Chromatin Assembly and Disassembly
The mechanisms effecting establishment, maintenance, and modification of that specific physical conformation of CHROMATIN determining the transcriptional accessibility or inaccessibility of the DNA.
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.
Chromosomal Proteins, Non-Histone
Promoter Regions, Genetic
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Chromatin Assembly Factor-1
A histone chaperone protein that plays a role in the deposition of NUCLEOSOMES on newly synthesized DNA. It is comprised of three different subunits of 48, 60, and 150 kDa molecular size. The 48 kDa subunit, RETINOBLASTOMA-BINDING PROTEIN 4, is also a component of several other protein complexes involved in chromatin remodeling.
In the interphase nucleus, a condensed mass of chromatin representing an inactivated X chromosome. Each X CHROMOSOME, in excess of one, forms sex chromatin (Barr body) in the mammalian nucleus. (from King & Stansfield, A Dictionary of Genetics, 4th ed)
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.
The portion of chromosome material that remains condensed and is transcriptionally inactive during INTERPHASE.
A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.
Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)
An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. The enzyme has a preference for double-stranded DNA.
Gene Expression Regulation
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.
Enzymes that catalyze acyl group transfer from ACETYL-CoA to HISTONES forming CoA and acetyl-histones.
Saccharomyces cerevisiae Proteins
Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.
The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.
In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The process by which a DNA molecule is duplicated.
Cell Cycle Proteins
Proteins that control the CELL DIVISION CYCLE. This family of proteins includes a wide variety of classes, including CYCLIN-DEPENDENT KINASES, mitogen-activated kinases, CYCLINS, and PHOSPHOPROTEIN PHOSPHATASES as well as their putative substrates such as chromatin-associated proteins, CYTOSKELETAL PROTEINS, and TRANSCRIPTION FACTORS.
RNA Polymerase II
Enhancer Elements, Genetic
Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.
Enzymes which catalyze the hydrolases of ester bonds within DNA. EC 3.1.-.
Gene Expression Regulation, Fungal
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.
Proteins that catalyze the unwinding of duplex DNA during replication by binding cooperatively to single-stranded regions of DNA or to short regions of duplex DNA that are undergoing transient opening. In addition DNA helicases are DNA-dependent ATPases that harness the free energy of ATP hydrolysis to translocate DNA strands.
Mature male germ cells derived from SPERMATIDS. As spermatids move toward the lumen of the SEMINIFEROUS TUBULES, they undergo extensive structural changes including the loss of cytoplasm, condensation of CHROMATIN into the SPERM HEAD, formation of the ACROSOME cap, the SPERM MIDPIECE and the SPERM TAIL that provides motility.
Protein Structure, Tertiary
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Cell Line, Tumor
A cell line derived from cultured tumor cells.
High Mobility Group Proteins
The complex series of phenomena, occurring between the end of one CELL DIVISION and the end of the next, by which cellular material is duplicated and then divided between two daughter cells. The cell cycle includes INTERPHASE, which includes G0 PHASE; G1 PHASE; S PHASE; and G2 PHASE, and CELL DIVISION PHASE.
The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
A group of enzymes which catalyze the hydrolysis of ATP. The hydrolysis reaction is usually coupled with another function such as transporting Ca(2+) across a membrane. These enzymes may be dependent on Ca(2+), Mg(2+), anions, H+, or DNA.
Gene Expression Regulation, Developmental
Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.
Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.
Mi-2 Nucleosome Remodeling and Deacetylase Complex
A enzyme complex involved in the remodeling of NUCLEOSOMES. The complex is comprised of at least seven subunits and includes both histone deacetylase and ATPase activities.
Glycosidic antibiotic from Streptomyces griseus used as a fluorescent stain of DNA and as an antineoplastic agent.
Amino Acid Sequence
p300-CBP Transcription Factors
A family of histone acetyltransferases that is structurally-related to CREB-BINDING PROTEIN and to E1A-ASSOCIATED P300 PROTEIN. They function as transcriptional coactivators by bridging between DNA-binding TRANSCRIPTION FACTORS and the basal transcription machinery. They also modify transcription factors and CHROMATIN through ACETYLATION.
Histone Deacetylase Inhibitors
Nucleic Acid Conformation
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.
Transcription Initiation Site
Protein Processing, Post-Translational
Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.
The specific patterns of changes made to HISTONES, that are involved in assembly, maintenance, and alteration of chromatin structural states (such as EUCHROMATIN and HETEROCHROMATIN). The changes are made by various HISTONE MODIFICATION PROCESSES that include ACETYLATION; METHYLATION; PHOSPHORYLATION; and UBIQUITINATION.
An evolutionarily-conserved 10-kDa nuclear protein that binds NUCLEOSOMES and may be involved in the process of CHROMATIN unfolding.
The membrane system of the CELL NUCLEUS that surrounds the nucleoplasm. It consists of two concentric membranes separated by the perinuclear space. The structures of the envelope where it opens to the cytoplasm are called the nuclear pores (NUCLEAR PORE).
Enzymes that catalyze the methylation of amino acids after their incorporation into a polypeptide chain. S-Adenosyl-L-methionine acts as the methylating agent. EC 2.1.1.
The residual framework structure of the CELL NUCLEUS that maintains many of the overall architectural features of the cell nucleus including the nuclear lamina with NUCLEAR PORE complex structures, residual CELL NUCLEOLI and an extensive fibrogranular structure in the nuclear interior. (Advan. Enzyme Regul. 2002; 42:39-52)
A group of simple proteins that yield basic amino acids on hydrolysis and that occur combined with nucleic acid in the sperm of fish. Protamines contain very few kinds of amino acids. Protamine sulfate combines with heparin to form a stable inactive complex; it is used to neutralize the anticoagulant action of heparin in the treatment of heparin overdose. (From Merck Index, 11th ed; Martindale, The Extra Pharmacopoeia, 30th ed, p692)
Within most types of eukaryotic CELL NUCLEUS, a distinct region, not delimited by a membrane, in which some species of rRNA (RNA, RIBOSOMAL) are synthesized and assembled into ribonucleoprotein subunits of ribosomes. In the nucleolus rRNA is transcribed from a nucleolar organizer, i.e., a group of tandemly repeated chromosomal genes which encode rRNA and which are transcribed by RNA polymerase I. (Singleton & Sainsbury, Dictionary of Microbiology & Molecular Biology, 2d ed)
Histone Deacetylase 1
A histone deacetylase subtype that is found along with HISTONE DEACETYLASE 2; RETINOBLASTOMA-BINDING PROTEIN 4; and RETINOBLASTOMA-BINDING PROTEIN 7 as core components of histone deacetylase complexes.
RNA, Small Interfering
Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
A family of histone molecular chaperones that play roles in sperm CHROMATIN decondensation and CHROMATIN ASSEMBLY in fertilized eggs. They were originally discovered in XENOPUS egg extracts as histone-binding factors that mediate nucleosome formation in vitro.
Locus Control Region
A sirtuin family member found primarily in the CYTOPLASM. It is a multifunctional enzyme that contains a NAD-dependent deacetylase activity that is specific for HISTONES and a mono-ADP-ribosyltransferase activity.
Ducts that serve exclusively for the passage of eggs from the ovaries to the exterior of the body. In non-mammals, they are termed oviducts. In mammals, they are highly specialized and known as FALLOPIAN TUBES.
Polycomb Repressive Complex 1
A multisubunit polycomb protein complex with affinity for CHROMATIN that contains methylated HISTONE H3. It contains an E3 ubiquitin ligase activity that is specific for HISTONE H2A and works in conjunction with POLYCOMB REPRESSIVE COMPLEX 2 to effect EPIGENETIC REPRESSION.
Silent Information Regulator Proteins, Saccharomyces cerevisiae
A set of nuclear proteins in SACCHAROMYCES CEREVISIAE that are required for the transcriptional repression of the silent mating type loci. They mediate the formation of silenced CHROMATIN and repress both transcription and recombination at other loci as well. They are comprised of 4 non-homologous, interacting proteins, Sir1p, Sir2p, Sir3p, and Sir4p. Sir2p, an NAD-dependent HISTONE DEACETYLASE, is the founding member of the family of SIRTUINS.
DNA Breaks, Double-Stranded
Interruptions in the sugar-phosphate backbone of DNA, across both strands adjacently.
Areas of increased density of the dinucleotide sequence cytosine--phosphate diester--guanine. They form stretches of DNA several hundred to several thousand base pairs long. In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. They are unmethylated except for those on the inactive X chromosome and some associated with imprinted genes.
Embryonic Stem Cells
The mechanisms of eukaryotic CELLS that place or keep the CHROMOSOMES in a particular SUBNUCLEAR SPACE.
Regulatory Elements, Transcriptional
Structures within the nucleus of fungal cells consisting of or containing DNA, which carry genetic information essential to the cell.
Highly repetitive DNA sequences found in HETEROCHROMATIN, mainly near centromeres. They are composed of simple sequences (very short) (see MINISATELLITE REPEATS) repeated in tandem many times to form large blocks of sequence. Additionally, following the accumulation of mutations, these blocks of repeats have been repeated in tandem themselves. The degree of repetition is on the order of 1000 to 10 million at each locus. Loci are few, usually one or two per chromosome. They were called satellites since in density gradients, they often sediment as distinct, satellite bands separate from the bulk of genomic DNA owing to a distinct BASE COMPOSITION.
Silencer Elements, Transcriptional
Regulatory Sequences, Nucleic Acid
Red blood cells. Mature erythrocytes are non-nucleated, biconcave disks containing HEMOGLOBIN whose function is to transport OXYGEN.
Microscopy using an electron beam, instead of light, to visualize the sample, thereby allowing much greater magnification. The interactions of ELECTRONS with specimens are used to provide information about the fine structure of that specimen. In TRANSMISSION ELECTRON MICROSCOPY the reactions of the electrons that are transmitted through the specimen are imaged. In SCANNING ELECTRON MICROSCOPY an electron beam falls at a non-normal angle on the specimen and the image is derived from the reactions occurring above the plane of the specimen.
A homologous family of regulatory enzymes that are structurally related to the protein silent mating type information regulator 2 (Sir2) found in Saccharomyces cerevisiae. Sirtuins contain a central catalytic core region which binds NAD. Several of the sirtuins utilize NAD to deacetylate proteins such as HISTONES and are categorized as GROUP III HISTONE DEACETYLASES. Several other sirtuin members utilize NAD to transfer ADP-RIBOSE to proteins and are categorized as MONO ADP-RIBOSE TRANSFERASES, while a third group of sirtuins appears to have both deacetylase and ADP ribose transferase activities.
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Reverse Transcriptase Polymerase Chain Reaction
A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
Transcriptional Elongation Factors
Transcription factors whose primary function is to regulate the rate in which RNA is transcribed.
A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Nucleosome Assembly Protein 1
A histone chaperone that facilitates nucleosome assembly by mediating the formation of the histone octamer and its transfer to DNA.
Oligonucleotide Array Sequence Analysis
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.
Gene Expression Profiling
Electrophoretic Mobility Shift Assay
An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.
Methyl-CpG-Binding Protein 2
A DNA-binding protein that interacts with methylated CPG ISLANDS. It plays a role in repressing GENETIC TRANSCRIPTION and is frequently mutated in RETT SYNDROME.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
Origin Recognition Complex
Recombinant Fusion Proteins
Gene Knockdown Techniques
Poly Adenosine Diphosphate Ribose
In Situ Hybridization, Fluorescence
A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.
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.
Matrix Attachment Region Binding Proteins
Proteins that bind to the MATRIX ATTACHMENT REGIONS of DNA.
E1A-Associated p300 Protein
A member of the p300-CBP transcription factors that was originally identified as a binding partner for ADENOVIRUS E1A PROTEINS.
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.
Fluorescence Recovery After Photobleaching
A method used to study the lateral movement of MEMBRANE PROTEINS and LIPIDS. A small area of a cell membrane is bleached by laser light and the amount of time necessary for unbleached fluorescent marker-tagged proteins to diffuse back into the bleached site is a measurement of the cell membrane's fluidity. The diffusion coefficient of a protein or lipid in the membrane can be calculated from the data. (From Segen, Current Med Talk, 1995).
RNA, Long Noncoding
A class of untranslated RNA molecules that are typically greater than 200 nucleotides in length and do not code for proteins. Members of this class have been found to play roles in transcriptional regulation, post-transcriptional processing, CHROMATIN REMODELING, and in the epigenetic control of chromatin.
Sp1 Transcription Factor
Promoter-specific RNA polymerase II transcription factor that binds to the GC box, one of the upstream promoter elements, in mammalian cells. The binding of Sp1 is necessary for the initiation of transcription in the promoters of a variety of cellular and viral GENES.
Polycomb Repressive Complex 2
Retinoblastoma-Binding Protein 4
A retinoblastoma-binding protein that is involved in CHROMATIN REMODELING, histone deacetylation, and repression of GENETIC TRANSCRIPTION. Although initially discovered as a retinoblastoma binding protein it has an affinity for core HISTONES and is a subunit of chromatin assembly factor-1 and polycomb repressive complex 2.
Members of the beta-globin family. In humans, they are encoded in a gene cluster on CHROMOSOME 11. They include epsilon-globin, gamma-globin, delta-globin and beta-globin. There is also a pseudogene of beta (theta-beta) in the gene cluster. Adult HEMOGLOBIN is comprised of two ALPHA-GLOBIN chains and two beta-globin chains.
Jumonji Domain-Containing Histone Demethylases
A family of histone demethylases that share a conserved Jumonji C domain. The enzymes function via an iron-dependent dioxygenase mechanism that couples the conversion of 2-oxoglutarate to succinate to the hydroxylation of N-methyl groups.
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.
