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)

The purpose of this study was to generate a transcriptional profile specific for mutant p53 in triple-negative breast cancer (TNBC), representing potential novel therapeutic targets. The highly heterogeneous TNBC tumor subgroup is established as having a poor clinical outcome. There are currently no targeted therapies for women with TNBC; consequently, there is an unmet clinical need to identify targetable pathways. Approximately 75% of these tumors are known to harbour a mutation in Tp53 (mutp53). Chromatin Immunoprecipitation Sequencing (ChIP-Seq) for mutp53 and ETS-1 (a known mutp53 interactor) was carried out using the D0-1 (sc-126) and sc-20 antibodies respectively, in the MDA-MB-468 TNBC cell line. The aim of these ChIP-seq experiments was to identify sites bound by endogenous R273H mutp53 and ETS-1 and to confirm that target genes were co-regulated. We identified 282 novel mutp53 specific genomic binding sites and 37 mutant p53 and ETS1 shared binding sites. In-house data analysis and ...
The Hippo pathway is an important regulator of cell growth and stem cell activity. When Hippo signaling is inactive, the transcriptional coactivator YAP and its paralogue TAZ translocate to the nucleus, where they bind TEAD transcription factors and regulate genes that result in increased organ size and tumorigenesis. Despite the importance of this pathway in cancer, the factors recruited by YAP/TAZ and TEADs and the binding sites of YAP/TAZ on chromatin remain largely unknown. Galli and colleagues used chromatin immunoprecipitation sequencing (ChIP-seq) in liver cancer cells to analyze the genome-wide occupancy of YAP, TEAD1, TEAD4, and TAZ, which revealed that YAP and TAZ have redundant occupancy patterns at a small subset of TEAD-bound distal regulatory enhancer elements. The YAP-bound enhancers were highly active with a higher density of activating histone marks than the average enhancer and high expression of the associated target genes. Twenty-five percent of the YAP-bound enhancers were ...
The Hippo pathway is an important regulator of cell growth and stem cell activity. When Hippo signaling is inactive, the transcriptional coactivator YAP and its paralogue TAZ translocate to the nucleus, where they bind TEAD transcription factors and regulate genes that result in increased organ size and tumorigenesis. Despite the importance of this pathway in cancer, the factors recruited by YAP/TAZ and TEADs and the binding sites of YAP/TAZ on chromatin remain largely unknown. Galli and colleagues used chromatin immunoprecipitation sequencing (ChIP-seq) in liver cancer cells to analyze the genome-wide occupancy of YAP, TEAD1, TEAD4, and TAZ, which revealed that YAP and TAZ have redundant occupancy patterns at a small subset of TEAD-bound distal regulatory enhancer elements. The YAP-bound enhancers were highly active with a higher density of activating histone marks than the average enhancer and high expression of the associated target genes. Twenty-five percent of the YAP-bound enhancers were ...
DESCRIPTION. MixChIP is a probabilistic method for identifying cell type specific TF binding sites from heterogeneous chromatin immunoprecipitation sequencing (ChIP-seq) data. ...
I am a research technician for the ENCyclopedia Of DNA Elements (ENCODE) Project. The goal of the project is to identify all functional elements in the human genome through high-throughput sequencing. This project uses Bacterial Artificial Chromosomes (BAC) Recombineering to tag transcription factors with GFP in order to perform Chromatin Immunoprecipitation Sequencing (ChIP-Seq). Once the BAC is transfected into K562 cells, I maintain the stable cell lines. After I extract the chromatin from the cells, I sonicate the chromatin then perform ChIP. Finally, the purified DNA generated from ChIP is sequenced using next generation sequencing.. ...
Experimental designs that take advantage of high-throughput sequencing to generate datasets include RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), sequencing of 16S rRNA gene fragments, metagenomic analysis and selective growth experiments. In each case the underlying data are similar and are composed of counts of sequencing reads mapped to a large number of features in each sample. Despite this underlying similarity, the data analysis methods used for these experimental designs are all different, and do not translate across experiments. Alternative methods have been developed in the physical and geological sciences that treat similar data as compositions. Compositional data analysis methods transform the data to relative abundances with the result that the analyses are more robust and reproducible. Data from an in vitro selective growth experiment, an RNA-seq experiment and the Human Microbiome Project 16S rRNA gene abundance dataset were examined by ALDEx2, a
BACKGROUND & AIMS: Little is known about mechanisms that underlie postnatal hepatocyte maturation and fibrosis at the chromatin level. We investigated the transcription of genes involved in maturation and fibrosis in postnatal hepatocytes of mice, focusing on the chromatin compaction the roles of the Polycomb repressive complex 2 histone methyltransferases EZH1 and EZH2. METHODS: Hepatocytes were isolated from mixed background C57BL/6J-C3H mice, as well as mice with liver-specific disruption of Ezh1 and/or Ezh2, at postnatal day 14 and 2 months after birth. Liver tissues were collected and analyzed by RNA sequencing, H3K27me3 chromatin immunoprecipitation sequencing, and sonication-resistant heterochromatin sequencing (a method to map heterochromatin and euchromatin). Liver damage was characterized by histologic analysis. RESULTS: We found more than 3000 genes differentially expressed in hepatocytes during liver maturation from postnatal day 14 to month 2 after birth. Disruption of Ezh1 and Ezh2 ...
Chromatin immunoprecipitation sequencing(ChIP-seq) rwas performed with the Diagenode recombinant antibody directed against H3K9me3 on sheared chromatin from 4 million K562 cells.
何謂ChIP-Seq? ChIP–seq ( Chromatin immunoprecipitation sequencing )是指染色質免疫沉澱後,所獲得的DNA片段進行高通量
Chromatin alterations are fundamental hallmarks of cancer. To study chromatin alterations in primary gastric adenocarcinomas, we perform nanoscale chromatin immunoprecipitation sequencing of multiple.. He is also the co-founder and scientific adviser of Centaurus Therapeutics Inc., a US-based biotechnology company developing new therapeutics to combat the metabolic underpinnings of chronic diseases.. However, simultaneous oesophageal pH monitoring showed that 7 of the 31 patients (23%) had abnormal acid reflux despite adequate gastric acid suppression. This suggests that the antireflux mechanism in BO patients is poor, allowing even small amounts of acid to reflux in the oesophagus.. Figure 5: PI3Kδ-S but not PI3Kδ-L is resistant to small-molecule inhibition of PI3K/AKT/mTOR signalling and proliferation. Figure 6: PI3Kδ-S but not PI3Kδ-L is resistant to small-molecule inhibition.. Polycystic ovarian syndrome (PCOS) is a highly variable syndrome and one of the most common female endocrine ...
L.Y.Wang, M. Snyder, M. Gerstein In order to understand the molecular mechanisms of gene regulation, a robust method is required to discriminate transcription factor binding sites from non-binding sites on a genomic scale. Experimental methods such as ChIP-chip experiments (microarray-based readout of chromatin immuno-precipitation assays), though gaining great success, remain time-consuming, expensive, and noisy. Traditional computational methods for binding site identification, such as consensus sequences, profile methods, and HMMs, are known to generate high false positive rates when applied genome-wide. They are based on training only with positive data, the small numbers of known binding sites. Thus, we are motivated to propose a new computational method to discover transcription-factor binding sites that synthesizes the noisy data from ChIP-chip experiments with known positive binding-site patterns. Our method (which we call BoCaTFBS) uses a boosted cascade of classifiers, where each ...
I have chip-seq data on histone modifications. Ive been scouring literature and blogs on Chip-seq analysis involving normalizing to input and normalizing across samples using spiked-in samples. There doesnt seem to be a cohesive differential binding analysis approach that can incorporate input normalization along with spike-in normalization. It seems most of the diff. binding approaches involves using RNA-seq methods (EdgeR, DESeq2) on read counts over genomic windows. I can substitute normalization factors used in these RNA-seq packages with spike-in normalization factors, but how do I account for input? Is blacklisting sites that are not different from input really the best way? Transforming the counts over input via log2fc or subtraction is not statistically sound (other bioinformaticians seems to agree).. Ive looked at the input signal for my data and have found signal patterns in areas consistent with some of my histone markers. This makes me think that I should really normalize my IP to ...
