Chromatin Assembly and Disassembly
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
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.
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).
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.
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.
Saccharomyces cerevisiae Proteins
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.
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
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.
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.
Gene Expression Regulation, Developmental
Mi-2 Nucleosome Remodeling and Deacetylase Complex
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.
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
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.
Locus Control Region
Polycomb Repressive Complex 1
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
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
Regulatory Elements, Transcriptional
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
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
Transcriptional Elongation Factors
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
Oligonucleotide Array Sequence Analysis
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
Origin Recognition Complex
Recombinant Fusion Proteins
Gene Knockdown Techniques
Poly Adenosine Diphosphate Ribose
In Situ Hybridization, Fluorescence
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
E1A-Associated p300 Protein
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.
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
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
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)
... recent chromatin publications and news Protocol for in vitro Chromatin Assembly ENCODE threads Explorer Chromatin patterns at ... Elements of chromatin structure: histones, nucleosomes, and fibres, p. 1-26. In S. C. R. Elgin (ed.), Chromatin structure and ... When the chromatin decondenses, the DNA is open to entry of molecular machinery. Fluctuations between open and closed chromatin ... When chromatin is condensed, the nucleus becomes more rigid. When chromatin is decondensed, the nucleus becomes more elastic ...
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 ...
... s may serve as a marker of cancer activity. Chromatin bridges may form by any number of processes wherein ... Chromatin bridges are easiest and most readily visible when observing chromosomes stained with DAPI. DNA bridges appear to be a ... Chromatin bridge is a mitotic occurrence that forms when telomeres of sister chromatids fuse together and fail to completely ... A chromatin bridge may also be observed using indirect immunofluorescence, in which anti-tubulin emits a green coloration when ...
The developmentally regulated process of resolving bivalent chromatin is aided by the activity of ATP-chromatin remodelers such ... However, in bivalent chromatin, both types of regulators are interacting with the same domain at the same time. Bivalent ... Bivalent chromatin domains are found in embryonic stem (ES) cells and play an important role in cell differentiation. When ... Bivalent chromatin are segments of DNA, bound to histone proteins, that have both repressing and activating epigenetic ...
Epigenetics & Chromatin
"Epigenetics & Chromatin". Epigenetics & Chromatin. Retrieved 2020-10-29. "Epigenetics & Chromatin". Epigenetics & Chromatin. ... "Epigenetics & Chromatin". Epigenetics & Chromatin. Retrieved 2020-10-29. "Epigenetics & Chromatin". Epigenetics & Chromatin. ... "Epigenetics & Chromatin". Epigenetics & Chromatin. Retrieved 2020-10-29. "Epigenetics & Chromatin". Journal Citation Reports ... "Archive of "Epigenetics & Chromatin"". www.ncbi.nlm.nih.gov. Retrieved 2020-11-05. "Epigenetics & Chromatin". Socolar. ...
A chromatin variant corresponds to a section of the genome that differs in chromatin states across cell types/states within an ... Chromatin variants range in sizes. The smallest chromatin variants cover a few hundred DNA base pairs, such as seen at ... The largest chromatin variants capture a few thousand DNA base pairs, such as seen at Large Organized Chromatin Lysine domains ... Chromatin variants are found across the genome, inclusive of repetitive and non-repetitive DNA sequence. ...
... is the dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the ... MBInfo - Chromatin MBInfo - DNA Packaging YouTube - Chromatin, Histones and Modifications YouTube - Epigenetics Overview ... Epigenetics Histone Nucleosomes Chromatin Histone acetyltransferase Transcription factors CAF-1 (Chromatin assembly factor-1 ... Wang GG, Allis CD, Chi P (September 2007). "Chromatin remodeling and cancer, Part II: ATP-dependent chromatin remodeling". ...
Active chromatin sequence
At the active chromatin sequence site deacetylation can caused the gene to be repressed if not being expressed. Chromatin Sabo ... Active chromatin may also be called euchromatin. ACSs may occur in non-expressed gene regions which are assumed to be "poised" ... An active chromatin sequence (ACS) is a region of DNA in a eukaryotic chromosome in which histone modifications such as ... Roh TY, Cuddapah S, Zhao K (2005). "Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping ...
Chromatin assembly factor 1
Hoek M, Stillman B (October 2003). "Chromatin assembly factor 1 is essential and couples chromatin assembly to DNA replication ... Chromatin assembly factor-1 (CAF-1) is a protein complex - including Chaf1a (p150), Chaf1b (p60), and p48 subunits in humans, ... However, loss of function in p48 would alter how well the complex is able to chaperone chromatin, but would not stop it as a ... Volk, Andrew; Crispino, John D. (August 2015). "The role of the chromatin assembly complex (CAF-1) and its p60 subunit (CHAF1b ...
Sperm Chromatin Structure Assay
... (SCSA) is a diagnostic approach that detects sperm abnormality with a large extent of DNA ... "Sperm Chromatin Structure Assay (SCSA) , Center for Women's Health , OHSU". www.ohsu.edu. Retrieved 2021-03-31. Evenson, Donald ... The small AO molecules penetrate through the sperm chromatin in access to double-stranded DNA and single-stranded DNA in intact ... Evenson, D.P. (1999-04-01). "Utility of the sperm chromatin structure assay as a diagnostic and prognostic tool in the human ...
