DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.DNA: 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).Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.DNA, Single-Stranded: A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.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.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Poly(A)-Binding Proteins: Proteins that bind to the 3' polyadenylated region of MRNA. When complexed with RNA the proteins serve an array of functions such as stabilizing the 3' end of RNA, promoting poly(A) synthesis and stimulating mRNA translation.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Nuclear Proteins: 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.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.Bacterial Proteins: Proteins found in any species of bacterium.DNA Helicases: 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.DNA Replication: The process by which a DNA molecule is duplicated.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Cell Line: Established cell cultures that have the potential to propagate indefinitely.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.Viral Proteins: Proteins found in any species of virus.Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Replication Protein A: A single-stranded DNA-binding protein that is found in EUKARYOTIC CELLS. It is required for DNA REPLICATION; DNA REPAIR; and GENETIC RECOMBINATION.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Zinc Fingers: Motifs in DNA- and RNA-binding proteins whose amino acids are folded into a single structural unit around a zinc atom. In the classic zinc finger, one zinc atom is bound to two cysteines and two histidines. In between the cysteines and histidines are 12 residues which form a DNA binding fingertip. By variations in the composition of the sequences in the fingertip and the number and spacing of tandem repeats of the motif, zinc fingers can form a large number of different sequence specific binding sites.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.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.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.HeLa Cells: 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.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Plasmids: 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.Cell Nucleus: 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)DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.RNA, Messenger: 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.Poly T: A group of thymine nucleotides in which the phosphate residues of each thymine nucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Tacrolimus Binding Proteins: A family of immunophilin proteins that bind to the immunosuppressive drugs TACROLIMUS (also known as FK506) and SIROLIMUS. EC 5.2.1.-Kinetics: The rate dynamics in chemical or physical systems.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.Protein Conformation: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).Poly(A)-Binding Protein I: A poly(A) binding protein that has a variety of functions such as mRNA stabilization and protection of RNA from nuclease activity. Although poly(A) binding protein I is considered a major cytoplasmic RNA-binding protein it is also found in the CELL NUCLEUS and may be involved in transport of mRNP particles.CCAAT-Enhancer-Binding Proteins: A class of proteins that were originally identified by their ability to bind the DNA sequence CCAAT. The typical CCAAT-enhancer binding protein forms dimers and consists of an activation domain, a DNA-binding basic region, and a leucine-rich dimerization domain (LEUCINE ZIPPERS). CCAAT-BINDING FACTOR is structurally distinct type of CCAAT-enhancer binding protein consisting of a trimer of three different subunits.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Transfection: 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.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.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.NFI Transcription Factors: Transcription factors that were originally identified as site-specific DNA-binding proteins essential for DNA REPLICATION by ADENOVIRUSES. They play important roles in MAMMARY GLAND function and development.DNA Footprinting: 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)Leucine Zippers: DNA-binding motifs formed from two alpha-helixes which intertwine for about eight turns into a coiled coil and then bifurcate to form Y shaped structures. Leucines occurring in heptad repeats end up on the same sides of the helixes and are adjacent to each other in the stem of the Y (the "zipper" region). The DNA-binding residues are located in the bifurcated region of the Y.Binding, Competitive: The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.Helix-Turn-Helix Motifs: The first DNA-binding protein motif to be recognized. Helix-turn-helix motifs were originally identified in bacterial proteins but have since been found in hundreds of DNA-BINDING PROTEINS from both eukaryotes and prokaryotes. They are constructed from two alpha helices connected by a short extended chain of amino acids, which constitute the "turn." The two helices are held at a fixed angle, primarily through interactions between the two helices. (From Alberts et al., Molecular Biology of the Cell, 3d ed, p408-9)Insulin-Like Growth Factor Binding Proteins: A family of soluble proteins that bind insulin-like growth factors and modulate their biological actions at the cellular level. (Int J Gynaecol Obstet 1992;39(1):3-9)Molecular Weight: The sum of the weight of all the atoms in a molecule.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Y-Box-Binding Protein 1: Y-box-binding protein 1 was originally identified as a DNA-binding protein that interacts with Y-box PROMOTER REGIONS of MHC CLASS II GENES. It is a highly conserved transcription factor that regulates expression of a wide variety of GENES.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Consensus Sequence: A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.Fungal Proteins: Proteins found in any species of fungus.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Chromatography, Affinity: A chromatographic technique that utilizes the ability of biological molecules to bind to certain ligands specifically and reversibly. It is used in protein biochemistry. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Homeodomain Proteins: Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL).Macromolecular Substances: Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.Cyclic AMP Response Element-Binding Protein: A protein that has been shown to function as a calcium-regulated transcription factor as well as a substrate for depolarization-activated CALCIUM-CALMODULIN-DEPENDENT PROTEIN KINASES. This protein functions to integrate both calcium and cAMP signals.Heterogeneous-Nuclear Ribonucleoproteins: A family of ribonucleoproteins that were originally found as proteins bound to nascent RNA transcripts in the form of ribonucleoprotein particles. Although considered ribonucleoproteins they are primarily classified by their protein component. They are involved in a variety of processes such as packaging of RNA and RNA TRANSPORT within the nucleus. A subset of heterogeneous-nuclear ribonucleoproteins are involved in additional functions such as nucleocytoplasmic transport (ACTIVE TRANSPORT, CELL NUCLEUS) of RNA and mRNA stability in the CYTOPLASM.DNA Primase: A single-stranded DNA-dependent RNA polymerase that functions to initiate, or prime, DNA synthesis by synthesizing oligoribonucleotide primers. EC 2.7.7.-.Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Fatty Acid-Binding Proteins: Intracellular proteins that reversibly bind hydrophobic ligands including: saturated and unsaturated FATTY ACIDS; EICOSANOIDS; and RETINOIDS. They are considered a highly conserved and ubiquitously expressed family of proteins that may play a role in the metabolism of LIPIDS.Polydeoxyribonucleotides: A group of 13 or more deoxyribonucleotides in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Structure-Activity Relationship: The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Helix-Loop-Helix Motifs: Recurring supersecondary structures characterized by 20 amino acids folding into two alpha helices connected by a non-helical "loop" segment. They are found in many sequence-specific DNA-BINDING PROTEINS and in CALCIUM-BINDING PROTEINS.Ultraviolet Rays: That portion of the electromagnetic spectrum immediately below the visible range and extending into the x-ray frequencies. The longer wavelengths (near-UV or biotic or vital rays) are necessary for the endogenous synthesis of vitamin D and are also called antirachitic rays; the shorter, ionizing wavelengths (far-UV or abiotic or extravital rays) are viricidal, bactericidal, mutagenic, and carcinogenic and are used as disinfectants.Octamer Transcription Factor-1: A ubiquitously expressed octamer transcription factor that regulates GENETIC TRANSCRIPTION of SMALL NUCLEAR RNA; IMMUNOGLOBULIN GENES; and HISTONE H2B genes.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Signal Transduction: 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.Basic-Leucine Zipper Transcription Factors: A large superfamily of transcription factors that contain a region rich in BASIC AMINO ACID residues followed by a LEUCINE ZIPPER domain.Genes, Reporter: Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.Deoxyribonuclease I: 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.Pseudomonas Phages: Viruses whose host is Pseudomonas. A frequently encountered Pseudomonas phage is BACTERIOPHAGE PHI 6.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Telomere-Binding Proteins: Proteins that specifically bind to TELOMERES. Proteins in this class include those that perform functions such as telomere capping, telomere maintenance and telomere stabilization.Drosophila Proteins: Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.DNA-Directed DNA Polymerase: DNA-dependent DNA polymerases found in bacteria, animal and plant cells. During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.G-Box Binding Factors: A family of transcription factors found primarily in PLANTS that bind to the G-box DNA sequence CACGTG or to a consensus sequence CANNTG.Host Cell Factor C1: A cellular transcriptional coactivator that was originally identified by its requirement for the stable assembly IMMEDIATE-EARLY PROTEINS of the HERPES SIMPLEX VIRUS. It is a nuclear protein that is a transcriptional coactivator for a number of transcription factors including VP16 PROTEIN; GA-BINDING PROTEIN; EARLY GROWTH RESPONSE PROTEIN 2; and E2F4 TRANSCRIPTION FACTOR. It also interacts with and stabilizes HERPES SIMPLEX VIRUS PROTEIN VMW65 and helps regulate GENETIC TRANSCRIPTION of IMMEDIATE-EARLY GENES in HERPES SIMPLEX VIRUS.Sulfolobus: A genus of aerobic, chemolithotrophic, coccoid ARCHAEA whose organisms are thermoacidophilic. Its cells are highly irregular in shape, often lobed, but occasionally spherical. It has worldwide distribution with organisms isolated from hot acidic soils and water. Sulfur is used as an energy source.Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.Templates, Genetic: Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Protein Structure, Secondary: The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.Two-Hybrid System Techniques: Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.Immunoglobulin J Recombination Signal Sequence-Binding Protein: A ubiquitously expressed sequence-specific transcriptional repressor that is normally the target of signaling by NOTCH PROTEINS.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.Chromatin: The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.Poly(A)-Binding Protein II: A poly(A) binding protein that is involved in promoting the extension of the poly A tails of MRNA. The protein requires a minimum of ten ADENOSINE nucleotides in order for binding to mRNA. Once bound it works in conjunction with CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR to stimulate the rate of poly A synthesis by POLY A POLYMERASE. Once poly-A tails reach around 250 nucleotides in length poly(A) binding protein II no longer stimulates POLYADENYLATION. Mutations within a GCG repeat region in the gene for poly(A) binding protein II have been shown to cause the disease MUSCULAR DYSTROPHY, OCULOPHARYNGEAL.High Mobility Group Proteins: A family of low-molecular weight, non-histone proteins found in chromatin.TATA-Box Binding Protein: A general transcription factor that plays a major role in the activation of eukaryotic genes transcribed by RNA POLYMERASES. It binds specifically to the TATA BOX promoter element, which lies close to the position of transcription initiation in RNA transcribed by RNA POLYMERASE II. Although considered a principal component of TRANSCRIPTION FACTOR TFIID it also takes part in general transcription factor complexes involved in RNA POLYMERASE I and RNA POLYMERASE III transcription.Cell Extracts: Preparations of cell constituents or subcellular materials, isolates, or substances.Tumor Cells, Cultured: Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.Adenoviruses, Human: Species of the genus MASTADENOVIRUS, causing a wide range of diseases in humans. Infections are mostly asymptomatic, but can be associated with diseases of the respiratory, ocular, and gastrointestinal systems. Serotypes (named with Arabic numbers) have been grouped into species designated Human adenovirus A-F.DNA Repair: 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.Replication Origin: A unique DNA sequence of a replicon at which DNA REPLICATION is initiated and proceeds bidirectionally or unidirectionally. It contains the sites where the first separation of the complementary strands occurs, a primer RNA is synthesized, and the switch from primer RNA to DNA synthesis takes place. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)DNA Damage: 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.Adenosine Triphosphatases: 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.DNA Polymerase III: A DNA-dependent DNA polymerase characterized in E. coli and other lower organisms but may be present in higher organisms. Use also for a more complex form of DNA polymerase III designated as DNA polymerase III* or pol III* which is 15 times more active biologically than DNA polymerase I in the synthesis of DNA. This polymerase has both 3'-5' and 5'-3' exonuclease activities, is inhibited by sulfhydryl reagents, and has the same template-primer dependence as pol II. EC 2.7.7.7.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).AT Rich Sequence: A nucleic acid sequence that contains an above average number of ADENINE and THYMINE bases.Inhibitor of Differentiation Proteins: Inhibitor of differentiation proteins are negative regulators of BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS. They inhibit CELL DIFFERENTIATION and induce CELL PROLIFERATION by modulating different CELL CYCLE regulators.TATA Box: A conserved A-T rich sequence which is contained in promoters for RNA polymerase II. The segment is seven base pairs long and the nucleotides most commonly found are TATAAAA.Rec A Recombinases: A family of recombinases initially identified in BACTERIA. They catalyze the ATP-driven exchange of DNA strands in GENETIC RECOMBINATION. The product of the reaction consists of a duplex and a displaced single-stranded loop, which has the shape of the letter D and is therefore called a D-loop structure.Transcription Factor AP-1: A multiprotein complex composed of the products of c-jun and c-fos proto-oncogenes. These proteins must dimerize in order to bind to the AP-1 recognition site, also known as the TPA-responsive element (TRE). AP-1 controls both basal and inducible transcription of several genes.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Response Elements: 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.Insulin-Like Growth Factor Binding Protein 3: One of the six homologous soluble proteins that bind insulin-like growth factors (SOMATOMEDINS) and modulate their mitogenic and metabolic actions at the cellular level.Calcium-Binding Proteins: Proteins to which calcium ions are bound. They can act as transport proteins, regulator proteins, or activator proteins. They typically contain EF HAND MOTIFS.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Gene Expression Regulation, Developmental: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.Periplasmic Binding Proteins: Periplasmic proteins that scavenge or sense diverse nutrients. In the bacterial environment they usually couple to transporters or chemotaxis receptors on the inner bacterial membrane.Bacteriophage T7: Virulent bacteriophage and type species of the genus T7-like phages, in the family PODOVIRIDAE, that infects E. coli. It consists of linear double-stranded DNA, terminally redundant, and non-permuted.Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.COS Cells: CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Chromatin Immunoprecipitation: 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.Poly dA-dT: Polydeoxyribonucleotides made up of deoxyadenine nucleotides and thymine nucleotides. Present in DNA preparations isolated from crab species. Synthetic preparations have been used extensively in the study of DNA.Hemizygote: An individual having only one allele at a given locus because of the loss of the other allele through a mutation (e.g., CHROMOSOME DELETION).CREB-Binding Protein: A member of the p300-CBP transcription factor family that was initially identified as a binding partner for CAMP RESPONSE ELEMENT-BINDING PROTEIN. Mutations in CREB-binding protein are associated with RUBINSTEIN-TAYBI SYNDROME.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Bacteriophage phi X 174: The type species of the genus MICROVIRUS. A prototype of the small virulent DNA coliphages, it is composed of a single strand of supercoiled circular DNA, which on infection, is converted to a double-stranded replicative form by a host enzyme.Cross-Linking Reagents: Reagents with two reactive groups, usually at opposite ends of the molecule, that are capable of reacting with and thereby forming bridges between side chains of amino acids in proteins; the locations of naturally reactive areas within proteins can thereby be identified; may also be used for other macromolecules, like glycoproteins, nucleic acids, or other.Tacrolimus Binding Protein 1A: A 12-KDa tacrolimus binding protein that is found associated with and may modulate the function of calcium release channels. It is a peptidyl-prolyl cis/trans isomerase which is inhibited by both tacrolimus (commonly called FK506) and SIROLIMUS.Luciferases: Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.Precipitin Tests: Serologic tests in which a positive reaction manifested by visible CHEMICAL PRECIPITATION occurs when a soluble ANTIGEN reacts with its precipitins, i.e., ANTIBODIES that can form a precipitate.Drosophila: A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.Oligonucleotide Probes: Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.DNA Probes: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.Latent TGF-beta Binding Proteins: A family of secreted multidomain proteins that were originally identified by their association with the latent form of TRANSFORMING GROWTH FACTORS. They interact with a variety of EXTRACELLULAR MATRIX PROTEINS and may play a role in the regulation of TGB-beta bioavailability.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.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.Virus Replication: The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.Point Mutation: A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.DNA, Superhelical: Circular duplex DNA isolated from viruses, bacteria and mitochondria in supercoiled or supertwisted form. This superhelical DNA is endowed with free energy. During transcription, the magnitude of RNA initiation is proportional to the DNA superhelicity.Proto-Oncogene Proteins: Products of proto-oncogenes. Normally they do not have oncogenic or transforming properties, but are involved in the regulation or differentiation of cell growth. They often have protein kinase activity.NF-kappa B: Ubiquitous, inducible, nuclear transcriptional activator that binds to enhancer elements in many different cell types and is activated by pathogenic stimuli. The NF-kappa B complex is a heterodimer composed of two DNA-binding subunits: NF-kappa B1 and relA.Ribonucleoproteins: Complexes of RNA-binding proteins with ribonucleic acids (RNA).RNA: 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)RNA Nucleotidyltransferases: Enzymes that catalyze the template-directed incorporation of ribonucleotides into an RNA chain. EC 2.7.7.-.Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.Insulin-Like Growth Factor Binding Protein 2: One of the six homologous soluble proteins that bind insulin-like growth factors (SOMATOMEDINS) and modulate their mitogenic and metabolic actions at the cellular level.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.Zinc: A metallic element of atomic number 30 and atomic weight 65.38. It is a necessary trace element in the diet, forming an essential part of many enzymes, and playing an important role in protein synthesis and in cell division. Zinc deficiency is associated with ANEMIA, short stature, HYPOGONADISM, impaired WOUND HEALING, and geophagia. It is known by the symbol Zn.Archaeal Proteins: Proteins found in any species of archaeon.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.Integration Host Factors: Bacterial proteins that are used by BACTERIOPHAGES to incorporate their DNA into the DNA of the "host" bacteria. They are DNA-binding proteins that function in genetic recombination as well as in transcriptional and translational regulation.DNA, Circular: Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)Blotting, Northern: Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Deinococcus: A genus of gram-positive aerobic cocci found in the soil, that is highly resistant to radiation, especially ionizing radiation (RADIATION, IONIZING). Deinococcus radiodurans is the type species.Genetic Complementation Test: A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.Adenoviridae: A family of non-enveloped viruses infecting mammals (MASTADENOVIRUS) and birds (AVIADENOVIRUS) or both (ATADENOVIRUS). Infections may be asymptomatic or result in a variety of diseases.Immunoblotting: Immunologic method used for detecting or quantifying immunoreactive substances. The substance is identified by first immobilizing it by blotting onto a membrane and then tagging it with labeled antibodies.Erythroid-Specific DNA-Binding Factors: A group of transcription factors that were originally described as being specific to ERYTHROID CELLS.Exodeoxyribonucleases: A family of enzymes that catalyze the exonucleolytic cleavage of DNA. It includes members of the class EC 3.1.11 that produce 5'-phosphomonoesters as cleavage products.Factor For Inversion Stimulation Protein: A highly abundant DNA binding protein whose expression is strongly correlated with the growth phase of bacteria. The protein plays a role in regulating DNA topology and activation of RIBOSOMAL RNA transcription. It was originally identified as a factor required for inversion stimulation by the Hin recombinase of SALMONELLA and Gin site-specific recombinase of BACTERIOPHAGE MU.Nerve Tissue ProteinsProtein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.PhosphoproteinsGenes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.T-Phages: A series of 7 virulent phages which infect E. coli. The T-even phages T2, T4; (BACTERIOPHAGE T4), and T6, and the phage T5 are called "autonomously virulent" because they cause cessation of all bacterial metabolism on infection. Phages T1, T3; (BACTERIOPHAGE T3), and T7; (BACTERIOPHAGE T7) are called "dependent virulent" because they depend on continued bacterial metabolism during the lytic cycle. The T-even phages contain 5-hydroxymethylcytosine in place of ordinary cytosine in their DNA.Arabidopsis Proteins: Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.Cullin Proteins: A family of structurally related proteins that were originally discovered for their role in cell-cycle regulation in CAENORHABDITIS ELEGANS. They play important roles in regulation of the CELL CYCLE and as components of UBIQUITIN-PROTEIN LIGASES.Chromomycins: A complex of several closely related glycosidic antibiotics from Streptomyces griseus. The major component, CHROMOMYCIN A3, is used as a fluorescent stain of DNA where it attaches and inhibits RNA synthesis. It is also used as an antineoplastic agent, especially for solid tumors.3T3 Cells: Cell lines whose original growing procedure consisted being transferred (T) every 3 days and plated at 300,000 cells per plate (J Cell Biol 17:299-313, 1963). Lines have been developed using several different strains of mice. Tissues are usually fibroblasts derived from mouse embryos but other types and sources have been developed as well. The 3T3 lines are valuable in vitro host systems for oncogenic virus transformation studies, since 3T3 cells possess a high sensitivity to CONTACT INHIBITION.Cercopithecus aethiops: A species of CERCOPITHECUS containing three subspecies: C. tantalus, C. pygerythrus, and C. sabeus. They are found in the forests and savannah of Africa. The African green monkey (C. pygerythrus) is the natural host of SIMIAN IMMUNODEFICIENCY VIRUS and is used in AIDS research.Insulin-Like Growth Factor Binding Protein 1: One of the six homologous proteins that specifically bind insulin-like growth factors (SOMATOMEDINS) and modulate their mitogenic and metabolic actions. The function of this protein is not completely defined. However, several studies demonstrate that it inhibits IGF binding to cell surface receptors and thereby inhibits IGF-mediated mitogenic and cell metabolic actions. (Proc Soc Exp Biol Med 1993;204(1):4-29)Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.Thermoproteus: A genus of obligately anaerobic ARCHAEA, in the family THERMOPROTEACEAE. They are found in acidic hot springs and water holes.Magnetic Resonance Spectroscopy: Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).

