlight and using protective measures such as sunscreen and hats to prevent skin cancer.

It's important to note that not all cancers can be prevented, and some may be caused by factors that are not yet understood or cannot be controlled. However, by taking these steps, individuals can reduce their risk of developing cancer and improve their overall health and well-being.

Wikimedia Commons has media related to Chromatin immunoprecipitation. Chromatin+immunoprecipitation at the US National Library ... Nelson J, Denisenko O, Bomsztyk K (2009). "The fast chromatin immunoprecipitation method". Chromatin Immunoprecipitation Assays ... Chromatin immunoprecipitation (ChIP) is a type of immunoprecipitation experimental technique used to investigate the ... on Unfixed Chromatin from Cells and Tissues to Analyze Histone Modifications Chromatin Immunoprecipitation (ChIP) of Protein ...

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

Chromatin immunoprecipitation of transcription factors can be used to map transcription factor binding sites in the genome. ... Collas, Philippe (May 2010). "The Current State of Chromatin Immunoprecipitation". Molecular Biotechnology. 45 (1): 87-100. doi ...

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

"Isolating human transcription factor targets by coupling chromatin immunoprecipitation". Genes Dev. 16 (2): 235-244. doi: ...

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

"Use of protein biotinylation in vivo for chromatin immunoprecipitation". Analytical Biochemistry. 325 (1): 68-76. doi:10.1016/j ... approach to study chromatin in proximity to a protein of interest". Genome Research. 23 (2): 331-40. doi:10.1101/gr.134874.111 ...

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

Chromatin immunoprecipitation allows binding sites of proteins to be identified. A genome-wide variation of this is known as ... Proteins that bind to chromatin are cross-linked in vivo, usually via fixation with formaldehyde. The chromatin is then ... Methyl-DNA immunoprecipitation followed by tiling array allows DNA methylation mapping and measurement across the genome. DNA ... segments of open chromatin that are more readily cleaved by DNaseI. DNaseI cleaving produces larger fragments of around 1.2kb ...

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

This can be determined using a chromatin immunoprecipitation (ChIP) assay. DNA-nucleosome interactions are characterized by two ... "Chromatin Immuprecipitation". www.bio.brandeis.edu. Krogan NJ, Dover J, Wood A, Schneider J, Heidt J, Boateng MA, Dean K, Ryan ... 2013). "Genome-wide chromatin state transitions associated with developmental and environmental cues". Cell. 152 (3): 642-654. ... It is thought that they achieve this through alterations in chromatin structure, such as histone modification and DNA ...

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

Weinmann AS, Bartley SM, Zhang T, Zhang MQ, Farnham PJ (October 2001). "Use of chromatin immunoprecipitation to clone novel E2F ... SUZ12, as part of Polycomb Repressive Complex 2 (PRC2), may be involved with chromatin silencing in conjunction with HOTAIR ... "Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs". Cell. 129 (7): 1311-23. doi ...

https://en.wikipedia.org/wiki/SUZ12

Weinmann AS, Bartley SM, Zhang T, Zhang MQ, Farnham PJ (October 2001). "Use of chromatin immunoprecipitation to clone novel E2F ...

https://en.wikipedia.org/wiki/BECN1

In 1984, John T. Lis innovated the Chromatin immunoprecipitation technique. In 1993, the Nuclear Ligation Assay was published, ... In 1879, Walther Flemming coined the term chromatin. In 1883, August Weismann connected chromatin with heredity. In 1884, ... Chromatin Immunoprecipitation Assays. review. Methods in Molecular Biology. Vol. 567. pp. 171-88. doi:10.1007/978-1-60327-414-2 ... In 1973/1974, chromatin fiber was discovered. In 1975, Pierre Chambon coined the term nucleosomes. In 1982, Chromosome ...

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

Chromatin Immunoprecipitation. Methods in Molecular Biology. Vol. 1689. pp. 83-101. doi:10.1007/978-1-4939-7380-4_8. ISBN 978-1 ... Bajic M, Maher KA, Deal RB (2018). "Identification of Open Chromatin Regions in Plant Genomes Using ATAC-Seq". Plant Chromatin ... "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and ... Open chromatin regions can be defined, for example, by standard peak calling of pseudo bulk ATAC-seq data. Further steps ...

https://en.wikipedia.org/wiki/ATAC-seq

Sengupta M, Jain V, Wilkinson BJ, Jayaswal RK (June 2012). "Chromatin immunoprecipitation identifies genes under direct VraSR ...

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

Chromatin immunoprecipitation (ChIP) techniques have been in use since 1984 to detect protein-DNA interactions. There have been ... Chromatin immunoprecipitation Chip-sequencing ChIP-on-chip Protein-DNA interaction Gilmour, DS; JT Lis (1983). "Detecting ... ChIP-exo is a chromatin immunoprecipitation based method for mapping the locations at which a protein of interest ( ... Cells are then collected, broken open, and the chromatin sheared and solubilized by sonication. An antibody is then used to ...

https://en.wikipedia.org/wiki/ChIP-exo

Chromatin-immunoprecipitation analysis confirms p53 binding to the promoter region of CCDC188. Significantly repressed CCDC188 ...

https://en.wikipedia.org/wiki/CCDC188

Chromatin immunoprecipitation (ChIP) in embryos, tissue specific and single cell approaches - which combined with genetic ... "Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP". Nature Protocols. 7 (5): ... Eileen E. M. Furlong FRS MAE is an Irish molecular biologist working in the fields of transcription, chromatin biology, ... "EMBL Conference - from Functional Genomics to Systems Biology -". "14th EMBL Conference - Transcription and Chromatin - Virtual ...