The Drosophila kismet gene is related to chromatin-remodeling factors and is required for both segmentation and segment identity. (1/12332)The Drosophila kismet gene was identified in a screen for dominant suppressors of Polycomb, a repressor of homeotic genes. Here we show that kismet mutations suppress the Polycomb mutant phenotype by blocking the ectopic transcription of homeotic genes. Loss of zygotic kismet function causes homeotic transformations similar to those associated with loss-of-function mutations in the homeotic genes Sex combs reduced and Abdominal-B. kismet is also required for proper larval body segmentation. Loss of maternal kismet function causes segmentation defects similar to those caused by mutations in the pair-rule gene even-skipped. The kismet gene encodes several large nuclear proteins that are ubiquitously expressed along the anterior-posterior axis. The Kismet proteins contain a domain conserved in the trithorax group protein Brahma and related chromatin-remodeling factors, providing further evidence that alterations in chromatin structure are required to maintain the spatially restricted patterns of homeotic gene transcription. (+info)
Gadd45, a p53-responsive stress protein, modifies DNA accessibility on damaged chromatin. (2/12332)This report demonstrates that Gadd45, a p53-responsive stress protein, can facilitate topoisomerase relaxing and cleavage activity in the presence of core histones. A correlation between reduced expression of Gadd45 and increased resistance to topoisomerase I and topoisomerase II inhibitors in a variety of human cell lines was also found. Gadd45 could potentially mediate this effect by destabilizing histone-DNA interactions since it was found to interact directly with the four core histones. To evaluate this possibility, we investigated the effect of Gadd45 on preassembled mononucleosomes. Our data indicate that Gadd45 directly associates with mononucleosomes that have been altered by histone acetylation or UV radiation. This interaction resulted in increased DNase I accessibility on hyperacetylated mononucleosomes and substantial reduction of T4 endonuclease V accessibility to cyclobutane pyrimidine dimers on UV-irradiated mononucleosomes but not on naked DNA. Both histone acetylation and UV radiation are thought to destabilize the nucleosomal structure. Hence, these results imply that Gadd45 can recognize an altered chromatin state and modulate DNA accessibility to cellular proteins. (+info)
A new element within the T-cell receptor alpha locus required for tissue-specific locus control region activity. (3/12332)Locus control regions (LCRs) are cis-acting regulatory elements thought to provide a tissue-specific open chromatin domain for genes to which they are linked. The gene for T-cell receptor alpha chain (TCRalpha) is exclusively expressed in T cells, and the chromatin at its locus displays differentially open configurations in expressing and nonexpressing tissues. Mouse TCRalpha exists in a complex locus containing three differentially regulated genes. We previously described an LCR in this locus that confers T-lineage-specific expression upon linked transgenes. The 3' portion of this LCR contains an unrestricted chromatin opening activity while the 5' portion contains elements restricting this activity to T cells. This tissue-specificity region contains four known DNase I hypersensitive sites, two located near transcriptional silencers, one at the TCRalpha enhancer, and another located 3' of the enhancer in a 1-kb region of unknown function. Analysis of this region using transgenic mice reveals that the silencer regions contribute negligibly to LCR activity. While the enhancer is required for complete LCR function, its removal has surprisingly little effect on chromatin structure or expression outside the thymus. Rather, the region 3' of the enhancer appears responsible for the tissue-differential chromatin configurations observed at the TCRalpha locus. This region, herein termed the "HS1' element," also increases lymphoid transgene expression while suppressing ectopic transgene activity. Thus, this previously undescribed element is an integral part of the TCRalphaLCR, which influences tissue-specific chromatin structure and gene expression. (+info)
A novel H2A/H4 nucleosomal histone acetyltransferase in Tetrahymena thermophila. (4/12332)Recently, we reported the identification of a 55-kDa polypeptide (p55) from Tetrahymena macronuclei as a catalytic subunit of a transcription-associated histone acetyltransferase (HAT A). Extensive homology between p55 and Gcn5p, a component of the SAGA and ADA transcriptional coactivator complexes in budding yeast, suggests an immediate link between the regulation of chromatin structure and transcriptional output. Here we report the characterization of a second transcription-associated HAT activity from Tetrahymena macronuclei. This novel activity is distinct from complexes containing p55 and putative ciliate SAGA and ADA components and shares several characteristics with NuA4 (for nucleosomal H2A/H4), a 1.8-MDa, Gcn5p-independent HAT complex recently described in yeast. A key feature of both the NuA4 and Tetrahymena activities is their acetylation site specificity for lysines 5, 8, 12, and 16 of H4 and lysines 5 and 9 of H2A in nucleosomal substrates, patterns that are distinct from those of known Gcn5p family members. Moreover, like NuA4, the Tetrahymena activity is capable of activating transcription from nucleosomal templates in vitro in an acetyl coenzyme A-dependent fashion. Unlike NuA4, however, sucrose gradient analyses of the ciliate enzyme, following sequential denaturation and renaturation, estimate the molecular size of the catalytically active subunit to be approximately 80 kDa, consistent with the notion that a single polypeptide or a stable subcomplex is sufficient for this H2A/H4 nucleosomal HAT activity. Together, these data document the importance of this novel HAT activity for transcriptional activation from chromatin templates and suggest that a second catalytic HAT subunit, in addition to p55/Gcn5p, is conserved between yeast and Tetrahymena. (+info)
Stable remodeling of tailless nucleosomes by the human SWI-SNF complex. (5/12332)The histone N-terminal tails have been shown previously to be important for chromatin assembly, remodeling, and stability. We have tested the ability of human SWI-SNF (hSWI-SNF) to remodel nucleosomes whose tails have been cleaved through a limited trypsin digestion. We show that hSWI-SNF is able to remodel tailless mononucleosomes and nucleosomal arrays, although hSWI-SNF remodeling of tailless nucleosomes is less effective than remodeling of nucleosomes with tails. Analogous to previous observations with tailed nucleosomal templates, we show both (i) that hSWI-SNF-remodeled trypsinized mononucleosomes and arrays are stable for 30 min in the remodeled conformation after removal of ATP and (ii) that the remodeled tailless mononucleosome can be isolated on a nondenaturing acrylamide gel as a novel species. Thus, nucleosome remodeling by hSWI-SNF can occur via interactions with a tailless nucleosome core. (+info)
Differential regulation of the human nidogen gene promoter region by a novel cell-type-specific silencer element. (6/12332)Transfection analyses of the human nidogen promoter region in nidogen-producing fibroblasts from adult skin revealed multiple positive and negative cis-acting elements controlling nidogen gene expression. Characterization of the positive regulatory domains by gel mobility-shift assays and co-transfection studies in Drosophila SL2 cells unequivocally demonstrated that Sp1-like transcription factors are essential for a high expression of the human nidogen gene. Analysis of the negative regulatory domains identified a novel silencer element between nt -1333 and -1322, which is bound by a distinct nuclear factor, by using extracts from adult but not from embryonal fibroblasts. In embryonal fibroblasts, which express significantly higher amounts of nidogen mRNA as compared with adult fibroblasts, this inhibitory nidogen promoter region did not affect nidogen and SV40 promoter activities. The silencer element seems to be active only in nidogen-producing cells. Therefore this regulatory element might function in vivo to limit nidogen gene expression in response to external stimuli. However, none of the identified regulatory elements, including the silencer, contribute significantly to cell-specific expression of the human nidogen gene. Instead we provide evidence that gene expression in epidermal keratinocytes that are not producing nidogen is repressed by methylation-specific and chromatin-dependent mechanisms. (+info)
Histone octamer transfer by a chromatin-remodeling complex. (7/12332)RSC, an abundant, essential chromatin-remodeling complex related to SWI/SNF complex, catalyzes the transfer of a histone octamer from a nucleosome core particle to naked DNA. The newly formed octamer-DNA complex is identical with a nucleosome in all respects. The reaction requires ATP and involves an activated RSC-nucleosome intermediate. The mechanism may entail formation of a duplex displacement loop on the nucleosome, facilitating the entry of exogeneous DNA and the release of the endogenous molecule. (+info)
Differential transcriptional activity associated with chromatin configuration in fully grown mouse germinal vesicle oocytes. (8/12332)It was previously shown that fully grown ovarian germinal vesicle (GV) oocytes of adult mice exhibit several nuclear configurations that differ essentially by the presence or absence of a ring of condensed chromatin around the nucleolus. These configurations have been termed, respectively, SN (surrounded nucleolus) and NSN (nonsurrounded nucleolus). Work from our and other laboratories has revealed ultrastructural and functional differences between these two configurations. The aims of the present study were 1) to analyze the equilibrium between the SN and the NSN population as a function of the age of the mice and the time after hCG-induced ovulation and 2) to study the polymerase I (pol I)- and polymerase II (pol II)-dependent transcription in both types of oocytes through the detection of bromouridine incorporated into nascent RNA. We show 1) that ovarian GV oocytes exhibiting the SN-type configuration can be found as soon as 17 days after birth in the C57/CBA mouse strain and 2) that the SN:NSN ratio of ovarian GV oocytes is very low just after hCG-induced ovulation and then increases progressively with the time after ovulation. Furthermore, we demonstrate that the SN configuration correlates strictly with the arrest of both pol I- and pol II-dependent transcription in mice at any age. Finally, we show that ribosomal genes are located at the outer periphery of the nucleolus in the NSN configuration and that pol I-dependent perinucleolar transcription sites correspond to specific ultrastructural features of the nucleolus. Altogether, these results provide clear-cut criteria delineating transcriptionally active GV oocytes from those that are inactive, and confirm that the SN-type configuration is mostly present in preovulatory oocytes. (+info)
The PBAP remodeling complex is required for histone H3.3 replacement at chromatin boundaries and for boundary functions |...
DNA is wrapped around a histone octamer to form the basic unit of chromatin structure. During embryogenesis, dynamic changes of chromatin structure and chromatin modification occur after fertilization; subsequently, the epigenetic information is inherited through many rounds of the cell cycle. Thus, chromatin is essential for the determination of cell identity. Two strategies are used to modulate a chromatin environment: the covalent modification of histone tails and energy-dependent chromatin remodeling. The acetylation, methylation or phosphorylation of histone tails can have profound effects on chromatin structure and transcription (Jenuwein and Allis, 2001). Chromatin remodeling reactions are catalyzed by large protein complexes that use the energy of ATP hydrolysis to alter the structure or positioning of nucleosomes (Becker and Hörz, 2002; Clapier and Cairns, 2009). In addition to these events, histone variants play important roles in modulating chromatin structure (Henikoff and Ahmad, ...
Chromatin Protocols - University of Manitoba Libraries
Preparation of Chromatin Assembly Extracts from Preblastoderm Drosophila Embryos -- Analysis of Reconstituted Chromatin Using a Solid-Phase Approach -- In Vivo Chromatin Decondensation Assays: Molecular Genetic Analysis of Chromatin Unfolding Characteristics of Selected Proteins -- DNA Methyltransferase Probing of Chromatin Structure Within Populations and on Single Molecules -- Visualization of the Expression of HMGN Nucleosomal Binding Proteins in the Developing Mouse Embryo and in Adult Mouse Tissues -- Drug-Induced Premature Chromosome Condensation (PCC) Protocols: Cytogenetic Approaches in Mitotic Chromosome and Interphase Chromatin -- Analysis of DNA Topology in Yeast Chromatin -- Preparation and Analysis of Uniquely Positioned Mononucleosomes -- Monitoring DNA Breaks in Optically Highlighted Chromatin in Living Cells by Laser Scanning Confocal Microscopy -- Methods to Study Transcription-Coupled Repair in Chromatin -- Cytometric Analysis of DNA Damage: Phosphorylation of Histone H2AX as a ...
p53 is a chromatin accessibility factor for nucleotide excision repair of DNA damage - White Rose Research Online
One of the longest standing problems in DNA repair is how cells relax chromatin in order to make DNA lesions accessible for global nucleotide excision repair (NER). Since chromatin has to be relaxed for efficient lesion detection, the key question is whether chromatin relaxation precedes lesion detection or vice versa. Chromatin accessibility factors have been proposed but not yet identified. Here we show that p53 acts as a chromatin accessibility factor, mediating UV-induced global chromatin relaxation. Using localized subnuclear UV irradiation, we demonstrate that chromatin relaxation is extended over the whole nucleus and that this process requires p53. We show that the sequence for initiation of global NER is as follows: transcription-associated lesion detection; p53-mediated global chromatin relaxation; and global lesion detection. The tumour suppressor p53 is crucial for genomic stability, a role partially explained by its pro-apoptotic capacity. We demonstrate here that p53 is also a ...
High-Frequency Promoter Firing Links THO Complex Function to Heavy Chromatin Formation - Research - Aarhus University
The THO complex is involved in transcription, genome stability, and messenger ribonucleoprotein (mRNP) formation, but its precise molecular function remains enigmatic. Under heat shock conditions, THO mutants accumulate large protein-DNA complexes that alter the chromatin density of target genes (heavy chromatin), defining a specific biochemical facet of THO function and a powerful tool of analysis. Here, we show that heavy chromatin distribution is dictated by gene boundaries and that the gene promoter is necessary and sufficient to convey THO sensitivity in these conditions. Single-molecule fluorescence insitu hybridization measurements show that heavy chromatin formation correlates with an unusually high firing pace of the promoter with more than 20 transcription events per minute. Heavy chromatin formation closely follows the modulation of promoter firing and strongly correlates with polymerase occupancy genome wide. We propose that the THO complex is required for tuning the dynamic of ...
A cis-element within the ARF locus mediates repression of p16INK4A expression via long-range chromatin interactions | PNAS
Loss of function of CDKN2A/B, also known as INK4/ARF [encoding p16INK4A, p15INK4B, and p14ARF (mouse p19Arf)], confers susceptibility to cancers, whereas its up-regulation during organismal aging provokes cellular senescence and tissue degenerative disorders. To better understand the transcriptional regulation of p16INK4A, a CRISPR screen targeting open, noncoding chromatin regions adjacent to p16INK4A was performed in a human p16INK4A-P2A-mCherry reporter cell line. We identified a repressive element located in the 3′ region adjacent to the ARF promoter that controls p16INK4A expression via long-distance chromatin interactions. Coinfection of lentiviral dCas9-KRAB with selected single-guide RNAs against the repressive element abrogated the ARF/p16INK4A chromatin contacts, thus reactivating p16INK4A expression. Genetic CRISPR screening identified candidate transcription factors inhibiting p16INK4A regulation, including ZNF217, which was confirmed to bind the ARF/p16INK4A interaction loop. In ...
CAME: Identification of chromatin accessibility from nucleosome occupancy and methylome sequencing<...
TY - JOUR. T1 - CAME. T2 - Identification of chromatin accessibility from nucleosome occupancy and methylome sequencing. AU - Piao, Yongjun. AU - Lee, Seong Keon. AU - Lee, Eun Joon. AU - Robertson, Keith D. AU - Shi, Huidong. AU - Ryu, Keun Ho. AU - Choi, Jeong Hyeon. PY - 2017/4/15. Y1 - 2017/4/15. N2 - Motivation: Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, Methyltransferase Accessibility Protocol for individual templates-Bisulfite Genome Sequencing (MAPit-BGS) and nucleosome occupancy and methylome sequencing (NOMe-seq) have been developed for simultaneously profiling chromatin accessibility and DNA methylation on single molecules. Therefore, there is a great demand in developing computational methods to identify chromatin ...
The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions |...
Here, we introduce the 3D Genome Browser, http://3dgenome.org , which allows users to conveniently explore both their own and over 300 publicly available chromatin interaction data of different types. We design a new binary data format for Hi-C data that reduces the file size by at least a magnitude and allows users to visualize chromatin interactions over millions of base pairs within seconds. Our browser provides multiple methods linking distal cis-regulatory elements with their potential target genes. Users can seamlessly integrate thousands of other omics data to gain a comprehensive view of both regulatory landscape and 3D genome structure.
Biochemical and functional differences of chromatin assembled replication-coupled or independent in Xenopus laevis egg extracts...
Two main chromatin assembly pathways ensure the proper transmission of chromatin organization and chromatin-based information throughout the cell cycle. A replication-dependent (RD) pathway that couples chromatin assembly to DNA synthesis and a replication-independent (RI) pathway. Whether these pathways contribute to the establishment of chromatin domains like heterochromatin or euchromatin by introducing modifications on histones or modulating chromatin structure remains unknown. Using Xenopus laevis egg extracts we monitored RD and RI chromatin assembly on single-stranded and double-stranded DNA templates. Even though RD assembly proceeded faster than RI assembly the histone content and saturation level with nucleosomes were similar. Despite these comparable topological features, the hydrodynamic behavior of both chromatin species in sucrose gradient centrifugation clearly differed. The RD assembled chromatin ran at lower sucrose concentrations than the RI created chromatin suggesting ...
Contribution of non-histone proteins to chromatin structure and stability
Histones are responsible for packaging the genomes of almost all eukaryotes into fundamental repeating nucleosome units. The packaging must facilitate compaction into the cell nucleus but also enable dynamic access to the genome. A variety of mechanisms exist for targeting enzymes to undertake local opening of chromatin such as at active genes or for DNA repair. However, larger scale transitions in chromatin also occur where extended genome regions have altered chromatin organisation. This often involves abundant non-histone chromatin proteins that switch chromatin between states that are not well understood at the structural level. The contribution of highly basic non-histone chromatin proteins in vitro has been investigated using the HMGA2 protein implicated in human stem cell chromatin opening, and the Hematodinium DVNP protein which is suggested to replace histones as the dominant packaging protein in this dinoflagellate. These two proteins are compared to histone H1 which stabilises ...
Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation |...
1. Li X-Y, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD. The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol. 2011;12: R34. doi: 10.1186/gb-2011-12-4-r34 21473766. 2. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, et al. The accessible chromatin landscape of the human genome. Nature. 2012;489: 75-82. doi: 10.1038/nature11232 22955617. 3. Klemm SL, Shipony Z, Greenleaf WJ. Chromatin accessibility and the regulatory epigenome. Nat Rev Genet. 2019;20: 207-220. doi: 10.1038/s41576-018-0089-8 30675018. 4. Wu J, Huang B, Chen H, Yin Q, Liu Y, Xiang Y, et al. The landscape of accessible chromatin in mammalian preimplantation embryos. Nature. 2016;534: 652-657. doi: 10.1038/nature18606 27309802. 5. Clark SJ, Argelaguet R, Kapourani C-A, Stubbs TM, Lee HJ, Alda-Catalinas C, et al. scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in ...
A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets | Genome...
The different chromatin features display distinct spatial patterns. It is thus worthwhile to explore the relationship between these patterns and the level of gene expression. Making use of RNA-seq data obtained from the different stages of C. elegans, we quantified the expression level of each gene. For each bin, we then calculated the correlation between the gene expression levels and the average signals of each chromatin feature of the bin. Figure 2b shows the spatial variation of these correlation coefficients around TSSs and TTSs. According to the correlation patterns, there are two main types of chromatin features: ones that are positively correlated with gene expression (such as H3K79me1, H3K79me2 and H3K79me3); and ones that are negatively correlated with gene expression (such as H3K9me2 and H3K9me3). While some features show largely uniform correlations across the 16-kb regions, some others are more variable across the regions. For example, H3K79me2 has a high correlation coefficient ...
NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data | BMC Genomics | Full Text
Biomedical applications of high-throughput sequencing methods generate a vast amount of data in which numerous chromatin features are mapped along the genome. The results are frequently analysed by creating binary data sets that link the presence/absence of a given feature to specific genomic loci. However, the nucleosome occupancy or chromatin accessibility landscape is essentially continuous. It is currently a challenge in the field to cope with continuous distributions of deep sequencing chromatin readouts and to integrate the different types of discrete chromatin features to reveal linkages between them. Here we introduce the NucTools suite of Perl scripts as well as MATLAB- and R-based visualization programs for a nucleosome-centred downstream analysis of deep sequencing data. NucTools accounts for the continuous distribution of nucleosome occupancy. It allows calculations of nucleosome occupancy profiles averaged over several replicates, comparisons of nucleosome occupancy landscapes between
Chromatin fibers observed in situ in frozen hydrated sections. Native fiber diameter is not correlated with nucleosome repeat...
Chromatin fibers have been observed and measured in frozen hydrated sections of three types of cell (chicken erythrocytes and sperm of Patiria miniata and Thyone briareus) representing an approximately 20-bp range of nucleosomal repeat lengths. For sperm of the starfish P. miniata, it was possible to obtain images of chromatin fibers from cells that were swimming in seawater up to the moment of cryo-immobilization, thus providing a record of the native morphology of the chromatin of these cells. Glutaraldehyde fixation produced no significant changes in the ultrastructure or diameter of chromatin fibers, and fiber diameters observed in cryosections were similar to those recorded after low temperature embedding in Lowicryl K11M. Chromatin fiber diameters measured from cryosections of the three types of nuclei were similar, a striking contrast to the situation for chromatin isolated from these cell types, where a strong positive correlation between diameter and nucleosomal repeat length has been ...
Chromatin Structure and Gene Expression - Sarah C. Elgin - Hardcover | Rent 9780199635764 | 0199635765
Due to advances in molecular biology techniques, chromatin structure and function has re-emerged as a key research area in the investigation of gene regulation and expression. This indispensable new book provides the busy researcher with an overview of all the latest research in this important area. Topicality and breadth of coverage is assured by the contributions of an international group of over 30 leading scientists in this field. Contents list: Elements of chromatin structure: histones, nucleosomes, fibers; DNA structure: implications for chromatin structure and function; Replication and assembly; Promoter potentiation and activation: chromatin structure and transcriptional induction of heat shock genes; Initiation of expression: remodelling genes; Transcription on chromatin templates; Chromatin structure and epigenetic regulation in yeast; Epigenetic regulation in Drosophilia: a conspiracy of silence; Boundaries and domains; Epigenetic regulation in mammalian cells.Elgin, Sarah C. is the ...