Chromatin target of prmt1
... is a protein that in humans is encoded by the CHTOP gene. This gene encodes a small nuclear protein ... "Entrez Gene: Chromatin target of PRMT1". Zullo AJ, Michaud M, Zhang W, Grusby MJ (May 2009). "Identification of the small ... a novel chromatin target of protein arginine methyltransferases". Molecular and Cellular Biology. 30 (1): 260-72. doi:10.1128/ ...
Chromatin accessibility complex 1
... is a protein that in humans is encoded by the CHRAC1 gene. CHRAC1 is a histone-fold protein ... "Entrez Gene: Chromatin accessibility complex 1". Retrieved 2016-10-26. This article incorporates text from the United States ...
In pathology, salt-and-pepper chromatin, also salt-and-pepper nuclei and stippled chromatin, refers to cell nuclei that ... A pheochromocytoma showing finely granular chromatin. H&E stain. Salt-and-pepper chromatin (pheochromocytoma). H&E stain. ... Neuroendocrine tumour of the lung with salt-and-pepper chromatin. H&E stain. Neuroendocrine tumour of the small intestine with ... Salt-and-pepper chromatin - nature.com. Salt-and-pepper nucleus - upmc.edu. (Pathology). ...
Chromatin structure remodeling (RSC) complex
There are four subfamilies of chromatin remodelers: SWI/SNF, INO80, ISW1, and CHD. The RSC complex is a 15-subunit chromatin ... RSC (Remodeling the Structure of Chromatin) is a member of the ATP-dependent chromatin remodeler family. The activity of the ... While there are many similarities between these two chromatin remodeling complexes, they remodel different parts of chromatin. ... After this chromatin remodeling complex was discovered, the RSC complex was found when its components, Snf2 and Swi2p, were ...
... (also called "open chromatin") is a lightly packed form of chromatin (DNA, RNA, and protein) that is enriched in ... Chromatin. Atlas of plant and animal histology". mmegias.webs.uvigo.es. Retrieved 2021-12-02. Enukashvily NI (January 2013). " ... Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin - Tedesco M, ... October 2021). "Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin". ...
Timothy J. Richmond
Their work on the nucle-osome core particle, the fun-da-mental repeat-ing unit of chro-matin, resul-ted ul-ti-mately in its ... They have since de-term-ined the organ-iz-a-tion of nucle-osomes in the chro-matin fiber. He was the postdoctoral supervisor of ... Richmond's work provides a basis for integrating decades of biochemical, physical, and genetic studies of chromatin. His focus ... 2003 (over 1450 citations) Dorigo, Benedetta; Schalch, Thomas; Bystricky, Kerstin; Richmond, Timothy J. (2003). "Chromatin ...
Histone code Nucleosome Chromatin Other histone proteins: Histone H1 Histone H2A Histone H3 Histone H4 Bhasin M, Reinherz EL, ... Histone H2B is one of the 5 main histone proteins involved in the structure of chromatin in eukaryotic cells. Featuring a main ... These are highly involved in condensing chromatin from the beads-on-a-string conformation to a 30-nm fiber. Similar to other ... The wrapping continues until all chromatin has been packaged with the nucleosomes. Histone H2B is a structural protein that ...
"Chromatin Network". Retrieved 1 March 2012. Kouzarides T (February 2007). "Chromatin modifications and their function". Cell. ... The genomic DNA of eukaryotes associates with histones to form chromatin. The level of chromatin compaction depends heavily on ... See Histone#Chromatin regulation. Abnormal expression or activity of methylation-regulating enzymes has been noted in some ... Histone methylation is a principal epigenetic modification of chromatin that determines gene expression, genomic stability, ...
Cold Spring Harbor Laboratory
... chromatin dynamics; structural biology; advanced proteomics; mass spectrometry; advanced microscopy. Cancer ...
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. 8 (5): 405-424. doi:10.1023/A:1009262819961 ... Also, different isotypes show different localization and bind to chromatin with different affinities. Therefore a model has ...
Histones are proteins which are involved in the folding and compaction of the chromatin. There are several different types of ... 2021). "Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer". Gut. 71 (5 ... In general, DNA methylation attracts proteins which fold that section of the chromatin and repress the related genes. The ... This persistent hyperglycemic environment is leads to DNA methylation as well because the chemistry within chromatin in the ...
The complexes formed by the looping of the DNA are known as chromatin. The basic structural unit of chromatin is the nucleosome ... Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of ... This led to chromatin states which define genomic regions by grouping the interactions of different proteins and/or histone ... Chromatin states are also useful in identifying regulatory elements that have no defined sequence, such as enhancers. This ...
During interphase, the genetic material in the nucleus consists of loosely packed chromatin. At the onset of prophase, ... A, normal mitosis; B, chromatin bridge; C, multipolar mitosis; D, ring mitosis; E, dispersed mitosis; F, asymmetrical mitosis; ... Kadauke S, Blobel GA (April 2013). "Mitotic bookmarking by transcription factors". Epigenetics & Chromatin. 6 (1): 6. doi: ... non-attached condensed chromatin in the area of the mitotic figure) indicates high risk human papillomavirus infection-related ...