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

Chromatin immunoprecipitation demonstrates that LUX binds to the PRR9 promoter to repress it. Additionally, ELF3 has been shown ...

https://en.wikipedia.org/wiki/Pseudo-response_regulator

ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of ... The third step is called chromatin immunoprecipitation, which is what ChIP is short for. The ChIP process enhances specific ... August 2007). "Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel ... The second step is the process of chromatin fragmentation which breaks up the chromatin in order to get high quality DNA pieces ...

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

"Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis". ...

https://en.wikipedia.org/wiki/E2F3

"Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis". ... interaction between chromatin assembly factor 1 and HP1 proteins". Molecular Cell. 4 (4): 529-40. doi:10.1016/S1097-2765(00) ... as well as interacting with a variety of chromatin-associated, non-histone proteins. HP1α is 191 amino acids in length ... while the C-terminal CSD homodimerizes and interacts with a variety of other chromatin-associated, non-histone related proteins ...

https://en.wikipedia.org/wiki/CBX5_(gene)

"Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis". ...

https://en.wikipedia.org/wiki/E2F2

Hearnes JM, Mays DJ, Schavolt KL, Tang L, Jiang X, Pietenpol JA (November 2005). "Chromatin immunoprecipitation-based screen to ... Knocking down LOXL2 results in lower levels of H3K4ox, resulting in chromatin decompaction, thus continuing activation of DNA ... January 2020). "LOXL2-mediated H3K4 oxidation reduces chromatin accessibility in triple-negative breast cancer cells". Oncogene ...

https://en.wikipedia.org/wiki/FAM227B

... (also known as ChIP-chip) is a technology that combines chromatin immunoprecipitation ('ChIP') with DNA microarray ... Introduced in 2007, ChIP sequencing (ChIP-seq) is a technology that uses chromatin immunoprecipitation to crosslink the ... Aparicio, O; Geisberg, JV; Struhl, K (2004). Chromatin immunoprecipitation for determining the association of proteins with ... and application of genome-wide chromatin immunoprecipitation experiments, Genomics 83 (2004) 349-360. Royce TE, Rozowsky JS, ...

https://en.wikipedia.org/wiki/ChIP-on-chip

"Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing - PubMed". ...

https://en.wikipedia.org/wiki/Michael_P._Snyder

2002). "Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray ...

https://en.wikipedia.org/wiki/GAS2L1

2002). "Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray ... 2003). "Acetylation-dependent chromatin reorganization by BRDT, a testis-specific bromodomain-containing protein". Mol. Cell. ... 2001). "Enhancement of the p300 HAT activity by HIV-1 Tat on chromatin DNA". Virology. 289 (2): 312-26. doi:10.1006/viro. ... 2004). "Identification of chromatin-related protein interactions using protein microarrays". Proteomics. 3 (11): 2101-7. doi: ...

https://en.wikipedia.org/wiki/HIST2H4A

2002). "Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray ...

https://en.wikipedia.org/wiki/CSDA_(gene)

The most commonly used method for identifying transcription factor binding sites is chromatin immunoprecipitation (ChIP). This ... Teif VB, Rippe K (October 2010). "Statistical-mechanical lattice models for protein-DNA binding in chromatin". Journal of ... For most other transcription factors, the nucleosome should be actively unwound by molecular motors such as chromatin ... Narlikar GJ, Fan HY, Kingston RE (February 2002). "Cooperation between complexes that regulate chromatin structure and ...

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

2002). "Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray ... The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher ... 2001). "Enhancement of the p300 HAT activity by HIV-1 Tat on chromatin DNA". Virology. 289 (2): 312-326. doi:10.1006/viro. ... El Kharroubi A, Piras G, Zensen R, Martin MA (1998). "Transcriptional activation of the integrated chromatin-associated human ...

https://en.wikipedia.org/wiki/HIST1H2BJ

2002). "Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray ...

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

2002). "Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray ... The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher ... 2001). "Enhancement of the p300 HAT activity by HIV-1 Tat on chromatin DNA". Virology. 289 (2): 312-26. doi:10.1006/viro. ... El Kharroubi A, Piras G, Zensen R, Martin MA (1998). "Transcriptional activation of the integrated chromatin-associated human ...

https://en.wikipedia.org/wiki/HIST1H2AG

2002). "Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray ...

https://en.wikipedia.org/wiki/MFAP1

Histone modification was first detected on a genome wide level through the coupling of chromatin immunoprecipitation (ChIP) ... Chromatin packaging of DNA varies depending on the cell cycle stage and by local DNA region. The degree to which chromatin is ... However instead of isolating a DNA-binding transcription factor or enhancer protein through chromatin immunoprecipitation, the ... By remodeling chromatin structure and changing the density of DNA packaging, gene expression can thus be modulated. Chromatin ...