Structural Biochemistry/30nm chromatin fibers - Wikibooks, open books for an open world
There are variety of models and techniques to observe the presence of the 30nm fibers but it has been more observed that highly compacted chromatin fiber like 30nm fibers are not necessarily present for any gene regulation such as folding of DNA. Instead, 10 nm chromatin can be condensed enough into compacted domains through frequent bending and making 10nm fibers close to each other. In other words, it does not require to have 30nm fibers but is sufficient to have 10 nm chromatin fibers that is organized in genome to explain the complexities of nuclear organization and gene regulation. ...
Selective recognition of histone variant H2A.Z gives insight into mechanism of chromatin remodeling----Institute of Biophysics...
Chromatin compacts DNA to an extreme extend and allows eukaryotic genome fit the size of the nucleus. On the other hand, however, it must process the ability to untighten DNA and to permit the cellular machinery access to genome. Chromatin consists of nucleosomes in which a protein core is constituted by four canonical histones H2A, H2B, H3, H4 and wrapped around by 147 bp of DNA. Histone variants, and the chromatin remodelling machinery, can reorganize the compaction of chromatin and thus be important for epigenetic regulation of gene expression.. Histone variant H2A.Z is a universal mark of dynamic nucleosomes. H2A.Z is essential for growth, development and viability of a number of species including mammals. H2A.Z plays critical roles in multiple biological processes including gene transcription and replication, DNA repair, and genome integrity. The chromatin incorporation of H2A.Z is catalysed by SRCAP, an ATP-dependent, multi-component chromatin remodelling complex. The YL1 subunit of SRCAP ...
CTCF binding and higher order chromatin structure of the H19 locus are maintained in mitotic chromatin
The genetic information encoded by the DNA sequence, can be expressed in different ways. Genomic imprinting is an epigenetic phenomenon that results in monoallelic expression of imprinted genes in a parent of origin-dependent manner. Imprinted genes are frequently found in clusters and can share common regulatory elements. Most of the imprinted genes are regulated by Imprinting Control Regions (ICRs). H19/Igf2 region is a well known imprinted cluster, which is regulated by insulator function of ICR located upstream of the H19 gene. It has been proposed that the epigenetic control of the insulator function of H19 ICR involves organization of higher order chromatin interactions.. In this study we have investigated the role of post-translational modification in regulating insulator protein CTCF (CCCTC-binding factor). The results indicated novel links between poly(ADP-ribosyl)ation and CTCF, which are essential for regulating insulators function.. We also studied the higher order chromatin ...
Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding...
TY - JOUR. T1 - Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns. AU - Srivastava, Divyanshi. AU - Mahony, Shaun. PY - 2019/1/1. Y1 - 2019/1/1. N2 - Transcription factors (TFs) selectively bind distinct sets of sites in different cell types. Such cell type-specific binding specificity is expected to result from interplay between the TFs intrinsic sequence preferences, cooperative interactions with other regulatory proteins, and cell type-specific chromatin landscapes. Cell type-specific TF binding events are highly correlated with patterns of chromatin accessibility and active histone modifications in the same cell type. However, since concurrent chromatin may itself be a consequence of TF binding, chromatin landscapes measured prior to TF activation provide more useful insights into how cell type-specific TF binding events became established in the first place. Here, we review the various sequence and chromatin ...
Studies toward in vitro reconstitution of plant chromatin , WCU NC DOCKS (North Carolina Digital Online Collection of Knowledge...
Abstract: To study the relation between chromatin structure and DNA function in detail it is necessary to have an in vitro procedure for assembling nucleosomes on a naked DNA template with properties similar to native chromatin. Such procedures exist for yeast and animal model systems but have not been developed for plants. The goal of this project was to lay the groundwork for developing a chromatin assembly extract from plants. Extracts from various plant materials were tested to determine their suitability for chromatin reconstitution. Tissues from plants are thought to have much higher levels of protease and nuclease activities than those of animals or yeast. Therefore, methods to determine the relative activity of proteases and nucleases had to be developed to determine if the template DNA, histones, and chromatin assembly proteins could survive the chromatin assembly reaction. Additionally, methods to streamline the isolation of maize nuclei and purification of histones were developed. ...
Nuclear Chromatin Decondensation (N.C.D.) - Nuclear Chromatin Decondensation (N.C.D.) Exporter, Importer, Manufacturer,...
HI-TECH SOLUTIONS - Exporter, Importer, Manufacturer, Distributor & Supplier of Nuclear Chromatin Decondensation (N.C.D.) based in New Delhi, India
Biology | Free Full-Text | Myogenic Differential Methylation: Diverse Associations with Chromatin Structure | HTML
Employing a new algorithm for identifying differentially methylated regions (DMRs) from reduced representation bisulfite sequencing profiles, we identified 1972 hypermethylated and 3250 hypomethylated myogenic DMRs in a comparison of myoblasts (Mb) and myotubes (Mt) with 16 types of nonmuscle cell cultures. DMRs co-localized with a variety of chromatin structures, as deduced from ENCODE whole-genome profiles. Myogenic hypomethylation was highly associated with both weak and strong enhancer-type chromatin, while hypermethylation was infrequently associated with enhancer-type chromatin. Both myogenic hypermethylation and hypomethylation often overlapped weak transcription-type chromatin and Polycomb-repressed-type chromatin. For representative genes, we illustrate relationships between DNA methylation, the local chromatin state, DNaseI hypersensitivity, and gene expression. For example, MARVELD2 exhibited myogenic hypermethylation in transcription-type chromatin that overlapped a silenced promoter in Mb
The Hsp90 Molecular Chaperone Regulates the Transcription Factor Network Controlling Chromatin Accessibility<...
TY - JOUR. T1 - The Hsp90 Molecular Chaperone Regulates the Transcription Factor Network Controlling Chromatin Accessibility. AU - Gvozdenov, Zlata. AU - Bendix, Lindsey D.. AU - Kolhe, Janhavi. AU - Freeman, Brian C.. PY - 2019/12/6. Y1 - 2019/12/6. N2 - Genomic events including gene regulation and chromatin status are controlled by transcription factors. Here we report that the Hsp90 molecular chaperone broadly regulates the transcription factor protein family. Our studies identified a biphasic use of Hsp90 in which early inactivation (15 min) of the chaperone triggered a wide reduction of DNA binding events along the genome with concurrent changes to chromatin structure. Long-term loss (6 h) of Hsp90 resulted in a decline of a divergent yet overlaying pool of transcription factors that produced a distinct chromatin pattern. Although both phases involve protein folding, the early point correlated with Hsp90 acting in a late folding step that is critical for DNA binding function, whereas ...
Download Methods In Enzymology Vol. 376 Chromatin And Chromatin Remodeling Enzymes Part B
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ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes
Bysani M, Agren R, Davegårdh C, Volkov P, Rönn T, Unneberg P, Bacos K, Ling C Sci Rep 9 (1) - [2019-12-00; online 2019-05-23] Impaired insulin secretion from pancreatic islets is a hallmark of type 2 diabetes (T2D). Altered chromatin structure may contribute to the disease. We therefore studied the impact of T2D on open chromatin in human pancreatic islets. We used assay for transposase-accessible chromatin using sequencing (ATAC-seq) to profile open chromatin in islets from T2D and non-diabetic donors. We identified 57,105 and 53,284 ATAC-seq peaks representing open chromatin regions in islets of non-diabetic and diabetic donors, respectively. The majority of ATAC-seq peaks mapped near transcription start sites. Additionally, peaks were enriched in enhancer regions and in regions where islet-specific transcription factors (TFs), e.g. FOXA2, MAFB, NKX2.2, NKX6.1 and PDX1, bind. Islet ATAC-seq peaks overlap with 13 SNPs associated with T2D (e.g. rs7903146, rs2237897, rs757209, rs11708067 and ...
Heterochromatin protein 1 recruitment and chromatin conformational dynamics at the single-molecule level
Chromatin is the template on which DNA-associated transactions take place in eukaryotic organisms. Nucleosomes consisting of the four histones H2A, H2B, H3 and H4 each organize 150bp of DNA and constitute a first layer of chromatin. The three-dimensional organization of chromatin as well as histone post-translational modifications (PTMs) regulate recruitment of chromatin-associated effector proteins (effectors). Heterochromatin protein 1 (HP1) is an effector associated with silenced genome regions. HP1 recognizes histone H3 trimethylated at lysine 9 (H3 K9me3) and can dimerize. This results in a protein with two binding domains allowing multivalent engagement of target chromatin. HP1 can further promote chromatin condensation and inter-fiber contacts. The effector p53 binding protein (53BP1) is a key regulator in the DNA damage repair pathway. It is known to target a trio of PTMs; H4 dimethylated at K20 (H4 K20me2), H2A(.X) ubiquitylated at K15 (H2A.X K15ub) and H2A.X phosphorylated at S139 ...
Transcription of isolated mouse liver chromatin<...
TY - JOUR. T1 - Transcription of isolated mouse liver chromatin. AU - Bacheler, Lee T.. AU - Smith, Kirby D.. PY - 1976. Y1 - 1976. N2 - Analysis of RNA transcription from isolated mouse liver chromatin has been undertaken by means of RN A-excess hybridizations with small amounts of radioactive DNA. This analysis indicates that mouse liver chromatin is a restricted template for the in vitro synthesis of RNA complements to repetitive DNA, but more RNA species are synthesized than are found in the RNA isolated from mouse liver nuclei. Extraction with 0.5 M NaCl destroys the template restriction of isolated chromatin. RNA synthesized in vitro from DNA or chromatin templates by Escherichia coli RNA polymerase, as well as in vivo mouse liver nuclear RNA, were each hybridized to 125I-labeled DNA of high, intermediate, or low reiteration frequency. Chromatin-primed and nuclear RNA saturate a smaller portion of each DNA fraction than does DNA-primed RNA. However, chromatin-primed RNA saturates more high ...
Editing the Epigenome: Plasticity and Memory of Chromatin Structure</span>
Principal Investigator: Oliver Bell. In metazoans, packaging of genomic DNA into the nucleosomal protein scaffold of chromatin provides an opportunity to tightly regulate accessibility and readout of the genetic information. In particular, chemical modifications of nucleosomes and DNA have emerged as important determinants of genome accessibility. However, the dynamic regulation of chromatin state and its contribution to epigenetic inheritance of gene expression has remained enigmatic and a key challenge in the field of chromatin biology.. We have developed a novel technology that allows for rapid addition and removal of chromatin regulatory activities to a gene locus in any murine cell type. The Chromatin in vivo Assay (CiA) employs small molecules, which simultaneously bind two distinct peptide domains to induce dimerization between a chromatin modifier and a DNA binding protein. The CiA approach provides high temporal control allowing us to study the kinetics and epigenetic memory of histone ...
PLOS ONE: RNA Is an Integral Component of Chromatin that Contributes to Its Structural Organization
Chromatin structure is influenced by multiples factors, such as pH, temperature, nature and concentration of counterions, post-translational modifications of histones and binding of structural non-histone proteins. RNA is also known to contribute to the regulation of chromatin structure as chromatin-induced gene silencing was shown to depend on the RNAi machinery in S. pombe, plants and Drosophila. Moreover, both in Drosophila and mammals, dosage compensation requires the contribution of specific non-coding RNAs. However, whether RNA itself plays a direct structural role in chromatin is not known. Here, we report results that indicate a general structural role for RNA in eukaryotic chromatin. RNA is found associated to purified chromatin prepared from chicken liver, or cultured Drosophila S2 cells, and treatment with RNase A alters the structural properties of chromatin. Our results indicate that chromatin-associated RNAs, which account for 2%-5% of total chromatin-associated nucleic acids, are polyA−
PLOS Genetics: Histone H2A C-Terminus Regulates Chromatin Dynamics, Remodeling, and Histone H1 Binding
Author Summary Histones are the main protein components of chromatin. The N-terminal tails of histones stick out from the nucleosomes, the building blocks of chromatin, and are involved in the regulation of all DNA-dependent processes. Only Histone H2A has an additional C-terminal tail and currently very little is known about the function of this tail. The H2A C-terminus protrudes from the nucleosome and is located where the DNA enters and leaves the nucleosome. We show here that it can interact with the linker histone H1 that is important for higher order chromatin structure. We also find that this tail is involved in regulating nucleosome dynamics and mobility of H2A itself. The C-terminal H2A tail has also an important function in regulating the activity of chromatin remodelers, enzymes that can reposition nucleosomes. Furthermore we find that cells expressing C-terminally truncated H2A are more sensitive to stress, demonstrating that this tail is important for cellular homeostasis. Together our
Three-dimensional analysis of the arrangement of compact chromatin in the nucleus of G0rat lymphocytes | SpringerLink
The arrangement of compact chromatin of G0 lymphocytes was studied in three-dimensional reconstructions of the ensemble of the chromatin and of individual compact chromatin bodies. Rat spleen was seri
Chromatin organisation and cancer prognosis: a pan-cancer study
Background Chromatin organisation affects gene expression and regional mutation frequencies and contributes to carcinogenesis. Aberrant organisation of DNA has been correlated with cancer prognosis in analyses of the chromatin component of tumour cell nuclei using image texture analysis. As yet, the methodology has not been sufficiently validated to permit its clinical application. We aimed to define and validate a novel prognostic biomarker for the automatic detection of heterogeneous chromatin organisation. Methods Machine learning algorithms analysed the chromatin organisation in 461 000 images of tumour cell nuclei stained for DNA from 390 patients (discovery cohort) treated for stage I or II colorectal cancer at the Aker University Hospital (Oslo, Norway). The resulting marker of chromatin heterogeneity, termed Nucleotyping, was subsequently independently validated in six patient cohorts: 442 patients with stage I or II colorectal cancer in the Gloucester Colorectal Cancer Study (UK); 391 ...
Scientists Find No Proof For 30 NM Chromatin Fibers In The Mouse Genome - Redorbit
Scientists in Canada and the United States have used three-dimensional imaging techniques to settle a long-standing debate about how DNA and structural proteins are packaged into chromatin fibers. The researchers, whose findings are published in EMBO reports, reveal that the mouse genome consists of 10-nm chromatin fibers but did not find evidence for the wider 30-nm fibers that were previously thought to be important components of the DNA architecture.. DNA is an exceptionally long molecule that can reach several meters in length. This means it needs to be packaged into a highly compact state to fit within the limited space of the cell nucleus, said David Bazett-Jones, Senior Scientist at the Hospital for Sick Children, Toronto, and Professor at the University of Toronto, Canada. For the past few decades, scientists have favored structural models for chromatin organization where DNA is first wrapped around proteins in nucleosomes. In one possible model, the strand of repeating nucleosomes is ...
Transposition of Native Chromatin for Fast and Sensitive Epigenomic Profiling of Open Chromatin, DNA-binding Proteins and...
We describe an assay for transposase-accessible chromatin using sequencing (ATAC-seq), based on direct in vitro transposition of sequencing adaptors into native chromatin, as a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-s …
Poly(ADP-ribosyl)ation directs recruitment and activation of an ATP-dependent chromatin remodeler | PNAS
Posttranslational modifications play a key role in recruiting chromatin remodeling and modifying enzymes to specific regions of chromosomes to modulate chromatin structure. Alc1 (amplified in liver cancer 1), a member of the SNF2 ATPase superfamily with a carboxy-terminal macrodomain, is encoded by an oncogene implicated in the pathogenesis of hepatocellular carcinoma. Here we show that Alc1 interacts transiently with chromatin-associated proteins, including histones and the poly(ADP-ribose) polymerase Parp1. Alc1 ATPase and chromatin remodeling activities are strongly activated by Parp1 and its substrate NAD and require an intact macrodomain capable of binding poly(ADP-ribose). Alc1 is rapidly recruited to nucleosomes in vitro and to chromatin in cells when Parp1 catalyzes PAR synthesis. We propose that poly(ADP-ribosyl)ation of chromatin-associated Parp1 serves as a mechanism for targeting a SNF2 family remodeler to chromatin. ...
Large-scale Comparative Study of Hi-C-based Chromatin 3D Structure Modeling Methods
Chromatin is a complex polymer molecule in eukaryotic cells, primarily consisting of DNA and histones. Many works have shown that the 3D folding of chromatin structure plays an important role in DNA expression. The recently proposed Chro- mosome Conformation Capture technologies, especially the Hi-C assays, provide us an opportunity to study how the 3D structures of the chromatin are organized. Based on the data from Hi-C experiments, many chromatin 3D structure modeling methods have been proposed. However, there is limited ground truth to validate these methods and no robust chromatin structure alignment algorithms to evaluate the performance of these methods. In our work, we first made a thorough literature review of 25 publicly available population Hi-C-based chromatin 3D structure modeling methods. Furthermore, to evaluate and to compare the performance of these methods, we proposed a novel data simulation method, which combined the population Hi-C data and single-cell Hi-C data without ad ...
Chromatin remodeling proteins: New insights in human malignancy and targeted cancer therapy
Beijing, China - Chromatin remodeling proteins (chromatin remodelers) are essential and powerful regulators for critical DNA-templated cellular processes, such as DNA replication, recombination, gene transcription/repression, and DNA damage repair. These molecular and genetic processes are important for a wide spectrum of cellular functions, including cell cycle, death, differentiation, pluripotency, and genome integrity. Recently, many scientific reports have shown that chromatin remodeling proteins could be promising new targets for the treatment of human malignancy.. This is a hot and exciting research topic for cancer researchers, and our article provides an updated understanding on the functions and mechanisms of chromatin remodelers in human cancers, says Dr. Chun Zhang, the principle investigator of the Department of Nuclear Medicine of Beijing Chao-Yang Hospital and Capital Medical University of China.. Chromatin remodeling is an energy-driven process in which chromatin remodelers use ...