... and chromatin. This occurs through the synthesis of a new nuclear envelope that forms around the chromatin gathered at each ... The nuclear envelope is broken down in this stage, long strands of chromatin condense to form shorter more visible strands ... The nucleolus reforms as the chromatin reverts back to the loose state it possessed during interphase. The division of the ... Chromatin. 7 (1): 25. doi:10.1186/1756-8935-7-25. PMC 4247682. PMID 25435919. Hetzer MW (March 2010). "The nuclear envelope". ...
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 ...
Chromatin. 13 (1): 12. doi:10.1186/s13072-020-00334-y. ISSN 1756-8935. PMC 7059380. PMID 32138783. Wang, Qin; Dai, Tianyue; Sun ...
Jeanteur P (2008). Epigenetics and Chromatin. Springer. ISBN 9783540852360. Kaneko S, Li G, Son J, Xu CF, Margueron R, Neubert ... Heterochromatin is tightly packed chromatin which limits the accessibility of transcription machinery to the underlying DNA, ... Chromatin. 6 (1): 3. doi:10.1186/1756-8935-6-3. PMC 3606351. PMID 23448518. Martin C, Zhang Y (November 2005). "The diverse ... due to PRC2/EZH2-EED-mediated H3K27 methylation and subsequent recruitment of PRC1 which facilitates condensation of chromatin ...
Talbert, P.; Meers, M.P.; Henikoff, S. (2019). "Old cogs, new tricks: the evolution of gene expression in a chromatin context ... Chromatin. 10 (55): 55. doi:10.1186/s13072-017-0162-0. PMC 5704553. PMID 29179736. Erives, A.; Levine, M. (2004). "Coordinate ...
"Chromatin Immuprecipitation". www.bio.brandeis.edu. Krogan NJ, Dover J, Wood A, Schneider J, Heidt J, Boateng MA, Dean K, Ryan ... 2013). "Genome-wide chromatin state transitions associated with developmental and environmental cues". Cell. 152 (3): 642-654. ... It is thought that they achieve this through alterations in chromatin structure, such as histone modification and DNA ... To a large extent, differences in transcription factor binding are determined by the chromatin accessibility of their binding ...
ChromDB Contains 9,341 chromatin-associated proteins, including RNAi-associated proteins, for a broad range of organisms. ... "ChromDB::Chromatin Database". Archived from the original on 2019-04-10. Retrieved 2010-01-29. Cremofac "Home". epigenomics.ca. ... CREMOFAC Contains 1725 redundant and 720 non-redundant chromatin-remodeling factor sequences in eukaryotes. The Krembil Family ...
Photo Gallery - Chromatin & Gene Expression Group
NLM Intramural Research - Networks, Gene Regulation, and Chromatin
Spatially mapped single-cell chromatin accessibility | Nature Communications
... single-cell profiling of chromatin states. sciMAP-ATAC produces data of equivalent quality to non-spatial sci-ATAC and retains ... where we produce spatial trajectories and integrate our data with non-spatial single-nucleus RNA and other chromatin ... single-cell combinatorial indexing on Microbiopsies Assigned to Positions for the Assay for Transposase Accessible Chromatin, ... Chromatin accessibility analysis. The filtered bam file was used for chromatin accessibility peak calling for each of the five ...
Cardiff researcher finds chromatin in volcano - News - Cardiff University
Chromatin Dynamics News, Articles | The Scientist Magazine®
Detailed analyses of cohesins movements indicate how this protein complex hauls chromatin fibers to package DNA into loops. ... Detailed analyses of cohesins movements indicate how this protein complex hauls chromatin fibers to package DNA into loops. ... Detailed analyses of cohesins movements indicate how this protein complex hauls chromatin fibers to package DNA into loops. ... By manipulating DNA sequences that guide genome-folding, researchers confirm an existing model of chromatin structure inside ...
Dopamine modification on chromatin linked to addiction | National Institutes of Health (NIH)
Dopamine modification on chromatin linked to addiction. At a Glance. *Researchers found that dopamine can modify the structure ... In chromatin, DNA (yellow) is wound around histone proteins (blue). Chemical changes to histones can affect the way the genes ... Chemical modifications of chromatin-the structure that DNA and proteins called histones are packed into to form chromosomes-can ...
General Term: Chromatin
Chromatin. A complex of ,!g,DNA and basic proteins (as histone) in ,!g,eukaryotic cells that is condensed into ,!g,chromosomes ... There are two types: heterochromatic which is densely coiled chromatin that appears as nodules in or along chromosomes and ... Euchromatic is the less coiled and genetically active portion of chromatin that is largely composed of genes. ...
ADNP Controls Gene Expression Through Local Chromatin Architecture by Association With BRG1 and CHD4
Recent studies have suggested that ADNP functions as an important chromatin regulator. However, how ADNP-regulated chromatin ... ADNP Controls Gene Expression Through Local Chromatin Architecture by Association With BRG1 and CHD4 Front Cell Dev Biol. 2020 ... Here we show that ADNP interacts with two chromatin remodelers, BRG1 and CHD4. ADNP is required for proper establishment of ... Thus, our work revealed a key role of ADNP in the establishment of local chromatin landscape and structure of developmental ...