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

Nagai S, Davis RE, Mattei PJ, Eagen KP, Kornberg RD (2017). "Chromatin potentiates transcription". Proc Natl Acad Sci U S A. ... A method employing very gentle cell lysis in yeast followed by co-immunoprecipitation with an antibody to a mediator subunit ( ... Mediator is involved in "looping" of chromatin, which brings distant regions of a chromosome into closer physical proximity. ... 2013). "Activating RNAs associate with mediator to enhance chromatin architecture and transcription" (PDF). Nature. 494 (7438 ...

https://en.wikipedia.org/wiki/Mediator_(coactivator)

The histone mark acetylation can be detected in a variety of ways: 1. Chromatin Immunoprecipitation Sequencing (ChIP-sequencing ... 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 ...

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

... through in vitro techniques such as yeast 2-hybrid screens and immunoprecipitation. This interaction has been specifically ... as well as many other corepressor molecules leading to transcription repression via chromatin remodelling. EVI1 interaction ...

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

The JUN protein was found to interact with C18orf63 through antibait co-immunoprecipitation. The JUN protein binds to the USP28 ... "Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes". Molecular Systems Biology ...

https://en.wikipedia.org/wiki/C18orf63

Chromatin Immunoprecipitation results in production of complex mixtures of relatively short DNA fragments, which is challenging ...

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

Analysis of chromatin immunoprecipitation revealed that AI-10-49 treatment results in the displacement of the SWI/SNF complex ... June 2018). "CBFβ-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia". Cell. ... December 2017). "CBFβ-SMMHC Inhibition Disrupts Enhancer Chromatin Dynamics and Represses MYC Transcriptional Program in Inv ( ... and disrupts enhancer chromatin dynamics which in turn induces apoptosis by repressing MYC. Furthermore, this study suggests ...

https://en.wikipedia.org/wiki/AI-10-49

Chromatin Immuno-Precipitation, or (ChIP), is an alternative method to assay protein binding at specific loci of the genome. ... Germann S, Juul-Jensen T, Letarnec B, Gaudin V (October 2006). "DamID, a new tool for studying plant chromatin profiling in ... As well as detection of standard protein-DNA interactions, DamID can be used to investigate other aspects of chromatin biology ... Cheetham SW, Brand AH (January 2018). "RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites". ...

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

... (Sonication of Cross-linked Chromatin Sequencing) is a method in molecular biology used for determining the sequences ... since it follows the same steps except it doesn't require immunoprecipitation. Auerbach, R. K.; Euskirchen, G.; Rozowsky, J.; ... "Mapping accessible chromatin regions using Sono-Seq". Proceedings of the National Academy of Sciences. 106 (35): 14926-14931. ... of those DNA regions in the genome near regions of open chromatin of expressed genes. It is also known as "Input" in the Chip- ...

https://en.wikipedia.org/wiki/Sono-Seq

If the caspase of interest was detected, it meant that it was bound to survivin in the immunoprecipitation step implicating ... During prophase, as the chromatin condenses so that it is visible under the microscope, survivin starts to move to the ... Instead, it is observed that modification of the chromatin inside of the promoter region may be responsible for the ... Evidence of the heterodimerization of survivin splice variants with survivin was shown with co-immunoprecipitation experiments ...

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

It was detected that human FOXO1 is linked with the cyclin D1 promoter using chromatin immunoprecipitation assays (ChIP assays ...

https://en.wikipedia.org/wiki/Forkhead_box_protein_O1

Other methylation assays have been proposed or used in research settings, including methylated DNA immunoprecipitation and ... implications for a role of chromatin structure in the pathogenesis of the disease". Chromosome Research. 2 (3): 225-234. doi: ...

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

... (Microfluidic Oscillatory Washing-based Chromatin ImmunoPrecipitation followed by sequencing) is a microfluidic ... The preparation of chromatin fragments from cells or nuclei and sequencing library using ChIP DNA is largely the same as in ... In the process, a packed bed of beads is formed to drastically increase the adsorption efficiency of chromatin fragments. An ... overall process of MOWChIP-seq is similar to that of conventional ChIP-seq assay except that the chromatin immunoprecipitation ...

https://en.wikipedia.org/wiki/MOWChIP-seq

Chromatin immunoprecipitation followed by sequencing) experiments. Find Individual Motif Occurrences (FIMO) is a tool for ... Chromatin immunoprecipitation followed by sequencing) experiments. In the interest of computational efficiency, DREME finds ...

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

https://en.wikipedia.org/wiki/H2BK5ac

https://en.wikipedia.org/wiki/H3K36ac

Chromatin Immunoprecipitation (ChIP) data for SMIM19 in mice even more confidently display ubiquitously medium to high ... Rafique S, Thomas JS, Sproul D, Bickmore WA (August 2015). "Estrogen-induced chromatin decondensation and nuclear re- ...

https://en.wikipedia.org/wiki/SMIM19

S-transferase M3 promoter and functional analysis in a glioma cell line using allele-specific chromatin immunoprecipitation". ...

https://en.wikipedia.org/wiki/GSTM3

Immunoprecipitation kinase assays revealed that cyclin C has Rb kinase activity. Furthermore, unlike cyclins D and E, cyclin ... there is some speculation that it may directly phosphorylate them or be involved in chromatin remodeling. Rim15 has also been ... Finally, co-immunoprecipitation assays revealed that cyclin-dependent kinase 3 (cdk3) promotes G0 exit by forming a complex ... lineage decisions in embryonic stem cells as well as control quiescence in hair follicle and muscle stem cells via chromatin ...