Conference Scene: Chromatin, replication and chromosomal stability. - Inserm
The Chromatin, Replication and Chromosomal Stability Conference took place on June 20-21 in Stockholm, Sweden. In this article, I outline the broad scientific program of the meeting which reflected the wide diversity in epigenetics research. Distinct histone modifications are linked with specific chromatin structures and intranuclear positioning, thereby impacting replication timing and replication initiation, which in turn are related to gene expression and cell differentiation. Interference in any of these interconnected mechanisms can result in DNA breakage and lead to the activation of repair pathways. The DNA repair mechanisms again are influenced by the chromatin structure. In summary, the conference highlighted the functional implication of epigenetics in chromatin compaction, transcription regulation, replication control and DNA repair. The tight control of all these mechanisms defines the final cellular character.
p53 Chromatin Epigenetic Domain Organization and p53 Transcription | Molecular and Cellular Biology
In this report, we show that p53 is organized into two epigenetic domains with distinct chromatin structures, CpG methylation, histone compositions, and modifications, as well as associated regulatory factors. The open chromatin conformation, unmethylated CpG, and histone modifications associated the first domain are characteristic of an active chromatin, whereas the characteristics of the second domain, with full CpG methylation, nuclease resistance, and unacetylated histones, are reminiscent of inactive chromatin.. The promoter region has been known to be organized into a nucleosome-free structure (32), but whether this structure is due to the absence of histones or to a novel organization of the histone-DNA complex has not been investigated. The ChIP technique allows us to address this question, and we show that nuclease hypersensitivity and the absence of a nucleosomal DNA ladder in epigenetic domain I are associated with the depletion of the H2a/H2b dimer. Previous studies have shown that ...
ArchAlign: Coordinate-free chromatin alignment reveals novel architectures<...
TY - JOUR. T1 - ArchAlign. T2 - Coordinate-free chromatin alignment reveals novel architectures. AU - Lai, William K.M.. AU - Buck, Michael J.. PY - 2010/12/23. Y1 - 2010/12/23. N2 - To facilitate identification and characterization of genomic functional elements, we have developed a chromatin architecture alignment algorithm (ArchAlign). ArchAlign identifies shared chromatin structural patterns from high-resolution chromatin structural datasets derived from next-generation sequencing or tiled microarray approaches for user defined regions of interest. We validated ArchAlign using well characterized functional elements, and used it to explore the chromatin structural architecture at CTCF binding sites in the human genome. ArchAlign is freely available at http://www.acsu.buffalo.edu/~mjbuck/ArchAlign.html.. AB - To facilitate identification and characterization of genomic functional elements, we have developed a chromatin architecture alignment algorithm (ArchAlign). ArchAlign identifies shared ...
piRNA clusters and open chromatin structure | Mobile DNA | Full Text
Transposable elements (TEs) are major structural components of eukaryotic genomes; however, mobilization of TEs generally has negative effects on the host genome. To counteract this threat, host cells have evolved genetic and epigenetic mechanisms that keep TEs silenced. One such mechanism involves the Piwi-piRNA complex, which represses TEs in animal gonads either by cleaving TE transcripts in the cytoplasm or by directing specific chromatin modifications at TE loci in the nucleus. Most Piwi-interacting RNAs (piRNAs) are derived from genomic piRNA clusters. There has been remarkable progress in our understanding of the mechanisms underlying piRNA biogenesis. However, little is known about how a specific locus in the genome is converted into a piRNA-producing site. In this review, we will discuss a possible link between chromatin boundaries and piRNA cluster formation.
A role for MeCP2 in switching gene activity via chromatin unfolding and HP1γ displacement
Methyl-CpG-binding protein 2 (MeCP2) is generally considered to act as a transcriptional repressor, whereas recent studies suggest that MeCP2 is also involved in transcription activation. To gain insight into this dual function of MeCP2, we assessed the impact of MeCP2 on higher-order chromatin structure in living cells using mammalian cell systems harbouring a lactose operator and reporter gene-containing chromosomal domain to assess the effect of lactose repressor-tagged MeCP2 (and separate MeCP2 domains) binding in living cells. Our data reveal that targeted binding of MeCP2 elicits extensive chromatin unfolding. MeCP2-induced chromatin unfolding is triggered independently of the methyl-cytosine-binding domain. Interestingly, MeCP2 binding triggers the loss of HP1gamma at the chromosomal domain and an increased HP1gamma mobility, which is not observed for HP1alpha and HP1beta. Surprisingly, MeCP2-induced chromatin unfolding is not associated with transcriptional activation. Our study suggests ...
Multiple modes of PRC2 inhibition elicit global chromatin alterations in H3K27M pediatric glioma | Science Advances
A primary challenge in the H3K27M field has been to resolve the contradictory observations indicating that PRC2 has a high affinity for H3K27M peptides, yet PRC2 and H3K27M are often mutually excluded from chromatin in H3K27M DIPG (4, 6, 9, 10). Our studies revealed that interaction of H3K27M with PRC2 is a dynamic process that cannot be captured by static, steady-state approaches. Namely, there is an initial phase after H3K27M is expressed and incorporated into chromatin, followed by PRC2 recruitment to H3K27M-containing chromatin, presumably due to its higher affinity toward H3K27M (Fig. 2C). However, in the next phase, PRC2 is released from H3K27M, as they do not colocalize at steady-state conditions in both isogenic 293 T-REx systems (e.g., this study, Figs. 2 and 3) and the H3K27M DIPG themselves (6). This dynamic model therefore accommodates both the finding of high H3K27M and PRC2 affinity in select assays and their failure to be stably colocalized on chromatin in cells. In line with the ...
Critical Role for the Histone H4 N Terminus in Nucleosome Remodeling by ISWI | Molecular and Cellular Biology
The assembly of eukaryotic genomes into chromatin is a highly complex and delicate task; the cell must efficiently package and condense the DNA into the eukaryotic nucleus while maintaining specific regions of accessible chromatin to enable important functions with chromatin substrates. While the chromatin structure must remain highly dynamic in order to accommodate changes in the expression of some genes, it also serves to stably maintain the functional states of other genes through epigenetic mechanisms (45, 51). Recently, genetic and biochemical analyses have identified a broad class of multisubunit chromatin remodeling complexes which are likely to play important roles both in the process of chromatin opening and in the maintenance of chromatin in a dynamic or flexible state (26, 48, 53). These complexes remodel or reorganize nucleosomes in a wide range of in vitro assays which test for altered accessibility of nucleosomal DNA.. Nucleosome remodeling complexes are modular entities. The ...
Androgen Receptor Deregulation Drives Bromodomain-Mediated Chromatin Alterations in Prostate Cancer. - Nuffield Department of...
Global changes in chromatin accessibility may drive cancer progression by reprogramming transcription factor (TF) binding. In addition, histone acetylation readers such as bromodomain-containing protein 4 (BRD4) have been shown to associate with these TFs and contribute to aggressive cancers including prostate cancer (PC). Here, we show that chromatin accessibility defines castration-resistant prostate cancer (CRPC). We show that the deregulation of androgen receptor (AR) expression is a driver of chromatin relaxation and that AR/androgen-regulated bromodomain-containing proteins (BRDs) mediate this effect. We also report that BRDs are overexpressed in CRPCs and that ATAD2 and BRD2 have prognostic value. Finally, we developed gene stratification signature (BROMO-10) for bromodomain response and PC prognostication, to inform current and future trials with drugs targeting these processes. Our findings provide a compelling rational for combination therapy targeting bromodomains in selected patients in
Sperm chromatin analysis by flow cytometry « REPROBIO
Our group has experience using different techniques for assessing sperm chromatin status in different species (fish, amphibians, mammals). We have used the Comet assay, SCD (Halomax, Halosperm, etc.), SCSA and TUNEL. Currently, we are routinely carrying out SCSA analyses in spermatozoa from several species, including human.. We are open to collaborations with other groups that would be interested in analysing the sperm chromatin but currently do not have the time or resources to carry it out. We are collaborating with several groups that simply store their samples frozen and ship them to our lab from time to time, in order to perform the analyses.. Contact Dr. F. Martínez-Pastor for more information.. ...
Abstract 10470: Nucleosome Positioning is a Mechanism of Global Chromatin Structural Remodeling in Cardiac Hypertrophy |...
The re-expression of fetal cardiac genes during disease requires coordinated chromatin remodeling. Local chromatin packing around the nucleosome protein complex is understood with atomic resolution; however, higher level properties of chromatin packing in the cardiovascular system are unknown. We hypothesized that nucleosome occupancy (i.e. exact positioning of nucleosomes at given loci) is a feature that regulates altered gene expression in hypertrophy. To investigate mechanisms that establish chromatin structure, genome-wide nucleosome location in heart was determined by Micrococcal Nuclease treatment followed by next-generation sequencing (MNase-Seq). A total of 137.4M Illumina reads were acquired from normal and hypertrophic myocardium, and Novoalign used to align them to the mouse genome mm9 with an average mapping percentage of 59%. Resulting occupancy profiles from normal and diseased cardiac myocytes exhibit global (i.e. chromosome scale) similarities, but local (i.e. gene/promoter ...
Differential Salt Fractionation of Nuclei to Analyze Chromatin-associated Proteins from Cultured Mammalian Cells -BIO-PROTOCOL
Nucleosomes are the core units of cellular chromatin and are comprised of 147 base pairs (bp) of DNA wrapped around an octamer of histone proteins. Proteins such as chromatin remodelers, transcription factors, and DNA repair proteins interact dynamically with chromatin to regulate access to DNA, control gene transcription, and maintain genome integrity. The extent of association with chromatin changes rapidly in response to stresses, such as immune activation, oxidative stress, or viral infection, resulting in downstream effects on chromatin conformation and transcription of target genes. To elucidate changes in the composition of proteins associated with chromatin under different conditions, we adapted existing protocols to isolate nuclei and fractionate cellular chromatin using a gradient of salt concentrations. The presence of specific proteins in different salt fractions can be assessed by Western blotting or mass spectrometry, providing insight into the degree to which they are associated with
Chromatin shearing from tissue protocol using Diagenodes Chromatin shearing optimization kit - Low SDS and Bioruptor<sup>®<...
This protocol describes the chromatin preparation from fresh or frozen tissues. The isolated chromatin can be used for chromatin immunoprecipitation assays using Diagenode&rsquo...
Effects of chromatin structure on the enzymatic and DNA binding functions of DNA methyltransferases DNMT1 and Dnmt3a in vitro<...
TY - JOUR. T1 - Effects of chromatin structure on the enzymatic and DNA binding functions of DNA methyltransferases DNMT1 and Dnmt3a in vitro. AU - Robertson, Andrea K.. AU - Geiman, Theresa M.. AU - Sankpal, Umesh Tanaji. AU - Hager, Gordon L.. AU - Robertson, Keith D.. PY - 2004/9/10. Y1 - 2004/9/10. N2 - DNA methylation is an epigenetic modification of the genome critical for numerous processes, including transcriptional repression and maintenance of chromatin structure. Recent studies have revealed connections between DNA methylation and other epigenetic modifications such as ATP-dependent chromatin remodeling. It remains unclear, however, exactly how chromatin and epigenetic chromatin modifications affect the biological properties of the DNA methyltransferases (DNMT1, DNMT3A, and DNMT3B). Using a highly purified system and the 5S rDNA gene as free DNA or assembled into a mononucleosome, we have compared the effects of chromatin structure on DNMT1 and Dnmt3a. The catalytic efficiency for ...
Modeling apoptotic chromatin condensation in normal cell nuclei. Requirement for intranuclear mobility and actin involvement<...
TY - JOUR. T1 - Modeling apoptotic chromatin condensation in normal cell nuclei. Requirement for intranuclear mobility and actin involvement. AU - Widlak, Piotr. AU - Palyvoda, Olena. AU - Kumala, Slawomir. AU - Garrard, William T.. N1 - Copyright: Copyright 2008 Elsevier B.V., All rights reserved.. PY - 2002/6/14. Y1 - 2002/6/14. N2 - Hallmarks of the terminal stages of apoptosis are genomic DNA fragmentation and chromatin condensation. Here, we have studied the mechanism of condensation both in vitro and in vivo. We found that DNA fragmentation per se of isolated nuclei from non-apoptotic cells induced chromatin condensation that closely resembles the morphology seen in apoptotic cells, independent of ATP utilization, at physiological ionic strengths. Interestingly, chromatin condensation was accompanied by release of nuclear actin, and both condensation and actin release could be blocked by reversibly pretreating nuclei with Ca2+, Cu2+, diamide, or low pH, procedures shown to stabilize ...
Chromatin assembly coupled to DNA repair: a new role for chromatin assembly factor I - CSHL Scientific Digital Repository
DNA repair in the eukaryotic cell disrupts local chromatin organization. To investigate whether the resetting of nucleosomal arrays can be linked to the repair process, we developed model systems, with both Xenopus egg extract and human cell extracts, to follow repair and chromatin assembly in parallel on circular DNA templates. Both systems were able to carry out nucleotide excision repair of DNA lesions. We observed that UV-dependent DNA synthesis occurs simultaneously with chromatin assembly, strongly indicating a mechanistic coupling between the two processes. A complementation assay established that chromatin assembly factor I (CAF1) is necessary for this repair associated chromatin formation.. ...
Deficiency of the multi-copy mouse Y gene Sly causes sperm DNA damage and abnormal chromatin packaging | Journal of Cell Science
Even relatively minor errors in chromatin remodeling during spermiogenesis are associated with sperm DNA damage and infertility, yet little is known about the etiology. Mice with severe NPYq deletions are infertile due to severe sperm differentiation defects (Ward and Burgoyne, 2006; Yamauchi et al., 2009). We have recently observed that sperm from these mice presented abnormal chromatin packaging and DNA damage. Moreover, when these sperm were injected into the oocytes, a significant increase of oocyte arrest at pronuclei stage and of chromosome aberrations in the fertilized eggs were noted (Yamauchi et al., 2010). Here we provide evidence that the deficiency of NPYq encoded gene Sly is associated with sperm DNA damage and poor sperm chromatin condensation, and propose that SLY plays a role in spermatid-specific chromatin remodeling.. How can Sly/SLY be involved in sperm DNA damage phenotype? SLY protein has been shown to control the postmeiotic expression of ,100 genes, the majority of which ...
A native chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in strawberry fruits | Plant Methods ...
Covalent modifications of histones and histone variants have great influence on chromatin structure, which is involved in the transcriptional regulation of gene expression. Chromatin immunoprecipitation (ChIP) is a powerful tool for studying in vivo DNA-histone interactions. Strawberry is a model for Rosaceae and non-climacteric fruits, in which histone modifications have been implicated to affect fruit development and ripening. However, a validated ChIP method has not been reported in strawberry, probably due to its high levels of polysaccharides which affect the quality of prepared chromatin and the efficiency of immunoprecipitation. We describe a native chromatin immunoprecipitation (N-ChIP) protocol suitable for strawberry by optimizing the parameters for nuclei isolation, chromatin extraction, DNA fragmentation and validation analysis using quantitative real-time PCR (qRT-PCR). The qRT-PCR results show that both the active mark H3K36me3 and the silent mark H3K9me2 are efficiently immunoprecipitated
Chromatin remodelers, their implication in cancer and therapeutic potential - University of Regensburg Publication Server
The chromatin remodeling complexes alter chromatin structures. They remodel nucleosomes in ATP-dependent manner and have essential roles in DNA damage repair, recombination, replication and transcriptional control. Increasing evidences indicate that subunits of chromatin remodelers are mutated and/or deregulated in a number of human cancers, and how they influence the cancer gene expression program during cancer initiation and progression is becomming clearer. Therefore, chromatin remodeling complexes arose as promising new targets for the treatment of human cancers. In this review, chromatin remodeling complexes, their epigenetic reader domains and available inhibitors are described. The insights into the misregulated chromatin remodelers pathways in human malignancies and the novel approach targeting deregulated chromatin remodelers to improve chemotherapy efficiency are discussed. ...
Mechanistic stochastic model of histone modification pattern formation | Epigenetics & Chromatin | Full Text
The activity of a single gene is influenced by the composition of the chromatin in which it is embedded. Nucleosome turnover, conformational dynamics, and covalent histone modifications each induce changes in the structure of chromatin and its affinity for regulatory proteins. The dynamics of histone modifications and the persistence of modification patterns for long periods are still largely unknown. In this study, we present a stochastic mathematical model that describes the molecular mechanisms of histone modification pattern formation along a single gene, with non-phenomenological, physical parameters. We find that diffusion and recruitment properties of histone modifying enzymes together with chromatin connectivity allow for a rich repertoire of stochastic histone modification dynamics and pattern formation. We demonstrate that histone modification patterns at a single gene can be established or removed within a few minutes through diffusion and weak recruitment mechanisms of histone modification
Alleviation of historic H1-mediated transcriptional repression and chromatin compaction by the acidic activation region in...
TY - JOUR. T1 - Alleviation of historic H1-mediated transcriptional repression and chromatin compaction by the acidic activation region in chromosomal protein HMG-14. AU - Ding, Hanfei. AU - Bustin, Michael. AU - Hansen, Ulla. PY - 1997/10/1. Y1 - 1997/10/1. N2 - Histone H1 promotes the generation of a condensed, transcriptionally inactive, higher-order chromatin structure. Consequently, historic H1 activity must be antagonized in order to convert chromatin to a transcriptionally competent, more extended structure. Using simian virus 40 minichromosomes as a model system, we now demonstrate that the nonhistoric chromosomal protein HMG-14, which is known to preferentially associate with active chromatin, completely alleviates historic H1-mediated inhibition of transcription by RNA polymerase II. HMG-14 also partially disrupts histone H1-dependent compaction of chromatin. Both the transcriptional enhancement and chromatin-unfolding activities of HMG-14 are mediated through its acidic, C-terminal ...