ChIP-chip and ChIP-seq data analysis workflow. ChIP-chip data (fold enrichment of immunoprecipitated material over genomic DNA) and/or ChIP-seq data are mapped to a reference genome. Control bound and unbound regions are visually inspected and validated by comparison to standard ChIP and qPCR. Genomic regions where signal is significantly greater than expected by chance (user-defined threshold) are identified as bound. Bound regions are then compared to a database of genomic elements of interest (e.g. promoters) to identify bound elements. Note that absence of detected binding from a genomic region may result from absence of complementary probes upon the array (ChIP-chip), masking of repetitive regions (ChIP-chip and ChIP-seq), or unmappable regions (ChIP-seq). ... Pol II distribution detected by ChIP, ChIP-chip, and ChIP-seq. Drosophila S2 cells were crosslinked, sonicated, and total Pol II (Rpb3) was immunoprecipitated. Pol II ChIP signal at the Tl promoter region was quantified with qPCR ...
Mapping the chromosomal locations of transcription factors, nucleosomes, histone modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the key tasks of modern biology, as evidenced by the Encyclopedia of DNA Elements (ENCODE) Project. To this end, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is the standard methodology. Mapping such protein-DNA interactions in vivo using ChIP-seq presents multiple challenges not only in sample preparation and sequencing but also for computational analysis. Here, we present step-by-step guidelines for the computational analysis of ChIP-seq data. We address all the major steps in the analysis of ChIP-seq data: sequencing depth selection, quality checking, mapping, data normalization, assessment of reproducibility, peak calling, differential binding analysis, controlling the false discovery rate, peak annotation, visualization, and motif analysis. At each step in our guidelines we discuss some of the software
Chromatin immunoprecipitation (ChIP) allows enrichment of genomic regions which are associated with specific transcription factors, histone modifications, and indeed any other epitopes which are present on chromatin. The original ChIP methods used site-specific PCR and Southern blotting to confirm which regions of the genome were enriched, on a candidate basis. The combination of ChIP with genomic tiling arrays (ChIP-chip) allowed a more unbiased approach to map ChIP-enriched sites. However, limitations of microarray probe design and probe number have a detrimental impact on the coverage, resolution, sensitivity, and cost of whole-genome tiling microarray sets for higher eukaryotes with large genomes. The combination of ChIP with high-throughput sequencing technology has allowed more comprehensive surveys of genome occupancy, greater resolution, and lower cost for whole genome coverage. Herein, we provide a comparison of high-throughput sequencing platforms and a survey of ChIP-seq analysis tools,
We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors in vivo. We used ChIP-seq to map STAT1 targets in interferon-γ (IFN-γ)-stimulated and unstimulated human HeLa S3 cells, and compared the methods performance to ChIP-PCR and to ChIP-chip for four chromosomes. By ChIP-seq, using 15.1 and 12.9 million uniquely mapped sequence reads, and an estimated false discovery rate of less than 0.001, we identified 41,582 and 11,004 putative STAT1-binding regions in stimulated and unstimulated cells, respectively. Of the 34 loci known to contain STAT1 interferon-responsive binding sites, ChIP-seq found 24 (71%). ChIP-seq targets were enriched in sequences similar to known STAT1 binding motifs. Comparisons with two ChIP-PCR data sets suggested that ChIP-seq sensitivity was between 70% and 92% and specificity was at least 95%.
Genome-wide assessment of protein-DNA interaction by chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq) is a key technology for studying transcription factor (TF) localization and regulation of gene expression. Signal-to-noise-ratio and signal specificity in ChIP-seq studies depend on many variables, including antibody affinity and specificity. Thus far, efforts to improve antibody reagents for ChIP-seq experiments have focused mainly on generating higher quality antibodies. Here we introduce KOIN (knockout implemented normalization) as a novel strategy to increase signal specificity and reduce noise by using TF knockout mice as a critical control for ChIP-seq data experiments. Additionally, KOIN can identify hyper ChIPable regions as another source of false-positive signals. As the use of the KOIN algorithm reduces false-positive results and thereby prevents misinterpretation of ChIP-seq data, it should be considered as the gold standard for future ChIP-seq analyses,
Before interpreting the biological results from ChIP-chip or ChIP-seq data using the Cistrome platform, researchers can upload raw data from their microarray or sequencing facilities and then preprocess those data using Cistrome peak-calling tools. Alternatively, researchers can also upload intermediate results from their own analysis tools. As illustrated in Figure 1, the peak calling step generates two types of intermediate files: peak location files (in BED format), indicating the predicted transcription factor binding sites or histone modification sites, and signal profile files (in WIGGLE format) of binding or histone modification across the genome.. Several methods can be used to import data into Cistrome. The Upload File function can import a file from the users computer or from an HTTP or FTP file server in the same manner as in Galaxy. In most cases, sequencing facilities will manage the low level base calling and read mapping processes. The least processed Cistrome data formats that ...
Background Context-dependent transcription factor (TF) binding is one reason for differences in gene expression patterns between different cellular states. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identifies genome-wide TF binding sites for one particular context-the cells used in the experiment. But can such ChIP-seq data predict TF binding in other cellular contexts and is it possible to distinguish context-dependent from ubiquitous TF binding? Results We compared ChIP-seq data on TF binding for multiple TFs in two different cell types and found that on average only a third of ChIP-seq peak regions are common to both cell types. Expectedly, common peaks occur more frequently in certain genomic contexts, such as CpG-rich promoters, whereas chromatin differences characterize cell-type specific TF binding. We also find, however, that genotype differences between the cell types can explain differences in binding. Moreover, ChIP-seq signal intensity and peak ...
We propose to apply the emerging technology of Chromatin Immunoprecipitation on microarrays (ChIP chip) to identify the direct targets of transcription factors (TFs) known to be involved in breast and colon cancers. During the R21 phase of the project, we plan to identify these targets using a newly developed set of oligonucleotide microarrays that contain 15 million 50mer probes that tile through the non-repetitive sequence of the human genome at 100 bp resolution. We will validate that our ChIP chip protocols work with this new tiling array set. We will also develop and refine two new protocols, microarray reuse and 4-color hybridizations, that will allow economical use of this tiling array set so that it will be a more practical tool for research labs. In the R33 phase of this project, we will use this tiling array set to identify the direct targets of 9 TFs known to be involved in breast and colon cancers. Once we have collected the direct targets of these TFs, we will develop custom arrays ...
Amplification problem in DNA isolated after ChIP experiment, - posted in Genetics and Genomics: I am trying to work out a ChIP experiment. After my ChIP experiment, the DNA I am getting in INPUT is showing problem with amplification. In an RT PCR experiment when I am taking 1ul of this INPUT DNA, It shows a CT value of 36. While on increasing the volume of INPUT dna to 4ul in RT PCR, it does not even get amplified in 40 cycles. I am using diagenode Ipure kit for DNA isol...
Nucleus Collection contains over 1100 mAbs against diverse targets such as ssDNA, dsDNA, DNA modifying enzymes and transcription factors
Skeletal muscle collection includes over 185 mAbs against myosin isoforms for myofiber typing, MyoD and myogenin TFs, and Troponin complex I and T
TY - JOUR. T1 - Genome-wide analysis of the chromatin composition of histone H2A and H3 variants in mouse embryonic stem cells. AU - Yukawa, Masashi. AU - Akiyama, Tomohiko. AU - Franke, Vedran. AU - Mise, Nathan. AU - Isagawa, Takayuki. AU - Suzuki, Yutaka. AU - Suzuki, Masataka G.. AU - Vlahovicek, Kristian. AU - Abe, Kuniya. AU - Aburatani, Hiroyuki. AU - Aoki, Fugaku. PY - 2014/3/21. Y1 - 2014/3/21. N2 - Genome-wide distribution of the majority of H2A and H3 variants (H2A, H2AX, H2AZ, macroH2A, H3.1, H3.2 and H3.3) was simultaneously investigated in mouse embryonic stem cells by chromatin immunoprecipitation sequencing. Around the transcription start site, histone variant distribution differed between genes possessing promoters of high and low CpG density, regardless of their expression levels. In the intergenic regions, regulatory elements were enriched in H2A.Z and H3.3, whereas repeat elements were abundant in H2A and macroH2A, and H3.1, respectively. Analysis of H2A and H3 variant ...
BayesPeak - Bayesian Analysis of ChIP-seq Data, This package is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data.. ChIPpeakAnno - Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges.. Chipseq - A package for analyzing chipseq data. Tools for helping process short read data for chipseq experiments. ChIPseqR - ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.. ChIPsim - A general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.. DESeq - Differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count ...