The surface ectoderm is essential for nephric duct formation in intermediate mesoderm. (1/69904)

The nephric duct is the first epithelial tubule to differentiate from intermediate mesoderm that is essential for all further urogenital development. In this study we identify the domain of intermediate mesoderm that gives rise to the nephric duct and demonstrate that the surface ectoderm is required for its differentiation. Removal of the surface ectoderm resulted in decreased levels of Sim-1 and Pax-2 mRNA expression in mesenchymal nephric duct progenitors, and caused inhibition of nephric duct formation and subsequent kidney development. The surface ectoderm expresses BMP-4 and we show that it is required for the maintenance of high-level BMP-4 expression in lateral plate mesoderm. Addition of a BMP-4-coated bead to embryos lacking the surface ectoderm restored normal levels of Sim-1 and Pax-2 mRNA expression in nephric duct progenitors, nephric duct formation and the initiation of nephrogenesis. Thus, BMP-4 signaling can substitute for the surface ectoderm in supporting nephric duct morphogenesis. Collectively, these data suggest that inductive interactions between the surface ectoderm, lateral mesoderm and intermediate mesoderm are essential for nephric duct formation and the initiation of urogenital development.  (+info)

Separation of shoot and floral identity in Arabidopsis. (2/69904)

The overall morphology of an Arabidopsis plant depends on the behaviour of its meristems. Meristems derived from the shoot apex can develop into either shoots or flowers. The distinction between these alternative fates requires separation between the function of floral meristem identity genes and the function of an antagonistic group of genes, which includes TERMINAL FLOWER 1. We show that the activities of these genes are restricted to separate domains of the shoot apex by different mechanisms. Meristem identity genes, such as LEAFY, APETALA 1 and CAULIFLOWER, prevent TERMINAL FLOWER 1 transcription in floral meristems on the apex periphery. TERMINAL FLOWER 1, in turn, can inhibit the activity of meristem identity genes at the centre of the shoot apex in two ways; first by delaying their upregulation, and second, by preventing the meristem from responding to LEAFY or APETALA 1. We suggest that the wild-type pattern of TERMINAL FLOWER 1 and floral meristem identity gene expression depends on the relative timing of their upregulation.  (+info)

Novel regulation of the homeotic gene Scr associated with a crustacean leg-to-maxilliped appendage transformation. (3/69904)

Homeotic genes are known to be involved in patterning morphological structures along the antero-posterior axis of insects and vertebrates. Because of their important roles in development, changes in the function and expression patterns of homeotic genes may have played a major role in the evolution of different body plans. For example, it has been proposed that during the evolution of several crustacean lineages, changes in the expression patterns of the homeotic genes Ultrabithorax and abdominal-A have played a role in transformation of the anterior thoracic appendages into mouthparts termed maxillipeds. This homeotic-like transformation is recapitulated at the late stages of the direct embryonic development of the crustacean Porcellio scaber (Oniscidea, Isopoda). Interestingly, this morphological change is associated with apparent novelties both in the transcriptional and post-transcriptional regulation of the Porcellio scaber ortholog of the Drosophila homeotic gene, Sex combs reduced (Scr). Specifically, we find that Scr mRNA is present in the second maxillary segment and the first pair of thoracic legs (T1) in early embryos, whereas protein accumulates only in the second maxillae. In later stages, however, high levels of SCR appear in the T1 legs, which correlates temporally with the transformation of these appendages into maxillipeds. Our observations provide further insight into the process of the homeotic leg-to-maxilliped transformation in the evolution of crustaceans and suggest a novel regulatory mechanism for this process in this group of arthropods.  (+info)

Apontic binds the translational repressor Bruno and is implicated in regulation of oskar mRNA translation. (4/69904)

The product of the oskar gene directs posterior patterning in the Drosophila oocyte, where it must be deployed specifically at the posterior pole. Proper expression relies on the coordinated localization and translational control of the oskar mRNA. Translational repression prior to localization of the transcript is mediated, in part, by the Bruno protein, which binds to discrete sites in the 3' untranslated region of the oskar mRNA. To begin to understand how Bruno acts in translational repression, we performed a yeast two-hybrid screen to identify Bruno-interacting proteins. One interactor, described here, is the product of the apontic gene. Coimmunoprecipitation experiments lend biochemical support to the idea that Bruno and Apontic proteins physically interact in Drosophila. Genetic experiments using mutants defective in apontic and bruno reveal a functional interaction between these genes. Given this interaction, Apontic is likely to act together with Bruno in translational repression of oskar mRNA. Interestingly, Apontic, like Bruno, is an RNA-binding protein and specifically binds certain regions of the oskar mRNA 3' untranslated region.  (+info)

Transcriptional repression by the Drosophila giant protein: cis element positioning provides an alternative means of interpreting an effector gradient. (5/69904)

Early developmental patterning of the Drosophila embryo is driven by the activities of a diverse set of maternally and zygotically derived transcription factors, including repressors encoded by gap genes such as Kruppel, knirps, giant and the mesoderm-specific snail. The mechanism of repression by gap transcription factors is not well understood at a molecular level. Initial characterization of these transcription factors suggests that they act as short-range repressors, interfering with the activity of enhancer or promoter elements 50 to 100 bp away. To better understand the molecular mechanism of short-range repression, we have investigated the properties of the Giant gap protein. We tested the ability of endogenous Giant to repress when bound close to the transcriptional initiation site and found that Giant effectively represses a heterologous promoter when binding sites are located at -55 bp with respect to the start of transcription. Consistent with its role as a short-range repressor, as the binding sites are moved to more distal locations, repression is diminished. Rather than exhibiting a sharp 'step-function' drop-off in activity, however, repression is progressively restricted to areas of highest Giant concentration. Less than a two-fold difference in Giant protein concentration is sufficient to determine a change in transcriptional status of a target gene. This effect demonstrates that Giant protein gradients can be differentially interpreted by target promoters, depending on the exact location of the Giant binding sites within the gene. Thus, in addition to binding site affinity and number, cis element positioning within a promoter can affect the response of a gene to a repressor gradient. We also demonstrate that a chimeric Gal4-Giant protein lacking the basic/zipper domain can specifically repress reporter genes, suggesting that the Giant effector domain is an autonomous repression domain.  (+info)

A Drosophila doublesex-related gene, terra, is involved in somitogenesis in vertebrates. (6/69904)

The Drosophila doublesex (dsx) gene encodes a transcription factor that mediates sex determination. We describe the characterization of a novel zebrafish zinc-finger gene, terra, which contains a DNA binding domain similar to that of the Drosophila dsx gene. However, unlike dsx, terra is transiently expressed in the presomitic mesoderm and newly formed somites. Expression of terra in presomitic mesoderm is restricted to cells that lack expression of MyoD. In vivo, terra expression is reduced by hedgehog but enhanced by BMP signals. Overexpression of terra induces rapid apoptosis both in vitro and in vivo, suggesting that a tight regulation of terra expression is required during embryogenesis. Terra has both human and mouse homologs and is specifically expressed in mouse somites. Taken together, our findings suggest that terra is a highly conserved protein that plays specific roles in early somitogenesis of vertebrates.  (+info)

Requirement of a novel gene, Xin, in cardiac morphogenesis. (7/69904)

A novel gene, Xin, from chick (cXin) and mouse (mXin) embryonic hearts, may be required for cardiac morphogenesis and looping. Both cloned cDNAs have a single open reading frame, encoding proteins with 2,562 and 1,677 amino acids for cXin and mXin, respectively. The derived amino acid sequences share 46% similarity. The overall domain structures of the predicted cXin and mXin proteins, including proline-rich regions, 16 amino acid repeats, DNA-binding domains, SH3-binding motifs and nuclear localization signals, are highly conserved. Northern blot analyses detect a single message of 8.9 and 5.8 kilo base (kb) from both cardiac and skeletal muscle of chick and mouse, respectively. In situ hybridization reveals that the cXin gene is specifically expressed in cardiac progenitor cells of chick embryos as early as stage 8, prior to heart tube formation. cXin continues to be expressed in the myocardium of developing hearts. By stage 15, cXin expression is also detected in the myotomes of developing somites. Immunofluorescence microscopy reveals that the mXin protein is colocalized with N-cadherin and connexin-43 in the intercalated discs of adult mouse hearts. Incubation of stage 6 chick embryos with cXin antisense oligonucleotides results in abnormal cardiac morphogenesis and an alteration of cardiac looping. The myocardium of the affected hearts becomes thickened and tends to form multiple invaginations into the heart cavity. This abnormal cellular process may account in part for the abnormal looping. cXin expression can be induced by bone morphogenetic protein (BMP) in explants of anterior medial mesoendoderm from stage 6 chick embryos, a tissue that is normally non-cardiogenic. This induction occurs following the BMP-mediated induction of two cardiac-restricted transcription factors, Nkx2.5 and MEF2C. Furthermore, either MEF2C or Nkx2.5 can transactivate a luciferase reporter driven by the mXin promoter in mouse fibroblasts. These results suggest that Xin may participate in a BMP-Nkx2.5-MEF2C pathway to control cardiac morphogenesis and looping.  (+info)

Characterization of an amphioxus paired box gene, AmphiPax2/5/8: developmental expression patterns in optic support cells, nephridium, thyroid-like structures and pharyngeal gill slits, but not in the midbrain-hindbrain boundary region. (8/69904)