Genome Instability and Chromatin Remodeling Section | National Institute on Aging
Genome Instability and Chromatin Remodeling Section Weidong Wang, PhD, Chief The Genome Instability and Chromatin Remodeling ... Home Research & Funding Labs at NIA Laboratory of Genetics & Genomics Genome Instability and Chromatin Remodeling Section ... Chromatin-remodeling complexes that regulate transcription, replication and repair.. Findings and Publications Yan Z, Delannoy ... several chromatin-remodeling complexes (BAF, PBAF, NURD), and Top3b-TDRD3 topoisomerase complex. Given that Top3b is the first ...
Citation Form | EPIGENETICS-AND-CHROMATIN | Manuscript | Citation Machine
Post-doctoral Fellow - Chromatin, epigenetics | Center for Cancer Research
... and repressed chromatin (heterochromatin). The functional organization of chromatin is important for regulation of ... 2021). We are currently addressing the question of how LSH molecular function alters chromatin structure and maintains genomic ... nucleosome occupancy and DNA methylation and are crucial for organization of the genome into active chromatin (euchromatin) ... and repressed chromatin (heterochromatin). The functional organization of chromatin is important for regulation of ...
NIH VideoCast - Chromatin Responses to DNA Damage
Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions
However, they impact chromatin dynamics and should be reflected in particular in the motion of a single locus. We present here ... Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions. Author(s). Amitai, Assaf; ... Is it possible to extract tethering forces applied on chromatin from the statistics of a single locus trajectories imaged in ... "Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions." Edited by Alexandre V Morozov. ...
MeCP2 and Chromatin Compartmentalization - PubMed
... is a multifunctional epigenetic reader playing a role in transcriptional regulation and chromatin structure, which was linked ... MeCP2 and Chromatin Compartmentalization Annika Schmidt et al. Cells. 2020. . Free PMC article Show details Display options ... MeCP2 and Chromatin Compartmentalization Annika Schmidt 1 , Hui Zhang 1 , M Cristina Cardoso 1 ... Idris M, Coussement L, Alves MM, De Meyer T, Melotte V. Idris M, et al. Epigenetics Chromatin. 2023 Aug 3;16(1):31. doi: ...
Chromatin Immunoprecipitation Sequencing - MeSH - NCBI
Chromatin Immunoprecipitation Sequencing. A technique for identifying the BINDING SITES on nucleic acid sequences that are ... Therapeutic Techniques and Equipment CategoryInvestigative TechniquesGenetic TechniquesChromatin ImmunoprecipitationChromatin ... and Equipment CategoryInvestigative TechniquesImmunologic TechniquesImmunoprecipitationChromatin ImmunoprecipitationChromatin ... and Equipment CategoryInvestigative TechniquesGenetic TechniquesSequence AnalysisHigh-Throughput Nucleotide SequencingChromatin ...
CHROMATIN ASSEMBLY AND FORMALDEHYDE TOXICITY
... suggesting inhibition of chromatin assembly. Defective chromatin assembly causes dysregulation of gene expression and genomic ... Our preliminary results further show that formaldehyde reduces the total amount of histone in the chromatin fraction and the ... In Aim 2, we will determine the impact of aberrant chromatin assembly on formaldehyde-induced changes in gene expression, ... In Aim 3, we will investigate whether formaldehyde exposure compromises chromatin assembly in vivo. The proposed concept that a ...
Genes | Free Full-Text | Contribution of Topological Domains and Loop Formation to 3D Chromatin Organization
... or a weaker architectural role in chromatin loop formation. TAD borders directly impact on chromatin dynamics by restricting ... We discuss how sub-TAD chromatin dynamics, constrained into a recently described statistical helix conformation, can produce ... organization of the eukaryote genomes and discusses the relationship to chromatin loop formation. CTCF protein appears as a ... Recent investigations on 3D chromatin folding revealed that the eukaryote genomes are both highly compartmentalized and ...
Insights into chromatin structure and dynamics in plants | John Innes Centre
The packaging of chromatin into the nucleus of a eukaryotic cell requires an extraordinary degree of compaction and physical ... The packaging of chromatin into the nucleus of a eukaryotic cell requires an extraordinary degree of compaction and physical ... In this review, we focus on these aspects of chromatin organization and discuss novel approaches such as live cell imaging and ... tools likely to give significant insights into our understanding of the very dynamic nature of chromatin and chromatin ...
JCI - CDK8 and CDK19 regulate intestinal differentiation and homeostasis via the chromatin remodeling complex SWI/SNF
The Mediator kinase module bound and phosphorylated key components of the chromatin remodeling complex switch/sucrose non- ... CDK8 and CDK19 regulate intestinal differentiation and homeostasis via the chromatin remodeling complex SWI/SNF. ... CDK8 and CDK19 regulate intestinal differentiation and homeostasis via the chromatin remodeling complex SWI/SNF. ... coordinated by the interaction between the chromatin remodeling complex SWI/SNF and Mediator kinase. ...