The technique of chromatin immunoprecipitation (ChIP) is a powerful method for identifying in vivo DNA binding sites of transcription factors and for studying chromatin modifications. Unfortunately, the large number of cells needed for the standard ChIP protocol has hindered the analysis of many biologically interesting cell populations that are difficult to obtain in large numbers. New ChIP methods involving the use of carrier chromatin have been developed that allow the one-gene-at-a-time analysis of very small numbers of cells. However such methods are not useful if the resultant sample will be applied to genomic microarrays or used in ChIP-sequencing assays. Therefore, we have miniaturized the ChIP protocol such that as few as 10,000 cells (without the addition of carrier reagents) can be used to obtain enough sample material to analyze the entire human genome. We demonstrate the reproducibility of this MicroChIP technique using 2.1 million feature high-density oligonucleotide arrays and ...
With the microarray technology rapidly advanced, tiling arrays have quickly become one of the most powerful tools in genome-wide investigations. High density tiling arrays [1] can be used to address many biological problems such as transcriptome mapping, protein-DNA interaction mapping (ChIP-chip) and array CGH among others [2]. ChIP-chip [3], the focus of the paper, is a technique that combines chromatin immunoprecipitation (ChIP) with microarray technology (chip). It allows efficient, scalable and comprehensive identification of binding sites and profiles of DNA-binding proteins [4]. High density ChIP-chip tiling arrays not only help us map the binding sites of a protein in the genome, but also allow us to better understand the binding events of the protein by clearly displaying the binding occupancy profiles. Several methods have been proposed to analyze the ChIP-chip data; for example, Joint Binding De-convolution (JBD) [5] uses a probabilistic graphical model to improve spatial resolution ...
Single nucleotide polymorphisms (SNPs) have been associated with many aspects of human development and disease, and many non-coding SNPs associated with disease risk are presumed to affect gene regulation. We have previously shown that SNPs within transcription factor binding sites can affect transcription factor binding in an allele-specific and heritable manner. However, such analysis has relied on prior whole-genome genotypes provided by large external projects such as HapMap and the 1000 Genomes Project. This requirement limits the study of allele-specific effects of SNPs in primary patient samples from diseases of interest, where complete genotypes are not readily available. In this study, we show that we are able to identify SNPs de novo and accurately from ChIP-seq data generated in the ENCODE Project. Our de novo identified SNPs from ChIP-seq data are highly concordant with published genotypes. Independent experimental verification of more than 100 sites estimates our false discovery rate at
EZ-Magna ChIP™ HiSens Chromatin Immunoprecipitation Kit Single day chromatin immunoprecipitation (ChIP) kit containing all necessary reagents to enable ChIP from low input amounts of chromatin obtained from either cells or tissues using magnetic A/G beads. Control primers included. - Find MSDS or SDS, a COA, data sheets and more information.
Chromatin immunoprecipitation followed by genome-wide chip hybridization (ChIP-chip), provides a tool for identifying transcription factor (TF) binding sites in the upstream regulatory regions of genes that are differentially expressed in alternative phenotypes or under different environmental conditions (Sun et al. 2010; Qin et al. 2011; Vernes et al. 2011; Yu et al. 2011; Cho et al. 2012; Kwon et al. 2012; Federowicz et al. 2014). By combining ChIP-chip hybridization analyses with mutational analyses and genome-wide transcription profiling, transcriptional networks regulating phenotypic transitions and the expression of alternative phenotypes can be developed (Sun et al. 2010; Qin et al. 2011; Vernes et al. 2011; Wang et al. 2011; Cho et al. 2012; Kwon et al. 2012; Federowicz et al. 2014). However, while ChIP-chip analyses provide the locations of binding sites, they do not assess functionality (Anderson et al. 1989; Li et al. 2008; Cooke et al. 2009; Ucar et al. 2009; Qin et al. 2011; Carey ...
Peak calling is a fundamental step in the analysis of data generated by ChIP-seq or similar techniques to acquire epigenetics information. Current peak callers are often hard to parameterise and may therefore be difficult to use for non-bioinformaticians. In this paper, we present the ChIP-seq analysis tool available in CLC Genomics Workbench and CLC Genomics Server (version 7.5 and up), a user-friendly peak-caller designed to be not specific to a particular *-seq protocol. We illustrate the advantages of a shape-based approach and describe the algorithmic principles underlying the implementation. Thanks to the generality of the idea and the fact the algorithm is able to learn the peak shape from the data, the implementation requires only minimal user input, while still being applicable to a range of *-seq protocols. Using independently validated benchmark datasets, we compare our implementation to other state-of-the-art algorithms explicitly designed to analyse ChIP-seq data and provide an evaluation
Background TF-TFBS-TFT triplets -Transcription factors(TF) regulate transcription factor target(TFT) through binding to transcription factor DNA binding sites(TFBS).
This function reads in transcription factor information given the selected transcription factor target gene database. The information is downloaded via the AnnotationHub package and merged, if necessary.
Chromatrap® offers a one-of-a-kind solid state patented technology, which is characterized by unmatched sensitivity. This makes it possible for users to perform Chromatin immunoprecipitation (ChIP) assays using only 1000 cells per immunoprecipitation.
Chromatin Immunoprecipitation determines the in vivo chromatin binding sites of a transcription factor or other protein of interest. ...
www.millipore.com/epigenetics Cat # Agarose ChIP Kits 17-295 17-371 17-245 17-229 Tools for Chromatin Immunoprecipitation ...
1) Any replication of the Lin et al. paper needs to include both RNA profiling and ChIP-seq experiments. The Lin et al. paper has been quite controversial and was based in very large part on ChIP-seq data and its interpretation. Many of the conclusions were based on very subtle changes in data profiles. Subsequently, two papers were published in Nature (Walz et al. and Sabo et al.) that challenge the global claims of Lin et al. In both papers, the authors worked hard to accumulate comprehensive ChIP-seq and RNA expression data in carefully designed experimental systems. While some aspects of the Lin et al. paper may be correct, both Nature papers conclude that there is a set of defined target genes that are far more Myc responsive than others. Hence, reproducing only a subset of the Lin et al. experiments is unlikely to add anything new or resolve controversial claims.. The authors do not propose to reproduce the critical ChIP-seq data and they do not propose any analysis of RNAPII profiles that ...
Chromatin immunoprecipitation (ChIP) is an assay for interrogating protein-DNA interactions that is increasingly being used for drug target discove...
Labomics offers research tools for life science: Genome Editing tools - TALEN CRISPR ,RNA, microRNA, DNA & protein analysis, magnetic beads separation, immuno-precipitation, virus isolation, shRNA clones collection, microRNA clones collection, cDNA ready for expression clones collection, More than 95000 highly characterized antibodies (Lifespan, Everest, BioHit, LabOmics).
Labomics offers research tools for life science: Genome Editing tools - TALEN CRISPR ,RNA, microRNA, DNA & protein analysis, magnetic beads separation, immuno-precipitation, virus isolation, shRNA clones collection, microRNA clones collection, cDNA ready for expression clones collection, More than 95000 highly characterized antibodies (Lifespan, Everest, BioHit, LabOmics).
Recently, several non-classical functions of histone modification regulators (HMRs), independent of their known histone modification substrates and products, have been reported to be essential for specific cellular processes. However, there is no framework designed for identifying such functions systematically. Here, we develop ncHMR detector, the first computational framework to predict non-classical functions and cofactors of a given HMR, based on ChIP-seq data mining. We apply ncHMR detector in ChIP-seq data-rich cell types and predict non-classical functions of HMRs. Finally, we experimentally reveal that the predicted non-classical function of CBX7 is biologically significant for the maintenance of pluripotency.
BIC/miR-155 expression is not necessarily regulated by FoxP3.(A) Schematic overview of the ChIP-Seq analysis workflow. Genomic loci of all significantly and rep
Hojo, H. et al. Sp7/Osterix Is restricted to bone-forming vertebrates where it acts as a Dlx co-factor in osteoblast specification. Dev. Cell 37, 1-16 (2016).. This study used ChIP-seq and RNA-seq to analyze the role of the transcription factor Sp7/Osterix during bone formation in mice. The authors generated a transgenic mouse line in which a biotin motif and three FLAG epitopes were attached to the C-terminus of the Sp7 protein to enable the binding sites of Sp7 could be identified by ChIP. ThruPLEX DNA-seq kit was used to generate ChIP-seq libraries to identify osteoblast enhancers. The authors concluded that the appearance of Sp7 within the Sp family was likely to have played a key role in the emergence of bone-forming osteoblasts during vertebrate evolution.. Read now » ...