Chromatin assembly factor 1 is essential and couples chromatin assembly to DNA replication in vivo - CSHL Scientific Digital...
De novo chromatin assembly maintains histone density on the daughter strands in the wake of the replication fork. The heterotrimer chromatin assembly factor 1 (CAF-1) couples DNA replication to histone deposition in vitro, but is not essential for yeast cell proliferation. Depletion of CAF-1 in human cell lines demonstrated that CAF-1 was required for efficient progression through S-phase. Cells lacking CAF-1 accumulated in early and mid S-phase and replicated DNA slowly. The checkpoint kinase Chk1, but not Chk2, was phosphorylated in response to CAF-1 depletion, consistent with a DNA replication defect. CAF-1-depleted cell extracts completely lacked DNA replication-coupled chromatin assembly activity, suggesting that CAF-1 is required for efficient S-phase progression in human cells. These results indicate that, in contrast to yeast, human CAF-1 is necessary for coupling chromatin assembly with DNA replication.. ...
Analysis of chromatin structure by in vivo formaldehyde cross-linking<...
TY - JOUR. T1 - Analysis of chromatin structure by in vivo formaldehyde cross-linking. AU - Orlando, Valerio. AU - Strutt, Helen. AU - Paro, Renato. PY - 1997/2. Y1 - 1997/2. N2 - Recent advances leave no doubt that higher order chromatin structures play a fundamental role in many developmentally important mechanisms of gene regulation. In particular analyses in genetic model systems like yeast and Drosophila uncovered novel proteins that are involved in the regulation of chromatin structures. Many of these proteins do not bind directly to DNA but interact in large multimeric complexes. To identify the DNA elements regulated by these multiprotein complexes, alternative approaches to the standard methods of DNA-protein analysis had to be devised. Here we present a method that preserves the architecture of the higher order chromatin structures by crosslinking cells in vivo with formaldehyde. An immunoprecipitation strategy is then used to identify the DNA targets of chromosomal proteins of ...
Cis-acting sequences regulating expression of the human alpha-globin cluster lie within constitutively open chromatin. -...
Current models suggest that tissue-specific genes are arranged in discrete, independently controlled segments of chromatin referred to as regulatory domains. Transition from a closed to open chromatin structure may be an important step in the regulation of gene expression. To determine whether the human alpha-globin cluster, like the beta-globin cluster, lies within a discrete, erythroid-specific domain, we have examined the long-range genomic organization and chromatin structure around this region. The alpha genes lie adjacent to at least four widely expressed genes. The major alpha-globin regulatory element lies 40 kb away from the cluster within an intron of one of these genes. Therefore, unlike the beta cluster, cis-acting sequences controlling alpha gene expression are dispersed within a region of chromatin that is open in both erythroid and nonerythroid cells. This implies a difference in the hierarchical control of alpha- and beta-globin expression.
Partial purification of the template-active fraction of chromatin: A preliminary report - CaltechAUTHORS
A fraction of rat-liver chromatin that is transcriptionally active in vivo has been purified 6- to 7-fold over whole chromatin. This was accomplished by selectively shearing chromatin with DNase II followed by fractionating the released portion on the basis of its solubility properties in 2 mM MgCl2. The resulting soluble material comprises 11% of the total chromatin DNA and is impoverished in histone and enriched in nonhistone protein. Compared with unsheared chromatin, this minor fraction exhibits marked differences in chromosomal protein species. DNA renaturation studies indicate that this fraction is composed of a specific subset of whole genomal DNA sequences. Furthermore, DNA·RNA hybridization experiments suggest that almost 60% of the nonrepetitious DNA sequences of this minor fraction could code for cellular RNA. ...
Nase I Hypersensitive Site Assay of Chromatin Assembled in Xenopus Oocytes - Thyroid Hormone
DNase I hypersensitive site assay is perhaps the most widely used assay for detection of changes in chromatin structure. Studies of many spatially or temporally regulated genes, such as P-globin, have revealed the correlation of formation of DNase I hypersensitive sites with the status of transcription (22). This assay has also been used extensively in analyses of chromatin structure in injected Xenopus oocytes (24). Although the mechanism for the formation of DNase I hypersensitive sites is still not fully understood, the detection of DNase I hypersensitive sites are widely interpreted as results of chromatin remodeling induced by the binding of transcription factors.. 1. Inject 15-20 oocytes with DNA and with or without mRNA encoding TR/RXR (100 ng/ pL, 27.6 nL/oocyte) and treated with or without 50 nM T3. Incubate the oocytes overnight at 18°C incubator.. 2. Collect healthy oocytes and wash the oocytes once with 500 pL of MBSH buffer.. 3. To 15-20 oocytes, add 240 pL of DNase I buffer. ...
Sequence-Specific Targeting of Dosage Compensation in Drosophila Favors an Active Chromatin Context
The Drosophila MSL complex mediates dosage compensation by increasing transcription of the single X chromosome in males approximately two-fold. This is accomplished through recognition of the X chromosome and subsequent acetylation of histone H4K16 on X-linked genes. Initial binding to the X is thought to occur at entry sites that contain a consensus sequence motif (MSL recognition element or MRE). However, this motif is only similar to 2 fold enriched on X, and only a fraction of the motifs on X are initially targeted. Here we ask whether chromatin context could distinguish between utilized and non-utilized copies of the motif, by comparing their relative enrichment for histone modifications and chromosomal proteins mapped in the modENCODE project. Through a comparative analysis of the chromatin features in male S2 cells (which contain MSL complex) and female Kc cells (which lack the complex), we find that the presence of active chromatin modifications, together with an elevated local GC ...
Intasome architecture and chromatin density modulate retroviral integration into nucleosome | Retrovirology | Full Text
Retroviral integration depends on the interaction between intasomes, host chromatin and cellular targeting cofactors as LEDGF/p75 or BET proteins. Previous studies indicated that the retroviral integrase, by itself, may play a role in the local integration site selection within nucleosomal target DNA. We focused our study on this local association by analyzing the intrinsic properties of various retroviral intasomes to functionally accommodate different chromatin structures in the lack of other cofactors. Using in vitro conditions allowing the efficient catalysis of full site integration without these cofactors, we show that distinct retroviral integrases are not equally affected by chromatin compactness. Indeed, while PFV and MLV integration reactions are favored into dense and stable nucleosomes, HIV-1 and ASV concerted integration reactions are preferred into poorly dense chromatin regions of our nucleosomal acceptor templates. Predicted nucleosome occupancy around integration sites identified in
Large-scale organization of ribosomal DNA chromatin is regulated by Tip5 - Publikationsserver der Universität Regensburg
The DNase I accessibility and chromatin organization of genes within the nucleus do correlate to their transcriptional activity. Here, we show that both serum starvation and overexpression of Tip5, a key regulator of ribosomal RNA gene (rDNA) repression, dictate DNase I accessibility, facilitate the association of rDNA with the nuclear matrix and thus regulate large-scale rDNA chromatin organization. Tip5 contains four AT-hooks and a TAM (Tip5/ARBP/MBD) domain, which were proposed to bind matrix-attachment regions (MARs) of the genome. Remarkably, the TAM domain of Tip5 functions as nucleolar localization and nuclear matrix targeting module, whereas AT-hooks do not mediate association with the nuclear matrix, but they are required for nucleolar targeting. These findings suggest a dual role for Tip5s AT-hooks and TAM domain, targeting the nucleolus and anchoring to the nuclear matrix, and suggest a function for Tip5 in the regulation of higher-order rDNA chromatin structure. ...
Thyroid hormone receptor actions on transcription in amphibia: The roles of histone modification and chromatin disruption |...
Thyroid hormone (T3) plays diverse roles in adult organ function and during vertebrate development. The most important stage of mammalian development affected by T3 is the perinatal period when plasma T3 level peaks. Amphibian metamorphosis resembles this mammalian postembryonic period and is absolutely dependent on T3. The ability to easily manipulate this process makes it an ideal model to study the molecular mechanisms governing T3 action during vertebrate development. T3 functions mostly by regulating gene expression through T3 receptors (TRs). Studies in vitro, in cell cultures and reconstituted frog oocyte transcription system have revealed that TRs can both activate and repress gene transcription in a T3-dependent manner and involve chromatin disruption and histone modifications. These changes are accompanied by the recruitment of diverse cofactor complexes. More recently, genetic studies in mouse and frog have provided strong evidence for a role of cofactor complexes in T3 signaling in vivo.
Thyroid hormone receptor actions on transcription in amphibia: The roles of histone modification and chromatin disruption |...
Thyroid hormone (T3) plays diverse roles in adult organ function and during vertebrate development. The most important stage of mammalian development affected by T3 is the perinatal period when plasma T3 level peaks. Amphibian metamorphosis resembles this mammalian postembryonic period and is absolutely dependent on T3. The ability to easily manipulate this process makes it an ideal model to study the molecular mechanisms governing T3 action during vertebrate development. T3 functions mostly by regulating gene expression through T3 receptors (TRs). Studies in vitro, in cell cultures and reconstituted frog oocyte transcription system have revealed that TRs can both activate and repress gene transcription in a T3-dependent manner and involve chromatin disruption and histone modifications. These changes are accompanied by the recruitment of diverse cofactor complexes. More recently, genetic studies in mouse and frog have provided strong evidence for a role of cofactor complexes in T3 signaling in vivo.
Nucleosome acidic patch-targeting binuclear ruthenium compounds induce aberrant chromatin condensation | DR-NTU
The acidic patch is a highly electronegative cleft on the histone H2A-H2B dimer in the nucleosome. It is a fundamental motif for protein binding and chromatin dynamics, but the cellular impact of targeting this potentially therapeutic site with exogenous molecules remains unclear. Here, we characterize a family of binuclear ruthenium compounds that selectively target the nucleosome acidic patch, generating intra-nucleosomal H2A-H2B cross-links as well as inter-nucleosomal cross-links. In contrast to cisplatin or the progenitor RAPTA-C anticancer drugs, the binuclear agents neither arrest specific cell cycle phases nor elicit DNA damage response, but rather induce an irreversible, anomalous state of condensed chromatin that ultimately results in apoptosis. In vitro, the compounds induce misfolding of chromatin fibre and block the binding of the regulator of chromatin condensation 1 (RCC1) acidic patch-binding protein. This family of chromatin-modifying molecules has potential for applications ...
Mapping and Characterization of DNase I Hypersensitive Sites in Arabidopsis Chromatin : Plant and Cell Physiology - oi
Recent genome-wide analyses of yeast and human chromatin revealed the widespread prevalence of DNase I hypersensitive sites (DNase I HSs) at gene regulatory regions with possible roles in eukaryotic gene regulation. The presence of DNase I HSs in plants has been described for only a few genes, and we analyzed the chromatin structure of an 80 kb genomic region containing 30 variably expressed genes by DNase I sensitivity assay at 500 bp resolution in Arabidopsis. Distinct DNase I HSs were found at the 5′ and/or 3′ ends of most genes irrespective of their expression levels. Further analysis of well-characterized genes showed that the DNase I HSs occurred near cis-regulatory elements in the promoters of these genes. Upon transcriptional activation of a heat-inducible gene, the DNase I HS was extended into the vicinity of a cis-element and adjacent TATA element in the promoter. Concomitant with this change in DNase I HS, histones were acetylated, removed from the promoter, and a transcription ...
An alternative beads‐on‐a‐string chromatin architecture in Thermococcus kodakarensis | EMBO Reports
T. kodakarensis MNase digestion. T. kodakarensis strain KOD1  was cultivated under anaerobic conditions at 85 °C and an insoluble unfixed chromatin fraction prepared from cells at the late‐log/stationary‐phase transition . Chromatin was digested with 1 unit/ml of MNase, or 0.1 units/ml of DNase I for 1 h at 37 °C in the presence of 10 μg/μl RNase A. De‐proteinized genomic DNA was digested with 0.03 units/ml of MNase .. S. cerevisiae MNase digestion. EUROSCARF wild‐type reference strain BY4742 was grown and chromatin digestion (pooled triplicate samples) performed as described , with chromatin in unfixed detergent‐permeabilised yeast spheroplasts incubated with 600 units/ml of MNase for 3 min at 37 °C. Illumina DNA sequencing. NEBNext DNA sample prep master mix set 1 was used for Illumina adaptor ligation. Adaptor ligates were size selected on polyacrylamide gels to preserve the size distribution of the fragments before sequencing in 100 nucleotide paired end mode ...
Actin-related proteins in the nucleus: life beyond chromatin remodelers -ORCA
Since their discovery in the mid-1990s, nuclear actin-related proteins (ARPs) have gained attention for their roles as structural components of ATP-dependent chromatin-remodeling complexes. These remodelers can move nucleosomes along the DNA, evict them from chromatin, and exchange histone variants to alter chromatin states locally. Chromatin-remodeling facilitates DNA-templated processes such as transcription regulation, DNA replication, and repair. Consistent with a role for ARPs in shaping chromatin structure, recent genetic studies show that they affect developmental and cell-type specific transcriptional programming. Here, we focus on recent results that suggest a specific contribution of ARPs to long-range interactions in the nucleus, and review evidence indicating that some ARPs may act independently of chromatin-remodeling machines.. ...
Serval - Chromatin Loop Extrusion and Chromatin Unknotting.
It has been a puzzle how decondensed interphase chromosomes remain essentially unknotted. The natural expectation is that in the presence of type II DNA topoisomerases that permit passages of double-stranded DNA regions through each other, all chromosomes should reach the state of topological equilibrium. The topological equilibrium in highly crowded interphase chromosomes forming chromosome territories would result in formation of highly knotted chromatin fibres. However, Chromosome Conformation Capture (3C) methods revealed that the decay of contact probabilities with the genomic distance in interphase chromosomes is practically the same as in the crumpled globule state that is formed when long polymers condense without formation of any knots. To remove knots from highly crowded chromatin, one would need an active process that should not only provide the energy to move the system from the state of topological equilibrium but also guide topoisomerase-mediated passages in such a way th
B138 Background: Treatment of breast cancer cells with histone deacetylase (HDAC) inhibitors results in chromatin decondensation and the sensitization of cancer cells to DNA damaging agents such as topoisomerase II inhibitors. We previously reported that the HDAC inhibitors induced chromatin decondensation through the down-regulation of heterochromatin maintenance proteins such as heterochromatin protein 1 (HP1), structural maintenance of chromatin proteins (SMC) 1-5 and DNA methyltransferase 1 (DNMT1). Here we report the role of HDAC2 in the expression of heterochromatin maintenance proteins, chromatin decondensation and DNA damage induced by topoisomerase inhibition. Methods: HDAC2 was selectively depleted using siRNA transfection. HDAC2 depleted cells were evaluated by microarray and Western blot analysis for changes in HP1, DNMT1 and SMC mRNA and protein expression. Chromatin decondensation was evaluated by electron microscopy. DNA damage and cell death induced by the topoisomerase ...
Cp190 - Centrosome-associated zinc finger protein CP190 - Drosophila melanogaster (Fruit fly) - Cp190 gene & protein
Component of the gypsy chromatin insulator complex which is required for the function of the gypsy chromatin insulator and other endogenous chromatin insulators. Chromatin insulators are regulatory elements which establish independent domains of transcriptional activity within eukaryotic genomes. Insulators have two defining properties; they can block the communication between an enhancer and a promoter when placed between them and can also buffer transgenes from position effect variegation (PEV). Insulators are proposed to structure the chromatin fiber into independent domains of differing transcriptional potential by promoting the formation of distinct chromatin loops. This chromatin looping may involve the formation of insulator bodies, where homotypic interactions between individual subunits of the insulator complex could promote the clustering of widely spaced insulators at the nuclear periphery. Within the gypsy insulator complex, this protein may directly bind to insulator DNA at sites distinct
Work | Exploring the Roles of cis- and trans-Factors in Modulating Higher Order Chromatin Structure and Gene Expression | ID:...
Gene expression is tightly regulated at the level of transcription through cooperation between cis-regulatory elements and trans-factors that bind to the regulatory elements. Together, these factors regulate the higher order chromatin structure which establishes domains that organize the genome and coordinate gene expression. However, the molecular mechanisms controlling transcription of individual loci within a topological domain (TAD) are not fully understood. The cystic fibrosis transmembrane conductance regulator (CFTR) gene provides a paradigm for investigating these mechanisms. CFTR occupies a TAD bordered by CTCF/cohesin binding sites within which are cell-type-selective cis-regulatory elements for the locus. We showed previously that intronic and extragenic enhancers, when occupied by specific transcription factors, are recruited to the CFTR promoter by a looping mechanism to drive gene expression. Here we use a combination of CRISPR/Cas9 editing of cis-regulatory elements and ...
The Yeast Histone Chaperone Chromatin Assembly Factor 1 Protects Against Double-Strand DNA-Damaging Agents | Genetics
We have shown for the first time that the function of CAF-1 is important for viability following double-strand DNA repair. Furthermore, CAF-1 functions genetically in both homologous recombination and NHEJ, and its function during double-strand DNA repair is dependent on the interaction between CAF-1 and PCNA. Given the biochemical role of CAF-1 in DNA synthesis-coupled chromatin assembly, we propose that CAF-1 mediates chromatin assembly during double-strand DNA repair in vivo.. We have observed sensitivity of CAF-1 mutants to a variety of double-strand DNA-damaging agents. A systematic analysis of the yeast deletion collection also isolated the cac2Δ as a mutant sensitive to MMS (Chang et al. 2002). Similarly, mutants of the genes encoding Arabidopsis CAF-1, fas1, and fas2 are sensitive to MMS (Takeda et al. 2004). Given the role of CAF-1 in chromatin assembly during NER of single-strand lesions and the sensitivity of CAF-1 mutants to UV irradiation (Gaillard et al. 1996; Kaufman et al. 1997; ...