On the basis of developmental gene expression, the vertebrate central nervous system comprises: a forebrain plus anterior midbrain, a midbrain-hindbrain boundary region (MHB) having organizer properties, and a rhombospinal domain. The vertebrate MHB is characterized by position, by organizer properties and by being the early site of action of Wnt1 and engrailed genes, and of genes of the Pax2/5/8 subfamily. Wada and others (Wada, H., Saiga, H., Satoh, N. and Holland, P. W. H. (1998) Development 125, 1113-1122) suggested that ascidian tunicates have a vertebrate-like MHB on the basis of ascidian Pax258 expression there. In another invertebrate chordate, amphioxus, comparable gene expression evidence for a vertebrate-like MHB is lacking. We, therefore, isolated and characterized AmphiPax2/5/8, the sole member of this subfamily in amphioxus. AmphiPax2/5/8 is initially expressed well back in the rhombospinal domain and not where a MHB would be expected. In contrast, most of the other expression domains of AmphiPax2/5/8 correspond to expression domains of vertebrate Pax2, Pax5 and Pax8 in structures that are probably homologous - support cells of the eye, nephridium, thyroid-like structures and pharyngeal gill slits; although AmphiPax2/5/8 is not transcribed in any structures that could be interpreted as homologues of vertebrate otic placodes or otic vesicles. In sum, the developmental expression of AmphiPax2/5/8 indicates that the amphioxus central nervous system lacks a MHB resembling the vertebrate isthmic region. Additional gene expression data for the developing ascidian and amphioxus nervous systems would help determine whether a MHB is a basal chordate character secondarily lost in amphioxus. The alternative is that the MHB is a vertebrate innovation.  (+info)