https://en.wikipedia.org/wiki/G0_phase

A year later, the terms "MNase-Seq" and "MNase-ChIP", for micrococcal nuclease digestion with chromatin immunoprecipitation, ... MNase digestion of chromatin was key to early studies of chromatin structure; being used to determine that each nucleosomal ... It generally maintains chromatin structure, so results from ATAC-seq can be used to directly assess chromatin accessibility, ... As of February 2020, MNase-seq is still applied to assay accessibility in chromatin. Chromatin is dynamic and the positioning ...

https://en.wikipedia.org/wiki/MNase-seq

https://en.wikipedia.org/wiki/H4K91ac

Chromatin immunoprecipitation studies demonstrate that SIRT7 localizes to rDNA, and coimmunoprecipitation shows that SIRT7 ... This suggests that SIRT7 plays a crucial role in connecting the function of chromatin remodeling complexes to RNA Pol I ... "Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in ...

https://en.wikipedia.org/wiki/Sirtuin_7

Chromatin immunoprecipitation. Chromatin was extracted from 5 × 106 cells. Briefly, cells were crosslinked with 1% formaldehyde ... One-twentieth of the precleared chromatin was used as the input for the Chromatin immunoprecipitation (ChIP) assay. The ... Having unveiled a multimeric nuclear complex consisting of β-arr1, YAP and mutp53, we performed chromatin immunoprecipitation ( ... Chromatin was sheared by sonication, centrifuged and diluted in 50 mM Tris pH 8.0, 0.5% NP-40, 0.2 M NaCl, 0.5 mM EDTA. ...

https://www.nature.com/articles/s41467-019-11045-8?error=cookies_not_supported&code=c1988f35-6ee7-4a15-a258-22d715986de6

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https://dshb.biology.uiowa.edu/custitem16/MIgG2c,RIgG2b/custitem40/Chromatin-Immunoprecipitation,Immunoprecipitation?custitem16%2F-kappa-light-chain%2CMIgG2c%2Fcustitem34%2FVertebrates=

Identifying chromatin features that regulate gene expression distribution * [The role of three-dimensional chromatin structure ... Identifying chromatin features that regulate gene expression distribution * [The role of three-dimensional chromatin structure ... Purification of nanogram-range immunoprecipitated DNA in ChIP-seq utility Chromatin immunoprecipitation-sequencing (ChIP-seq) ... Histone variants in archaea and the evolution of combinatorial chromatin complexity. Nucleosomes in eukaryotes act as platforms ...

https://chipready.com/tag/culture-cells-meaning/

Chromatin Immunoprecipitation. Chromatin immunoprecipitation (ChIP) was performed as follows: following treatments, cells were ... Regulation of IL-23R Occurs Through Direct Chromatin Remodeling. A ChIP analysis of the IL-23R promoter from A549 cells pre- ... The ChIP analysis confirms that chromatin remodeling is directly involved with the induction of IL-23R gene expression. ... The antibodies used for immunoprecipitation were as follows: pan acetyl-histone H3 (H3Ac) (Millipore, Cat#06-599), pan acetyl- ...

https://www.frontiersin.org/articles/10.3389/fonc.2013.00162/full

FREE Answer to What is Chromatin Immunoprecipitation (ChIP) and how does it work? ... What is Chromatin Immunoprecipitation (ChIP) and how does it work?. What is Chromatin Immunoprecipitation (ChIP) and how does ... Describe the steps of the chromatin immunoprecipitation assay. What is outsourcing and how does it reduce risk? Not how does it ... Working of Chromatin Immunoprecipitation (ChIP) -. *Examination of the availability of protein-DNA interaction at steady state ...

https://justaaa.com/biology/365928-what-is-chromatin-immunoprecipitation-chip-and

However, deletion of Dnmt3a has a minor effect on TET1 binding on chromatin, indicating that TET1 may limit DNA methylation ... Ten percent of chromatin was kept as input. Immunoprecipitation was performed overnight at 4 °C using M280-streptavidin (Thermo ... Chromatin immunoprecipitation. Biotin-Streptavidin ChIP was performed as described, with some modifications [41]. After a 16-h ... genome-wide binding maps of DNMT3A1 were generated by biotin-based chromatin immunoprecipitation (ChIP) followed by high- ...

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1464-7

Chromatin immunoprecipitation. Request a detailed protocol Cells (1 × 106) were cross-linked with 0.5 M DSG in PBS for 45 min ... Sonicated chromatin was incubated for 3 hr at 4°C with 5-15 μg of normal IgG or specific antibodies. Antibodies used were as ... Using immunoprecipitation assays in HEK293T cells, we detected overexpressed HA-PPARγ2 in a protein complex with FLAG-TRIM23 ( ... Transfection, immunoprecipitation, and immunoblot analysis. Request a detailed protocol HEK293T cells were transfected by the ...

https://elifesciences.org/articles/5615

This was confirmed by chromatin immunoprecipitation (ChIP) assay, which revealed that Runx1t1 binds to the promoter region of ...

https://pubmed.ncbi.nlm.nih.gov/24586690/

Chromatin immunoprecipitation assay. The chromatin immunoprecipitation assay was performed on frozen human colon tissues, ... we performed a chromatin immunoprecipitation (ChIP) assay. Briefly, chromatin was isolated from colon tissues from ulcerative ... Chromatin immunoprecipitation assays of human ulcerative colitis and CACC samples indicated that IL13 via STAT6 directly ... Chromatin was precipitated with 4 μg of anti-pSTAT6 (Thermo Fisher Scientific) or anti-p-p65 (Santa Cruz Biotechnology) at 4°C ...