Chromatin, Inc. - Mergers & Acquisitions (M&A), Partnerships & Alliances and Investment Report - 2016/11/10 - MarketLine...
Project Synopsis:|br/||br/|Marketlines Company Mergers & Acquisitions (M&A), Partnerships & Alliances and Investments reports offer a comprehensive breakdown of the organic and inorganic growth activity undertaken by an organization to sustain its competitive advantage.|br/||br/|Project Description:|br/||br/|Marketlines Chromatin, Inc. Mergers & Acquisitions (M&A), Partnerships & Alliances and Investments report includes business description, detailed reports on mergers and acquisitions (M&A), divestments, capital raisings, venture capital investments, ownership and partnership transactions undertaken by Chromatin, Inc. since January 2007.|br/||br/|Scope:|br/||br/|- Provides intelligence on Chromatin, Inc.s M&A, strategic partnerships and alliances, capital raising and private equity transactions.|br/|- Detailed reports of various financial transactions undertaken by Chromatin, Inc. and its subsidiaries since 2007.|br/|- Information about key financial and legal advisors for Chromatin, Inc.s
Dissertation or Thesis | The Biological Significance of BRG1 Mutations | ID: nc580n25t | Carolina Digital Repository
Eukaryotic organisms package DNA into chromatin for compact storage in the cell nucleus, but this packaging process results in transcriptional repression of genes. Chromatin remodeling complexes have evolved to overcome the transcriptional repression caused by chromatin packaging of DNA into nucleosomes by histones. One example of a chromatin remodeling complex is the SWI/SNF complex in yeast which uses ATP to drive the chromatin apart and make DNA accessible to transcription factors. The yeast SWI2 protein was discovered as the catalytic subunit of the yeast SWI/SNF chromatin remodeling complex and is required for the complex to counteract the repressive nature of chromatin. BRG1 and BRM, SWI2 homologs, are part of human chromatin remodeling complexes and have been shown to play a redundant role in the regulation of certain cell cycle and cellular adhesion genes, as well as cellular pathways. Recent studies showing loss of BRG1 in human tumor cell lines and primary tissue samples, BRG1 ...
Localization of TFIIB binding regions using serial analysis of chromatin occupancy | BMC Molecular Biology | Full Text
RNA Polymerase II (RNAP II) is recruited to core promoters by the pre-initiation complex (PIC) of general transcription factors. Within the PIC, transcription factor for RNA polymerase IIB (TFIIB) determines the start site of transcription. TFIIB binding has not been localized, genome-wide, in metazoans. Serial analysis of chromatin occupancy (SACO) is an unbiased methodology used to empirically identify transcription factor binding regions. In this report, we use TFIIB and SACO to localize TFIIB binding regions across the rat genome. A sample of the TFIIB SACO library was sequenced and 12,968 TFIIB genomic signature tags (GSTs) were assigned to the rat genome. GSTs are 20-22 base pair fragments that are derived from TFIIB bound chromatin. TFIIB localized to both non-protein coding and protein-coding loci. For 21% of the 1783 protein-coding genes in this sample of the SACO library, TFIIB binding mapped near the characterized 5 promoter that is upstream of the transcription start site (TSS). However,
CSynth: A Dynamic Modelling and Visualisation Tool for 3D Chromatin Structure - MRC Weatherall Institute of Molecular Medicine
The 3D structure of chromatin in the nucleus is important for gene expression and regulation. Chromosomal conformation capture techniques, such as Hi-C, generate large amounts of data showing interaction points on the genome but these are hard to interpret using standard tools. We have developed CSynth, a high performance 3D genome browser and real time chromatin restraint-based modeller to visualise dynamic and interactive models of chromatin capture data. CSynth does its calculations in the GPU hence is much faster than existing modelling software to infer and visualise the chromatin structure which also allow real-time interaction with the modelling parameters. It also allows straightforward comparison of interaction data and the results of third party 3D modelling outputs. In addition we include an option to view and manipulate these complicated structures using Virtual Reality (VR) allowing scientists to immerse themselves in the models for further understanding. This VR component has also proven
Oligodendrocyte precursor differentiation and survival requires chromatin remodeling by Chd7 and Chd8 [RNA-seq] - omicX
Oligodendrocyte precursor cells (OPCs) constitute the main proliferative cells in the adult brain, and deregulation of OPC proliferation-differentiation balance results in either glioma formation or defective adaptive (re)myelination. OPC differentiation requires significant genetic reprogramming implicating chromatin remodeling. Mounting evidence indicates that chromatin remodelers play important roles during normal development and their mutations are associated with neurodevelopmental defects, with CHD7 haploinsuficiency being the cause of CHARGE syndrome and CHD8 being one of the strongest Autism Spectrum Disorder (ASD) high-risk associated genes. Here, we report on uncharacterized functions of the chromatin remodelers Chd7 and Chd8 in OPCs. Their OPC-chromatin-binding profile combined with transcriptome and chromatin accessibility analyses of Chd7-deleted OPCs, demonstrates that Chd7 protects non-proliferative OPCs from apoptosis by chromatin-closing and transcriptional repression of p53.
Radiation-induced alterations of histone post-translational modification levels in lymphoblastoid cell lines | Radiation...
It is becoming increasingly evident that the cellular response towards DNA damage is affected by the structure of the chromatin region surrounding the damage site , while at the same time the chromatin structure is affected by the damage response . DNA double-strand breaks (DSBs) elicit a response in an Mbp-large chromatin region surrounding the break that involves alterations in several post-translational modifications (PTMs). Phosphorylation of histone variant H2AX at serine 139 (S139) to yield γ-H2AX is a hallmark step in the cellular response to DSB. The γ-H2AX chromatin domains, which can be visualized as ionizing radiation induced foci (IRIF), delineate regions where a large variety of signalling and repair proteins accumulate .. Immunofluorescence detection of PTMs demonstrated alterations in several modifications in the γ-H2AX domain following DSB induction that are associated with regulation of chromatin accessibility, recruitment of DNA damage response factors, and ...
Antibodies to Histone Modifications - Antibodies in Chromatin Remodeling | Sigma-Aldrich
In eukaryotic cells DNA is associated with histones and other proteins to form chromatin. The basic unit of chromatin is the nucleosome consisting of 140 bp of DNA wrapped around an octameric core of the four conserved histones H2A, H2B, H3 and H4.The relatively unstructured and highly charged N-terminal tail domains of histones, are central to the processes that modulate chromatin structure. A diverse and elaborate array of post-translational modifications that include acetylation, phosphorylation, methylation, ubiquitination and ADP-ribosylation, occur on the N-terminal tail domains of histones. Acetylation of lysine residues within these N-terminal domains by histone acetyl-transferases (HATs), is associated with transcriptional activation. This modification results in remodeling of the nucleosome structure into an open conformation more accessible to transcription complexes. In most species, histone H3 is primarily acetylated at lysines 9, 14, 18 and 23. Acetylation at lysine 9 appears to
Chromatin - Simple English Wikipedia, the free encyclopedia
Chromatin is the complex combination of DNA and proteins that makes up chromosomes. It is found inside the nuclei of eukaryotic cells. Chromatin is divided into heterochromatin (condensed) and euchromatin (extended) forms. Heterochromatin is composed mostly of satellite DNA tandem repeats. The active components of chromatin are DNA and histone proteins, although other proteins also occur. The functions of chromatin are: ...
DOAB: Directory of Open Access Books
Abstract. NETosis, a form of cell death that manifests by the release of decondensed chromatin to the extracellular space, provides valuable insights into mechanisms and consequences of cellular demise. Because extracellular chromatin can immobilize microbes, the extended nucleohistone network was called a neutrophil extracellular trap (NET), and the process of chromatin release was proposed to serve an innate immune defense function. Extracellular chromatin NETs were initially observed in studies of neutrophils and are most prominent in these types of granulocytes. Subsequent studies showed that other granulocytes and, in a limited way, other cells of the innate immune response may also release nuclear chromatin following certain kinds of stimulation. Variations of NETosis were noted with cells that remain temporarily motile after the release of chromatin. Numerous stimuli for NETosis were discovered, including bacterial breakdown products, inflammatory stimuli, particulate matter, certain ...
Beyond the Identification of Transcribed Sequences: Functional and Expression Analysis
ARONOW. Stepwise chromatin restructuring and unexpected rules for interaction of distributed cis-elements that form a locus control region in vivo. Catherine Ley-Ebert, Carolyn Florio, John Maier, Chris Cost and Bruce Aronow. Childrens Hospital Research Foundation and the University of Cincinnati, Cincinnati, Ohio, USA. We have performed a mutational analysis of the human adenosine deaminase (ADA) gene thymic locus control region in transgenic mice using CAT reporter genes. We examined in detail gene expression, chromatin structure based on low and high resolution MNase and DNAse hypersensitivity, restriction enzyme accessibility, and histone acetylation state analyses using chromatin immune precipitations. Mutations and perturbations of LCR cis-elements led to variably compromised LCR function and the formation of several common distinguishable chromatin structures.. Our results suggest that the ADA thymic LCR is formed by the interaction of distributed cis-elements that consist of a 200 97bp ...
ATP-dependent chromatin remodeler Ino80 replaces histone H3 with CENP-A at centromeres
This organism was chosen because it has epigenetically defined regional centromeres whose chromatin and protein compositions are similar to those of their human counterparts, to identify factors responsible for the replacement of histone H3 with CENP-A at centromeres.. In this report, the KAIST research group systematically analyzed the roles of the ATP-dependent chromatin-remodelers in the centromeric chromatin assembly of fission yeast as they serve as strong candidates for such factors ...
Chromatin, Chromatid, Chromsome Terminology - General Biology Discussion - BioForum
Chromatin, Chromatid, Chromsome Terminology - posted in General Biology Discussion: Some Questions to which I have found different/conflicting answers depending on what I have read or who I have talked to. Thanks in Advance. 1-Chromatin, chromosomes, and chromatid all consist of DNA AND some sort of proteins? 2-Is the following statement accurate: ALL types/forms of chromatin material and chromatids consist of chromosomes BUT not all types of chromosomes are chromatin or chromatids? 3-An...
Emerging roles of telomeric chromatin alterations in cancer | Journal of Experimental & Clinical Cancer Research | Full Text
Telomeres, the nucleoprotein structures that cap the ends of eukaryotic chromosomes, play important and multiple roles in tumorigenesis. Functional telomeres need the establishment of a protective chromatin structure based on the interplay between the specific complex named shelterin and a tight nucleosomal organization. Telomere shortening in duplicating somatic cells leads eventually to the destabilization of the telomere capping structure and to the activation of a DNA damage response (DDR) signaling. The final outcome of this process is cell replicative senescence, which constitute a protective barrier against unlimited proliferation. Cells that can bypass senescence checkpoint continue to divide until a second replicative checkpoint, crisis, characterized by chromosome fusions and rearrangements leading to massive cell death by apoptosis. During crisis telomere dysfunctions can either inhibit cell replication or favor tumorigenesis by the accumulation of chromosomal rearrangements and neoplastic
CSHLPress.com - drosophila mutagenesis
COLD SPRING HARBOR, N.Y. (Monday, June 1, 2009) - High-throughput whole-genome analysis is becoming a standard laboratory approach for investigating cellular processes. Next-generation sequencing is replacing microarrays as the technique of choice for genome-scale analysis, because it offers advantages in both sensitivity and scale. The June issue of Cold Spring Harbor Protocols (www.cshprotocols.org/TOCs/toc6_09.dtl) features Native Chromatin Preparation and Illumina/Solexa Library Construction from Keji Zhao and colleagues at the National Heart, Lung and Blood Institute (http://public.nhlbi.nih.gov/Staff/Home/UserInputForPerson.aspx?OID=895&LabId=lmi). The article describes sample preparation for sequencing of chromatin-immunoprecipitated DNA (ChIP-Seq) to analyze histone modification patterns using native chromatin and the Solexa/Illumina Genome Analyzer. Step-by-step instructions are given for purification of human CD4+ T cells from lymphocytes and chromatin fragmentation using micrococcal ...
Chromatin remodeling activities act on UV-damaged nucleosomes and modu by Helene Gaillard, Daniel J. Fitzgerald et al.
Nucleosomes inhibit DNA repair in vitro, suggesting that chromatin remodeling activities might be required for efficient repair in vivo. To investigate how structural and dynamic properties of nucleosomes affect damage recognition and processing, we investigated repair of UV lesions by photolyase on a nucleosome positioned at one end of a 226-bp-long DNA fragment. Repair was slow in the nucleosome but efficient outside. No disruption or movement of the nucleosome was observed after UV irradiation and during repair. However, incubation with the nucleosome remodeling complex SWI/SNF and ATP altered the conformation of nucleosomal DNA as judged by UV photo-footprinting and promoted more homogeneous repair. Incubation with yISW2 and ATP moved the nucleosome to a more central position, thereby altering the repair pattern. This is the first demonstration that two different chromatin remodeling complexes can act on UV-damaged nucleosomes and modulate repair. Similar activities might relieve the inhibitory
Books by Subject - Lane Medical Library - Stanford University School of Medicine
Epigenetics is the study of heritable changes in gene expression that occur independent of changes in the primary DNA sequence. Chromatin structure defines the state in which genetic information is organized in the cell. The organization of this structure greatly influences the abilities of genes to be activated or silenced. In eukaryotic cells, 146 base pairs of DNA is wrapped around the histone octamer (two H2A/H2B dimers and one H3/H4 tetramer) forming the nucleosomes, the basic unit of chromatin. The nucleosome cores are connected by linker DNA sequences to further package into higher-order chromatin structures. In addition to the core histones, each histone contains an unstructured N-terminal tail. The histone tails are the sites of most of the post-translational modifications (PTMs), such as acetylation, methylation and phosphorylation. These modifications regulate the structure and function of chromatin through two general mechanisms. In the first model, histone modifications may play a ...
chromatin condensation and cleavage
cleavage to large fragments (50-200 kD) probably occurs before cleavage to ladder sizes--Sikorska & Walker, Biochem. Cell Biol. 1994, released ca Feb, 1995--and the condensation can occur before distinct ladders are seen--Oberhammer, Sikorska, & others, ca 2 years ago. There have been a couple of very recent papers on the condensation, but it is certainly not a chromosome-by- chromosome condensation as in mitosis. Richard A. Lockshin/Dept. Biol. Sci. St. Johns U. 8000 Utopia Pkwy Jamaica NY 11439 USA/Phone 718: 990-1854/ Fax 718: 380-8543 [email address may change soon] In article ,40ld4r$fio at masala.cc.uh.edu, lhe at crick.bchs.uh.edu (Lihua He) writes: ,Dear Netters: ,We had a vote on the following question in a group meeting and we got a tie, so ,could you please help us. ,The question is: does chromatin cleavage occur earlier or later than chromatin ,condensation during apoptosis? ,Is there any difference between chromatin condensation of an apoptotic cell and ,of a normal cell cycle? ...
Nucleosome Repeat Length
In chromatin neighboring nucleosomes are separated by the linker DNA and in many cases also by the linker histone H1 as well as ... NRL can be determined genome-wide for the chromatin in a given cell type and state, or locally for a large enough genomic ... van Holde KE (1989). Chromatin. New York: Springer-Verlag. p. 497. ISBN 978-1-4612-8123-8. Valouev A, Johnson SM, Boyd SD, ... It was shown that ordered nucleosome positioning arises only in the presence of ATP-dependent chromatin remodeling. Furthermore ...
"Chromatin Network". Retrieved 1 March 2012. Kouzarides T (February 2007). "Chromatin modifications and their function". Cell. ... See Histone#Chromatin regulation. Abnormal expression or activity of methylation-regulating enzymes has been noted in some ... In eukaryotic cells, the genome is tightly condensed into chromatin (composed of DNA and histone proteins), so enzymes, such as ... Methylation of histones is important biologically because it is the principal epigenetic modification of chromatin that ...
Cold Spring Harbor Laboratory
... chromatin dynamics; structural biology; advanced proteomics; mass spectrometry; advanced microscopy. Cancer Research Principal ...
Linker histone H1 variants
The linker histone H1 is a protein family forming a critical component of eukaryotic chromatin. H1 histones bind to the linker ... However, at the level of local chromatin organization, individual variants can regulate a subset of specific genes both in a ... inactive chromatin: distribution in human fetal fibroblasts". Chromosome Research: An International Journal on the Molecular, ... Also, different isotypes show different localization and bind to chromatin with different affinities. Therefore a model has ...
During interphase, the genetic material in the nucleus consists of loosely packed chromatin. At the onset of prophase, ... Kadauke S, Blobel GA (April 2013). "Mitotic bookmarking by transcription factors". Epigenetics & Chromatin. 6 (1): 6. doi: ... chromatin fibers condense into discrete chromosomes that are typically visible at high magnification through a light microscope ...
Chromatin is a combination of proteins and DNA found in the nucleus, and it undergoes many structural changes as different ... Chromatin in the cell can be found in two states: condensed and uncondensed. The latter, known as euchromatin, is ... The process of chromatin remodeling involves several enzymes, including HATs, that assist in the reformation of nucleosomes and ... Controlling the chromatin remodeling process within cancer cells may provide a novel drug target for cancer research. Attacking ...