TY - JOUR. T1 - Crystallographic studies of a novel DNA-binding domain from the yeast transcriptional activator Ndt80. AU - Montano, Sherwin P.. AU - Pierce, Michael. AU - Coté, Marie L.. AU - Vershon, Andrew K.. AU - Georgiadis, Millie. PY - 2002/12/1. Y1 - 2002/12/1. N2 - The Ndt80 protein is a transcriptional activator that plays a key role in the progression of the meiotic divisions in the yeast Saccharomyces cerevisiae. Ndt80 is strongly induced during the middle stages of the sporulation pathway and binds specifically to a promoter element called the MSE to activate transcription of genes required for the meiotic divisions. Here, the preliminary structural and functional studies to characterize the DNA-binding activity of this protein are reported. Through deletion analysis and limited proteolysis studies of Ndt80, a novel 32 kDa DNA-binding domain that is sufficient for DNA-binding in vitro has been defined. Crystals of the DNA-binding domain of Ndt80 in two distinct lattices have been ...
p53 is an allosterically regulated protein with a latent DNA-binding activity. Posttranslational modification of a carboxy-terminal regulatory site in vitro, by casein kinase II and protein kinase C, can activate the sequence-specific DNA-binding function of the wild-type protein. The latent form of...
DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
Interactions between proteins and DNA play an important role in many essential biological processes such as DNA replication, transcription, splicing, and repair. The identification of amino acid residues involved in DNA-binding sites is critical for understanding the mechanism of these biological activities. In the last decade, numerous computational approaches have been developed to predict protein DNA-binding sites based on protein sequence and/or structural information, which play an important role in complementing experimental strategies. At this time, approaches can be divided into three categories: sequence-based DNA-binding site prediction, structure-based DNA-binding site prediction, and homology modeling and threading. In this article, we review existing research on computational methods to predict protein DNA-binding sites, which includes data sets, various residue sequence/structural features, machine learning methods for comparison and selection, evaluation methods, performance comparison of
The manipulation of DNA by proteins is central to the life of a cell. It is critical for processes ranging from replication and recombination to transcription and the repair of DNA damage. Introduction to Protein-DNA Interactions, written by Gary Stormo, provides an up-to-date and interdisciplinary perspective on protein-DNA interactions, with an emphasis on DNA-binding proteins…
XRCC genes (X-ray cross-complementing group) were discovered mainly for their roles in protecting mammalian cells against damage caused by ionizing radiation. Studies determined that these genes are important in the genetic stability of DNA. Although the loss of some of these genes does not necessarily confer high levels of sensitivity to radiation, they have been found to represent ... more ...
IRF-4 binds with LANA through its DNA-binding domain in vitro.(A) IRF-4 binds to C-terminal domain of LANA in vitro. The 35S-radiolabeled in vitro-translated pr
iDNA-Prot,dis: identifying DNA-binding proteins by incorporating amino acid distance-pairs and reduced alphabet profile into the general pseudo amino acid ...
Lachke, Salil A.; OConnell, Daniel J.; Aboukhalil, Anton; Choe, Sung E.; Turbe-Doan, Annick; Robertson, Erin A.; Amendt, Brad A. et al. (PLoS ONE, 2012) Link to Published Version ...
DDB1 was originally identified as a large subunit of damaged DNA-binding protein (DDB), which plays a role in DNA repair. DDB1 also functions as an adaptor molecule of Cul4/DDB1 ubiquitin E3 ligase and participates in various cellular processes. ...
Acts as a transcriptional repressor of the GATA3 promoter. Sequence-specific DNA-binding factor that binds to the 5-AGGTCTC-3 sequence within the…
Acts as a transcriptional repressor of the GATA3 promoter. Sequence-specific DNA-binding factor that binds to the 5-AGGTCTC-3 sequence within the…
The ssb gene, coding for single-stranded-DNA-binding protein (SSB), was cloned from four marine Shewanella strains that differed in their temperature and pressure optima and ranges of growth. All four Shewanella ssb genes complemented Escherichia coli ssb point and deletion mutants, with efficiencies that varied with temperature and ssb gene source. The Shewanella SSBs are the largest bacterial SSBs identified to date (24.9-26.3 kDa) and may be divided into conserved amino- and carboxy-terminal regions and a highly variable central region. Greater amino acid sequence homology was observed between the Shewanella SSBs as a group (72-87%) than with other bacterial SSBs (52-69%). Analysis of the amino acid composition of the Shewanella SSBs revealed several features that could correlate with pressure or temperature adaptation. SSBs from the three low-temperature-adapted Shewanella strains were an order of magnitude more hydrophilic than that from the mesophilic strain, and differences in the distribution of
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Looking for online definition of DNA-binding protein RFX8 in the Medical Dictionary? DNA-binding protein RFX8 explanation free. What is DNA-binding protein RFX8? Meaning of DNA-binding protein RFX8 medical term. What does DNA-binding protein RFX8 mean?
Summary Evidence is presented here which indicates that the adenovirus DNA-binding protein (DBP) is phosphorylated at a tyrosine residue early in infection. This was suggested by the discovery that a proportion of the label in 32P-labelled DBP was resistant to alkali, and was substantiated by acid hydrolysis of DBP immunoprecipitates and by immunoblotting with a monoclonal antibody against phosphotyrosine. Treatment of [35S] methionine-labelled DBPs with chymotrypsin produced fragments of apparent M r 45K and 39K whereas digestion of 32P-labelled DBP resulted in fragments of 45K and 26K. Consideration of the distribution of 32P label and its alkali stability in these fragments suggested that chymotrypsin cleaved populations of DBP at different sites depending on their phosphorylation states. The conservation, in all of the seven adenovirus serotypes sequenced, of a tyrosine residue (at amino acid 195 in adenovirus type 2) together with its surrounding residues, suggests that phosphorylation
The human transcription enhancer factor-1 (TEF-1) belongs to a family of evolutionarily conserved proteins that have a DNA binding TEA domain. TEF-1 shares a 98% homology with Drosophila scalloped (sd) in the DNA binding domain and a 50% similarity in the activation domain. We have expressed human TEF-1 in Drosophila under the hsp-70 promoter and find that it can substitute for Sd function. The transformants rescue the wingblade defects as well as the lethality of loss-of-function alleles. Observation of reporter activity in the imaginal wing discs of the enhancer-trap alleles suggests that TEF-1 is capable of promoting sd gene regulation. The functional capability of the TEF-1 product was assessed by comparing the extent of rescue by heat shock (hs)-TEF-1 with that of hs-sd. The finding that TEF-1 can function in vivo during wingblade development offers a potent genetic system for the analysis of its function and in the identification of the molecular partners of TEF-1.. ...
The molecular determinants necessary and sufficient for recognition of its specific DNA target are contained in the C-domain (H-NSctd) of nucleoid-associated protein H-NS. H-NSctd protects from DNaseI cleavage a few short DNA segments of the H-NS-sensitive hns promoter whose sequences closely match the recently identified H-NS consensus motif (tCGt/aTa/tAATT) and, ... read more alone or fused to the protein oligomerization domain of phage λ CI repressor, inhibits transcription from the hns promoter in vitro and in vivo. The importance of H-NS oligomerization is indicated by the fact that with an extended hns promoter construct (400 bp), which allows protein oligomerization, DNA binding and transcriptional repression are highly and almost equally efficient with native H-NS and H-NSctd::λCI and much less effective with the monomeric H-NSctd. With a shorter (110 bp) construct, which does not sustain extensive protein oligomerization, transcriptional repression is less effective, but native H-NS, ...
TY - JOUR. T1 - A proteolytic fragment from the central region of p53 has marked sequence-specific DNA-binding activity when generated from wild-type but not from oncogenic mutant p53 protein. AU - Bargonetti, Jill. AU - Manfredi, James J.. AU - Chen, Xinbin. AU - Marshak, Daniel R.. AU - Prives, Carol. PY - 1993. Y1 - 1993. N2 - p53 is a sequence-specific DNA-binding oligomeric protein that can activate transcription from promoters bearing p53-binding sites. Whereas the activation region of p53 has been identified within the amino terminus, the location of the specific DNA-binding domain has not been reported. Thermolysin treatment of p53 protein generates a stable protease-resistant fragment that binds with marked specificity to p53 DNA-binding sites. Amino-terminal sequencing of the fragment located the thennolysin cleavage site to residue 91. Because the fragment does not contain the cdc2 phosphorylation site at Ser-315, we conclude that the the site-specific DNA-binding domain of p53 spans ...
TY - JOUR. T1 - Determination of binding constants for cooperative site-specific protein-DNA interactions using the gel mobility-shift assay. AU - Senear, D. F.. AU - Brenowitz, M.. PY - 1991/9/9. Y1 - 1991/9/9. N2 - We have investigated the question of whether the gel mobility-shift assay can provide data that are useful to the demonstration of cooperativity in the site-specific binding of proteins to DNA. Three common patterns of protein-DNA interaction were considered: (i) the cooperative binding of a protein to two sites (illustrated by the Escherichia coli Gal repressor); (ii) the cooperative binding of a bidentate protein to two sites (illustrated by the E. coli Lac repressor); and (iii) the cooperative binding of a protein to three sites (illustrated by the λcI repressor). A simple, rigorous, and easily extendable statistical mechanical approach to the derivation of the binding equations for the different patterns is presented. Both stimulated and experimental data for each case are ...
Naturally elaborated membrane bleb fractions BI and BII of Neisseria gonorrhoeae contain both linear and circular DNAs. Because little is known about the interactions between DNA and blebs, studies were initiated to identify specific proteins that bind DNA in elaborated membrane blebs. Western immunoblots of whole-cell and bleb proteins from transformation-competent and DNA-uptake-deficient (dud) mutants were probed with single- or double-stranded gonococcal DNA, pBR322, or synthetic DNA oligomers containing intact or altered gonococcal transformation uptake sequences. The specificity and sensitivity of a nonradioactive DNA-binding protein assay was evaluated, and the assay was used to visualize DNA-protein complexes on the blots. The complexes were then characterized by molecular mass, DNA-binding specificity, and expression in bleb fractions. The assay effectively detected blotted DNA-binding proteins. At least 17 gonococcal DNA-binding proteins were identified; unique subsets occurred in BI ...
Purpose To evaluate the prognostic significance of DNA excision repair gene polymorphisms, excision repair cross-complementation group 1 ( ERCC1) and X-ray repair complementing defective repair in...
An inducible program of inflammatory gene expression is a hallmark of antimicrobial defenses. This response is controlled by a collaboration involving signal-dependent activation of transcription factors, transcriptional co-regulators, and chromatin-modifying factors. Here we have identified a highly conserved Zinc finger DNA binding protein CNBP (also called ZNF9) upregulated in myeloid cells exposed to lipopolysaccharide. CNBP resides primarily in the cytosol and upon TLR4 engagement, CNBP translocate to the nucleus. To investigate the functional consequences of these events, we generated mice lacking CNBP and characterized the role of CNBP in controlling the inducible transcriptional program using a combination of RNA-sequencing and multiplex gene expression analysis (Nanostring). In response to an array of signals such as LPS, CNBP-deficient macrophages were impaired in their ability to induce important immune genes including IL12p40 and IL6 amongst others. CNBP-deficient cells showed normal ...
Author Summary The main role of transcription factors is to modulate the expression levels of functionally related genes in response to environmental and cellular cues. For this process to be precise, the transcription factor needs to locate and bind specific DNA sequences in the genome and needs to bind these sites with a strength that appropriately adjusts the amount of gene expressed. Both specific protein-DNA interactions and transcription factor activity are intimately coupled, because they are both dependent upon the biochemical properties of the DNA-binding domain. Here we experimentally probe how variable these properties are using a novel in vivo selection assay. We observed that the specific binding preferences for the transcription factor MarA and its transcriptional activity can be altered over a large range with a few mutations and that selection on one function will impact the other. This work helps us to better understand the mechanism of transcriptional regulation and its evolution, and
XPB antibody (excision repair cross-complementation group 3) for IHC-P, WB. Anti-XPB pAb (GTX55844) is tested in Human, Mouse, Rat samples. 100% Ab-Assurance.
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Binding of transcriptional activators to a promoter is a prerequisite process in transcriptional activation. It is well established that the efficiency of activator binding to a promoter is determined by the affinity of direct interactions between the DNA-binding domain of an activator and its specific target sequences. However, I describe here that activator binding to a promoter is augmented in vivo by the effects of two other determinants that have not been generally appreciated: (i) the number of activator binding sites present in a promoter and (ii) the potency of activation domains of activators. Multiple sites within a promoter can cooperatively recruit cognate factors regardless of whether they contain an effective activation domain. This cooperativity can result in the synergistic activation of transcription. The second effect is the enhancement of activator binding to a promoter by the presence of activation domains. In this case, activation domains are not simply tethered to the ...
Genes expressed in erythroid cells contain binding sites for a cell-specific nuclear factor, GF-1 (NF-E1, Eryf 1), believed to be an important transcriptional regulator. Previously we characterized murine GF-1 as a 413-amino acid polypeptide containing two cysteine-cysteine regions reminiscent of zinc-finger DNA-binding domains. By cross-hybridization to the finger domain of murine GF-1 we have isolated cDNA encoding the human homolog. Peptide sequencing of purified human GF-1 confirmed the authenticity of the human cDNA. The predicted primary sequence of human GF-1 is highly similar to that of murine GF-1, particularly in the DNA-binding region. Although the DNA-binding domains of human, murine, and chicken proteins are remarkably conserved, the mammalian polypeptides are strikingly divergent from the avian counterpart in other regions, most likely those responsible for transcriptional activation. By hybridization to panels of human-rodent DNAs we have assigned the human GF-1 locus to Xp21-11. ...
The human ERYF1 gene (summary) NF-E1 DNA-binding protein GATA1, locus Xp11.23 [§§; †] containing 2 finger motifs referred to as ERYF1 of an erythroid-specific gene. The cDNA for the human ERYF1 gene is almost identical to that of chicken and mouse GATA1 gene consisting of 2 zinc finger type motifs its activator domain contains the binding…
Tumor protein p53, encoded in humans by the TP53 gene, was originally identified based on its interaction with the large T antigen of simian virus 40 (SV40). p53 is expressed at low levels in most cell types but is upregulated in many transformed (cancer) cell lines. In response to cellular stress, p53 regulates over 100 target genes that control cell cycle arrest, apoptosis, senescence, DNA repair, and metabolic changes. p53 protein has multiple domains that include DNA-binding, transactivation, and oligomerization activities. Mutations in the TP53 gene cause loss of tumor suppression activity and are found in more than 50% of human tumors. Multiple isoforms of p53 are known, with distinct DNA-binding and transcriptional activation properties. p53 is also known as cellular tumor antigen p53, p53 tumor suppressor, transformation-related protein 53, BCC7, LFS1, TRP53, and antigen NY-CO-13.. ...
DNA-binding proteins from starved cells (DPS) are proteins that belong to the ferritin superfamily and are characterized by strong similarities but also distinctive differences with respect to "canonical" ferritins. DPS proteins are part of a complex bacterial defence system that protects DNA against oxidative damage and are distributed widely in the bacterial kingdom. DPS are highly symmetrical dodecameric proteins of 200 kDa characterized from a shell-like structure of 2:3 tetrahedral symmetry assembled from identical subunits with an external diameter of ~ 9 nm and a central cavity of ~ 4.5 nm in diameter. Dps proteins belong to the ferritin superfamily and the DNA protection is afforded by means of a double mechanism: The first was discovered in Escherichia coli Dps in 1992 and has given the name to the protein family; during stationary phase, Dps binds the chromosome non-specifically, forming a highly ordered and stable dps-DNA co-crystal within which chromosomal DNA is condensed and ...
Zinc finger proteins contain DNA-binding domains and have a wide variety of functions, most of which encompass some form of transcriptional activation or repression. The majority of zinc finger proteins contain a Krueppel-type DNA binding domain and a KRAB domain, which is thought to interact with KAP1, thereby recruiting histone modifying proteins. Zinc finger protein 75 (ZNF75), also known as ZNF82, is a 289 amino acid member of the Krueppel C2H2-type zinc finger protein family. Localized to the nucleus, ZNF75 contains five C2H2- type zinc fingers and one KRAB domain through which it is thought to be involved in DNA-binding and transcriptional regulation ...
As a commentator up-thread noted, any slip-and-slide model of sequence-specific DNA binding activity by transcription factors fails the sniff test: how is the activator (or repressor) able to effectively scan the nucleotide side-groups to achive site-specificity when the latter are coated with histones (in most eukaryotes) and with other attendant DNA-binding molecules (in all organisms). The notion that the chromosomal DNA molecule exists in all of its double-helical beauty for all proteins to probe seems rather tired and readily debunked to my mind. Ive been a hesitant skeptic of the histone code as anything other than correlative observations, but given the ubiquitous habit of histone compaction of large chromosomal segments, some portions of which obviously remain accessible to transcription factors, it seems clear to me that were missing some vital pieces of the puzzle.. Delete ...