https://aacrjournals.org/cancerimmunolres/article/8/2/167/469841/Cross-talk-between-Colon-Cells-and-Macrophages

Chromatin Immunoprecipitation Assay. Chromatin immunoprecipitation (ChIP) assay was performed by using the Magna ChIP Assay Kit ... The results obtained so far suggest that the reduction of HbA1c levels is unable to reprogram the adverse chromatin pattern ... 3A). Accordingly, we found that the chromatin-modifying enzyme SIRT1 involved in H3 deacetylation (29) was downregulated in ... DNA methylation is an important repressor of gene expression, whereas acetylation of histone tails favors an open chromatin, ...

https://diabetesjournals.org/diabetes/article/66/9/2472/40094/Impact-of-Glycemic-Variability-on-Chromatin

Genome-wide chromatin immunoprecipitation sequencing (Chip-Seq) data. 100. 50. Genome-wide DNA methylation data ...

https://www.ninds.nih.gov/about-ninds/guidance-policy/ninds-interpretation-nih-gds-policy

Find de novo protein motifs from chromatin immunoprecipitation data.. Highlights:. *W-ChIPMotifs is a web application tool for ...

https://www.hsls.pitt.edu/obrc/index.php?page=URL1257434299

Validated for Western Blotting, Immunoprecipitation. Highly specific and rigorously validated in-house, Hamartin/TSC1 (D43E2) ... ChIP-Chromatin Immunoprecipitation. *C&R-CUT&RUN. *C&T-CUT&Tag. *DB-Dot Blot ... Proceed to immunoprecipitation below.. Immunoprecipitation. IMPORTANT: Appropriate isotype controls are highly recommended in ... Immunoprecipitation for Native Proteins. This protocol is intended for immunoprecipitation of native proteins utilizing Protein ...

https://www.cellsignal.com/products/primary-antibodies/hamartin-tsc1-d43e2-rabbit-mab/6935

Chromatin immunoprecipitation (ChIP). OCI-Ly3 cells in T75 flask were cross-linked by 1% formaldehyde. Glycine was used to ... Chromatin immunoprecipitation (ChIP) assays were used to identify whether JMJD3 expression influenced H3K27 trimethylation in ... the majority of lesions targeting histone or chromatin modification are also a prominent feature of the DLBCL [19, 29-31]. In ... The DNA purified from both input control samples and immunoprecipitations were subjected to PCR amplification for a 300 bp ...

https://www.oncotarget.com/article/8836/text/

Pilot ENCODE Chromatin Immunoprecipitation. Affy ChIP. hide. show. LI/UCSD ChIP. hide. show. Sanger ChIP-chip. hide. show. ...

http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&singleSearch=knownCanonical&position=TAPT1

Chromatin is implicated in contributing to the cellular heterogeneity in gene expression,sup,10-16,/sup,. Fully understan … ... Chromatin Immunoprecipitation Actions. * Search in PubMed * Search in MeSH * Add to Search ... scPCOR-seq enables co-profiling of chromatin occupancy and RNAs in single cells Lixia Pan # 1 , Wai Lim Ku # 1 , Qingsong Tang ... scPCOR-seq enables co-profiling of chromatin occupancy and RNAs in single cells Lixia Pan et al. Commun Biol. 2022. . ...

https://www.ncbi.nlm.nih.gov/pubmed/?term=35804086

Chromatin Immunoprecipitation (ChIP) for Yeast (PDF). PANDEY Protocols *18O - labeling trypsin digest protocol for relative ...

https://commonfund.nih.gov/bbpn/methods

... with sequencing and chromatin immunoprecipitation (ChIP) sequencing. Detailed protocols are contained in the Online ... Murine BM c-kit+ cells were enriched for bulk RNA sequencing, assay for transposase-accessible chromatin (ATAC) ... Increased chromatin accessibility and enhancer activation were consistently observed at the Egr1 locus in Asxl1-/-Jak2VF BM c- ... Mechanistically, we demonstrated that Asxl1 deletion results in increased chromatin accessibility and enhancer activation at ...

https://haematologica.org/article/view/haematol.2021.280320

Chromatin Assembly and Disassembly*/drug effects; Chromatin Immunoprecipitation; Dioxins/pharmacology; Estradiol/pharmacology; ... Coimmunoprecipitation and chromatin immunoprecipitation (ChIP)-reChIP studies documented that E2- or dioxin-promoted formation ... Title: Aryl hydrocarbon receptor modulation of estrogen receptor α-mediated gene regulation by a multimeric chromatin complex ...

https://tools.niehs.nih.gov/portfolio/index.cfm?do=portfolio.publicationDetail&id=1849915

Chromatin Immunoprecipitation. *real-time RT-PCR. *quantitative PCR. *Freelance Writing in Health and Science ... When I began my graduate research project in developmental neurobiology I gravitated towards investigating what role chromatin ...

https://www.ideaconnection.com/innovative-people/robin-webster/problem-solver.html

It uses peak centers from ChIP-seq (chromatin immunoprecipitation followed by sequencing) as input data. Our algorithm, T-KDE, ...