Jeanteur, Philippe (2008). Epigenetics and Chromatin. Springer. Kaneko S, Li G, Son J, Xu CF, Margueron R, Neubert TA, Reinberg ... Heterochromatin is tightly packed chromatin which limits the accessibility of transcription machinery to the underlying DNA, ... Chromatin. 6 (1): 3. doi:10.1186/1756-8935-6-3. PMC 3606351 . PMID 23448518. Martin C, Zhang Y (2005). "The diverse functions ... due to PRC2/EZH2-EED-mediated H3K27 methylation and subsequent recruitment of PRC1 which facilitates condensation of chromatin ...
The primary chromatin binding region was shown to localize to the C-repeat region. The chromatin-binding region was ... The Xist RNA directly binds to the inactive X-chromosome through a chromatin binding region of the RNA transcript. The Xist ... One theory is that Tsix is involved in chromatin modification at the Xist locus and another is that transcription factors of ... Navarro P, Pichard S, Ciaudo C, Avner P, Rougeulle C (Jun 2005). "Tsix transcription across the Xist gene alters chromatin ...
Chromosome conformation capture
Walther Flemming coined the term chromatin . In 1883, August Weismann connected chromatin with heredity. In 1884, Albrecht ... In 1973/1974, chromatin fiber was discovered. In 1975, Chambon coined the term nucleosomes. In 1982, Chromosome territories ... performed Hi-C experiment and found a prostate cancer risk region (7p15.2) in an anchor point for a repressive chromatin ... In 1888, Sutton and Boveri proposed the theory of continuity of chromatin during the cell cycle In 1889, Wilhelm von Waldemeyer ...
... chromatin remodeling, and X-chromosome inactivation in somatic cells. H2A.X and canonical H2A have diverged several times in ... Epigenetics Chromatin. doi:10.1186/s13072-016-0109-x. PMID 28096900. HistoneDB 2.0 - Database of histones and variants at NCBI ... Chromatin. 5:7. doi:10.1186/1756-8935-5-7. PMID 22650316. "Histone Variants Database 2.0". National Center for Biotechnology ...
Chromatin. 8: 3. doi:10.1186/1756-8935-8-3. ISSN 1756-8935. PMC 4363358 . PMID 25788984. T. Strachan and A. Read (2004). Human ... HP1 is involved in the chromatin condensing process that makes DNA inaccessible for transcription. Genetic disorders that ...
It is also associated with changes in chromatin conformation. The classical example is the Drosophila wm4 (speak white-mottled- ... According to this model, the heterochromatin forces an altered chromatin conformation on the euchromatic region. Due to this, ... codes for a chromatin protein containing a conserved domain common to several transcriptional regulators". Proc Natl Acad Sci U ... Chromatin. 2: 1. doi:10.1186/1756-8935-2-1. ISSN 1756-8935. Hermann J. Muller (1930). "Types of visible variations induced by X ...
Nucleosome Histone Chromatin Other histone proteins: Histone H1 Histone H2A Histone H3 Histone H4 Bhasin M, Reinherz EL, Reche ... Histone H2B is one of the 5 main histone proteins involved in the structure of chromatin in eukaryotic cells. Featuring a main ... These are highly involved in condensing chromatin from the beads-on-a-string conformation to a 30-nm fiber. Similar to other ... The wrapping continues until all chromatin has been packaged with the nucleosomes. Histone H2B is a structural protein that ...
Nagai S, Davis RE, Mattei PJ, Eagen KP, Kornberg RD (2017). "Chromatin potentiates transcription". Proc Natl Acad Sci U S A. ... Mediator is involved in "looping" of chromatin, which brings distant regions of a chromosome into closer physical proximity. ... 2013). "Activating RNAs associate with mediator to enhance chromatin architecture and transcription". Nature. 494 (7438): 497- ...
The list of chromatin remodeling enzymes is extensive and many have specific roles within the nucleus. For example, in 2016 ... Chromatin remodeling enzymes: These enzymes are responsible for promoting euchromatin or heterochromatin formation by a number ... A/B compartment-associated regions are on the multi-Mb scale and correlate with either open and expression-active chromatin ("A ... The quantity and organisation of these nucleosomes can affect the accessibility of local chromatin. This has a knock-on effect ...
Apoptotic DNA fragmentation
Burgoyne, Leigh A.; Burgoyne, Leigh A. (1973-05-15). "Chromatin sub-structure. The digestion of chromatin DNA at regularly ... In 1973, Hewish and Burgoyne, during the study of subchromatin structure, found that chromatin is accessible to the Ca++/Mg++ ... Ceskova, M.; Matyásová, J; Cejková, M (1976-12-31). "DNA in chromatin of irradiated lymphoid tissues degrades in vivo into ... Walker, P. R.; Pandey, S.; Sikorska, M. (1995). "Degradation of chromatin in apoptotic cells". Cell death and differentiation. ...
His lab studies the Myc oncogene and other factors that regulate stem and cancer cell chromatin including histone variant H3.3 ... ". "Endogenous mammalian histone H3.3 exhibits chromatin-related functions during development". Epigenetics and Chromatin. doi: ... studying Myc regulation of chromatin in stem cells and cancers of the nervous system. During his postdoctoral studies, ...
Burgoyne, Hewish (1973). "Chromatin sub-structure. The digestion of chromatin DNA at regularly spaced sites by a nuclear ... Since then, over several decades, chromatin theory has evolved. Chromatin subunit models as well as the notion of the ... Nucleosome Histone Chromatin Allfrey, VG; Mirsky, AE (May 1, 1964). "Structural Modifications of Histones and their Possible ... Specific remodeling proteins are constantly altering the chromatin structure by breaking the bonds between the DNA and ...
Proliferating cell nuclear antigen
Moggs JG, Grandi P, Quivy JP, Jónsson ZO, Hübscher U, Becker PB, Almouzni G (February 2000). "A CAF-1-PCNA-mediated chromatin ... Miura M (1999). "Detection of chromatin-bound PCNA in mammalian cells and its use to study DNA excision repair". J. Radiat. Res ... Balajee AS, Geard CR (March 2001). "Chromatin-bound PCNA complex formation triggered by DNA damage occurs independent of the ... chromatin remodeling and epigenetics. Many proteins interact with PCNA via the two known PCNA-interacting motifs PCNA- ...
Max Planck Institute of Immunobiology and Epigenetics
The Department of Chromatin Regulation, under Asifa Akhtar, aims to study chromatin and epigenetic mechanisms within gene ... "Department of Chromatin Regulation". Retrieved 16 April 2015. "Department of Developmental Immunobiology". Retrieved 16 April ...
Studies of chromatin structure. Removal of nucleic acids from laboratory protein preparations allowing for protein folding and ...
Molecular models of DNA
Peripheral chromatin is absent. Although the nuclei are not visible in unstained preparations, the karyosomes are readily ... Endolimax nana nuclei have a large endosome somewhat off-center and small amounts of visible chromatin or none at all. Cysts ... There is no peripheral chromatin on the nuclear membrane. The cytoplasm, which is coarsely granular and often highly vacuolated ...
Nuclear receptor coregulators
3. Chromatin acceptor sites". J Biol Chem. 246 (13): 4188-97. PMID 5559842. Yamamoto K, Alberts B (1975). "The interaction of ... Fryer, C. J. & Archer, T. K. (1998). "Chromatin remodelling by the glucocorticoid receptor requires the BRG1 complex". Nature. ... including SWI/SNF chromatin remodeling machines, SRC/p160s and TRAP/DRIP. The model accommodates the ability of membrane G ... such as E6-AP ATP-coupled chromatin remodeling complexes, such as the SWI/SNF/BRG-1 complex Protein methylases, such as CARM-1 ...
First, the chromatin content is far from being dilute, and second, the numbers of the participating molecules are sometimes so ... Most of the time, between cell divisions, chromatin is optimized to allow easy access of transcription factors to active genes ... doi:10.1016/s0959-440x(98)80063-8. Schiessel H (2003). "The physics of chromatin". J. Physics: Cond. Mat. 15: R699-R774. ... During the cell division, chromatin compaction increases even more to form chromosomes, which can cope with large mechanical ...
International Max Planck Research School for Molecular and Cellular Life Sciences
... chromatin & DNA biology; 4.) signaling & cell communication; 5.) biophysics, membranes & transport; 6.) multiscale imaging & ...
Norman Maclean (biologist)
422 Maclean, N., Matthews, H.R. & Bradbury, E.M. (1981). DNA- Chromatin and Chromosomes. Oxford: Blackwell Scientific pp. 281 ...
Rando, O J; J. Paulsson (2006). "Noisy silencing of chromatin". Cell. 11 (2): 134-6. doi:10.1016/j.devcel.2006.07.012. PMID ...
RNA polymerase II holoenzyme
Chromatin structure inhibition is the process wherein the promoter is hidden by chromatin structure. Chromatin structure is ... Chromatin structure-oriented factors are more complex than for initiation control. Often the chromatin-altering factor becomes ... See: chromatin, histone, and nucleosome RNA Pol II catalysis improving factors. Improve the Vmax or Km of RNA Pol II, so ... See: chromatin, histone, and nucleosome. These methods of control can be combined in a modular method, allowing very high ...
In chromatin, those proteins which remain after the histones have been removed, are classified as non-histone proteins. ... Chromatin Cohesin Condensin Hartwell, Leland; L. Hood; M. Goldberg; A. Reynolds; L. Silver; R. Veres (2004). Genetics: From ...
Webpage devoted to Chromatin Structure Info
... James R. Bone jrbone at odin.mdacc.tmc.edu Sat Jan 25 14:37:19 EST 1997 *Previous ... with emphasis on the proteins that modify chromatin structure, and the effects that these modifications have on cell function. ... Thanks, Jim bone Chromatin Structure and Function Page http://rampages.onramp.net/~jrbone/chrom.html ... message is to announce the creation of a new WWW resource deidicated to spreading information regarding the study of chromatin ...
Genes | Free Full-Text | Impact of Chromatin on HIV Replication
This review highlights critical host factors that influence chromatin structure and organization and that also impact HIV ... Furthermore, recent attempts to target chromatin associated factors to reduce the HIV proviral load are discussed. ... Chromatin influences Human Immunodeficiency Virus (HIV) integration and replication. ... Keywords: HIV; chromatin; integration; transcription; latency HIV; chromatin; integration; transcription; latency ►▼ Figures ...
Scientists Find No Proof For 30 NM Chromatin Fibers In The Mouse Genome - Redorbit
Chromatin is the complex of DNA and proteins that is the fundamental constituent of chromosomes in the nucleus of the cell. The ... The 10-nm model of chromatin fibers provides sufficient access to DNA to allow potential target sites to be reached. The 30-nm ... This approach allows for visual analysis of chromatin fibers without the need to add chemical agents to improve the contrast of ... "Our results revealed that the 30-nm chromatin fiber model is not consistent with the structure we found in our three- ...
Structural Biochemistry/30nm chromatin fibers - Wikibooks, open books for an open world
Presence of 30nm Chromatin fibers, essential?. It is essential for eukaryotic genomes to be folded and compacted to fit ... 30nm chromatin fiber models. The molecular model of the 30nm fiber includes the one-start solenoid, two-start helix ... Most of the chromatin is observed as 10nm fibers rather than 30nm. This technique proves that majority of genome is compacted ... Instead, 10 nm chromatin can be condensed enough into compacted domains through frequent bending and making 10nm fibers close ...
Biology | Free Full-Text | Myogenic Differential Methylation: Diverse Associations with Chromatin Structure | HTML
For LSP1, alternative promoter usage and active promoter-type chromatin were linked to highly specific myogenic or lymphogenic ... DMRs co-localized with a variety of chromatin structures, as deduced from ENCODE whole-genome profiles. Myogenic ... For example, MARVELD2 exhibited myogenic hypermethylation in transcription-type chromatin that overlapped a silenced promoter ... Both myogenic hypermethylation and hypomethylation often overlapped weak transcription-type chromatin and Polycomb-repressed- ...
Transcription, chromatin condensation, and gene migration | JCB
Large-scale chromatin structure of inducible genes: transcription on a condensed, linear template. J. Cell Biol. 185:87-100. ... Large-scale chromatin unfolding and remodeling induced by VP16 acidic activation domain. J. Cell Biol. 145:1341-1354. ... Large-scale chromatin decondensation and recondensation regulated by transcription from a natural promoter. J. Cell Biol. 154: ... Visualizing chromatin organization and dynamics during transcription. (A) The arrays are composed of a single human or mouse ...
Chromatin - Wikipedia
Recent chromatin publications and news] Protocol for in vitro Chromatin Assembly ENCODE threads Explorer Chromatin patterns at ... Elements of chromatin structure: histones, nucleosomes, and fibres, p. 1-26. In S. C. R. Elgin (ed.), Chromatin structure and ... When the chromatin decondenses, the DNA is open to entry of molecular machinery. Fluctuations between open and closed chromatin ... The spatial arrangement of the chromatin within the nucleus is not random - specific regions of the chromatin can be found in ...
Sperm Chromatin | SpringerLink
The Relationship Between Chromatin Structure and DNA Damage in Mammalian Spermatozoa Kenneth Dominguez, Chris D. R. Arca, W. ... Sperm Chromatin Dispersion Test: Technical Aspects and Clinical Applications Jaime Gosálvez, Carmen López-Fernández, José Luís ... Assisted reproductive technologies Chromatin DNA DNA repair Histones Male gamete morphogenesis Male infertility Nucleoproteins ... Sperm Chromatin Structure Assay (SCSA®): 30 Years of Experience with the SCSA® ...
... everything you need for studying or teaching Chromatin. ... Immediately download the Chromatin summary, chapter-by-chapter ... Chromatin Chromatin is a network of deoxyribonucleic acid (DNA) and nucleoproteins that constitutes a chromosome. Chromatin can ... Chromatin Chromatin is a network of deoxyribonucleic acid (DNA) and nucleoproteins that constitutes a chromosome. Chromatin can ...
Chromatin immunoprecipitation - Wikipedia
Generally, native chromatin is used as starting chromatin. As histones wrap around DNA to form nucleosomes, they are naturally ... Chromatin immunoprecipitation at the US National Library of Medicine Medical Subject Headings (MeSH) EpigenomeNOE.com Chromatin ... However, it demands highly specific primers for detection of the target cell chromatin from the foreign carrier chromatin ... Mild formaldehyde crosslinking followed by nuclease digestion has been used to shear the chromatin. Chromatin fragments of 400 ...
Chromatin | biology | Britannica.com
... compact fibre called chromatin. An extreme example of the ordered folding and compaction that chromatin can undergo is seen ... during cell division, when the chromatin of each chromosome condenses and is divided between two daughter cells (see below Cell ... Other articles where Chromatin is discussed: cell: DNA packaging: …a dense, ... a dense, compact fibre called chromatin. An extreme example of the ordered folding and compaction that chromatin can undergo is ...
Chromatin potentiates transcription | PNAS
... because chromatin reconstituted with purified histones differs from chromatin assembled in vivo. Reconstituted chromatin lacks ... S1 A and B) (10, 11). PHO5 chromatin isolated in this way was indistinguishable from chromatin at the chromosomal locus on the ... Dependence of chromatin transcription on protein factors and acetyl-CoA. (A) Repressed PHO5 chromatin was transcribed as in Fig ... C) Effect of gcn5 bromoΔ SAGA on chromatin transcription. Repressed (pho4Δ) PHO5 chromatin was transcribed as in Fig. 1C with ...
Chromatin Remodeling | SpringerLink
Reflecting this singular role for chromatin, numerous approaches have evolved in the laboratory over the past three decades to ... Chromatin is of central importance to gene regulation in eukaryotes. ... Chromatin is of central importance to gene regulation in eukaryotes. Reflecting this singular role for chromatin, numerous ... Analysis of Chromatin Structure in Plant Cells Mala Singh, Amol Ranjan, Krishan Mohan Rai, Sunil Kumar Singh, Verandra Kumar, ...
Chromatin | Define Chromatin at Dictionary.com
Chromatin definition, the readily stainable substance of a cell nucleus, consisting of DNA, RNA, and various proteins, that ... chromatin. Historical Examples. of chromatin. *. While these changes are going on in the chromatin the Amphiaster forms. ... Origin of chromatin. First recorded in 1880-85; chromat- + -in2. Related formschro·ma·tin·ic, adjectivechro·ma·toid, adjective ... Word Origin and History for chromatin. n.. protoplasm in cell nuclei, 1882, from German, coined 1879 by German anatomist ...
Chromatin Looping [image] | EurekAlert! Science News
Chromatin Protocols | Srikumar P. Chellappan | Springer
Protocols for reconstitution of chromatin on solid supports for analysis, preparation of positioned mononucleosomes, techniques ... this thorough volume is organized such that it begins with techniques related to the study of chromatin structure. ... Analysis of DNA Replication Associated Chromatin Decondensation: In Vivo Assay for Understanding Chromatin Remodeling ... Chromatin Protocols. Editors. * Srikumar P. Chellappan Series Title. Methods in Molecular Biology. Series Volume. 1288. ...
Chromatin rules. - PubMed - NCBI
Chromatin rules.. Li Y1, Huang S1.. Author information. 1. 1 Department of Biochemistry and Molecular Biology, University of ... Binding of pioneer transcription factors remodels the repressive chromatin and leads to H3K4me1 poised enhancers. The H3K4me1 ... lineage/cell-specific enhancers are silent by repressive chromatin structure. ...
rDNA Chromatin - Universität Regensburg
To investigate rDNA chromatin we have applied a technique called Chromatin Endogenous Cleavage (ChEC) (Schmid et al., 2004). In ... Most importantly the chromatin structure of the isolated material conserves important features of the chromatin in vivo (Figure ... Chromatin is defined as the entity composed of the DNA - encoding the genetic information - and associated proteins. Chromatin ... Below you find more details about our work on rDNA chromatin, PHO5 chromatin and the isolation of native chromosomal domains. ...