DNA binding capacity of Orf8 and Orf16 by electrophoretic mobility shift assays (EMSAs). Preparation of DNA substrate is graphically shown in panel A. US8 and U
Progression through the cell cycle is essential for the continued existence of all uni- and multicellular organisms. It is crucial for the survival of a cell that its DNA is correctly replicated. In mammals, the onset of DNA replication is regulated by the activity of the heterodimeric E2F-DP transcription factor. The mammalian E2F family contains six proteins (E2F1, E2F2, E2F3, E2F4, E2F5 and E2F6) (Trimarchi and Lees, 2002). All E2Fs have an N-terminally located DNA-binding domain immediately followed by a dimerization domain, allowing them to pair with a dimerization partner (DP1 or DP2). Dimerization of E2F with DP is a prerequisite for high affinity, sequence-specific binding to the E2F consensus DNA-binding site. E2F activity is negatively regulated by retinoblastoma (Rb), which binds to the transcriptional activation domain of the E2F-DP factor, rendering it inactive. Moreover, the recruitment by Rb of DNA-modifying enzymes, such as histone deacetylases and polycomb proteins, leads to ...
Enhancer factor C, EFC, EF-C, MHC class II regulatory factor RFX, MHC class II regulatory factor RFX1, regulatory factor X, 1 (influences HLA class II expression), Regulatory factor X 1, RFX, trans-acting regulatory factor 1, Transcription factor ...
Predicted to have DNA-binding transcription factor activity and sequence-specific DNA binding activity. Involved in pericyte cell differentiation and vascular smooth muscle cell development. Predicted to localize to the nucleus. Is expressed in head mesenchyme; pharyngeal arch 1; and pharyngeal arch 2. Orthologous to human FOXF2 (forkhead box F2 ...
The present invention provides a process of transfecting a cell with a polynucleotide mixed with one or more amphipathic compounds and an effective amount of a DNA-binding protein. Exemplary and preferred DNA-binding proteins are H1, H2A, and H2B. Exemplary and preferred amphipathic compounds are cationic amphipathic compounds.
Vol 9: Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome.. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
HSSB, MSTP075, MST075, replication protein A 70 kDa DNA-binding subunit, replication protein A1 (70kD), replication protein A1, 70kDa, REPA1RF-A protein 1, Replication factor A protein 1, RF-A, RP-A, RPA70RP-A p70, Single-stranded DNA-binding ...
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Although bats are recognized as major reservoir hosts of emerging infectious diseases, Joffrin and colleagues highlight that a significant knowledge gap on transmission mechanisms remains and needs further exploration. They question whether bat bites are the exception rather than the rule, and ask whether other animals can transmit bat-borne pathogens. They conclude by questioning what we can learn from bat-to-bat transmission.. ...
Summary: The human protein DNA Interactome (hPDI) database holds experimental protein-DNA interaction data for humans identified by protein microarray assays. The unique characteristics of hPDI are that it contains consensus DNA-binding sequences not only for nearly 500 human transcription factors but also for ,500 unconventional DNA-binding proteins, which are completely uncharacterized previously. Users can browse, search and download a subset or the entire data via a web interface. This database is freely accessible for any academic purposes.. Availability: http://bioinfo.wilmer.jhu.edu/PDI/. Contact: [email protected] ...
GT:ID BAD55361.1 GT:GENE BAD55361.1 GT:PRODUCT putative DNA-binding protein GT:DATABASE GIB00210CH01 GT:ORG nfar0 GB:ACCESSION GIB00210CH01 GB:LOCATION complement(531217..531633) GB:FROM 531217 GB:TO 531633 GB:DIRECTION - GB:PRODUCT putative DNA-binding protein GB:PROTEIN_ID BAD55361.1 LENGTH 138 SQ:AASEQ MADFAARLNKLFETVHPPGRKPHTNAEVAAALTASGHPISKPYLSQLRSGQRTNPSDETVAALAKFFKVKPDYFFNDIYAAKIDHDLELLSQLQGYGLRRLSSRAFDLSEESQNLLTSMAEKLRASEGLPEIPPDGTE GT:EXON 1,1-138:0, BL:SWS:NREP 1 BL:SWS:REP 1-,69,Y1416_COXBU,7e-04,37.9,58/100, RP:PDB:NREP 1 RP:PDB:REP 6-,104,2ao9A,3e-07,10.1,99/117, HM:PFM:NREP 1 HM:PFM:REP 33-,74,PF01381,4.7e-10,36.1,36/55,HTH_3, RP:SCP:NREP 1 RP:SCP:REP 6-,104,2ao9A1,2e-07,10.1,99/117,a.4.1.17, HM:SCP:REP 39-,77,2a6cA1,0.00055,33.3,39/0,a.35.1.13,1/1,lambda repressor-like DNA-binding domains, OP:NHOMO 42 OP:NHOMOORG 31 OP:PATTERN -------------------------------------------------------------------- ...
High-resolution computational models of genome binding events. A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors
GT:ID BAD57449.1 GT:GENE BAD57449.1 GT:PRODUCT putative DNA-binding protein GT:DATABASE GIB00210CH01 GT:ORG nfar0 GB:ACCESSION GIB00210CH01 GB:LOCATION 2771120..2771977 GB:FROM 2771120 GB:TO 2771977 GB:DIRECTION + GB:PRODUCT putative DNA-binding protein GB:PROTEIN_ID BAD57449.1 LENGTH 285 SQ:AASEQ MQQAVAERGPTVLRIALGGQLRKLRESRNITREAAGDAIRGSHAKISRLELGRTGFKERDIRDLLTLYGVVDPAERESFLDLARRANEPGWWHRYSDLLPQWFGQYLGLEQAAWKIRTYEAHLVPGLLQTPDYARAVLALGSDDADTDRRVDVRRRRQEILRRPEPPIVWAVLDEAALHRPVGGVQVHRAQIEHLIELAALPNVTLQVLPYSAGEHAAAGASFSILRFAEAELPDVVYLEHLTSALYLDRTQDLALYRSVMDRLSVQALAPDKSVDWLKNFAAGL GT:EXON 1,1-285:0, SEG 143-,163,ddadtdrrvdvrrrrqeilrr, RP:PDB:NREP 1 RP:PDB:REP 3-,90,2csfA,5e-08,8.0,88/101, HM:PFM:NREP 1 HM:PFM:REP 21-,74,PF01381,6.3e-06,24.5,53/55,HTH_3, RP:SCP:NREP 1 RP:SCP:REP 17-,116,1s4kA,5e-07,20.8,96/120,a.35.1.6, HM:SCP:REP 9-,70,1y9qA1,1.7e-05,29.0,62/0,a.35.1.8,1/1,lambda repressor-like DNA-binding domains, OP:NHOMO 191 OP:NHOMOORG 14 OP:PATTERN ...
In living cells, DNA-binding proteins regulate the activity of various genes so that different cells carry out the right tasks at the right time. For this to work, the DNA-binding proteins need to find the right DNA site sufficiently quickly. The research team behind the new study has previously succeeded in determining that it takes only a few minutes for an individual protein molecule to look through the millions of nearly identical binding alternatives and find the right place to bind. This is nevertheless slower than what is predicted by the established theoretical model for how DNA-binding proteins find their way to the proper place by alternating between diffusing in the cell cytoplasm and along DNA strands ...
This motif was first noticed as a feature of the crystal structure of the bacteriophage l Cro protein. The structure of this small regulatory protein contained two a-helices separated by 34 Ã… - the pitch of a DNA double helix. Model building studies showed that these two a-helices would fit into two successive major grooves. As the structures of a number of other bacterial regulatory proteins (the CRP protein and the bacteriophage l cI repressor) were solved, the same structural motif - called a helix-turn-helix - was observed. It consists of two a-helices separated by a short turn (it is not a b turn). One helix binds to recognition elements within the major groove of DNA; the other helps to keep the binding helix properly positioned with respect to the rest of the molecule. This motif, common in bacterial DNA-binding proteins, also occurs in the eukaryotic homeobox proteins ...
1PER: THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES
Does anyone use DNA binding proteins expressed in rabbit reticulocyte lysates to do gel shift assays? This system would allow easy and quick expression of a suspected DNA binding protein that I could study (much easier than trying to express and purify the protein). I would specifically like to know if the other proteins in the system or maybe even the DNA added would somehow interfere in a gel shift assay (although I guess its no different than using cell/nuclear extracts). If anyone has experience with this or know of a reference could you please let me know? Thanks. -- Steve Some day I will get the hell out of Wisconsin Rodems Then I am here for the Lee family renioun ... shur-wajo-shur ...
The calling card method provides an accurate and reproducible way to detect transcription factor binding that is orthogonal to ChIP and may be useful for analysis of the many TFs that appear to be recalcitrant to ChIP analysis (perhaps due to poor antibody quality).. While many calling card clusters show high concordance with ChIP-seq peaks, there are a number of peaks discordant between the two methods. Other orthogonal methods for measuring genomic data can generate disparate results at certain loci; for example, DNA methylation assayed by bisulfite-based sequencing methods and by immunoprecipitation enrichment methods yield similar, but not identical, results, particularly in terms of quantification (Harris et al. 2010). Of principal concern is the constraint on piggyBac to insert almost exclusively at the sequence TTAA, which can prevent the TF-PBase from recording its visit to regions devoid of that tetranucleotide. We observed ∼1% PB insertions at non-TTAA sites, raising the prospect of ...
Binds double-stranded DNA. Binds preferentially to supercoiled DNA and cruciform DNA structures. Seems to be involved in transcriptional regulation. May function as a transcriptional repressor. Could have a role in the regulation of hematopoietic differentiation through activation of unknown target genes. Controls cellular proliferation by modulating the functions of cell cycle regulatory factors including p53/TP53 and the retinoblastoma protein. May be involved in TP53-mediated transcriptional activation by enhancing TP53 sequence-specific DNA binding and modulating TP53 phosphorylation status. Seems to be involved in energy-level-dependent activation of the ATM/ AMPK/TP53 pathway coupled to regulation of autophagy. May be involved in regulation of TP53-mediated cell death also involving BRCA1. May be involved in the senescence of prostate epithelial cells. Involved in innate immune response by recognizing viral dsDNA in the cytosol and probably in the nucleus. After binding to viral DNA in the ...
Gene target information for Ssbp3 - single-stranded DNA binding protein 3 (house mouse). Find diseases associated with this biological target and compounds tested against it in bioassay experiments.
Filtering by: Creator Maria A. Schumacher Remove constraint Creator: Maria A. Schumacher Degree Ph.D. Remove constraint Degree: Ph.D. Department Dept. of Biochemistry and Molecular Biology Remove constraint Department: Dept. of Biochemistry and Molecular Biology Keyword crystallography Remove constraint Keyword: crystallography Keyword repressor proteins Remove constraint Keyword: repressor proteins Keyword dna-binding proteins Remove constraint Keyword: dna-binding proteins Collection Scholars Archive Remove constraint Collection: Scholars Archive ...
Filtering by: Date 1995 Remove constraint Date: 1995 Keyword dna-binding proteins Remove constraint Keyword: dna-binding proteins Keyword x-ray Remove constraint Keyword: x-ray School School of Medicine Remove constraint School: School of Medicine ...
Complete information for SSBP2 gene (Protein Coding), Single Stranded DNA Binding Protein 2, including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium
X-Ray Repair Cross Complementing 1 (XRCC1) plays a role in excision repair of DNA after ionizing irradiation. XRCC1 interacts with human…
Complete information for SSBP2 gene (Protein Coding), Single Stranded DNA Binding Protein 2, including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium
Genetic information processingDNA metabolismDNA replication, recombination, and repairsingle-stranded DNA-binding protein (TIGR00621; HMM-score: 163) ...
Others utilize interventions tailored to patients but do not describe the clinical decision-making process utilized to develop and modify interventions. Analysis of the mouse SREBP-1c gene promoter revealed an RXR/LXR DNA-binding site that is essential for this regulation. Identification of professional ...
SSBP2兔多克隆抗体(ab118880)可与人样本反应并经WB, IHC实验严格验证。中国75%以上现货,所有产品均提供质保服务,可通过电话、电邮或微信获得本地专属技术支持。
Meaning and definition of the name Boris. Learn the meaning of Boris, learn about the origin of the name Boris and find other information about the name Boris.
XRCC3兔多克隆抗体(ab97390)可与人样本反应并经WB, ICC/IF实验严格验证,被1篇文献引用。所有产品均提供质保服务,中国75%以上现货。
GO Terms Descrition:, periodic partitioning by pair rule gene, central nervous system development, RNA polymerase II distal enhancer sequence-specific DNA binding, positive regulation of transcription from RNA polymerase II promoter, trunk segmentation, cell fate specification, RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription, regulation of transcription from RNA polymerase II promoter, blastoderm segmentation, negative regulation of transcription from RNA polymerase II promoter, regulation of transcription, DNA-templated, sequence-specific DNA binding transcription factor activity, nucleus, sequence-specific DNA binding, gonadal mesoderm development, segmentation, posterior head segmentation, germ cell migration ...
DNA-binding activity of a maize heat shock transcription factor (HSF) was induced by heat shock of a whole cell extract at 44°C. Addition of the calcium ion chelator EGTA reduced the binding of the HSF to heat shock element (HSE) in vitro. Re-addition of CaCl2 to the sample pretreated with EGTA restored the ability of the HSF to bind to DNA. DNA-binding activity of the HSF was also induced by directly adding CaCl2 to a whole cell extract at non-heat-shock temperature, but not by MgCl2. During HS at 44°C, calmodulin (CaM) antagonists chlorpromazine (CPZ) and N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide (W7) inhibited DNA-binding activity of the HSF in a concentration-dependent manner, but N-(6-aminohexyl)-1-naphthalenesulfonamide (W5), an inactive structural analogue of W7, did not. Addition of antiserum specific to CaM reduced the binding of the HSF to HSE. Re-addition of CaM to the sample pretreated with antiserum could restore the binding activity of the HSF. DNA-binding activity of ...
GO Terms Descrition:, positive regulation of transcription from RNA polymerase II promoter, anterior/posterior axis specification, cell fate specification, RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity, transcription, DNA-templated, compound eye development, ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity, torso signaling pathway, terminal region determination, Bolwigs organ morphogenesis, DNA binding, sequence-specific DNA binding, sequence-specific DNA binding transcription factor activity, zinc ion binding, nucleus, regulation of cell cycle, intracellular receptor signaling pathway, steroid hormone mediated signaling pathway, steroid hormone receptor activity, regulation of transcription, DNA-templated, neuroblast division, optic lobe placode development, ring gland development, gastrulation, cell fate commitment ...
[46 Pages Report] Check for Discount on TAR DNA-Binding Protein 43 (TDP-43) - Pipeline Review, H1 2016 report by Global Markets Direct. Global Markets Directs, TAR DNA-Binding Protein 43 (TDP-...
Single-stranded DNA-binding proteins (SSBs), including replication protein A (RPA) in eukaryotes, play a central role in DNA replication, recombination, and repair. SSBs utilise an oligonucleotide/oligosaccharide-binding (OB) fold domain to bind DNA, and typically oligomerise in solution to bring multiple OB fold domains together in the functional SSB. SSBs from hyperthermophilic crenarchaea, such as Sulfolobus solfataricus, have an unusual structure with a single OB fold coupled to a flexible C-terminal tail. The OB fold resembles those in RPA, whilst the tail is reminiscent of bacterial SSBs and mediates interaction with other proteins. One paradigm in the field is that SSBs bind specifically to ssDNA and much less strongly to RNA, ensuring that their functions are restricted to DNA metabolism. Here, we use a combination of biochemical and biophysical approaches to demonstrate that the binding properties of S. solfataricus SSB are essentially identical for ssDNA and ssRNA. These features may ...
TY - JOUR. T1 - Custom DNA-binding proteins come of age. T2 - Polydactyl zinc-finger proteins. AU - Segal, David. AU - Barbas, Carlos F.. PY - 2001/12/1. Y1 - 2001/12/1. N2 - Artificial transcription factors based on modified zinc-finger DNA-binding domains have been shown to activate or repress the transcription of endogenous genes in multiple organisms. Advances in both the construction of novel zinc-finger proteins and our understanding of the characteristics of a productive regulatory site have fueled these achievements.. AB - Artificial transcription factors based on modified zinc-finger DNA-binding domains have been shown to activate or repress the transcription of endogenous genes in multiple organisms. Advances in both the construction of novel zinc-finger proteins and our understanding of the characteristics of a productive regulatory site have fueled these achievements.. UR - http://www.scopus.com/inward/record.url?scp=0035712253&partnerID=8YFLogxK. UR - ...
Mutations in genes encoding components of the mitochondrial DNA (mtDNA) replication machinery cause mtDNA depletion syndromes (MDSs), which associate ocular features with severe neurological syndromes. Here, we identified heterozygous missense mutations in single-strand binding protein 1 (SSBP1) in 5 unrelated families, leading to the R38Q and R107Q amino acid changes in the mitochondrial single-stranded DNA-binding protein, a crucial protein involved in mtDNA replication. All affected individuals presented optic atrophy, associated with foveopathy in half of the cases. To uncover the structural features underlying SSBP1 mutations, we determined a revised SSBP1 crystal structure. Structural analysis suggested that both mutations affect dimer interactions and presumably distort the DNA-binding region. Using patient fibroblasts, we validated that the R38Q variant destabilizes SSBP1 dimer/tetramer formation, affects mtDNA replication, and induces mtDNA depletion. Our study showing that mutations in ...
DNA-dependent protein kinase (DNA-PK) consists of a 460 kDa subunit that contains the catalytic domain (DNA-PKcs) complexed with two polypeptides of 70 kDa and 80 kDa (Ku70 and Ku80) which comprise the Ku autoantigen. DNA-PKcs requires association with DNA via Ku for catalytic activation and is implicated in double strand break repair, V(D)J recombination and transcription. We have utilised a cell-free system of concentrated Xenopus laevis egg extracts to investigate the regulation and possible functions of DNA-PK. Recently, we have shown that this system can reproduce events of apoptosis, including activation of an apoptotic protease that cleaves poly(ADP-ribose) polymerase. Here, we report that DNA-PK is rapidly inactivated with the onset of apoptosis in this system. Loss of activity is concomitant with cleavage of the catalytic subunit, whereas the Ku subunits are stable. Cleavage and inactivation of DNA-PKcs is prevented by prior addition of the anti-apoptotic protein Bcl-2 or inhibition of ...
The avian acute leukemia virus (E26) induces a mixed erythroidmyeloid leukemia in chickens and carries two distinct oncogenes, v-myb and v-ets. The viral protein responsible for transformation is a gag-myb-ets fusion protein that is located in the nucleus of the transformed cells. The cellular homologue of v-ets (c-ets-1) is highly expressed in lymphoid cells and differs from the v-ets gene at its carboxy terminal region. Here, we show that both the c-ets-1 and v-ets gene products are DNA-binding proteins and their DNA-binding activity is located in the carboxy terminal (46 amino acid residues) region. It appears that this DNA-binding activity is modulated by the extreme carboxy terminal region. The amino acid sequences of the putative ets DNA-binding domain at its carboxy terminal region showed a helix-turn-helix secondary structure. Exchanging the nonhomologous extreme carboxy terminal regions of c-ets-1 with v-ets gene sequences showed differences in DNA-binding affinity, indicating that ...