Chromatin reader domains of UHRF1 and cancerous DNA hypermethylation
UHRF1 chromatin reader domains contribute to DNA hypermethylation in colorectal cancer cells. To dissect the role of UHRF1, the ... Chromatin reader domains of DNMT-targeting protein, UHRF1, are responsible for cancerous DNA hypermethylation. Tue, 08/20/2019 ... Using colorectal cancer cells, the team found that chromatin reader domains of UHRF1 maintain cancerous DNA hypermethylation. ... Home » Antibody News » Chromatin reader domains of DNMT-targeting protein, UHRF1, are responsible for cancerous DNA ...
The New Techniques Revealing the Varied Shapes of Chromatin | NIH Common Fund
We revised our look, but we still have all the same great content! Cant find something you need? Please contact [email protected].. ...
Active chromatin and noncoding RNAs: an intimate relationship. | California's Stem Cell Agency
An emerging class of enhancer-like lncRNAs may link chromosome structure to chromatin state and establish active chromatin ... An emerging class of enhancer-like lncRNAs may link chromosome structure to chromatin state and establish active chromatin ... Eukaryotic genomes are packaged into chromatin, where diverse histone modifications can demarcate chromatin domains that ... Eukaryotic genomes are packaged into chromatin, where diverse histone modifications can demarcate chromatin domains that ...
Chromatin and Splicing - Igh
Our objectives now are to better understand the role of chromatin, enhancers and long non-coding RNAs in the onset and ... Splicing-associated chromatin signatures: a combinatorial and position-dependent role for histone marks in splicing definition. ... The regulation of alternative splicing is a multilayer process in which chromatin (in blue), long non-coding RNAs (in purple) ... Unexpectedly, in the past 20 years, chromatin and epigenetic modifications have been shown to play an important role in the ...
RFA-RM-20-003: Real Time Chromatin Dynamics and Function (U01 Clinical Trial Not Allowed)
Real Time Chromatin Dynamics and Function (U01 Clinical Trial Not Allowed) RFA-RM-20-003. RMOD ... These include: 1) better means of studying chromatin dynamics in live cells and in complex tissues, which will likely imply a ... A description of how the proposed work will dramatically impact our ability to study and understand aspects of chromatin ... Applications that focus on technologies that do not allow the continuous monitoring of chromatin structure and dynamics in live ...
SARS-CoV-2 restructures host chromatin architecture. - International Association for the Study of Pain (IASP)
These findings show that SARS-CoV-2 acutely rewires host chromatin, facilitating future studies of the long-term epigenomic ... Some viruses restructure host chromatin, influencing gene expression, with implications for disease outcome. Whether this ... finding widespread host chromatin restructuring that features widespread compartment A weakening, A-B mixing, reduced intra-TAD ...
High-Mobility Group Non-Histone Chromatin Protein Proteins
Order High-Mobility Group Non-Histone Chromatin Protein Proteins from many different species. Find the right product on ... High-Mobility Group Non-Histone Chromatin Protein Proteins by Origin. Find High-Mobility Group Non-Histone Chromatin Protein ... High-Mobility Group Non-Histone Chromatin Protein Proteins by Source. Find High-Mobility Group Non-Histone Chromatin Protein ... High-Mobility Group Non-Histone Chromatin Protein Proteins by Protein Type. Find High-Mobility Group Non-Histone Chromatin ...
Physical Biology of Chromatin - D. Jost
Our research tackles important questions regarding the coupling between 3D structure and functions of chromatin. Our objective ... our research addresses generic or specific biological questions on chromatin and gene regulation by developing physical and ... is to provide some universal principles driving chromatin folding and regulation, while contextualizing our approaches to ... Filed under: chromatin, epigenetics, Approches quantitatives de lexpression et de la dynamique des génomes, 3D chromosome ...
Chromatin replication and epigenome maintenance - Staff
Animals, Cell Division, Chromatin, Chromatin Assembly and Disassembly, DNA Replication, Epigenesis, Genetic, Epigenomics, ... Chromatin replication and epigenome maintenance. Research output: Contribution to journal › Review › peer-review ... Chromatin and nuclear structure influence where and when DNA replication initiates, whereas the replication process itself ... During cell division the entire genome must be accurately replicated and the chromatin landscape reproduced on new DNA. ...