Chromatin | Definition of Chromatin at Dictionary.com
Chromatin definition, the readily stainable substance of a cell nucleus, consisting of DNA, RNA, and various proteins, that ... chromatin. *. During the resting stage this chromatin material may have the form of a thread, or may form a network of fibres ( ... chromaticity coordinates, chromaticity diagram, chromaticness, chromatics, chromatid, chromatin, chromatin body, chromatism, ... A brief account of a chromatin element resembling the accessory chromosome in Sagitta has been added for comparison. ...
Understanding chromatin's cancer connection | EurekAlert! Science News
New live-cell imaging technique allows Northwestern University researchers to study chromatins dynamic processes, including ... Understanding chromatins cancer connection New nanoscale imaging technique allows researchers to study chromatin in live cells ... understanding-chromatins-cancer-connection.. html More in Technology & Engineering. * New UTSA study shows wearable technology ... "We know that chromatin is a major player in complex diseases," Backman said. "We just havent had the techniques to study it. ...
Chromatin nucleolus definition | Drugs.com
Chromatin immunoprecipitation from 1000 cells
This makes it possible for users to perform Chromatin immunoprecipitation (ChIP) assays using only 1000 cells per ... Chromatin immunoprecipitation. The Chromatrap® ChIP-seq Protein A kit (Cat no 500189) was used for ChIP in accordance with the ... Chromatin preparation. For the study the human endometrial carcinoma cell line Hec50 (Holinka et al., 1996) was utilized for ... Sometimes samples are small, cell types can be hard to come by or are difficult because they offer only a low chromatin yield. ...
Epigenetics & Chromatin: Interactions and processes
... To mark the 2013 BioMed Central Epigenetics & Chromatin: Interactions and ... UpSETing chromatin during non-coding RNA production The packaging of eukaryotic DNA into nucleosomal arrays permits cells to ... Epigenetics & Chromatin: interactions and processes On 11 to 13 March 2013, BioMed Central will be hosting its inaugural ... The processes of chromatin disassembly and reassembly during DNA replication also h... ...
2020 Asilomar Chromatin, Chromosomes, and Epigenetics Conference - Participation Form
Thank you for your interest in participating in the 2020 Asilomar Chromatin, Chromosomes, & Epigenetics Conference (ACCEC)!. ... eventbrite registration link: https://www.eventbrite.com/e/asilomar-chromatin-chromosomes-epigenetics-conference-tickets- ...
tRNA genes as chromatin barriers | Nature Structural & Molecular Biology
... point toward a novel function for tRNA genes and a common mechanism of compartmentalizing and organizing eukaryotic chromatin. ... Chromatin barriers restrict silenced chromatin domains from invading active domains. A recent study shows that a tRNA gene ... Chromatin barriers restrict silenced chromatin domains from invading active domains. A recent study shows that a tRNA gene ... the Unit on Chromatin and Transcription, National Institute of Child Health and Human Development, US National Institutes of ...
Chromatin Remodeling | Curriki
... of chromatin organization and then proceeds to describe the process of chromatin remodeling through a review of chromatin ... This Teaching Resource provides lecture notes and slides for a class covering chromatin remodeling mechanisms and is part of ... of chromatin organization and then proceeds to describe the process of chromatin remodeling through a review of chromatin ... of chromatin organization and then proceeds to describe the process of chromatin remodeling through a review of chromatin ...
Chromatin : Biofuels Digest
Tag: Chromatin. The Sherpas: 7 biofuels feedstock developers clearing paths to the summit. October 9, 2012 , Jim Lane ... Chromatins Yield Machine: is instant gene-stacking a game-changer for energy crops?. [ 0 ] January 19, 2011 , admin ... Chromatin launches new SweetFuel sorghum hybrids at BioPro. [ 0 ] March 15, 2011 , admin ... Chromatin sorghum hybrids top trials for sugar yields. [ 0 ] February 16, 2011 , admin ...
Epigenomics chromatin biology therapeutics | Genetics | Cambridge University Press
Covers basic chromatin biology, imprinting at a genome-wide level, and epigenomics in disease biology and epidemiology, making ... The neurobiology of chromatin-associated mechanisms in the context of psychosis and mood spectrum disorders. 30. Genome-wide ... Part I. Basics of Chromatin Biology and Biochemistry:. 1. Introduction to epigenomics. 2. Epigenetics and its historical ... 3-D quantitative DNA methylation imaging for chromatin texture analysis in pharmacoepigenomics and toxicoepigenomics. Part IV. ...
Bipolar meiotic spindle formation without chromatin. - PubMed - NCBI
Bipolar meiotic spindle formation without chromatin.. Brunet S1, Polanski Z, Verlhac MH, Kubiak JZ, Maro B. ... Non-specific chromatin is sufficient, however, to promote spindle assembly in Xenopus cell-free extracts that contain ... We found that a bipolar spindle can form in vivo in the absence of any chromatin due to the establishment of interactions ...
Open chromatin reveals the functional maize genome | PNAS
2014) Chromatin accessibility: A window into the genome. Epigenetics Chromatin 7(1):33. ... Here, we identify the small portion (,1%) of the maize genome residing in open chromatin. We demonstrate that open chromatin ... DNA methylation rates also closely mirror the chromatin accessibility landscape. Cytosine hypomethylation of open chromatin is ... Given that our results support intergenic functional variation explained almost exclusively by open chromatin, these chromatin ...
Chromatin Immunoprecipitation - Methods and Protocols | Neus Visa | Springer
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-level regulation of biosynthetic gene clusters | Nature Chemical Biology
Modification of the chromatin landscape in fungal secondary metabolite clusters allows for a simple technological means to ... Chromatin-level regulation of biosynthetic gene clusters. *Jin Woo Bok1. na1, ... Chromatin-dependent regulation of secondary metabolite biosynthesis in fungi: is the picture complete? *Jérôme Collemare ... Deleting a Chromatin Remodeling Gene Increases the Diversity of Secondary Metabolites Produced by Colletotrichum higginsianum * ...
Illume Chroma Tins
Meeting Theme: Transcription/Chromatin
Transcription/Chromatin. Session: Structural Transitions in Chromatin - An Exploration of Mechanisms. • DNA Accessibility in ... The "Transcription/Chromatin" annual meeting theme will contain sessions titled: "Structural Transitions in Chromatin - An ... A session titled "Alternative Chromatin Structures" will illuminate the fact that nucleosome and chromatin structure is ... functions in the context of chromatin and is regulated by its multilayered structural organization. Likewise, chromatin ...
Controlling Chromatin Spreading | Science
Chromatin, Inc. Announces Five New Sorghum Products | Business Wire
Chromatin, Inc., an agriculture technology company, announced the development of five forage sorghum products designed to ... About Chromatin: Chromatin, Inc. develops sorghum for both traditional agriculture markets and for uses in new applications. It ... "Chromatin currently sells a strong lineup of forage sorghums," Jeff Widder, Chromatins Executive Vice President noted. "With ... Today, Chromatins products are sold in the U.S. and in more than 20 countries, where its sorghum seed is planted on over 4 ...
GenesHistone modificationsHistonesAbstractNucleosomeMethylationModificationsRole of ChromatinFibersEpigeneticsReplicationVitroGenome-wideGenomicProteinStructuralComplexesRegulatoryMolecularLocal chromatinLoopsOrganizationTranscription factorsRegulationChanges in the chromatinCellsMechanismsAccessibilityNuclearBiological
- Genes encoding chromatin remodeler proteins are the most frequently mutated genes in human cancer tissues, indicating their tumor suppressive functions and potential therapeutic usages for cancer treatment," says Dr. Pingyu Zhang from the Department of Gastroenterology, Hepatology and Nutrition at the University of Texas MD Anderson Cancer Center of USA, "We believe that chromatin remodelers will become therapeutic targets for cancer therapies in the future. (benthamscience.com)
- A variety of mechanisms exist for targeting enzymes to undertake local opening of chromatin such as at active genes or for DNA repair. (nuigalway.ie)
- Under heat shock conditions, THO mutants accumulate large protein-DNA complexes that alter the chromatin density of target genes (heavy chromatin), defining a specific biochemical facet of THO function and a powerful tool of analysis. (au.dk)
- Although transcriptional and proteolytic activation of ADD1/SREBP1c has been studied intensively, the mechanism by which insulin regulates expression of its target genes with ADD1/SREBP1c at the chromatin level is unclear. (elsevier.com)
- We hypothesize that CTCF interactions stabilize enhancer-promoter chromatin interaction domains, facilitating increased expression of genes in response to stimuli. (ru.nl)
- RESULTS: We use CTCF ChIA-PET data from the ENCODE project to show that CTCF-associated chromatin loops have a tendency to enclose regions of enhancer-regulated stimulus responsive genes, insulating them from neighboring regions of constitutively expressed housekeeping genes. (ru.nl)
- CONCLUSIONS: We provide computational evidence that CTCF-mediated chromatin interactions enclose domains of stimulus responsive enhancer-regulated genes, insulating them from nearby housekeeping genes. (ru.nl)
- The contribution of highly basic non-histone chromatin proteins in vitro has been investigated using the HMGA2 protein implicated in human stem cell chromatin opening, and the Hematodinium DVNP protein which is suggested to replace histones as the dominant packaging protein in this dinoflagellate. (nuigalway.ie)
- Chromatin remodeling is an energy-driven process in which chromatin remodelers use the energy of ATP hydrolysis to change the nucleosome structure. (benthamscience.com)
- Recently, Methyltransferase Accessibility Protocol for individual templates-Bisulfite Genome Sequencing (MAPit-BGS) and nucleosome occupancy and methylome sequencing (NOMe-seq) have been developed for simultaneously profiling chromatin accessibility and DNA methylation on single molecules. (elsevier.com)
- The basic unit of chromatin is the nucleosome, where ~146 base pair increments of the genome are wrapped and compacted around the core histone proteins. (rxivist.org)
- One such mechanism involves the Piwi-piRNA complex, which represses TEs in animal gonads either by cleaving TE transcripts in the cytoplasm or by directing specific chromatin modifications at TE loci in the nucleus. (biomedcentral.com)
- This organization regulates many nuclear processes, and is controlled in part by histone post-transtranslational modifications and chromatin-binding proteins. (rxivist.org)
- The dynamic nature of this state could enable known modulators of chromatin structure, such as post-translational modifications and chromatin binding proteins, to act upon it and consequently control nuclear processes such as transcription and DNA repair. (rxivist.org)
Role of Chromatin3
- Our lab is investigating the role of chromatin and RNA in controlling transcriptional and post-transcriptional gene regulatory processes. (caltech.edu)
- We are also aiming to identify the role of chromatin on post-transcriptional gene regulatory processes. (caltech.edu)
- In this review, we emphasize the role of chromatin boundaries in piRNA cluster formation. (biomedcentral.com)
- Presence of 30nm Chromatin fibers, essential? (wikibooks.org)
- These models were based on EM of buffer-extracted chromatin fibers and micrococcal nuclease-digested material. (wikibooks.org)
- However, cryo-EM studies demonstrated that the 30nm fibers were not present in the fully condensed chromatin, and it was proved by the absence of a 30nm peak in the power spectrum. (wikibooks.org)
- It relies on heavy metal contrast agent, and thus is hard to visualize chromatin fibers. (wikibooks.org)
- Most of the chromatin is observed as 10nm fibers rather than 30nm. (wikibooks.org)
- This technique proves that majority of genome is compacted into 10nm chromatin fibers. (wikibooks.org)
- There are variety of models and techniques to observe the presence of the 30nm fibers but it has been more observed that highly compacted chromatin fiber like 30nm fibers are not necessarily present for any gene regulation such as folding of DNA. (wikibooks.org)
- Instead, 10 nm chromatin can be condensed enough into compacted domains through frequent bending and making 10nm fibers close to each other. (wikibooks.org)
- In other words, it does not require to have 30nm fibers but is sufficient to have 10 nm chromatin fibers that is organized in genome to explain the complexities of nuclear organization and gene regulation. (wikibooks.org)
- Living without 30nm chromatin fibers. (wikibooks.org)
- Beijing, China - Chromatin remodeling proteins (chromatin remodelers) are essential and powerful regulators for critical DNA-templated cellular processes, such as DNA replication, recombination, gene transcription/repression, and DNA damage repair. (benthamscience.com)
- Conference Scene: Chromatin, replication and chromosomal stability. (inserm.fr)
- The Chromatin, Replication and Chromosomal Stability Conference took place on June 20-21 in Stockholm, Sweden. (inserm.fr)
- This analysis indicates that mouse liver chromatin is a restricted template for the in vitro synthesis of RNA complements to repetitive DNA, but more RNA species are synthesized than are found in the RNA isolated from mouse liver nuclei. (elsevier.com)
- RNA synthesized in vitro from DNA or chromatin templates by Escherichia coli RNA polymerase, as well as in vivo mouse liver nuclear RNA, were each hybridized to 125 I-labeled DNA of high, intermediate, or low reiteration frequency. (elsevier.com)
- When used as a template for in vitro RNA synthesis, such salt-extracted chromatin produced RN As that hybridize as large a portion of each DNA fraction as does DNA-primed RNA. (elsevier.com)
- To characterise mechanisms behind transitions in chromatin state driven by non-histone chromatin proteins HMGA2, H1 and DVNP were purified and included in in vitro assays to characterise their interaction with DNA and nucleosomes. (nuigalway.ie)
- A question arise from this that whether 30nm chromatin fiber must be present or not to constitute the template for active genomic material. (wikibooks.org)
- To facilitate identification and characterization of genomic functional elements, we have developed a chromatin architecture alignment algorithm (ArchAlign). (elsevier.com)
- Genomic events including gene regulation and chromatin status are controlled by transcription factors. (illinois.edu)
- Genomic DNA is highly compacted in the nucleus of eukaryotic cells as a nucleoprotein assembly called chromatin. (rxivist.org)
- These results indicate that under physiologically relevant conditions, LLPS is an intrinsic behavior of the chromatin polymer, and suggest a model in which the condensed phase reflects a genomic 'ground state' that can produce chromatin organization and compaction in vivo. (rxivist.org)
- ArchAlign identifies shared chromatin structural patterns from high-resolution chromatin structural datasets derived from next-generation sequencing or tiled microarray approaches for user defined regions of interest. (elsevier.com)
- We validated ArchAlign using well characterized functional elements, and used it to explore the chromatin structural architecture at CTCF binding sites in the human genome. (elsevier.com)
- This often involves abundant non-histone chromatin proteins that switch chromatin between states that are not well understood at the structural level. (nuigalway.ie)
- Taken together, our results suggest that the SWI/SNF chromatin remodeling complexes confer not only insulin-dependent gene expression but also insulin sensitivity in vivo via interaction with ADD1/SREBP1c. (elsevier.com)
- Chromatin profiling has been a method of choice for mapping regulatory sequences in cells that go through developmental transitions. (oregonstate.edu)
- Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. (elsevier.com)
- Due to advances in molecular biology techniques, chromatin structure and function has re-emerged as a key research area in the investigation of gene regulation and expression. (valorebooks.com)
- Thus, Hsp90 selectively governs the transcription factor process overseeing local chromatin structure. (illinois.edu)
- Long-term loss (6 h) of Hsp90 resulted in a decline of a divergent yet overlaying pool of transcription factors that produced a distinct chromatin pattern. (illinois.edu)
- Intriguingly, despite the broad chaperone impact on a variety of transcription factors, the operational influence of Hsp90 was at the level of chromatin with only a mild effect on gene regulation. (illinois.edu)
- Epigenetic regulation in mammalian cells.Elgin, Sarah C. is the author of 'Chromatin Structure and Gene Expression - Sarah C. Elgin - Hardcover' with ISBN 9780199635764 and ISBN 0199635765. (valorebooks.com)
- Motivation: Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. (elsevier.com)
Changes in the chromatin1
- Insulin enhanced recruitment of SWI/SNF chromatin remodeling factors to its target gene promoters with concomitant changes in the chromatin structures as well as gene expression. (elsevier.com)
- In human cells, there are four chromatin remodeler families: SWI/SNF, INO80, ISWI and CHD family. (benthamscience.com)
- This is a hot and exciting research topic for cancer researchers, and our article provides an updated understanding on the functions and mechanisms of chromatin remodelers in human cancers," says Dr. Chun Zhang, the principle investigator of the Department of Nuclear Medicine of Beijing Chao-Yang Hospital and Capital Medical University of China. (benthamscience.com)
- The DNA repair mechanisms again are influenced by the chromatin structure. (inserm.fr)
- Therefore, there is a great demand in developing computational methods to identify chromatin accessibility from MAPit-BGS and NOMe-seq. (elsevier.com)
- The efficiency and effectiveness of CAME were demonstrated through comparisons with other existing techniques on both simulated and real data, and the results show that our method not only can precisely identify chromatin accessibility but also outperforms other methods. (elsevier.com)
- Chromatin-primed and nuclear RNA saturate a smaller portion of each DNA fraction than does DNA-primed RNA. (elsevier.com)
- However, chromatin-primed RNA saturates more high and low reiteration frequency DNA than does nuclear RNA. (elsevier.com)
- Simultaneous hybridization of nuclear-and chromatin-primed RNA with 125 I-labeled DNA indicates that chromatin-primed RNA contains all of the sequences present in nuclear RNA. (elsevier.com)
- The consistent prognostic prediction of Nucleotyping in different biological and technical circumstances suggests that the marker of chromatin heterogeneity can be reliably assessed in routine clinical practice and could be used to objectively assist decision making in a range of clinical settings. (uio.no)