Hojo, H. et al. Sp7/Osterix Is restricted to bone-forming vertebrates where it acts as a Dlx co-factor in osteoblast specification. Dev. Cell 37, 1-16 (2016).. This study used ChIP-seq and RNA-seq to analyze the role of the transcription factor Sp7/Osterix during bone formation in mice. The authors generated a transgenic mouse line in which a biotin motif and three FLAG epitopes were attached to the C-terminus of the Sp7 protein to enable the binding sites of Sp7 could be identified by ChIP. ThruPLEX DNA-seq kit was used to generate ChIP-seq libraries to identify osteoblast enhancers. The authors concluded that the appearance of Sp7 within the Sp family was likely to have played a key role in the emergence of bone-forming osteoblasts during vertebrate evolution.. Read now » ...
This is Your Brain on Chips on Wyss Institute | How do you study something as complex as the human brain? Take it apart. Wyss researchers have created Organ…
A single quantum well doped by a negative delta-function potential (Delta-potential) in the barrier regions is analyzed in terms of the optical transitions in between subbands. The first two states of the quantum well do not change at all as a function of the strength of the delta-potential up to a certain value, whereas the third one gets lowered almost exponentially. An important point is that the delta-potential brings a state from the continuum to the bound region. There is a range of the... ...
Schematics of endocytosis of a single NP.The membrane is partitioned into three regions due to the wrapping: the bound region of area , the impacted region of a
Discover our guide covering some of the latest and most advanced ChIP-based techniques. Including ChIP-loop, ChIA-PET, ChIP-exo and ChIP-BS-seq.
The Lens serves almost all the patents and scholarly work in the world as a free, open and secure digital public good, with user privacy a paramount focus.
Catch & Release v2.0 High Throughput (HT) Immunoprecipitation Assay Kit- 96 well from Upstate,This kit allows for quick and reproducible immunoprecipitation (IP) by using a 96 well filter plate. The system is more reproducible than regular IPs, which are problematic with regards to washing the protein A/G agarose without disrupting the agarose bed. The binding of the antibody/antigen comple,biological,biology supply,biology supplies,biology product
Please note the sensitivity of ChIP-on-chip using this cutoff is about 50%. If you see a gene with binding ratio somewhere between 1.5 and 2, there is a good chance that it may be a CREB target, especially if there is a good CRE on the promoter. Manual ChIP might be needed to verify CREB binding for these genes ...
The RSEG software package is aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as H3K36me3 and H3K27me3 ...
Packet-based on-chip interconnection networks, or Network-on-Chips (NoCs) are progressively replacing global on-chip interconnections in ...
Immunoprecipitation vs conventional WB - posted in Protein and Proteomics: Hi, folks. Sorry in advance for my naive question, its because Ive been reading some articles lately with a lot of IP. So here it is: what are the differences between IP and standard WB, regarding results? What are the differences between you precipitating the desired protein with protein G or A and then, detecting it on a SDS gel, and detecting it just with the 1st AB and 2nd AB, as it is in a convention...
Imagine instead of using your loose change on chips and a soda in the office breakroom vending machine, you could get egg-and-croissant sandwiches, or garden salads and fresh apricots.
高い抗原親和性、特異性と安定した品質を兼ね備えたアブカムのウサギ・モノクローナル抗体 RabMAb® ab32074 交差種: Ms,Rat,Hu 適用: WB,IP,IHC-P,Flow Cyt,ChIP/Chip,ICC/IF
Otherwise known as Covid chips because this is the only occasion youll ever have enough time to make the fuckers. Theyre currently in the fridge after simmering them. If theyre
引用Abcams Anti-TFEB抗体- ChIP Grade (ab2636)的参考文献列表。为您列举引用本产品的发表文章,并提供信息包括论文文献数据库中的检索编号以便您搜寻文章
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diazoethane definition: Noun (uncountable) 1. (organic chemistry) The diazo compound, CH3-CH=N+=N-Aldrichimica Acta Volume 30 No 4 (pdf) from Sigma-AldrichDiazomethane reacts rapidly with Smiths diene to produce pyrazoline (R = H) by exclusive reaction...
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 ...
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 enhance 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 ...
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 ...
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 ...
The histone mark H3K4me1 can be detected in a variety of ways: 1. Chromatin Immunoprecipitation Sequencing (ChIP-sequencing) ... Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of ... Chromatin states are also useful in identifying regulatory elements that have no defined sequence, such as enhancers. This ... This led to chromatin states, which define genomic regions by grouping different proteins and/or histone modifications together ...
The histone mark H3K4me3 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 ... usually identified through chromatin immunoprecipitation) to identify active gene promoters. H3K4me3 promotes gene activation ... Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of ...
ChIP-PET: The combined use of chromatin immunoprecipitation (ChIP) and PET is used to detect regions of DNA bound by a protein ... The first ChIA-PET was developed by Fullwood et al.. (2009) to generate a map of the interactions between chromatin bound by ... ChIA-PET: The application of PET sequencing on chromatin interaction analysis. It is a genome-wide strategy for finding de novo ... An oestrogen-receptor-alpha-bound human chromatin interactome. Nature. 462: 58-64. Ng P, Wei CL, Sung WK et al. 2005. Gene ...
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 ...
... chromatin immunoprecipitation, mRNA expression profiling, transcriptional promoter and DNA methylation measurements. The lab ...
Chromatin Immunoprecipitation results in production of complex mixtures of relatively short DNA fragments, which is challenging ...
... is also used to crosslink proteins to DNA, as used in ChIP (chromatin immunoprecipitation) which is a ...
... and chromatin immunoprecipitation-sequencing (ChIP-seq). RNA-seq permits the direct identification of eRNAs by matching the ... Using explicit chromatin signature peaks, a significant proportion (~70%) of extragenic RNA Pol II transcription start sites ... It was proposed that the presence of these enzymes could also induce an opening of chromatin at enhancer regions, which are ... Enhancers that generate polyA+ eRNAs have a lower H3K4me1/me3 ratio in their chromatin signature than 2D-eRNAs. PolyA+ eRNAs ...
... chromatin immunoprecipitation MeSH E05.478.605.492 - precipitin tests MeSH E05.478.605.492.300 - flocculation tests MeSH ...
SRG1 was identified when chromatin immunoprecipitation (ChIP) assays showed that in Saccharomyces cerevisiae, even when SER3 ...
In contrast to chromatin immunoprecipitation (ChIP)-based methods of identifying DNA double-strand breaks (DSBs) by labeling ... Kozubek S, Lukásová E, Amrichová J, Kozubek M, Lisková A, Slotová J (June 2000). "Influence of cell fixation on chromatin ... The initial fixation step stabilizes chromatin and prevents the formation of additional DSBs during sample preparation. DSBs ...
... as seen in fluorescent-antibody staining of Drosophila polytene chromosomes and chromatin immunoprecipitation (ChIP) assays on ... FACT (facilitates chromatin transcription, sometimes facilitates chromatin transactions) is a heterodimeric protein complex ... Co-immunoprecipitation assays with tagged recombinant proteins showed that the Spt16 subunit interacts with H2A/H2B dimers and ... Orphanides, George; Wu, Wei-Hua; Lane, William S.; Hampsey, Michael; Reinberg, Danny (1999). "The chromatin-specific ...
Chromatin immunoprecipitation studies with the SrbA protein led to the identification of a second hypoxia regulator, SrbB.[19] ...
Chromatin immunoprecipitation with sequencing (ChIP-seq) is a method used to identify protein binding sites on DNA and assess ... Studies observing the chromatin landscapes of beige adipocytes have found that adipogenesis of these cells results from the ... "EBF2 transcriptionally regulates brown adipogenesis via the histone reader DPF3 and the BAF chromatin remodeling complex" ... formation of cell specific chromatin landscapes, which regulate the transcriptional program and, ultimately, control ...
The most commonly used method for identifying transcription factor binding sites is chromatin immunoprecipitation (ChIP).[81] ... 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 ... Chadwick LH, Wade PA (April 2007). "MeCP2 in Rett syndrome: transcriptional repressor or chromatin architectural protein?". ...
RNP Immunoprecipitation (RIP)[edit]. Similar to chromatin immunoprecipitation (ChIP) outlined above, but rather than targeting ... Chromatin immunoprecipitation (ChIP) is a method used to determine the location of DNA binding sites on the genome for a ... Protein complex immunoprecipitation (Co-IP)[edit]. Immunoprecipitation of intact protein complexes (i.e. antigen along with any ... Chromatin+immunoprecipitation at the US National Library of Medicine Medical Subject Headings (MeSH) ...
Chromatin immunoprecipitation. *Surface plasmon resonance. *Isothermal titration calorimetry. *X-ray crystallography. *Protein ...
Chromatin immunoprecipitation. *Surface plasmon resonance. *Isothermal titration calorimetry. *X-ray crystallography. *Protein ...