https://www.niehs.nih.gov/research/atniehs/labs/bb/pi/bioinformatics/studies/index.cfm

And using chromatin immunoprecipitation assays, what we see is, in fact, yes there are changes. For example, the p65 subunit of ... Thats what open chromatin and ATAC helps uncover. So we can see sites and sequences that are all in the host chromatin, ... Well be examining the brain in traditional means as well as doing single-cell work, and here well do combined chromatin ... It stands for Assay for Transposable Accessible Chromatin, followed by high throughput sequencing, the TN5 transposase cut open ...

https://www.nimh.nih.gov/news/media/2021/macrophage-infection-by-hiv-implications-for-pathogenesis-and-cure-day-one

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

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

The underlying principle of our strategy makes it suitable for being applied to a vast range of chromatin modifications without ... Chromatin immunoprecipitation (ChIP) is the reference method for investigating protein-DNA interactions and chromatin-binding ... Chromatin was eluted by incubating beads in TE supplemented with 1 % SDS at 65 °C for 20 min. Afterwards, chromatin underwent ... Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell ...

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-2285-7

Chromatin Immunoprecipitation (ChIP) Analysis of Protein-DNA Interactions. Tae Hoon Kim and Job Dekker. Formaldehyde Cross- ... Preparation of Cross-Linked Chromatin for ChIP. Tae Hoon Kim and Job Dekker. ChIP. Tae Hoon Kim and Job Dekker. ChIP- ... CLIP (Cross-Linking and Immunoprecipitation) Identification of RNAs Bound by a Specific Protein. Robert Darnell. TRANSCRIPTOME ...

https://www.cshlpress.com/default.tpl?action=full&cart=1670140383944144767&--eqskudatarq=1024&typ=ps&newtitle=Molecular%20Neuroscience%3A%20A%20Laboratory%20Manual

"Examining histone modifications with chromatin immunoprecipitation and quantitative PCR." Nature Education 1 no. 1 (2008): 118 ... Die Modifikation des Chromatins ist ein intrinsischer Mechanismus, der während der Entwicklung eingesetzt wird, um verschiedene ... Die Struktur der kondensierten DNA in Form des Chromatins und die zugehörigen Histonproteine können chemisch modifiziert werden ...

https://www.jove.com/science-education/10797/what-is-gene-expression?language=German

Gene expression and chromatin-immunoprecipitation-sequencing (ChIP-seq) of Runx1 and p300 identified functional Runx1 bound MK ... Here, we used chromatin immunoprecipitation (ChIP) on chip assays to map the chromosomal distribution of Drosophila PcG ... Finally, chromatin conformation analysis revealed that EcR-bound regions within BR-C, which span similar to 30 KBs, contacted ... How this is achieved in the context of a complex chromatin landscape is largely unknown. Here we show that the nuclear protein ...

https://www.weizmann.ac.il/math/tanay/publications

EpiQuik Tissue Chromatin Immunoprecipitation (ChIP) Kit P-2003 EpiGentek * EUR 1084.86 * EUR 312.40 ...

https://www.mayconsulting.cz/zaangazowanie-imunoinhibitorowego-receptor-pd-1-przez-nowego/

Purification of nanogram-range immunoprecipitated DNA in ChIP-seq utility Chromatin immunoprecipitation-sequencing (ChIP-seq) is a broadly used epigenetic strategy for investigating genome-wide protein-DNA interactions in cells and tissues. (chipready.com)
Chromatin immunoprecipitation (ChIP) coupled with microarray (ChIP-chip) or sequencing (ChIP- seq) is a widely used technique for understanding the genome-wide binding pattern of regulatory proteins. (sbir.gov)
He and his colleagues therefore developed novel sequencing-based methods to study the epigenome, such as ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with the Next Generation Sequencing technique, and micrococcal nuclease sequencing (MNase-Seq). (nih.gov)

It is a powerful assay technique that can be used to probe DNA-protein interaction within a cell's neutral chromatin environment. (justaaa.com)
We offer ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput sequencing) to assess genome-wide chromatin accessibility, transcription factor binding, and nucleosome positioning and CUT&RUN (Cleavage Under Targets and Release Using Nuclease) for genome-wide profiling of DNA-bound proteins. (mdanderson.org)
We investigated via chromatin immunoprecipitation (ChIP) assay whether or not non-androgen stimuli (β-estradiol and EGF) could lead to AR binding to the known androgen receptor elements (AREs) of several genes: prostate specific antigen (PSA), FK506 binding protein 5 (FKBP5), insulin-like growth factor 1 (IGF-1), cyclin-dependent kinase inhibitor 1A (CDKN1A), and transmembrane protease, serine 2 (TMPRSS2). (thermofisher.com)
Using HepG2 and SMMC-7721 cells that aberrantly overexpressed COMMD7 , we found that NF-κB directly binds with COMMD7 promoter and serves as an activator for COMMD7 transcription by luciferase reporter assay, chromatin immunoprecipitation (ChIP), and electrophoretic mobility shift assay (EMSA). (oncotarget.com)
5. A rapid micro chromatin immunoprecipitation assay (microChIP). (nih.gov)

In conclusion, we identified PfBDP7 as a chromatin binding protein that is a constitutive part of the P. falciparum BDP1/BDP2 core complex and established PfBDP1 and PfBDP7 as novel players in the silencing of heterochromatin regulated virulence gene families of the malaria parasite P. falciparum . (frontiersin.org)