Chromosomal translocations involving the Mixed Lineage Leukemia (MLL) gene lead to the expression of MLL fusion proteins and acute leukemia. MLL fusion protein-induced leukemia is aggressive, and often refractory to therapy, highlighting the importance of studying the pathogenesis of this disease. MLL fusion proteins upregulate wild-type MLL target genes, including HOX genes, and block hematopoietic differentiation, promoting leukemogenesis. However, the precise mechanism by which MLL fusion proteins upregulate HOX genes and block differentiation has been unclear. My thesis research shows that leukemia cells expressing the MLL fusion protein MLL-AF9 also express wild-type MLL from the non-translocated MLL allele. Wild-type MLL is required for MLL-AF9-mediated HOX gene upregulation and leukemogenesis. Menin, a nuclear DNA-binding protein, recruits both wild-type MLL and MLL-AF9 to HOX genes to activate their transcription, highlighting the central role of menin in this disease. We also found that menin
Institut National de la Sante et de la Recherche Medicale U124-IRCL, Lille, France. The BTB/POZ domain defines a newly characterized protein-protein interaction interface. It is highly conserved throughout metazoan evolution and generally found at the NH2 terminus of either actin-binding or, more commonly, nuclear DNA-binding proteins. By mediating protein binding in large aggregates, the BTB/POZ domain serves to organize higher order macromolecular complexes involved in ring canal formation or chromatin folding ...
DNA binding protein A (dbpA) belongs to the Y-box binding protein family, characterized by an 80 amino-acid cold shock domain that imparts DNA-binding activity. It is also known as cold shock domain protein A (CSDA), CSDA1, ZO-1-associated nucleic acid-binding protein (ZONAB), and single-strand DNA-binding protein NF-GMB. DbpA has been reported to bind to the promoter for granulocyte-macrophage colony-stimulating factor (GM-CSF) and act as a repressor of transcription. It also binds to full-length mRNA and small RNAs containing the consensus site UCCAUCA, suggesting a role as a repressor of translation. Mutations in the CSDA gene have been associated with hepatocarcinogenesis.. ...
The mechanisms underlying the development and progression of breast cancer are not fully understood, and this is particularly challenging because of its diverse etiologies [20]. However, it is clear that changes in gene expression are essential to drive different processes that occur during tumourigenesis [21]. Transcription factors control gene expression by binding to specific DNA sequences in gene promoters and often regulate multiple target genes. Because of this ability to control different target genes, deregulation of transcription factors can drive events associated with the initiation and progression of diseases such as cancer [22]. Previous studies have shown that the Brn-3b transcription factor is elevated in ,60% of primary breast cancers [1], and when increased, it significantly enhances proliferation and anchorage-independent growth in vitro and tumour growth in vivo [2, 3]. Elevated Brn-3b also confers resistance to growth-inhibitory stimuli and increases the migratory potential ...
Predicted to have RNA polymerase II distal enhancer sequence-specific DNA binding activity. Involved in brain development; cardioblast differentiation; and cell fate specification. Predicted to ... Predicted to have RNA polymerase II distal enhancer sequence-specific DNA binding activity. Involved in brain development; cardioblast differentiation; and cell fate specification. Predicted to localize to the nucleus. Is expressed in several structures, including mesoderm; nervous system; otic vesicle; pharyngeal arch; and pronephric duct. Orthologous to human HOXB5 (homeobox B5). ...
Members of the large ETS family of transcription factors (TFs) have highly similar DNA-binding domains (DBDs)-yet they have diverse functions and activities in physiology and oncogenesis. Some differences in DNA-binding preferences within this family have been described, but they have not been analysed systematically, and their contributions to targeting remain largely uncharacterized. We report here the DNA-binding profiles for all human and mouse ETS factors, which we generated using two different methods: a high-throughput microwell-based TF DNA-binding specificity assay, and protein-binding microarrays (PBMs). Both approaches reveal that the ETS-binding profiles cluster into four distinct classes, and that all ETS factors linked to cancer, ERG, ETV1, ETV4 and FLI1, fall into just one of these classes. We identify amino-acid residues that are critical for the differences in specificity between all the classes, and confirm the specificities in vivo using chromatin immunoprecipitation followed ...
Chorion-specific transcription factor GCMa is a protein that, in humans, is encoded by the GCM1 gene. This gene encodes a DNA-binding protein with a gcm-motif (glial cell missing motif). The encoded protein is a homolog of the Drosophila glial cells missing gene (gcm). This protein binds to the GCM-motif (A/G)CCCGCAT, a novel sequence among known targets of DNA-binding proteins. The N-terminal DNA-binding domain confers the unique DNA-binding activity of this protein. GRCh38: Ensembl release 89: ENSG00000137270 - Ensembl, May 2017 GRCm38: Ensembl release 89: ENSMUSG00000023333 - Ensembl, May 2017 "Human PubMed Reference:". "Mouse PubMed Reference:". Akiyama Y, Hosoya T, Poole AM, Hotta Y (Jan 1997). "The gcm-motif: a novel DNA-binding motif conserved in Drosophila and mammals". Proc Natl Acad Sci U S A. 93 (25): 14912-6. doi:10.1073/pnas.93.25.14912. PMC 26236 . PMID 8962155. "Entrez Gene: GCM1 glial cells missing homolog 1 (Drosophila)". Yamada K, Ogawa H, Honda S, et al. (1999). "A GCM motif ...
Sp2 transcription factor, also known as SP2, is a human gene.[1] This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters.[1] ...
TY - JOUR. T1 - Pin1-mediated Sp1 phosphorylation by CDK1 increases Sp1 stability and decreases its DNA-binding activity during mitosis. AU - Yang, Hang Che. AU - Chuang, Jian Ying. AU - Jeng, Wen Yih. AU - Liu, Chia I.. AU - Wang, Andrew H.J.. AU - Lu, Pei Jung. AU - Chang, Wen Chang. AU - Hung, Jan Jong. PY - 2014/12/16. Y1 - 2014/12/16. N2 - We have shown that Sp1 phosphorylation at Thr739 decreases its DNA-binding activity. In this study, we found that phosphorylation of Sp1 at Thr739 alone is necessary, but not sufficient for the inhibition of its DNA-binding activity during mitosis. We demonstrated that Pin1 could be recruited to the Thr739(p)-Pro motif of Sp1 to modulate the interaction between phospho-Sp1 and CDK1, thereby facilitating CDK1-mediated phosphorylation of Sp1 at Ser720, Thr723 and Thr737 during mitosis. Loss of the Cterminal end of Sp1 (amino acids 741-785) significantly increased Sp1 phosphorylation, implying that the C-terminus inhibits CDK1-mediated Sp1 phosphorylation. ...
View Notes - Lec20 from BCH 110 at UC Riverside. Lecture 20 Eukaryotic Gene Regulation 2 REGULATORY TRANSCRIPTION FACTORS & ACTIVATION MECHANISMS Lodish 6th edition Chapter 7 Lodish 5th edition
Using a reinoic acid receptor hybridization probe, we have isolated a mouse embryonic cDNA that encodes the germ cell nuclear factor (mGCNF). The in vitro translated protein binds specifically to the
One of the largest classes of regulatory proteins in animals, sequence-specific DNA binding transcription factors determine in which cells genes will be expressed and so control the development of an animal from a single cell to a morphologically complex adult. Understanding how this process is coordinated depends on knowing the number and types of genes that each transcription factor binds and regulates. Using immunoprecipitation of in vivo crosslinked chromatin coupled with DNA microarray hybridization (ChIP/chip), we have determined the genomic binding sites in early embryos of six transcription factors that play a crucial role in early development of the fruit fly Drosophila melanogaster. We find that these proteins bind to several thousand genomic regions that lie close to approximately half the protein coding genes. Although this is a much larger number of genes than these factors are generally thought to regulate, we go on to show that whereas the more highly bound genes generally look to ...
One of the largest classes of regulatory proteins in animals, sequence-specific DNA binding transcription factors determine in which cells genes will be expressed and so control the development of an animal from a single cell to a morphologically complex adult. Understanding how this process is coordinated depends on knowing the number and types of genes that each transcription factor binds and regulates. Using immunoprecipitation of in vivo crosslinked chromatin coupled with DNA microarray hybridization (ChIP/chip), we have determined the genomic binding sites in early embryos of six transcription factors that play a crucial role in early development of the fruit fly Drosophila melanogaster. We find that these proteins bind to several thousand genomic regions that lie close to approximately half the protein coding genes. Although this is a much larger number of genes than these factors are generally thought to regulate, we go on to show that whereas the more highly bound genes generally look to ...
One of the largest classes of regulatory proteins in animals, sequence-specific DNA binding transcription factors determine in which cells genes will be expressed and so control the development of an animal from a single cell to a morphologically complex adult. Understanding how this process is coordinated depends on knowing the number and types of genes that each transcription factor binds and regulates. Using immunoprecipitation of in vivo crosslinked chromatin coupled with DNA microarray hybridization (ChIP/chip), we have determined the genomic binding sites in early embryos of six transcription factors that play a crucial role in early development of the fruit fly Drosophila melanogaster. We find that these proteins bind to several thousand genomic regions that lie close to approximately half the protein coding genes. Although this is a much larger number of genes than these factors are generally thought to regulate, we go on to show that whereas the more highly bound genes generally look to ...
One of the largest classes of regulatory proteins in animals, sequence-specific DNA binding transcription factors determine in which cells genes will be expressed and so control the development of an animal from a single cell to a morphologically complex adult. Understanding how this process is coordinated depends on knowing the number and types of genes that each transcription factor binds and regulates. Using immunoprecipitation of in vivo crosslinked chromatin coupled with DNA microarray hybridization (ChIP/chip), we have determined the genomic binding sites in early embryos of six transcription factors that play a crucial role in early development of the fruit fly Drosophila melanogaster. We find that these proteins bind to several thousand genomic regions that lie close to approximately half the protein coding genes. Although this is a much larger number of genes than these factors are generally thought to regulate, we go on to show that whereas the more highly bound genes generally look to ...
EWSR1 encodes a multifunctional protein that is involved in various cellular processes, including gene expression, cell signaling, and RNA processing and transport. The protein includes an N-terminal transcriptional activation domain and a C-terminal RNA-binding domain. Chromosomal translocations between this gene and various genes encoding transcription factors result in the production of chimeric proteins that are involved in tumorigenesis. These chimeric proteins usually consist of the N-terminal transcriptional activation domain of this protein fused to the C-terminal DNA-binding domain of the transcription factor protein. Mutations in this gene, specifically a t(11;22)(q24;q12) translocation, are known to cause Ewing sarcoma as well as neuroectodermal and various other tumors.
Colorectal cancer (CRC) is one of the leading causes of cancer mortality and 5-Fluorouracil (5-FU) is the most common chemotherapy agent of CRC. A high level of X-ray repair cross complementing group 1 (XRCC1) in cancer cells has been associated with the drug resistance occurrence. Moreover, the activation of adenosine monophosphate (AMP)-activated protein kinase (AMPK) has been indicated to regulate the cancer cell survival. Thus, this study was aimed to examine whether XRCC1 plays a role in the 5-FU/AMPK agonist (AICAR)-induced cytotoxic effect on CRC and the underlying mechanisms. Human HCT-116 colorectal cells were used in this study. It was shown that 5-FU increases the XRCC1 expression in HCT-116 cells and then affects the cell survival through CXCR4/Akt signaling. Moreover, 5-FU combined with AICAR further result in more survival inhibition in HCT-116 cells, accompanied with reduced CXCR4/Akt signaling activity and XRCC1 expression. These results elucidate the role and mechanism of XRCC1 in the
These non-specific interactions are formed through basic residues in the histones making ionic bonds to the acidic sugar-phosphate backbone of the DNA, and are therefore largely independent of the base sequence. Chemical modifications of these basic amino acid residues include methylation, phosphorylation and acetylation. These chemical changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to transcription factors and changing the rate of transcription. Other non-specific DNA-binding proteins in chromatin include the high-mobility group proteins, which bind to bent or distorted DNA. These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that make up chromosom ...
For about 10 years until 2000, my labs research activities were focused on the mechanism of recombinational repair of double-strand breaks in DNA. We focused our efforts on two model systems: one involved the repair of restriction enzyme cleavages at specific mammalian chromosomal loci and the second explored the biochemical properties of purified yeast Rad51 protein, an essential catalyst for synapsing the broken ends of DNA with an intact homologue of that sequence. We also explored the roles of Rad52 and PRA (single-strand DNA binding protein) in the repair process.In 2000, I became Emeritus Professor in Biochemistry and stepped down from the Directorship of the Beckman Center. Much of my activities since then have been involved in writing a biography of the genetics pioneer George Beadle, published in 2003, plus articles for other publications elaborating on Beadles legacy for todays science. Over the years I have been and continue to be an activist in public policy issues affecting ...
Damaged DNA-binding protein 2 DDB2 protects against UV irradiation in human cells and Drosophila. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
BACKGROUND: Mycobacterium smegmatis is fast growing non-pathogenicmycobacteria. This organism has been widely used as a model organism tostudy the biology of other virulent and extremely slow growing specieslike Mycobacterium tuberculosis. Based on the homology of the N-terminalDNA binding domain, the recently sequenced genome of M. smegmatis has beenshown to possess several putative GntR regulators. A strikingcharacteristic feature of this family of regulators is that they possess aconserved N-terminal DNA binding domain and a diverse C-terminal domaininvolved in the effector binding and/or oligomerization. Since thephysiological role of these regulators is critically dependent uponeffector binding and operator sites, we have analysed and classified theseregulators into their specific subfamilies and identified their potentialbinding sites. RESULTS: The sequence analysis of M. smegmatis putativeGntRs has revealed that FadR, HutC, MocR and the YtrA-like regulators areencoded by 45, 8, 8 and 1 ...
Individual PREP1 and PBX1 are homeodomain transcriptional elements, whose biochemical and structural characterization hasnt yet been defined fully. of eukaryotic DNA-binding protein that control transcription of a wide selection of developmentally essential genes [1]. These protein talk about a 60 amino acidity DNA-binding domains which includes been conserved in series, system and framework of DNA-binding. While monomeric homeodomain protein exhibit a restricted capability to discriminate between different DNA sequences, their specificity is enhanced through the cooperative binding with various other DNA binding partners significantly. PBX1 (pre-B-cell leukemia homeobox 1) [2,3], and PREP1 (PBX-regulating proteins 1) also called PKNOX1 [4] both participate in the TALE category of homeodomain protein and form a solid and steady DNA-independent complicated [5]. PBX1 includes a nuclear localization indication and holds PREP1 in to the nucleus while subsequently PREP1 stops PBX1 nuclear export ...
Mitochondrial dysfunction has been linked to the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Functional studies of mitochondrial bioenergetics have focused mostly on superoxide dismutase 1 (SOD1) mutants, and showed that mutant human SOD1 impairs mitochondrial oxidative phosphorylation, calcium homeostasis, and dynamics. However, recent reports have indicated that alterations in transactivation response element DNA-binding protein 43 (TDP-43) can also lead to defects of mitochondrial morphology and dynamics. Furthermore, it was proposed that TDP-43 mutations cause oxidative phosphorylation impairment associated with respiratory chain defects and that these effects were caused by mitochondrial localization of the mutant protein. Here, we investigated the presence of bioenergetic defects in the brain of transgenic mice expressing human mutant TDP-43 (TDP-43A315T mice), patient derived fibroblasts, and human cells expressing mutant forms of TDP-43. In
Researchers] display estimates of the predicted transcription factors in five genomes in Table 1, ranging from about 300 in E. coli to over 3000 in humans. These constitute between 6% (in E. coli and yeast) and 8% (in human) of the encoded proteins in these organisms. van Nimwegens [ref 24 PMID 12957540] earlier observation that larger genomes tend to have more transcription factors per gene is in accordance with the trend seen in eukaryotes (Table 1)." See notes beneath ...
ESR1_HUMAN] Nuclear hormone receptor. The steroid hormones and their receptors are involved in the regulation of eukaryotic gene expression and affect cellular proliferation and differentiation in target tissues. Ligand-dependent nuclear transactivation involves either direct homodimer binding to a palindromic estrogen response element (ERE) sequence or association with other DNA-binding transcription factors, such as AP-1/c-Jun, c-Fos, ATF-2, Sp1 and Sp3, to mediate ERE-independent signaling. Ligand binding induces a conformational change allowing subsequent or combinatorial association with multiprotein coactivator complexes through LXXLL motifs of their respective components. Mutual transrepression occurs between the estrogen receptor (ER) and NF-kappa-B in a cell-type specific manner. Decreases NF-kappa-B DNA-binding activity and inhibits NF-kappa-B-mediated transcription from the IL6 promoter and displace RELA/p65 and associated coregulators from the promoter. Recruited to the NF-kappa-B ...