Chromatin immunoprecipitation. *Surface plasmon resonance. *Isothermal titration calorimetry. *X-ray crystallography. *Protein ...
Immunoprecipitation. *Chromatin immunoprecipitation. *Immunodiffusion *Ouchterlony double immunodiffusion. *Radial ...
Chromatin immunoprecipitation. *Surface plasmon resonance. *Isothermal titration calorimetry. *X-ray crystallography. *Protein ...
Immunoprecipitation. *Chromatin immunoprecipitation. *Immunodiffusion *Ouchterlony double immunodiffusion. *Radial ...
Chromatin immunoprecipitation. *Surface plasmon resonance. *Isothermal titration calorimetry. *X-ray crystallography. *Protein ...
Immunoprecipitation. *Chromatin immunoprecipitation. *Immunodiffusion *Ouchterlony double immunodiffusion. *Radial ...
Chromatin immunoprecipitation. *Surface plasmon resonance. *Isothermal titration calorimetry. *X-ray crystallography. *Protein ...
Methylated DNA immunoprecipitation (MeDIP), analogous to chromatin immunoprecipitation, immunoprecipitation is used to isolate ... inactive chromatin, termed heterochromatin. This link between DNA methylation and chromatin structure is very important. In ... In yeast at least, H3K36me3 recruits enzymes such as histone deacetylases to condense chromatin and prevent the activation of ... such as histone deacetylases and other chromatin remodeling proteins that can modify histones, thereby forming compact, ...
... including chromatin immunoprecipitation (together with its large-scale variants ChIP-on-chip and ChIP-Seq), fluorescent in situ ... Chromatin remodeling is not always inherited, and not all epigenetic inheritance involves chromatin remodeling.[45] ... One way that genes are regulated is through the remodeling of chromatin. Chromatin is the complex of DNA and the histone ... This chromatin remodeler can then cause changes to the state of the chromatin. Indeed, a bromodomain - a protein domain that ...
Exposing various ectopic DNA loci to natural lncRNAs can help show the effects of lncRNAs on gene expression and chromatin ... Transient reporter assays followed by confirmation with RNA Immunoprecipitation sequencing (RIP-qPCR) showed that all the three ... One of the major outstanding questions in the study of lncRNAs is whether effects on chromatin state or gene expression ... and regulating the chromatin state, and thereby the expression, of a given locus. Many ncRNAs have been discovered, but in many ...
Transcription - Actin is involved in chromatin reorganization,[80][107][115][116] transcription initiation and interaction with ... It was initially thought that it only bound with actin and tubulin, although recent immunoprecipitation studies have shown that ... Farrants AK (Jun 2008). "Chromatin remodelling and actin organisation". FEBS Letters. 582 (14): 2041-2050. doi:10.1016/j. ... Actin can also be a component of chromatin remodelling complexes as well as pre-mRNP particles (that is, precursor messenger ...
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 ...
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 ...
Chromatin+immunoprecipitation at the US National Library of Medicine Medical Subject Headings (MeSH) EpigenomeNOE.com Chromatin ... 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 ... These reports are considered the pioneering studies in the field of chromatin immunoprecipitation. XChIP was further modified ...
Analysis of chromatin immunoprecipitation revealed that AI-10-49 treatment results in the displacement of the SWI/SNF complex ... and disrupts enhancer chromatin dynamics which in turn induces apoptosis by repressing MYC. Furthermore, this study suggests ...
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". ...
... (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 ...
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 ...
... combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by ... Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. *Gordon ... We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel ... Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat ...
Hybridoma technology is used to fuse fusion a B cell and myeloma to form a hybridoma that produces identical monoclonal antibodies.
... chromatin immunoprecipitation sequencing (ChIP-seq), sequencing of 16S rRNA gene fragments, metagenomic analysis and selective ... These methods are diverse and include RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), and ... chromatin immunoprecipitation sequencing (ChIP-seq), sequencing of 16S rRNA gene fragments, metagenomic analysis and selective ...
Chromatin+immunoprecipitation at the US National Library of Medicine Medical Subject Headings (MeSH) EpigenomeNOE.com Chromatin ... 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 ... These reports are considered the pioneering studies in the field of chromatin immunoprecipitation. XChIP was further modified ...
This makes it possible for users to perform Chromatin immunoprecipitation (ChIP) assays using only 1000 cells per ... Chromatin immunoprecipitation. The Chromatrap® ChIP-seq Protein A kit (Cat no 500189) was used for ChIP in accordance with the ... Efficient Extraction and Immunoprecipitation of Chromatin from Complex Formalin Fixed Paraffin Embedded Tissue. ... Slurries were prepared for immunoprecipitation using 100 µl chromatin stock from each extraction, depending on the number of ...
This up-to-date volume includes protocols that illustrate the broad use of chromatin immunoprecipitation (ChIP) and ChIP- ... Chromatin Immunoprecipitation. Methods and Protocols. Editors: Visa, Neus, Jordán-Pla, Antonio (Eds.) ... Chromatin Immunoprecipitation from Mouse Embryonic Tissue or Adherent Cells in Culture, Followed by Next-Generation Sequencing ... Includes cutting-edge techniques for the study of chromatin immunoprecipitation. *Provides step-by-step detail essential for ...
Chromatin Immunoprecipitation Sequencing (ChIP Seq) News and Research. RSS ChIP-seq, or chromatin immunoprecipitation and ...
Immunoprecipitation. *Use the chromatin prepared from Step 2.2. Approximately 25 μg of DNA per IP is recommended. Dilute each ... After reading this ChIP protocol, review more ChIP assay / chromatin immunoprecipitation resources and products, or go straight ... This chromatin preparation will be used for the immunoprecipitation (IP) in Step 4. ... flexible Chromatin Extraction Kit ab117152 which is used to extract native, cross-linked, sheared or unsheared chromatin ...
Find out how to perform native chromatin immunoprecipitation with this detailed step-by-step protocol. ... Immunoprecipitation. *100-200 μg unfixed chromatin + 100-200 μl affinity purified antibody (50-100 μg Ig) and the final volume ... After reading this ChIP protocol, review more ChIP assay /chromatin immunoprecipitation resources and products, or go straight ... flexible Chromatin Extraction Kit ab117152 which is used to extract native, cross-linked, sheared or unsheared chromatin ...
Chromatin immunoprecipitation (ChIP) is a powerful research technique used to identify and analyze protein-DNA interactions ... Whatever your preferred method of chromatin preparation we have a ChIP kit suited to your needs. ...
A complete solution for Chromatin Immunoprecipitation including columns and reagents for DNA purification. ... The Imprint Chromatin Immunoprecipitation Kit combines speed and convenience with performance. ... View the Chromatin IP (ChIP) Troubleshooting Questions. View the poster Rapid and easy method for Chromatin IP (ChIP) analysis ... Successful chromatin immunoprecipitation requires an effective, specific, and high quality antibody. Not all antibodies work in ...
... these covalent modifications on the core histones are thought to play essential roles in chromatin organization and gene ... Chromatin Immunoprecipitation (ChIP) Protocol. In cells and tissues, the histone proteins that constitute the nucleosomes can ... View the protocol Chromatin Immunoprecipitation (ChIP) on Unfixed Chromatin from Cells and Tissues to Analyze Histone ... For other applications, chromatin immunoprecipitation should be performed on cross-linked chromatin. ...
Chromatin Immunoprecipitation, Chromatin Immunoprecipitation (ChIP) using Drosophila tissue, Chromatin Immunoprecipitation ... Chromatin Immunoprecipitation from Human Embryonic Stem Cells, Generation of High Quality Chromatin Immunoprecipitation DNA ... Efficient Chromatin Immunoprecipitation using Limiting Amounts of Biomass, Chromatin Immunoprecipitation (ChIP) Protocol for ... Chromatin Immunoprecipitation from Dorsal Root Ganglia Tissue following Axonal Injury, Chromatin Immunoprecipitation Assay ...
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G Chromatin Immunoprecipitation Kit Magna ChIP™ A/G Chromatin Immunoprecipitation Kit EZ-Magna ChIP™ A/G Chromatin ... A Chromatin Immunoprecipitation Kit Magna ChIP™ G Chromatin Immunoprecipitation Kit EZ-Magna ChIP™ A Chromatin ... Universal Chromatin Immunoprecipitation DNA Microarray Quad Kit Magna ChIP-Seq Chromatin Immunoprecipitation and Next ... Chromatin Immunoprecipitation Human Promoter 244K Microarray Kit Magna ChIP2™ Chromatin Immunoprecipitation Mouse Promoter 244K ...