Binding proteinsOrganizationDynamicsEmbryonic stemEukaryoticOpen chromatinComplexesHistone modificationsTranscriptionInteractionsModificationsChromosomesGenesTADsTranscriptionalStructureNuclearRegulationGenome-wideObserved in vivoVivoGenomesGenomicNucleosomeProteinAssayEnzymesBiologyLoopsRegulatesNucleosomesCombinatorialInteractionEnhancersInteractsNucleusMechanismsRoleRNAsSubsequentEnablesDomainsCellsComplex
- Chromatin structures are dynamically changed by nucleosome binding proteins . (bvsalud.org)
- NLM's networks, gene regulation, and chromatin research focuses on diverse aspects of gene regulation, such as chromatin organization, DNA conformation, DNA-protein interaction, DNA regulatory elements, and gene regulatory networks. (nih.gov)
- Epigenetic modifications comprise histone modifications, histone variants, nucleosome occupancy and DNA methylation and are crucial for organization of the genome into active chromatin (euchromatin) and repressed chromatin (heterochromatin). (cancer.gov)
- The functional organization of chromatin is important for regulation of transcription, cellular differentiation, and genome maintenance. (cancer.gov)
- This review presents the most recent advances in topological domains' organization of the eukaryote genomes and discusses the relationship to chromatin loop formation. (mdpi.com)
- CTCF protein appears as a central factor of these two organization levels having either a strong insulating role at TAD borders, or a weaker architectural role in chromatin loop formation. (mdpi.com)
- The packaging of chromatin into the nucleus of a eukaryotic cell requires an extraordinary degree of compaction and physical organization. (jic.ac.uk)
- In this review, we focus on these aspects of chromatin organization and discuss novel approaches such as live cell imaging and photobleaching as important tools likely to give significant insights into our understanding of the very dynamic nature of chromatin and chromatin regulatory processes. (jic.ac.uk)
- Stability and function of eukaryotic genomes are closely linked to chromatin structure and organization. (ku.dk)
- Research has revealed a hierarchical organization into chromosomal territories, compartments, domains, and eventually chromatin loops that serve to bring transcriptional enhancers in proximity of their target promoters. (fmi.ch)
- It has become increasingly apparent that proper control of gene expression requires complex organization of DNA at the level of chromatin. (nih.gov)
- Chromatin insulators are DNA-protein complexes that influence gene expression by establishing chromatin domains subject to distinct transcriptional controls, likely through alteration of their spatial organization. (nih.gov)
- With their new method performed in mouse embryonic stem cells, the researchers could confirm the existence of key structural features of chromosomes, notably TADs and chromatin loops. (fmi.ch)
- ATAC-Seq is based on transposase-mediated insertion of sequencing primers into open chromatin regions. (activemotif.com)
- Why study Open Chromatin? (activemotif.com)
- Figure 1: Active Motif's ATAC-Seq assay reliably detects regions of open chromatin. (activemotif.com)
- DNAse-Seq, which has long been the gold standard for generating genome-wide profiles of open chromatin, is shown above in blue. (activemotif.com)
- The underlying DNA sequence of differentially open chromatin regions can be analyzed to identify the most enriched transcription factor binding sites. (activemotif.com)
- The open chromatin profiles are similar to DNAse-Seq profiles generated by the ENCODE consortium. (activemotif.com)
- The Genome Instability and Chromatin Remodeling Section (GICRS), led by Weidong Wang, focuses on three main projects: (1) multiprotein complexes in DNA damage response and genome maintenance, (2) a dual-activity topoisomerase complex and its roles in DNA transcription, mRNA metabolism, coronavirus RNA replication, neurodevelopment and mental disorders, and (3) chromatin remodeling complexes and gene regulation. (nih.gov)
- The GICRS has successfully identified components of the Fanconi anemia core complex, Bloom syndrome complex, ATRX-syndrome complex, FANCM-MHF DNA remodeling complex, RNF8-FAAP20 ubiquitin cascade, several chromatin-remodeling complexes (BAF, PBAF, NURD), and Top3b-TDRD3 topoisomerase complex. (nih.gov)
- Chromatin-remodeling complexes that regulate transcription, replication and repair. (nih.gov)
- In particular, we have shown that non-coding RNAs and histone modifications can communicate with the splicing machinery via recruitment of chromatin/splicing-adaptor complexes. (cnrs.fr)
- Drosophila harbors the largest diversity of known chromatin insulator complexes. (nih.gov)
- ADNP is required for proper establishment of chromatin accessibility, nucleosome configuration, and bivalent histone modifications of developmental genes. (nih.gov)
- Bivalent chromatin is characterized by the simultaneous presence of H3K4me3 and H3K27me3, histone modifications generally associated with transcriptionally active and repressed chromatin, respectively. (nih.gov)
- Histone modifications and histone variants are also involved in regulating chromatin and nucleosome structures. (bvsalud.org)
- While BRD4 association with chromatin is known to de-compact it and activate transcription of key proto-oncogenes, the mechanism involved is currently unknown. (nih.gov)
- Consistent with its role in localized chromatin de-compaction, BRD4 HAT activity regulates transcription at these gene loci as well. (nih.gov)
- BRD4 HAT activity thus plays a key role in chromatin remodeling and transcription. (nih.gov)
- Change in gene expression associated with pancreatic cancer could be attributed to the variation in histone posttranslational modifications leading to subsequent remodeling of the chromatin template during transcription. (nih.gov)
- HiChIP contact analysis shows that global chromatin interactions are dramatically increased during FXR activation. (biorxiv.org)
- We demonstrate that chromatin conformation, including genome-wide interactions, TADs, intra-chromosomal and inter-chromosomal Foxa2-anchored loops, drastically changes upon addition of FXR agonist. (biorxiv.org)