Tumor protein p53, a nuclear protein, plays an essential role in the regulation of cell cycle, specifically in the transition from G0 to G1. It is found in very low levels in normal cells, however, in a variety of transformed cell lines, it is expressed in high amounts, and believed to contribute to transformation and malignancy. p53 is a DNA-binding protein containing DNA-binding, oligomerization and transcription activation domains. It is postulated to bind as a tetramer to a p53-binding site and activate expression of downstream genes that inhibit growth and/or invasion, and thus function as a tumor suppressor. Mutants of p53 that frequently occur in a number of different human cancers fail to bind the consensus DNA binding site, and hence cause the loss of tumor suppressor activity. Alterations of the TP53 gene occur not only as somatic mutations in human malignancies, but also as germline mutations in some cancer-prone families with Li-Fraumeni syndrome ...
Heat shock response in eukaryotes is transcriptionally regulated by conserved heat shock transcription factors (Hsfs). Hsf genes are represented by a large multigene family in plants and investigation of the Hsf gene family will serve to elucidate the mechanisms by which plants respond to stress. In recent years, reports of genome-wide structural and evolutionary analysis of the entire Hsf gene family have been generated in two model plant systems, Arabidopsis and rice. Maize, an important cereal crop, has represented a model plant for genetics and evolutionary research. Although some Hsf genes have been characterized in maize, analysis of the entire Hsf gene family were not completed following Maize (B73) Genome Sequencing Project. A genome-wide analysis was carried out in the present study to identify all Hsfs maize genes. Due to the availability of complete maize genome sequences, 25 nonredundant Hsf genes, named ZmHsfs were identified. Chromosomal location, protein domain and motif organization of
Looking for online definition of heat-shock transcription factor family member 5 in the Medical Dictionary? heat-shock transcription factor family member 5 explanation free. What is heat-shock transcription factor family member 5? Meaning of heat-shock transcription factor family member 5 medical term. What does heat-shock transcription factor family member 5 mean?
This proposed research project seeks to understand environmental stress-responsive gene expression mediated through Heat Shock Transcription Factor (HSF). This project will involve the following three components: 1) a study of the DNA-binding properties of HSF to different stress-responsive promoters using the electrophoretic mobility shift assay to determine the relative binding affinity, and chemical cross linking reagents to determine the multimerization state of HSF; 2) map the sites of phosphorylation on HCF in response to different cellular stress; 3) determine the importance of the phosphorylation of HCF in regulating stress-responsive gene expression in vivo by constructing site directed mutations in the HCF phosphorylation sites and replacing the endogenous copy of HCF with each mutated HCF. Cells expressing the mutationally altered HCF molecules will be tested for their ability to activate CUP transcription in response to heat and oxidative stress. For the first research goal, DNA ...
In vitro replication of papillomavirus DNA has been carried out with a combination of purified proteins and partially purified extracts made from human cells. DNA synthesis requires the viral E1 protein and the papillomavirus origin of replication. The E2 protein stimulates DNA synthesis in a binding site-independent manner. Papillomavirus DNA replication is also dependent on the cellular factors replication protein A, replication factor C, and proliferating-cell nuclear antigen as well as a phosphocellulose column fraction (IIA). Fraction IIA contains DNA polymerase alpha-primase and DNA polymerase delta. Both of these polymerases are essential for papillomavirus DNA replication in vitro. However, unlike the case with T-antigen-dependent replication from the simian virus 40 origin, purified DNA polymerase alpha-primase and delta cannot efficiently replace fraction IIA in the replication reaction. Hence, additional cellular factors seem to be required for papillomavirus DNA replication. ...
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... the protein binds to a non-specific site on the DNA and then it diffuses along the DNA chain until it locates a target site, a ... The in vivo model mentioned above clearly explains 3-D and 1-D diffusion along the DNA strand and the binding of proteins to ... Klenin, Konstantin V.; Merlitz, Holger; Langowski, Jörg; Wu, Chen-Xu (2006). "Facilitated Diffusion of DNA-Binding Proteins". ... 2013), during the process of protein sliding, the protein searches the entire length of the DNA chain using 3-D and 1-D ...
C3orf14-Chromosome 3 open reading frame 14: predicted DNA binding protein.. *C3orf23: encoding protein Uncharacterized protein ... TRAK1: trafficking kinesin-binding protein 1. *TRANK1: encoding protein Tetratricopeptide repeat and ankyrin repeat containing ... ZNF9: zinc finger protein 9 (a cellular retroviral nucleic acid binding protein) ... So CCDS's gene number prediction represents a lower bound on the total number of human protein-coding genes.[5] ...
ion channel binding. • protein binding. • RNA polymerase II transcription factor activity, sequence-specific DNA binding. • RNA ... ID2, GIG8, ID2A, ID2H, bHLHb26, inhibitor of DNA binding 2, HLH protein, inhibitor of DNA binding 2. ... DNA-binding protein inhibitor ID-2 is a protein that in humans is encoded by the ID2 gene.[5] ... The protein encoded by this gene belongs to the inhibitor of DNA binding (ID) family, members of which are transcriptional ...
Robison, K; McGuire, A. M.; Church, G. M. (1998). "A comprehensive library of DNA-binding site matrices for 55 proteins applied ... "Two DNA-binding proteins," Nature 290:736f, see [5], accessed 4 March 2015. ... G. M. Church, J. L. Sussman & S.-H. Kim, 1977, "Secondary structural complementarity between DNA and proteins," Proc. natn. ... his team has developed use of DNA array (aka DNA chip) synthesizers for combinatorial libraries and assembling large genome ...
... , a bacterial histone-like DNA-binding protein. *Wu Hu (disambiguation), an ancient Chinese term for multiple groups in China ...
sequence-specific DNA binding. • DNA binding. • transcription factor binding. • protein domain specific binding. • RNA ... transcription factor activity, sequence-specific DNA binding. • transcription regulatory region DNA binding. • ... HNF-3G is a member of the forkheadclass of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional ... regulation of transcription, DNA-templated. • transcription, DNA-templated. • spermatogenesis. • positive regulation of ...
sequence-specific DNA binding. • DNA binding. • RNA polymerase II regulatory region sequence-specific DNA binding. • protein ... protein binding. • protein heterodimerization activity. • nucleic acid binding. • transcription regulatory region DNA binding. ... identical protein binding. • RNA polymerase II transcription factor activity, sequence-specific DNA binding. ... Zinc finger protein Aiolos also known as Ikaros family zinc finger protein 3 is a protein that in humans is encoded by the ...
"MyoD is a sequence-specific DNA binding protein requiring a region of myc homology to bind to the muscle creatine kinase ... "Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection". ... When expressed, the myoD gene produces a protein referred to as MyoD (or MyoD1), which can bind certain DNA sequences, stop ... which is used to find the DNA-binding sites for proteins. Along with chemist Peter Dervan of Caltech and developmental ...
However, the shape feature of these molecules such as DNA and protein have also been studied and proposed to have an equivalent ... Alipanahi, B; Delong, A; Weirauch, MT; Frey, BJ (Aug 2015). "Predicting the sequence specificities of DNA- and RNA-binding ... Since presently-available DNA sequencing technologies are ill-suited for reading long sequences, large pieces of DNA (such as ... Sequence assembly refers to the reconstruction of a DNA sequence by aligning and merging small DNA fragments. It is an integral ...
Phosphocellulose chromatography utilizes the binding affinity of many DNA-binding proteins for phosphocellulose. The stronger a ... It is often used in biochemistry in the purification of proteins bound to tags. These fusion proteins are labeled with ... Fast protein liquid chromatography[edit]. Further information: Fast protein liquid chromatography. Fast protein liquid ... protein's interaction with DNA, the higher the salt concentration needed to elute that protein.[11] ...
The SRY protein, bound to the double helix of DNA. Ridley contemplates evolutionary psychology using the genes SRY on the Y ... The disaster of Creutzfeldt-Jakob disease in humans was found to be caused by the PRP gene which produces a prion protein that ... Recombinant DNA enabled genetic manipulation with restriction enzymes and a ligase. Genetic engineering has been highly ... "see and use the messages in their own DNA as they see fit." Silver describes the book as remarkable for focusing on "pure ...
Two beta strands with an alpha helix end folded over to bind a zinc ion. Important in DNA binding proteins. ... In most DNA motifs, for example, it is assumed that the DNA of that sequence does not deviate from the normal "double helical" ... In proteinsEdit. In proteins, a structural motif describes the connectivity between secondary structural elements. An ... In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a supersecondary structure, which ...
androgen receptor binding. • RNA binding. • ubiquitin protein ligase binding. • transcription regulatory region DNA binding. • ... tubulin binding. • metal ion binding. • enzyme binding. • zinc ion binding. • damaged DNA binding. • ligação a proteínas ... ubiquitin-protein transferase activity. • DNA binding. • transferase activity. • RNA polymerase II transcription coactivator ... RNA polymerase binding. • identical protein binding. Componente celular. • BRCA1-BARD1 complex. • condensed nuclear chromosome ...
... which in turn are often brought to the promoter DNA by an activator protein's binding to its own DNA binding site nearby.. In ... Identifying a Protein Binding Sites on DNA molecule YouTube tutorial video. *Pleiades Promoter Project - a research project ... In the case of a transcription factor binding site, there may be a single sequence that binds the protein most strongly under ... initial reversible binding of RNA polymerase, conformational changes in RNA polymerase, conformational changes in DNA, binding ...
Zinc finger: Two beta strands with an alpha helix end folded over to bind a zinc ion. Important in DNA binding proteins. Helix- ... In most DNA motifs, for example, it is assumed that the DNA of that sequence does not deviate from the normal "double helical" ... Sequence motif Short linear motif PROSITE Database of protein families and domains SCOP Structural classification of Proteins ... In proteins, a structural motif describes the connectivity between secondary structural elements. An individual motif usually ...
DNA binding. • sequence-specific DNA binding. • protein domain specific binding. • transcription factor activity, sequence- ... Forkhead box protein A2 is a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are ... transcription regulatory region DNA binding. • RNA polymerase II transcription factor activity, sequence-specific DNA binding. ... specific DNA binding. • transcription factor binding. • RNA polymerase II core promoter proximal region sequence-specific DNA ...
Wahls WP, Swenson G, Moore PD (June 1991). "Two hypervariable minisatellite DNA binding proteins". Nucleic Acids Research. 19 ( ... Wahls WP, Swenson G, Moore PD (June 1991). "Two hypervariable minisatellite DNA binding proteins". Nucleic Acids Research. 19 ( ... These hotspots are binding sites for the PRDM9 Zinc Finger array. Upon binding to DNA, PRDM9 catalyzes trimethylation of ... minisatelite binding protein 3). This would later turn out to be the same PRDM9 protein independently identified later. In 2005 ...
"Transcriptional activity among high and low risk human papillomavirus E2 proteins correlates with E2 DNA binding". The Journal ... HeLa cells grown in culture and stained with antibody to tubulin (green), antibody to Ki-67 (red) and the blue DNA binding dye ... Human papillomaviruses (HPVs) are frequently integrated into the cellular DNA in cervical cancers. We mapped by FISH five HPV18 ... Multiphoton fluorescence image of cultured HeLa cells with a fluorescent protein targeted to the Golgi apparatus (orange), ...
The zinc does not directly contact the DNA that these proteins bind to. Instead, the cofactor is essential for the stability of ... For instance, at least 1000 human proteins (out of ~20,000) contain zinc-binding protein domains[3] although there may be up to ... Lead(II) Binding in Natural and Artificial Proteins". In Astrid S, Helmut S, Sigel RK. Lead: Its Effects on Environment and ... The oxygen binding site is a binuclear iron center. The iron atoms are coordinated to the protein through the carboxylate side ...
Patsialou A, Wilsker D, Moran E (2005). "DNA-binding properties of ARID family proteins". Nucleic Acids Research. 33 (1): 66-80 ... type winged-helix DNA-binding domain, and a conserved N-terminal AT-rich DNA interaction domain-the last domain for which the ... "Nomenclature of the ARID family of DNA-binding proteins". Genomics. 86 (2): 242-51. doi:10.1016/j.ygeno.2005.03.013. PMID ... The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Research. 7 (4): 273-81. ...
... proteins have weak DNA-binding capacity. Therefore, to effectively bind DNA, NFAT proteins must cooperate with other ... Nuclear import of NFAT proteins is opposed by maintenance kinases in the cytoplasm and export kinases in the nucleus. Export ... Calcium signaling is critical to NFAT activation because calmodulin (CaM), a well-known calcium sensor protein, activates the ... Macian F (June 2005). "NFAT proteins: key regulators of T-cell development and function". Nature Reviews. Immunology. 5 (6): ...
Patsialou A, Wilsker D, Moran E (2005). "DNA-binding properties of ARID family proteins". Nucleic Acids Research. 33 (1): 66-80 ... a novel ARID class DNA-binding protein, causes growth retardation and abnormal development of reproductive organs". Genome ... "Dynamics of the Mrf-2 DNA-binding domain free and in complex with DNA". Biochemistry. 40 (31): 9142-50. doi:10.1021/bi010476a. ... containing highly conserved putative DNA/chromatin binding motifs is specifically up-regulated in breast cancer". The Journal ...
Ring-shaped DNA-binding protein. Involved in primed adaptation in Type II CRISPR system.. [73]. ... binding double-stranded fragments of invading DNA, while Cas1 binds the single-stranded flanks of the DNA and catalyses their ... CRISPR Cascade protein (cyan) bound to CRISPR RNA (green) and viral DNA (red) ... This interference mechanism is modulated by a modulatory protein, PtiM, binds to one of the interference-mediating proteins, ...
As a result, the expulsion of membrane proteins allows negatively charged DNA to bind.[10] ...
"DNA-binding proteins and evolution of transcription regulation in the archaea". Nucleic Acids Res. 27 (23): 4658-70. PMC 148756 ... Misalnya, DNA polimerase termostabil, seperti Pfu DNA polimerase dari Pyrococcus furiosus, merevolusi biologi molekuler dengan ... itu diperkirakan hanya berisi 537 gen pengkode-protein.[125] Potongan independen kecil dari DNA, yang disebut plasmid, juga ... Protein yang terkait dengan komponen sitoskeleton organisme lain ada di arkea,[82] dan filamen terbentuk dalam sel mereka,[83] ...
"DNA-binding proteins and evolution of transcription regulation in the archaea". Nucleic Acids Res. 27 (23): 4658-70. PMC 148756 ... No membrane-bound organelles or nucleus. No membrane-bound organelles or nucleus. Membrane-bound organelles and nucleus. ... For example, thermostable DNA polymerases, such as the Pfu DNA polymerase from Pyrococcus furiosus, revolutionized molecular ... it is estimated to contain only 537 protein-encoding genes.[129] Smaller independent pieces of DNA, called plasmids, are also ...
RNA polymerase II regulatory region sequence-specific DNA binding. • DNA binding. • sequence-specific DNA binding. • ... Homeobox protein Hox-D8 is a protein that in humans is encoded by the HOXD8 gene.[5][6][7] ... 1989). "Complementary homeo protein gradients in developing limb buds". Genes Dev. 3 (5): 641-50. doi:10.1101/gad.3.5.641. PMID ... regulation of transcription, DNA-templated. • negative regulation of transcription from RNA polymerase II promoter. • positive ...
Schreiber J, Enderich J, Wegner M (May 1998). "Structural requirements for DNA binding of GCM proteins". Nucleic Acids Res. 26 ... in the process of DNA binding and in the redox regulation of DNA binding. The GCM domain as a new class of Zn-containing DNA- ... binding domain with no similarity to any other DNA-binding domain. The GCM domain consists of a large and a small domain ... Akiyama Y, Hosoya T, Poole AM, Hotta Y (December 1996). "The gcm-motif: a novel DNA-binding motif conserved in Drosophila and ...
Custom DNA-binding proteins come of age: Polydactyl zinc-finger proteins. Current Opinion in Biotechnology. 2001 Dec 1;12(6): ... Custom DNA-binding proteins come of age : Polydactyl zinc-finger proteins. / Segal, David; Barbas, Carlos F. ... Segal, D., & Barbas, C. F. (2001). Custom DNA-binding proteins come of age: Polydactyl zinc-finger proteins. Current Opinion in ... Segal, D & Barbas, CF 2001, Custom DNA-binding proteins come of age: Polydactyl zinc-finger proteins, Current Opinion in ...
Previous studies have suggested that the lysine-rich N-terminus of Dps proteins participates in DNA binding. Accordingly, ... The release of iron from the core upon DNA binding suggests that Dps-1 may be involved in the process of DNA degradation that ... Dodecameric Dps-1 can bind ? 22bp DNA duplexes with very high affinity (Kd ~0.4 nM); considering interactions in the DNA major ... Stoichiometric titration of dodecameric Dps-1 with 22 bp DNA revealed the presence of 6 DNA binding sites in each dodecamer. ...
The physical ends of eukaryotic chromosomes form a specialized nucleoprotein complex composed of DNA and DNA binding proteins. ... DNA binding proteins and the second paper shows the identification and initial characterization of a telomeric DNA binding ... the DNA portion of the nucleo-protein complex consists of simple tandem DNA repeats with one strand guanine rich. The protein ... presented in two recent papers represent different stages in the characterization of the telomeric DNA binding proteins. The ...
... Steve Rodems smrodems at students.wisc.edu Thu Apr 21 19:06:28 EST 1994 *Previous message: Has ... Does anyone use DNA binding proteins expressed in rabbit reticulocyte lysates to do gel shift assays? This system would allow ... easy and quick expression of a suspected DNA binding protein that I could study (much easier than trying to express and purify ... the protein). I would specifically like to know if the other proteins in the system or maybe even the DNA added would somehow ...