... can be used to study protein DNA complexes. Visit this page to learn more about how to optimize ... Sheared chromatin may be saved at -80°C prior to performing the immunoprecipitation. If you are saving the chromatin, we would ... Immunoprecipitation. Immunoprecipitation of chromatin-bound protein can be performed with Protein A, G, or A/G magnetic or ... Fixation and Chromatin Isolation. A successful ChIP experiment is dependent on high quality chromatin. Chromatin quality can be ...
Analysis of Histone Modifications in Rodent Pancreatic Islets by Native Chromatin Immunoprecipitation.. Sandovici I1,2, ... Histones represent the main protein components of the chromatin and undergo diverse covalent modifications that are very ... pancreatic islets from rodents and subsequently outline the methods used to immunoprecipitate and analyze the native chromatin ...
Measurement of protein-DNA interactions in vivo by chromatin immunoprecipitation.. Im H1, Grass JA, Johnson KD, Boyer ME, Wu J ... The chromatin is sonicated to generate small fragments, and an immunoprecipitation is conducted with an antibody against the ... These seemingly complex issues can be directly addressed by a powerful methodology termed the chromatin immunoprecipitation ( ... Chromatin-domain scanning coupled with quantitative analysis is a powerful means of dissecting mechanisms by which signaling ...
... Chromatin Crosslinking: How Much Time? Chromatin ... Learn how the optimal crosslinking time in Chromatin Immunoprecipitation (ChIP) can be influenced by sample type, and by target ...
ChIP-chip chromatin immunoprecipitation microarray RNA polymerase transcription factor transcription factor binding ... Ren B,d Dynlacht BD (2004) Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian ... Lee TI, Johnstone SE, Young RA (2006) Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat ... To better understand these interactions, researchers developed a method that couples chromatin immunoprecipitation with ...
This up-to-date volume includes protocols that illustrate the broad use of chromatin immunoprecipitation (ChIP) and ChIP- ... Chromatin Immunoprecipitation from Mouse Embryonic Tissue or Adherent Cells in Culture, Followed by Next-Generation Sequencing ... Chromatin Immunoprecipitation Assay in the Hyperthermoacidophilic Crenarchaeon, Sulfolobus acidocaldarius Kun Wang, Ann- ... ChIP-re-ChIP: Co-occupancy Analysis by Sequential Chromatin Immunoprecipitation Timothy V. Beischlag, Gratien G. Prefontaine, ...
Read our ChIP protocol and watch our video protocol to learn more about lysate preparation, chromatin cross-linking, DNA ... shearing by sonication, immunoprecipitation, reverse cross-linking, DNA purification, DNA amplification, and DNA quantification ...
Chromatin immunoprecipitation (ChIP) is a method used to determine the location of DNA binding sites on the genome for a ... Chromatin Immunoprecipitation Sequencing (ChIP-Seq) * Chromatin Immunoprecipitation Sequencing (ChIP-Seq) on the 5500xl Genetic ... Chromatin Immunoprecipitation Sequencing (ChIP-Seq) Sample Prep Products * Chromatin Immunoprecipitation Sequencing by Ion ... Chromatin immunoprecipitation (ChIP) is a method used to determine the location of DNA binding sites on the genome for a ...
The chromatin immunoprecipitation (ChIP) assay is a powerful method for analyzing epigenetic modifications and genomic DNA ... 2. Optimization of chromatin shearing Shearing the chromatin allows the chromatin to be soluble and dictates the resolution of ... Chromatin immunoprecipitation (ChIP) is a technique used in epigenetic research that takes a snapshot of protein-DNA ... Mechanical chromatin shearing. Sonication is commonly used for chromatin shearing as it produces random fragments. Since ...
A novel protocol for the preparation of chromatin from adult mouse skeletal muscle adapted to the study of gene regulation in ... The chromatin can be efficiently sonicated and is suitable for chromatin immunoprecipitation experiments, as illustrated by the ... com/fr/fr/home/life-science/epigenetics-noncoding-rna-research/chromatin-remodeling/chromatin-immunoprecipitation-chip/chip- ... For immunoprecipitation, add the appropriate amount of primary antibody (e.g., 1-2 µg per 10 µg of chromatin) and incubate ...
Chromatin Immunoprecipitation determines the in vivo chromatin binding sites of a transcription factor or other protein of ... Retrieved from "https://openwetware.org/mediawiki/index.php?title=Chromatin_Immunoprecipitation&oldid=287188" ...
Lee, H. R., W. Zhang, T. Langdon, W. Jin, H. Yan et al., 2005 Chromatin immunoprecipitation cloning reveals rapid evolutionary ... 2004). Chromatin immunoprecipitation (ChIP) using antisera to histone H3 variant CENH3 is an accepted method for showing that a ... Precise Centromere Mapping Using a Combination of Repeat Junction Markers and Chromatin Immunoprecipitation-Polymerase Chain ... Precise Centromere Mapping Using a Combination of Repeat Junction Markers and Chromatin Immunoprecipitation-Polymerase Chain ...
Chromatin immunoprecipitation combined with next-generation sequencing (ChIP-seq) is a powerful technique to investigate in ... vivo transcription factor (TF) binding to DNA, as well as chromatin marks.... ... Chromatin immunoprecipitation (ChIP) Chromatin Transcription factor (TF) Next-generation sequencing Arabidopsis Root ... Chromatin Immunoprecipitation Sequencing (ChIP-Seq) for Transcription Factors and Chromatin Factors in Arabidopsis thaliana ...
Chromatin Immunoprecipitation. Recommended controls include: No antibody negative control OR normal IgG negative control, ... Although it is preferable to proceed directly to the following steps, sheared chromatin can now be frozen at -80 C for up to 1 ... 1. Dilute each IP sample 1:10 by adding 75 ul sheared chromatin to 675 ul dilution buffer, along with appropriate protease ... Keep samples ice cold to prevent denaturing of chromatin. Conditions for fragmenting must be empirically derived, and vary ...
Animals, Chromatin Immunoprecipitation, Dendritic Cells, DNA, Gene Expression Regulation, High-Throughput Screening Assays, ... A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals.. ... Here, we develop a high-throughput Chromatin ImmunoPrecipitation (HT-ChIP) method to systematically map protein-DNA ... HT-ChIP was applied to define the dynamics of DNA binding by 25 TFs and 4 chromatin marks at 4 time-points following pathogen ...
Chromatrap® Chromatin Immunoprecipitation qPCR Assay Kit - Video Protocol shows step by step how to perform a Chromatin IP from ... It was developed to offer a faster, more sensitive method of chromatin immunoprecipitation. By avoiding the use of magnetic or ... Chromatrap® solid-state platform for Chromatin immunoprecipitation. Genome-wide mapping of protein-DNA interactions is ... The most widely used tool for examining these interactions is chromatin immunoprecipitation (ChIP) followed by massively ...
Immunoprecipitation of native chromatin: NChIP. Methods 31:76‐82. Ooi, S.L., Henikoff, J.G., and Henikoff, S. 2010. A native ... In vivo cross‐linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment. Methods ... A rapid micro chromatin immunoprecipitation assay (microChIP). Nat. Protoc. 3:1032‐1045. ... The use of biotin tagging in Saccharomyces cerevisiae improves the sensitivity of chromatin immunoprecipitation. Nucleic Acids ...