- chromosomal interactions are detected as ligation products after chromatin crosslinking with formaldehyde, which 'glues' proteins and DNA together in an irreversible manner. (fmi.ch)
- Chemical modifications of chromatin-the structure that DNA and proteins called histones are packed into to form chromosomes-can affect gene expression. (nih.gov)
- Unexpectedly, in the past 20 years, chromatin and epigenetic modifications have been shown to play an important role in the regulation of alternative splicing. (cnrs.fr)
- There are two types: heterochromatic which is densely coiled chromatin that appears as nodules in or along chromosomes and contains relatively few genes. (counterbalance.org)
- Chromatin fragments interact with many partners such as the nuclear membrane, other chromosomes or nuclear bodies, but the resulting forces cannot be directly measured in vivo. (mit.edu)
- The researchers went even further to characterize and sort cells based on: their complex patterns of gene expression, the presence or absence of chemical (or epigenetic) marks on their DNA, the way their chromosomes are packaged into chromatin , and their electrical properties. (nih.gov)
- A filamentary assembly of DNA and a protein structure base, primarily histone, chromatin is the form in which genes appear on chromosomes. (nih.gov)
- Euchromatic is the less coiled and genetically active portion of chromatin that is largely composed of genes. (counterbalance.org)
- Thus, our work revealed a key role of ADNP in the establishment of local chromatin landscape and structure of developmental genes by association with BRG1 and CHD4. (nih.gov)
- Here, we show that bivalent chromatin does not poise genes for rapid activation but protects promoters from de novo DNA methylation. (nih.gov)
- This raises the question of whether structures such as TADs and chromatin loops detected by 3C methods actually exist in living cells. (fmi.ch)
- Methyl-CpG binding protein 2 (MeCP2) is a multifunctional epigenetic reader playing a role in transcriptional regulation and chromatin structure, which was linked to Rett syndrome in humans. (nih.gov)
- Thus, these studies reveal a transcriptional mechanism of intestinal cell specification, coordinated by the interaction between the chromatin remodeling complex SWI/SNF and Mediator kinase. (jci.org)
- By manipulating DNA sequences that guide genome-folding, researchers confirm an existing model of chromatin structure inside the nucleus. (the-scientist.com)
- higher order chromatin structure. (nih.gov)
- 2021). We are currently addressing the question of how LSH molecular function alters chromatin structure and maintains genomic stability and cellular differentiation. (cancer.gov)
- An emerging class of enhancer-like lncRNAs may link chromosome structure to chromatin state and establish active chromatin domains. (ca.gov)
- changes in the chromatin structure of a gene were considered to be the passive consequence of the binding of these factors. (nih.gov)
- However, it is now clear that chromatin structure is an integral part of the process of gene regulation. (nih.gov)
- Our research tackles important questions regarding the coupling between 3D structure and functions of chromatin. (ens-lyon.fr)
- Chromatin and nuclear structure influence where and when DNA replication initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. (ku.dk)
- Micrococcal nuclease digestion showed an altered chromatin structure in hPaf1/PD2-KD cells. (nih.gov)
- Crick's notes for a seminar presentation on September 23, 1976 at the Salk Institute for Biological Studies on the structure of chromatin. (nih.gov)
- Crick had been interested in chromatin since he conducted studies of its structure with Alexander Rich in the mid-1950s. (nih.gov)
- Chromatin structure related to oncogenesis. (bvsalud.org)
- In this review article, we discuss the current progress toward understanding the relationship between chromatin structure and cancer development. (bvsalud.org)
- We have previously shown that pioneer factor Foxa2 opens chromatin for binding of nuclear receptors FXR and LXRα during acute ligand activation. (biorxiv.org)
- Overall, our results suggest that hPaf1/PD2 in association with MLL1 regulates methylation of H3K4 residues, as well as interacts and regulates nuclear shuttling of chromatin remodeling protein CHD1, facilitating its function in pancreatic cancer cells. (nih.gov)
- Undifferentiated tumours with histologic grade III, nuclear grade I, no lymphocytic infiltrate and involvement of overlying skin, nipple and areola were more often associated with low sex chromatin incidence. (who.int)
- The regulation of alternative splicing is a multilayer process in which chromatin (in blue), long non-coding RNAs (in purple) and RNA binding factors (in orange) work in an integrated way to establish the final splicing outcome. (cnrs.fr)
- In close connection with experimental biology, our research addresses generic or specific biological questions on chromatin and gene regulation by developing physical and computational models. (ens-lyon.fr)
- Our objective is to provide some universal principles driving chromatin folding and regulation, while contextualizing our approaches to fundamental, specific problems of 3D genomics. (ens-lyon.fr)
- Taking advantage of available genome-wide ChIP-seq and RNA-seq data from the ENCODE and ROADMAP Epigenomics project, we are now identifying the chromatin signatures that differentially mark included and excluded exons, to study what these events have in common in order to depict novel regulatory mechanisms of alternative splicing and improve the current prediction tools by adding to the splicing code the information embedded at the chromatin level. (cnrs.fr)
- This assay provides genome-wide profiles of open and accessible regions of chromatin that are indicative of active regulatory regions. (activemotif.com)
Observed in vivo1
- To conclude, the confined trajectories we observed in vivo reflect local interaction on chromatin. (mit.edu)