All ChIPAb+ antibodies are individually validated for chromatin precipitation, every lot, every time. (anobase.org)
After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES . (nih.gov)

PCR reactions should be performed in duplicate and should include a tube with no DNA to control for contamination, and a serial dilution of a 2% total input chromatin DNA (undiluted, 1:5, 1:25, 1:125), which is used to create a standard curve and determine amplification efficiency. (cellsignal.com)
Data is presented as percent input of each IP sample relative to input chromatin for each amplicon and ChIP sample as indicated. (anobase.org)

10. Chromatin Immunoprecipitation and Quantitative Real-Time PCR to Assess Binding of a Protein of Interest to Identified Predicted Binding Sites Within a Promoter. (nih.gov)

SimpleChIP ® Human MX1 Promoter Primers were tested on DNA isolated from cross-linked cells using the SimpleChIP ® Enzymatic Chromatin IP Kit (Magnetic Beads) #9003. (cellsignal.com)
These primers can be used to amplify DNA that has been isolated using chromatin immunoprecipitation (ChIP). (cellsignal.com)
Successful immunoprecipitation of HDAC1 associated DNA fragments was verified by qPCR using ChIP Primers, p21 flanking an Sp1 binding site in the human p21 promoter (Figure 1). (anobase.org)

4. Histone modifications and transcription factor binding on chromatin ChIP-PCR assays. (nih.gov)
Chromatin immunoprecipitation assays identified SOX2-binding sites on COL1A1 and COL1A2, indicating SOX2 as a transcription factor in collagen synthesis. (cdc.gov)

9. Linker histone epitopes are hidden by in situ higher-order chromatin structure. (nih.gov)
20. Chromatin immunoprecipitation (ChIP) for analysis of histone modifications and chromatin-associated proteins. (nih.gov)
His laboratory is studying how the interplay between transcription factors and various chromatin modifying enzymes, including both histone modifying enzymes and ATP-dependent chromatin remodeling complexes, regulates the dynamic epigenomic landscapes in various hematopoietic lineages. (nih.gov)

This led to the hypothesis that HDACs operate dynamically to reset chromatin after RNA polymerase II directs transcriptional elongation at active genes, whereas HDACs and HATs function together to maintain inactive genes at a poised state that can be induced rapidly in response to environmental cues. (nih.gov)

This study examined plasma cell -free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) as a noninvasive proxy to define molecular gene sets and sources of tissue injury in heart transplant patients . (bvsalud.org)
Chromatin immunoprecipitation and sequencing showed an increase in H3K27me3 'marks' and a dramatic shift in their location. (nih.gov)

Temporary cross-linking of protein and associated chromatin is done in live cells or tissues with the help of formaldehyde or UV. (justaaa.com)
LincRNAs were identified first in mammalian cells, and they are key regulators of diverse biological processes such as transcription and chromatin epigenetics [ 3 , 4 ]. (biomedcentral.com)
17. Chromatin Immunoprecipitation in Human and Yeast Cells. (nih.gov)
18. Chromatin immunoprecipitation in adult zebrafish red cells. (nih.gov)
U2OS cells (3 X 10E6 cell equivalents per IP) was subjected to chromatin immunoprecipitation using using 2 µg of either Normal Rabbit IgG, or 2 µg of Anti-HDAC1 and the Magna ChIP ® A Kit (Cat. (anobase.org)
This FOA requests proposals that will develop an affinity reagent resource for human transcription factors of the broadest possible utility, including possible detection of the target protein in a sample, immuno-chemical labeling of a tissue sample or cells, or immunoprecipitation of the target protein. (nih.gov)

To identify primary GR target genes, in which GR is a component of the transcriptional regulatory complex, we developed a strategy that uses chromatin immunoprecipitation to scan putative regulatory regions of target genes for sites occupied by specifically bound GR. We screened 11 glucocorticoid-regulated genes, and we identified GR-binding regions for eight of them (five induced and three repressed). (nih.gov)

The position of chromatin in regulating common gene expression has been extensively studied. (chipready.com)
2. Two-step cross-linking method for identification of NF-kappaB gene network by chromatin immunoprecipitation. (nih.gov)
14. Distinct alterations in chromatin organization of the two IGF-I promoters precede growth hormone-induced activation of IGF-I gene transcription. (nih.gov)
Setd1a and NURF mediate chromatin dynamics and gene regulation during erythroid lineage commitment and differentiation. (nih.gov)

Cell-free chromatin immunoprecipitation to detect molecular pathways in heart transplantation. (bvsalud.org)

Chromatin immunoprecipitation provides understanding of such mechanisms that clock and non-clock transcription factors along with co-regulators and chromatin modifications dictate circadian epigenome through cyclic alterations of chromatin structures and molecular functions in a concerted fashion. (elsevier.com)

Nucleosomes, the fundamental constructions used to bundle genetic info into chromatin, are topic to a various array of chemical modifications. (chipready.com)

Further Chromatin immunoprecipitation (ChIP) analysis confirmed that the KLF2 and active epigenetic marks (H3K27Ac and H3K4me3) were upregulated in the promoter region ATG7 during OB differentiation. (nih.gov)

It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA . (nih.gov)