  • We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors in vivo . (nature.com)
  • Experimental designs that take advantage of high-throughput sequencing to generate datasets include RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), sequencing of 16S rRNA gene fragments, metagenomic analysis and selective growth experiments. (biomedcentral.com)
  • These methods are diverse and include RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), and metagenomic and 16S rRNA gene amplification analysis of microbial populations. (biomedcentral.com)
  • Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identifies genome-wide TF binding sites for one particular context-the cells used in the experiment. (bibsys.no)
  • We show that by combining signal intensity with additional data-ranging from context independent information such as binding site conservation and position weight matrix scores to context dependent chromatin structure-we can predict whether a ChIP-seq peak is likely to be present in other cellular contexts. (bibsys.no)
  • MixChIP is a probabilistic method for identifying cell type specific TF binding sites from heterogeneous chromatin immunoprecipitation sequencing (ChIP-seq) data. (mybiosoftware.com)
  • Chromatin is immunoprecipitated with an anti-GFP Ab (ab290, Abcam) and the immunocomplexes are recovered with protein A/G magnetic beads (Millipore). (mendeley.com)
  • Expectedly, common peaks occur more frequently in certain genomic contexts, such as CpG-rich promoters, whereas chromatin differences characterize cell-type specific TF binding. (bibsys.no)
  • Chromatin is prepared and sonicated until fragments reach an average size of 500 bp. (mendeley.com)
  • To study chromatin alterations in primary gastric adenocarcinomas, we perform nanoscale chromatin immunoprecipitation sequencing of multiple. (livingnlimbo.com)
  • ChIP-seq, or chromatin immunoprecipitation and sequencing, is a technique that allows researchers to understand transcriptional regulation via mapping of protein-DNA interactions and epigenetic markers on a genome-wide scale. (news-medical.net)
  • Chromatin Immunoprecipitation is a powerful tool to study protein:DNA complexes and can be used to map transcription factor binding sites or to study epigenetic modifications. (biolegend.com)
  • Chromatin immunoprecipitation (ChIP) is a technique used in epigenetic research that takes a snapshot of protein-DNA interactions. (thermofisher.com)
  • Research assessing protein-DNA interactions at a genome-wide level can be used to understand chromatin dynamics and epigenetic modifications during normal development and disease. (thermofisher.com)
  • Of particular interest are DNA regions involved in gene regulation, nucleosome positions, and epigenetic modifications to chromatin such as DNA methylation and histone modifications. (thermofisher.com)
  • Understanding the epigenetic modifications to chromatin is critical for determining the influence of chromatin states on transcription and the dynamic interplay between the epigenome and gene regulatory networks. (thermofisher.com)
  • Chromatin immunoprecipitation coupled with next generation sequencing (ChIP-Seq) is a powerful and unbiased approach to study genome-wide DNA-protein interactions and epigenetic modifications ( 1 ). (life-science-alliance.org)
  • Progression of both cancer and aging include significant epigenetic components, but the chromatin changes that take place during cellular senescence are not known. (wiley.com)
  • Chromatin immunoprecipitation, or ChIP, is established in epigenetic research as a powerful method for investigating genome-wide DNA-protein interactions in the cell, aiding researchers in understanding chromatin dynamics and epigenetic mechanisms. (chipseq.com)
  • We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors in vivo . (nature.com)
  • Protein-DNA complexes are isolated by chromatin-immunoprecipitation and characterized by sequencing the associated DNA. (thermofisher.com)
  • Chromatin immunoprecipitation combined with next-generation sequencing (ChIP-seq) is a powerful technique to investigate in vivo transcription factor (TF) binding to DNA, as well as chromatin marks. (springer.com)
  • The most widely used tool for examining these interactions is chromatin immunoprecipitation (ChIP) followed by massively parallel sequencing (ChIP-seq) (fig. 1). (antibodies-online.com)
  • Chromatrap® utilizes the solid state technology in parallel with high throughput sequencing to deliver a precise ChIP-seq protocol from small cell numbers and chromatin concentrations (1-50 μg). (antibodies-online.com)
  • Specifically adapted for greater chromatin concentrations, Chromatrap® ChIP-seq now combines the dynamic range of Chromatrap® with the downstream analysis power of deep sequencing, allowing the genome wide identification of transcription factor binding sites and specific DNA associated protein modifications with no limitation in scale and resolution. (antibodies-online.com)
  • Isolation of protein-DNA interactions by chromatin immunoprecipitation (ChIP) followed by massively parallel DNA sequencing is an unbiased method for identifying and quantitating DNA sites that are associated to a chromatin-bound protein(s) of interest in any cell type or organism with known genomic sequence. (thermofisher.com)
  • These new kits enable target chromatin enrichment from both low and high amounts of input chromatin while delivering low backgrounds, high signal-to-noise ratios, and ultra-sensitive detection that is compatible with all commonly used downstream analysis applica¬tions including qPCR, next generation sequencing, and microarray. (merckmillipore.com)
  • Chromatin immunoprecipitation (ChIP) followed by next generation sequencing (ChIP-Seq) is a powerful technique to study transcriptional regulation. (life-science-alliance.org)
  • These seemingly complex issues can be directly addressed by a powerful methodology termed the chromatin immunoprecipitation (ChIP) assay. (nih.gov)
  • In a ChIP assay, DNA-protein complexes called chromatin are fixed to preserve the interactions. (antibodies-online.com)
  • Porvair Sciences has published an informative 8-page brochure providing scientists with a background to Chromatin Immunoprecipitation (ChIP), an introduction to Chromatrap® ChIP assay technology and how Chromatrap® compares to traditional bead based methodologies. (technologynetworks.com)
  • In zebrafish, this developmental period lasts for 3.3 h during which the embryo undergoes 10 rounds of synchronous Chromatin Immunoprecipitation Assay for Early Zebrafish Embryos (Prot59) cell divisions. (epigenesys.eu)
  • The Imprint ChIP Kit provides a complete solution for Chromatin Immunoprecipitation including columns and reagents for DNA purification and an integrated protocol for ChIP DNA amplification with our GenomePlex ® Whole Genome Amplification Kit ( WGA2 ). (sigmaaldrich.com)
  • Comparison of time required for protocol completion from fixation through purification using different Chromatin Immunoprecipitation kits. (sigmaaldrich.com)
  • A novel protocol for the preparation of chromatin from adult mouse skeletal muscle adapted to the study of gene regulation in muscle fibers by chromatin immunoprecipitation is presented. (jove.com)
  • This protocol offers a general guideline for immunoprecipitation with GenScript MagBeads . (genscript.com)
  • A detailed protocol on how to perform chromatin immunoprecipitation in solid tissue samples. (utexas.edu)
  • 2003). The ChIP protocol presented below describes in detail how to prepare and immuno-precipitate native chromatin. (epigenome-noe.net)
  • This protocol was adapted from methodology originally described by O'Neill and Turner (1995), and allows ChIP to be performed not only on chromatin from cultured cells, but also on freshly dissected and frozen tissues. (epigenome-noe.net)
  • The EZ-Magna HiSens ChIP kit provides a complete set of validated, quality controlled reagents, and a detailed protocol to enable ChIP from a wide range of input amounts of chromatin obtained from either cells or tissues. (emdmillipore.com)
  • Here we provide a robust Chromatin Immunoprecipitation (ChIP) protocol, allowing in vivo analyses of multiple chromatin modifications and binding of histone modifiers in different plant organs and tissues. (uzh.ch)
  • Chromatrap has announced a new patented protocol that is able to simply, quickly and efficiently enrich transcription factors from Native Chromatin. (technologynetworks.com)
  • In the September issue of Cold Spring Harbor Protocols ( www.cshprotocols.org/TOCs/toc9_09.dtl ), Michael Carey ( portal.ctrl.ucla.edu/biological-chemistry/institution/personnel?personnel_id=45403 ), Craig Peterson ( www.umassmed.edu/pmm/faculty/peterson.cfm ), and Stephen Smale ( dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=45693 ) present Chromatin Immunoprecipitation (ChIP) , an optimized protocol for use in mammalian cells. (cshlpress.org)
  • This protocol consists of an extraction of genomic DNA followed by a three-day immunoprecipitation procedure. (epigenesys.eu)
  • 1 Chromatin Immunoprecipitation A) Prepare a yeast culture (see the Galactose Induction Protocol for details). (docplayer.net)
  • Mild formaldehyde crosslinking followed by nuclease digestion has been used to shear the chromatin. (wikipedia.org)
  • Solomon MJ, Varshavsky A (1985) Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures. (springer.com)
  • Native Chromatin Immunoprecipitation (N-ChIP) is an alternative to traditional cross-linked (X-ChIP), which removes the need for fixing cells with formaldehyde prior to extraction. (technologynetworks.com)
  • B) Chromatin Crosslinking with Formaldehyde 1) When the culture is between 3x10 6 and 1x10 7 cells/ml dilute a sample 1:5 using YEP-lactate and then take the OD 600 (see misc. (docplayer.net)
  • We used formaldehyde assisted isolation of regulatory elements (FAIRE) to map genome-wide chromatin conformations. (wiley.com)
  • This up-to-date volume includes protocols that illustrate the broad use of chromatin immunoprecipitation (ChIP) and ChIP-related methods in a variety of biological research areas. (springer.com)