- Is it possible to extract tethering forces applied on chromatin from the statistics of a single locus trajectories imaged in vivo? (mit.edu)
- BRD4 HAT activity and H3K122 acetylation is responsible for nucleosome eviction and opening of the chromatin, as evidenced by the ability of BRD4, but not BRD4 HAT mutants, to evict nucleosomes both in vitro and in vivo. (nih.gov)
- Recent investigations on 3D chromatin folding revealed that the eukaryote genomes are both highly compartmentalized and extremely dynamic. (mdpi.com)
- The nucleosome , the primary unit of chromatin , consists of DNA and histone proteins , and is important for the maintenance of genomic DNA . (bvsalud.org)
- Histone mutations are present in many types of cancers , suggesting that chromatin and/or nucleosome structures could be closely related to cancer development. (bvsalud.org)
- Detailed analyses of cohesin's movements indicate how this protein complex hauls chromatin fibers to package DNA into loops. (the-scientist.com)
- Find High-Mobility Group Non-Histone Chromatin Protein Proteins for a variety of species such as anti-Candida albicans High-Mobility Group Non-Histone Chromatin Protein, anti-Emericella nidulans High-Mobility Group Non-Histone Chromatin Protein, anti-Schizosaccharomyces pombe High-Mobility Group Non-Histone Chromatin Protein. (antibodies-online.com)
- Find High-Mobility Group Non-Histone Chromatin Protein Proteins validated for a specific application such as ELISA. (antibodies-online.com)
- Also, a reduction in hPaf1 level resulted in reduced MLL1 expression and a corresponding decrease in the level of CHD1 (Chromohelicase DNA-binding protein 1), an ATPase dependent chromatin remodeling enzyme that specifically binds to H3K4 di and trimethyl marks. (nih.gov)
- Here, we present single-cell combinatorial indexing on Microbiopsies Assigned to Positions for the Assay for Transposase Accessible Chromatin, or sciMAP-ATAC, as a method for highly scalable, spatially resolved, single-cell profiling of chromatin states. (nature.com)
- Figure 2: Active Motif's ATAC-Seq assay distinguishes sample groups by identifying chromatin regions that are differentially open. (activemotif.com)
- Genome Survey of Chromatin-Modifying Enzymes in Threespine Stickleback: A Crucial Epigenetic Toolkit for Adaptation? (portlandpress.com)
- The National Cancer Institute (NCI) is seeking an outstanding, internationally recognized, and visionary leader in the field of chromatin biology to direct an internationally recognized research program in the current Laboratory of Receptor Biology and Gene Expression (LRBGE) in the NCI Center for Cancer Research (CCR). (nih.gov)
- Ligand-treated livers exhibit extensive redistribution of topological associated domains (TAD and substantial increase in Foxa2-anchored loops, suggesting Foxa2 is involved in dynamic chromatin conformational changes. (biorxiv.org)
- Human RNA polymerase II-association factor 1 (hPaf1/PD2) regulates histone methylation and chromatin remodeling in pancreatic cancer. (nih.gov)
- Required for DNA-binding by the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. (antibodies-online.com)
- Splicing-associated chromatin signatures: a combinatorial and position-dependent role for histone marks in splicing definition. (cnrs.fr)
- Inhibiting its interaction with chromatin has been a successful therapeutic strategy against many cancers including acute myeloid leukemia, Burkitt's lymphoma, breast, colon and lung cancer. (nih.gov)
- Our objectives now are to better understand the role of chromatin, enhancers and long non-coding RNAs in the onset and maintenance of a cell-specific splicing program, using as an inducible cell reprogramming model system the epithelial-to-mesenchymal transition (EMT), a process involved in early development and cancer metastasis. (cnrs.fr)
- Here we show that ADNP interacts with two chromatin remodelers, BRG1 and CHD4. (nih.gov)
- We apply sciMAP-ATAC to assess cortical lamination in the adult mouse primary somatosensory cortex and in the human primary visual cortex, where we produce spatial trajectories and integrate our data with non-spatial single-nucleus RNA and other chromatin accessibility single-cell datasets. (nature.com)
- However, how ADNP-regulated chromatin mechanisms control gene expression and stem cell fate commitment remains unclear. (nih.gov)
- Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. (ku.dk)
- Our group is looking for a postdoctoral candidate who has an interest in the relationship between chromatin and its role in human disease. (cancer.gov)
- Active chromatin and noncoding RNAs: an intimate relationship. (ca.gov)
- Home › About CIRM › Our Publications › Grantee publications › Active chromatin and noncoding RNAs: an intimate relationship. (ca.gov)
- While silent chromatin has been associated with long noncoding RNAs (lncRNAs) for some time, new studies suggest that noncoding RNAs also modulate the active chromatin state. (ca.gov)
- Moreover, recent studies have shown that loss of insulator activity in IDH1 mutant gliomas and T cell acute lymphoblastic leukemias leads to disruption of boundaries between chromatin domains and subsequent oncogene activation. (nih.gov)
- We hypothesized that Foxa2 also enables chromatin conformational changes during ligand activation. (biorxiv.org)
- Using colorectal cancer cells, the team found that chromatin reader domains of UHRF1 maintain cancerous DNA hypermethylation. (novusbio.com)
- The Mediator kinase module bound and phosphorylated key components of the chromatin remodeling complex switch/sucrose non-fermentable (SWI/SNF) in intestinal epithelial cells. (jci.org)
- Here we characterized the 3D genome and epigenome of human cells after SARS-CoV-2 infection, finding widespread host chromatin restructuring that features widespread compartment A weakening, A-B mixing, reduced intra-TAD contacts and decreased H3K27ac euchromatin modification levels. (iasp-pain.org)
- This protocol describes a procedure for generating and purifying wild type and mutant versions of the human INO80 chromatin remodeling complex. (jove.com)