Chromosome construction seize expertise can detect the three-dimensional building of chromatin. (chipready.com)

Recommended use: ~2 μg of antibody per chromatin immunoprecipitation (dependent upon biological context). (anobase.org)

The qPCR protocol and primer sequences are provided, allowing researchers to validate ChIP protocols when using our antibody in their chromatin context. (anobase.org)

1. Two-step cross-linking for analysis of protein-chromatin interactions. (nih.gov)

This controversy might have been influenced by the confounding effect of subtelomeric regions and interstitial telomeric sequences (ITSs) on telomeric chromatin structure analyses. (nih.gov)
We have developed a reliable procedure to study the chromatin structure of human telomeres independently of subtelomeres and ITSs. (nih.gov)

6. Acetylation of nucleosomal histones by p300 facilitates transcription from tax-responsive human T-cell leukemia virus type 1 chromatin template. (nih.gov)

Find de novo protein motifs from chromatin immunoprecipitation data. (pitt.edu)

Instruments are available for sample shearing, automated chromatin immunoprecipitation, automated library construction, library quality assessment and purification, and real-time qPCR. (nih.gov)
This FOA requests applications that will develop an affinity reagent resource of the broadest possible utility, including detection of the target protein in a sample, immuno-histochemical labeling of a tissue sample, or immunoprecipitation or other affinity capture of the target protein. (nih.gov)

The Epigenomics Profiling Core is pleased to announce that it now offers cfMeDIP (circulating cell-free methylated DNA immunoprecipitation) as part of its DNA methylation analysis repertoire. (mdanderson.org)
8. Analysis of in vivo transcription factor recruitment by chromatin immunoprecipitation of mouse embryonic kidney. (nih.gov)
16. Analysis of p300 occupancy at the early stage of stem cell differentiation by chromatin immunoprecipitation. (nih.gov)

Chromatin Immunoprecipitation (ChIP) is a method of determining the interaction between a protein of interest and a specific sequence of DNA. (justaaa.com)

7. Assessing sites of NF-κB DNA binding using chromatin immunoprecipitation. (nih.gov)

The change of H3K27me3 chromatin-binding pattern is directly related to cell cycle reentry and cell death of ATM-deficient neurons. (nih.gov)

Anatomy31

Organisms9

Diseases1

Chemicals and Drugs112

Analytical, Diagnostic and Therapeutic Techniques and Equipment28

Phenomena and Processes83

Information Science3

Specific targeting and constitutive association of histone deacetylase complexes during transcriptional repression. (1/5197)

Partially phosphorylated Pho4 activates transcription of a subset of phosphate-responsive genes. (2/5197)

Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. (3/5197)

Role of Saccharomyces single-stranded DNA-binding protein RPA in the strand invasion step of double-strand break repair. (4/5197)

ATF6 modulates SREBP2-mediated lipogenesis. (5/5197)

Formation, maintenance and consequences of the imprint at the mating-type locus in fission yeast. (6/5197)

MDR1 promoter hypermethylation in MCF-7 human breast cancer cells: changes in chromatin structure induced by treatment with 5-Aza-cytidine. (7/5197)

Spatial organization and dynamics of the association of Rec102 and Rec104 with meiotic chromosomes. (8/5197)

Chromatin

Chromatin Immunoprecipitation

Chromatin Assembly and Disassembly

Promoter Regions, Genetic

Histones

Transcription, Genetic

Transcription Factors

Protein Binding

Acetylation

Immunoprecipitation

Gene Expression Regulation

DNA-Binding Proteins

Response Elements

Binding Sites

Nucleosomes

Base Sequence

Precipitin Tests

Cell Line

Transcriptional Activation

Cell Line, Tumor

Repressor Proteins

Nuclear Proteins

Molecular Sequence Data

Electrophoretic Mobility Shift Assay

Gene Silencing

Histone Deacetylases

Chromosomal Proteins, Non-Histone

Sp1 Transcription Factor

DNA

Cell Nucleus

Epigenesis, Genetic

RNA, Messenger

RNA, Small Interfering

Methylation

Cells, Cultured

Trans-Activators

Histone Acetyltransferases

HeLa Cells

RNA Polymerase II

DNA Methylation

Reverse Transcriptase Polymerase Chain Reaction

Blotting, Western

Micrococcal Nuclease

Transfection

RNA Interference

Gene Expression Regulation, Neoplastic

Mutation

Genes, Reporter

Oligonucleotide Array Sequence Analysis

Hydroxamic Acids

Saccharomyces cerevisiae Proteins

Heterochromatin

p300-CBP Transcription Factors

Signal Transduction

Gene Knockdown Techniques

Lysine

Luciferases

Transcription Initiation Site

Histone-Lysine N-Methyltransferase

Saccharomyces cerevisiae

Enhancer Elements, Genetic

Histone Deacetylase 1

Phosphorylation

CCAAT-Binding Factor

Histone Deacetylase Inhibitors

Cell Cycle Proteins

Gene Expression Regulation, Developmental

Up-Regulation

Cell Differentiation

Protein Structure, Tertiary

Down-Regulation

DNA Primers

Deoxyribonuclease I

Homeodomain Proteins

Amino Acid Sequence

Gene Expression Profiling

E1A-Associated p300 Protein

Regulatory Elements, Transcriptional

Gene Expression Regulation, Enzymologic

Gene Expression Regulation, Fungal