  • Authoritative and practical, Chromatin Immunoprecipitation: Methods and Protocols features techniques, including bioinformatic analysis of ChIP data, will be of interest to a very broad research community in the fields of biochemistry, molecular biology, microbiology, and biomedicine. (springer.com)
  • Traditional immunoprecipitation (IP) uses agarose beads coated in protein A/G. Most of these IP protocols require more than three washing steps to eliminate background and non-specific binding. (genscript.com)
  • 2001). In these protocols ( Figure 1 ), the chromatin is fractionated by incubation of purified nuclei with micrococcal nuclease (MNase), an enzyme that cleaves preferentially the linker DNA between the nucleosomes (Drew, 1984). (epigenome-noe.net)
  • While the protocols for preparation of chromatin from tissue and cells are different, performance of ChIP itself is similar for both. (pancreapedia.org)
  • 3. Herring CD, Raffaelle M, Allen TE, Kanin EI, Landick R, Ansari AZ, Palsson BO (2005) Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarray. (springer.com)
  • 8. Chua YL, Mott E, Brown AP, MacLean D, Gray JC (2004) Microarray analysis of chromatin-immunoprecipitated DNA identifies specific regions of tobacco genes associated with acetylated histones. (springer.com)
  • Additional targets of CodY, a GTP-activated repressor of early stationary-phase genes in Bacillus subtilis , were identified by combining chromatin immunoprecipitation, DNA microarray hybridization, and gel mobility shift assays. (asm.org)
  • Here we identified 1,787 Smad2/3 binding sites in the promoter regions of over 25,500 genes by chromatin immunoprecipitation on microarray in HaCaT keratinocytes. (asm.org)
  • A successful ChIP experiment is dependent on high quality chromatin. (biolegend.com)
  • Chromatrap®, the novel solid-based matrix for ChIP assays, available from Porvair Sciences, has been successfully used to isolate high quality chromatin from a wide range of biological matrices by research groups around the world (see www.chromatrap.com ). (technologynetworks.com)
  • On their own, or in combination, these covalent modifications on the core histones are thought to play essential roles in chromatin organization and gene expression in eukaryotes. (sigmaaldrich.com)
  • Histones represent the main protein components of the chromatin and undergo diverse covalent modifications that are very important for gene regulation. (nih.gov)
  • Following lysis of cross-linked cells and immunoprecipitation of bacterial RNA polymerase, DNA associated with enriched RNA polymerase was hybridized to probes corresponding to different regions of known genes to determine the in vivo distribution and density of RNA polymerase at these genes. (wikipedia.org)
  • Chromatin-domain scanning coupled with quantitative analysis is a powerful means of dissecting mechanisms by which signaling pathways target genes within a complex genome. (nih.gov)
  • Serial analysis of chromatin occupancy identifies β-catenin target genes in colorectal carcinoma cells. (nature.com)
  • Chromatin immunoprecipitation (ChIP) analysis showed that these genes are direct targets of the SOX11 protein. (pubmedcentralcanada.ca)
  • Mutations in the spn-E and aub genes resulted in the increase of satellite transcript abundance in ovaries and the spn-E 1 mutation causes the accumulation of the histone H3 acetylated at lysine 9 (H3-AcK9) mark and transcription factor TAF1 in satellite chromatin. (genetics.org)
  • Here, we describe how ChIP can be performed on non-fixed chromatin from animal cells or tissues (fresh or frozen) to analyze histone modifications at specific chromosomal sites. (sigmaaldrich.com)
  • Analysis of Histone Modifications in Rodent Pancreatic Islets by Native Chromatin Immunoprecipitation. (nih.gov)
  • Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. (springer.com)
  • Ghavi-Helm Y, Zhao B, Furlong EE (2016) Chromatin immunoprecipitation for analyzing transcription factor binding and histone modifications in Drosophila. (springer.com)
  • With ChIP-seq you are able to investigate post translational modifications of chromatin and histone variants as well as nucleosome positioning . (antibodies-online.com)
  • These studies have been highly informative on the functions of specific histone modifications in, for instance, pericentric chromatin condensation (Peters, et al . (epigenome-noe.net)
  • Chromatin remodeling, histone modifications and other chromatin-related processes play a crucial role in gene regulation. (biomedcentral.com)
  • 52 copies in mammals) that are targeted for a wide range of post-translational modifications, providing a platform for interaction with chromatin modifiers and RNA processing machinery (Brookes and Pombo, 2009). (epigenesys.eu)
  • Here we describe the isolation of pancreatic islets from rodents and subsequently outline the methods used to immunoprecipitate and analyze the native chromatin obtained from these cells. (nih.gov)
  • For example, the most commonly used methods, '% of input' (%IP) and 'fold enrichment', may obscure the biological meaning of the ChIP signal by relating the signal intensity to an arbitrary amount of chromatin or to background levels, respectively. (biomedcentral.com)
  • Some other recent methods used prior ligation of barcoded adaptors to the chromatin digested by MNase, followed by a computational demultiplexing strategy to obtain profiles from samples of low cell numbers ( 9 ). (life-science-alliance.org)
  • Site-specific chromatin immunoprecipitation: a selective method to individually analyze neighboring transcription factor binding sites in vivo. (biomedsearch.com)
  • We use the oncogenic transcription factor c-Myc as proof-of-principle that human genome sequence analysis and scanning of a specific gene by chromatin immunoprecipitation can be coupled to identify target transcription factor binding sequences. (elsevier.com)
  • Hence, a scanning chromatin immunoprecipitation (SChIP) strategy is useful in analyzing functional transcription factor-binding sites. (elsevier.com)
  • Chromatin quality can be affected by lysis, fixation, and shearing conditions. (biolegend.com)
  • We detail all steps from material collection, fixation, chromatin preparation, immunoprecipitation, library preparation, and finally computational analysis based on a combination of publicly available tools. (springer.com)
  • Fujita, T. and Fujii, H. (2012) Efficient isolation of specific genomic regions by insertional chromatin immunoprecipitation (iChIP) with a second-generation tagged LexA DNA-binding domain. (scirp.org)
  • The Magna ChIP ® HiSens chromatin immunoprecipitation kit includes reagents, buffers, and beads for ChIP as well as materials for chromatin preparation and isolation from either cultured cells or tissues. (merckmillipore.com)
  • May 14, 2013, Darmstadt, Germany - Merck Millipore, the Life Science division of Merck , today introduced Magna ChIP ® HiSens chromatin immunoprecipitation kits for superior enrichment and detection of specific regions of chromatin-associated DNA. (merckmillipore.com)
  • Immunoprecipitation and wash steps are fast and easy with magnetic beads because the pellet forms on the side of the tube, even pulling completely out of the buffer. (activemotif.com)
  • The use of magnetic beads has recently gained popularity as a quicker, more accurate approach for immunoprecipitation. (genscript.com)
  • Single day chromatin immunoprecipitation (ChIP) kit containing all necessary reagents to enable ChIP from low input amounts of chromatin obtained from either cells or tissues using magnetic A/G beads. (emdmillipore.com)
  • Single day chromatin immunoprecipitation (ChIP) kit containing all necessary reagents to perform 22 individual chromatin immunoprecipitation (ChIP) reactions using magnetic A beads. (merckmillipore.com)
  • immunoprecipitation and micro-scale antibody purification. (genscript.com)
  • For a complete list of reagents included in ChIP-IT High Sensitivity or the High Sensitivity Chromatin Preparation Kits, please select the Contents tab below. (activemotif.com)
  • Two boxes containing all necessary reagents to perform 22 individual chromatin immunoprecipitation (ChIP) reactions. (emdmillipore.com)
  • In the first post of this ChIP series , we introduced the reader to the general concept and workflow of chromatin immunoprecipitation ( ChIP ), and provided advice on planning a ChIP experiment and preparing the necessary reagents. (whatisepigenetics.com)
  • Chromatin immuno-precipitation (ChIP) is performed by incubation of fractionated chromatin (input chromatin) with an antiserum directed against a chosen histone modification. (epigenome-noe.net)
  • We have developed a novel method, insertional chromatin immunoprecipitatin (iChIP), to isolate specific genomic regions retaining molecular interaction in order to perform non-biased identification of interacting molecules in vivo . (scirp.org)
  • A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. (broadinstitute.org)
  • However, to address in detail what happens at specific sites in vivo, chromatin immunoprecipitation (ChIP) is the method of choice. (sigmaaldrich.com)
  • Chromatin Crosslinking: How Much Time? (cellsignal.com)
  • However, chromatin shearing is challenging to control and varies depending upon cell density, extent of crosslinking, and cell type. (thermofisher.com)
  • Tiling arrays are increasingly used in chromatin immunoprecipitation (IP) experiments (ChIP on chip). (harvard.edu)
  • We propose endogenous controls for active and for repressed chromatin, and discuss various other controls that are essential for successful ChIP experiments. (biomedcentral.com)
  • Immunoprecipitation requires that the antibody be coupled to a solid substrate at some point in the procedure. (wikipedia.org)
  • Enzymatic chromatin shearing does not require specialized equipment, is generally reproducible (although it requires optimization for cell type), and requires minimal hands-on time. (thermofisher.com)