Each protein contains three DNA-binding motifs, known as AT-hooks, that bind in the minor groove of AT tracts in DNA. Multiple ... HMG-I proteins are DNA-binding proteins thought to affect the formation and function of transcription complexes. ... Multivalent DNA-binding properties of the HMG-1 proteins. J F Maher and D Nathans ... we demonstrate that high-affinity binding uses two or three appropriately spaced AT tracts as a single multivalent binding site ...
I need to purify some proteins which bind to DNA. I use DNA binding protein purification kit from Boerhinger with long ... DNA binding protein purification. Joel Baguet Joel.Baguet at ens-lyon.fr Mon Dec 14 11:37:15 EST 1998 *Previous message: Thank ... The protein-binding conditions are those for gel retardation assay. The results are very poor (about 1% with 35S in vitro ... concatamers of protein-binding oligonucleotide (obtainrd using self-primed PCR technique) ligated streptavidin magnetic ...
WT-DNA,. wild-type DNA;. MT-DNA,. mutant DNA;. BD,. binding domain;. HD,. homeodomain;. AD,. activation domain;. SAAB,. ... A) WT-DNA and MT-DNA binding sites were used as probes. (B) T7-KN1 was incubated with WT-DNA probe (W) or MT-DNA probe (M). (C ... KN1 and T7-KIP were mixed together in DNA binding assays at 1 ng or 10 ng of each protein per reaction. DNA-binding specificity ... This half site is also critical for DNA binding of the MEIS protein. Slight variations in these TALE HD DNA-binding motifs ...
The DNA-binding specificity of SOX9 and other SOX proteins.. Mertin S1, McDowall SG, Harley VR. ... How different SOX proteins achieve specific regulation of target genes is not known. We determined the DNA-binding specificity ... The optimal SOX9 binding sequence, AGAACAATGG, contained a core DNA-binding element AACAAT, flanked by 5 AG and 3 GG ... Our studies support the notion that SOX proteins achieve DNA sequence specificity through subtle preferences for flanking ...
When PB transposase is fused to a DNA-binding protein, it causes PB to integrate into the genome near the binding sites for ... "Calling Cards" for DNA-Binding Proteins in Mammalian Cells. Haoyi Wang, David Mayhew, Xuhua Chen, Mark Johnston and Robi David ... "Calling Cards" for DNA-Binding Proteins in Mammalian Cells. Haoyi Wang, David Mayhew, Xuhua Chen, Mark Johnston and Robi David ... "Calling Cards" for DNA-Binding Proteins in Mammalian Cells. Haoyi Wang, David Mayhew, Xuhua Chen, Mark Johnston and Robi David ...
... binds with high affinity to single-stranded DNA but does not bind well to double-stranded ... E. coli Single-Stranded DNA Binding Protein (SSB) consists of four identical 18.9kDa subunits that cooperatively bind to single ... This protein is involved in DNA replication and in recombination in vivo. ... Studying DNA replication and recombination. *DNA sequencing using the primer walking strategy with contiguous oligonucleotides ...
... we transplanted the DNA-binding region of MyoD intro helix 3 of protein Z. MyoD is a bHLH domain DNA-binding protein [17]. The ... MD Simulations of the Protein-DNA Complex. Simulations of the protein-DNA complexes were performed using Amber 10 [25]. Protein ... Protein Z and MyoD. Protein Z is derived from staphylococcal protein A and holds an IgG Fc-binding domain. It consists of a ... As mentioned before, four Amber simulations were performed to check the models DNA-binding abilities. Protein-DNA interactions ...
... the number of known DNA-binding proteins is very small compared to the large non-DNA-binding proteins and unknown proteins. DNA ... Among them, 525 are DNA-binding and 550 are non-DNA-binding protein sequences. All the protein sequences were taken from PDB [ ... K. K. Kumar, G. Pugalenthi, and P. N. Suganthan, "DNA-prot: identification of DNA binding proteins from protein sequence ... 17] constructed this independent dataset consisting of 93 DNA-binding and 93 non-DNA-binding protein sequences. They used ...
... a mono-ubiquitin-binding protein. FAN1 has a DNA branch-specific nuclease activity that is required for the removal and ... The nuclease FAN1 acts with Fanconi anemia proteins to help repair damaged DNA. ... The nuclease FAN1 acts with Fanconi anemia proteins to help repair damaged DNA. ... Mutations in 13 different genes implicated in repairing damaged DNA are known to be involved in the disease. Liu et al. have ...
We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their ... InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites ... protein]-cysteine S-methyltransferase, DNA binding (IPR014048). Key Species. Key species. Number of proteins. FASTA. Protein ... unclassified sequences unclassified sequences 262 proteins, FASTA , Protein IDs * Viruses Viruses 20 proteins, FASTA , Protein ...
The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex ... Histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under ... Protein disorder predictions are based on JRONN (Troshin, P. and Barton, G. J. unpublished), a Java implementation of RONN * ... The Protein Feature View requires a browser that supports SVG (Scalable Vector Graphics). Mouse over tracks and labels for more ...
The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex ... "single-stranded DNA-binding protein", "single-stranded DNA binding protein 1", "single-stranded DNA binding protein 1, ... White boxes represent UTRs (untranslated regions). Orange: protein coding regions. The black lines connecting boxes represent ...
... Kim J., Sif S., Jones B., ... The Ikaros gene family encodes zinc finger DNA-binding proteins essential for lineage determination and control of ... Here, we report that, in the nucleus of a T cell, a major fraction of Ikaros and Aiolos proteins associate with the DNA- ... European Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics. UniProt is an ELIXIR core ...
Tyrosine phosphorylation of DNA binding proteins by multiple cytokines. By AC Larner, M David, GM Feldman, K Igarashi, RH ... Tyrosine phosphorylation of DNA binding proteins by multiple cytokines. By AC Larner, M David, GM Feldman, K Igarashi, RH ... Tyrosine phosphorylation of DNA binding proteins by multiple cytokines Message Subject. (Your Name) has forwarded a page to you ... activated DNA binding proteins that recognized the IFN-gamma response region (GRR) located in the promoter of the Fc gamma RI ...
Abcam provides general protocols for DNA-Protein Binding Assay Kit (Colorimetric) (ab117139). Please download our pdf protocol ... Proteins and Peptides. Proteomics tools. Agonists, activators, antagonists and inhibitors. Lysates. Multiplex miRNA assays. By ... Epigenetics and Nuclear Signaling Chromatin Binding Proteins DNA / RNA binding Share by email ...
... DSpace/Manakin Repository. * DASH Home ... Differential Disruption of EWS-FLI1 Binding by DNA-Binding Agents Chen, Changmin; Wonsey, Diane R.; Lemieux, Madeleine E.; Kung ... CCAAT/Enhancer-Binding Protein \(\gamma\) Is a Critical Regulator of IL-1\(\beta\)-Induced IL-6 Production in Alveolar ... Cyclic AMP Responsive Element Binding Proteins Are Involved in Emergency Granulopoiesis through the Upregulation of CCAAT/ ...
The assay effectively detected blotted DNA-binding proteins. At least 17 gonococcal DNA-binding proteins were identified; ... lacked DNA-binding activity at the 11-kDa protein in BI. The segregation of DNA-binding proteins within BI and BII correlates ... Certain DNA-binding proteins had varied affinities for single- and double-stranded DNA, and the intact transformation uptake ... DNA-binding proteins in cells and membrane blebs of Neisseria gonorrhoeae. Message Subject (Your Name) has forwarded a page to ...
RFX binds the X1 box of MHC-II promoters (PubMed:9806546, PubMed:10072068, PubMed:10725724). May also potentiate the activation ... DNA-binding protein RFXANK. DNA-binding protein RFXANK (Regulatory factor X-associated ankyrin-containing protein, isoform CRA_ ... sp,O14593,RFXK_HUMAN DNA-binding protein RFXANK OS=Homo sapiens OX=9606 GN=RFXANK PE=1 SV=2 ... Protein. Similar proteins. Species. Score. Length. Source. O14593. Regulatory factor X-associated ankyrin-containing protein, ...
Many specific DNA-binding proteins bind to sites with dyad symmetry, and the bound form of the protein is a dimer. For some ... Dimerization of a specific DNA-binding protein on the DNA Message Subject. (Your Name) has forwarded a page to you from Science ... dimers form in solution and bind to DNA. LexA repressor of Escherichia coli has been used to test an alternative binding model ... A second monomer bound to an intact operator far more tightly than the first monomer; this cooperativity arose from protein- ...
Protein-DNA interactions are vitally important in a wide range of biological processes such as gene regulation and DNA ...
... and future directions in protein DNA-binding site prediction. In particular, we detail the meta-analysis of protein DNA-binding ... In the last decade, numerous computational approaches have been developed to predict protein DNA-binding sites based on protein ... sequence-based DNA-binding site prediction, structure-based DNA-binding site prediction, and homology modeling and threading. ... In this article, we review existing research on computational methods to predict protein DNA-binding sites, which includes data ...
  • I would specifically like to know if the other proteins in the system or maybe even the DNA added would somehow interfere in a gel shift assay (although I guess its no different than using cell/nuclear extracts). (bio.net)
  • Ku is an abundant nuclear protein and is present in vertebrates, insects, yeast, and worms. (nih.gov)
  • In 2006, TAR DNA-binding protein 43 (TDP-43), a highly conserved nuclear protein, was identified as the major disease protein in amyotrophic lateral sclerosis (ALS) and in the most common variant of frontotemporal lobar degeneration (FTLD), FTLD-U, which is characterized by cytoplasmic inclusions that stain positive for ubiquitin but negative for tau and alpha-synuclein. (rutgers.edu)
  • It involves incubation of nuclear extract proteins with 5'biotinylated double-stranded DNA probes and streptavidin-agarose beads. (springer.com)
  • DNA fragments encompassing SNPs, and risk or non‑risk alleles were immobilized onto the novel nanobeads and DNAbinding proteins were purified from the nuclear extracts of pancreatic β cells using these DNA‑immobilized nanobeads. (spandidos-publications.com)
  • Base J (β-D-glucosyl-hydroxymethyluracil) was discovered in the nuclear DNA of some pathogenic protozoa, such as trypanosomes and Leishmania, where it replaces a fraction of base T. We have found a J-Binding Protein 1 (JBP1) in these organisms, which contains a unique J-DNA binding domain (DB-JBP1) and a thymidine hydroxylase domain involved in the first step of J biosynthesis. (diva-portal.org)
  • The DNA is maintained by several nuclear-encoded proteins. (spandidos-publications.com)
  • The HD is a conserved structure that contains three α helices, and a sequence motif in the third helix recognizes and binds to the appropriate DNA sequence ( 15 ). (pnas.org)
  • Fbw7 recognizes a destruction signal on certain proteins that need to be degraded and brings them in close proximity to the enzymes that attach ubiquitin. (bio-medicine.org)
  • The studies discussed in this thesis unify experimental and theoretical techniques, both established and novel, in investigating the problem of how a protein that binds specific sites on DNA translocates to, recognizes, and stably binds to its target site or sites. (harvard.edu)
  • TDP-43 is a multi-functional RNA/DNA-binding protein well-conserved among many species including mammals and Drosophila. (sdbonline.org)
  • The individual A and B boxes (which, although broadly similar, show both structural and functional differences) exhibit many of the structure-specific properties of the whole protein. (biochemsoctrans.org)
  • This thesis includes structural biochemical work in combination with mutational and functional studies of proteins from both human and virus. (diva-portal.org)
  • We have also made progress toward understanding the functional implications of disorder in DNA binding / transcription. (cam.ac.uk)
  • The findings of this study indicate that our comparative method using novel nanobeads is effective for the identification of allele‑specific DNA‑binding proteins, which may provide important clues for the functional impact of disease‑associated non‑coding SNPs. (spandidos-publications.com)
  • Although individual members of the HU family have diverged in their DNA binding properties, even distant homologs display functional similarities, constraining negative supercoils and binding not only B-form but also structurally unusual DNA such as cruciforms ( Grove, 2011 ). (elifesciences.org)
  • At this time, how the absence of a functional SMAD protein leads to a tumor is unknown. (biologists.org)
  • Collectively, our findings suggest that CHD2 is a multi-functional protein working with the paraspeckle protein complex to facilitate both the pre-mRNA splicing process and the initial DNA repair process. (tennessee.edu)
  • These proteins, collectively referred to as MEIS, include the myeloid ecotropic viral integration site (MEIS) and pre-B cell homeobox (PBX)-regulating protein 1 (PREP1) family in vertebrates and Homothorax (HTH) in Drosophila ( 16 ). (pnas.org)
  • The biochemical function of the MEINOX domain in MEIS proteins is to mediate heterodimerization with another group of TALE HD proteins, PBX in vertebrates and extradenticle (EXD) in Drosophila ( 17 - 21 ). (pnas.org)
  • Bas van Steensel, of the University of Amsterdam, and colleagues tested their strategy in the fruit fly Drosophila melanogaster by pinpointing the binding sites of the three fly proteins HP-1, GAF and Sir2 that bind DNA. (genomenewsnetwork.org)
  • These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that form chromosomes. (wikipedia.org)
  • We discovered classes of DNA-binding factors that strictly avoided, could tolerate or tended to overlap with nucleosomes. (nih.gov)
  • The purpose of this study was to evaluate expression of methyl-CpG-binding protein 2 (MeCP2) in epiretinal membranes from patients with proliferative vitreoretinopathy (PVR) and to investigate effects of inhibition of MeCP2 and DNA methylation on transforming growth factor (TGF)-β-induced retinal pigment epithelial (RPE) cell transdifferentiation. (arvojournals.org)
  • T antigen also inactivates some of the most important proteins that protect cells against malignant transformation, including tumor suppressor proteins p53 and pRb. (bio-medicine.org)
  • In the Journal of Biological Chemistry paper, Dr. Welcker and Dr. Bruce Clurman report that T antigen also binds to another tumor suppressor, Fbw7. (bio-medicine.org)
  • Structure determined for p53 tumor suppressor protein as bound to DNA for anti-cancer activity ( More than half of human cancers involve. (bio-medicine.org)
  • The experiments presented in two recent papers represent different stages in the characterization of the telomeric DNA binding proteins. (nih.gov)
  • The first paper presents a structure-function study of the Oxytricha telomeric DNA binding proteins and the second paper shows the identification and initial characterization of a telomeric DNA binding activity from Xenopus laevis. (nih.gov)
  • From a larger perspective, our study shows that the genetic characterization of missense mutations, particularly in modular proteins, requires experimental verification. (biologists.org)
  • In all the species tested, the distribution of nucleoid proteins by their mol wts was similar, especially between the predominant proteins with mol wts of 10 to 40 kD. (deepdyve.com)
  • Ku contains ssDNA-dependent ATPase and ATP-dependent DNA helicase activities. (nih.gov)
  • Further, sequence domain families were mapped to structures in the protein databank (PDB) and the protein domain structure classification database (SCOP). (ncbs.res.in)
  • The results show that, in remarkable contrast to other phage SSBs, the Orf14(bIL67)-like proteins form a distinct, self-contained and well supported phylogenetic group connected to the archaeal SSBs. (sigmaaldrich.com)
  • All methods supported the recognition of these phage proteins as a new family within the SSB superfamily. (sigmaaldrich.com)
  • Here we introduce a new approach for the screening of DNA binding proteins, using a phage library based on a phage display technique. (ejbiotechnology.info)
  • In principal, a complementary DNA (cDNA) library based on the recombinant bacteriophage T7 expressing target proteins on its capsid (phage display) is constructed. (ejbiotechnology.info)
  • These phage particles are hybridized with a biotinylated target DNA fragment which is immobilized on the surface of streptavidin paramagnetic particle (SA-PMP). (ejbiotechnology.info)
  • The phage particles are released from the target DNA fragment by a nuclease treatment and the recovered phages are used to the next round of hybridization. (ejbiotechnology.info)
  • We could validate that our new application of phage display is a superior method for isolation of DNA binding proteins with a broad range of potential applications. (ejbiotechnology.info)
  • Many specific DNA-binding proteins bind to sites with dyad symmetry, and the bound form of the protein is a dimer. (sciencemag.org)
  • The lac repressor protein is a dimer of two identical subunits and each one binds a short segment with the core sequence ATTGT. (blogspot.com)
  • This naturally occurring form contains a pairing of two p53 proteins, called a dimer, that then binds to a second p53 dimer in a similar way to create the precisely oriented four-protein complex, called a tetramer, that binds DNA. (bio-medicine.org)
  • Now, in a new study featured as a "paper of the week" and on the cover of the July 21 issue of the Journal of Biological Chemistry, researchers at The Wistar Institute have successfully determined the three-dimensional structure of the p53 protein bound as a dimer to DNA and used the structure to produce an accurate model of the p53 tetramer bound to DNA. (bio-medicine.org)
  • One new insight from the current study, for example, is that the point of contact between the two core domains of a pair of p53 proteins forming a dimer tracks to a part of the protein often mutated in cancers. (bio-medicine.org)
  • This suggests that the interface between the two proteins of the dimer is likely as important for the proper functioning of the tetramer as its interface with DNA, which also depends on the interface of the core domains of the two p53 proteins that form a dimer. (bio-medicine.org)
  • In seeking to determine the structure of p53 bound to DNA, the challenge for the scientists was that their efforts to crystallize the p53 dimer bound to DNA consistently resulted in structures that could not bind to DNA. (bio-medicine.org)
  • There's an inactive form of the p53 dimer that's unable to bind DNA in the correct fashion," Marmorstein explains. (bio-medicine.org)
  • The core domain is what's binding the DNA, but within the dimer, the two cores have to be in the proper orientation to bind DNA. (bio-medicine.org)
  • That allowed us to trap the form of the p53 dimer that's compatible with DNA binding. (bio-medicine.org)
  • Fanconi anemia patients suffer a number of symptoms, including increased sensitivity to chemicals that cross-link DNA strands of the double helix together. (sciencemag.org)
  • The DNA double helix consists of two strands coiled around each other. (elifesciences.org)
  • I use DNA binding protein purification kit from Boerhinger with long concatamers of protein-binding oligonucleotide (obtainrd using self-primed PCR technique) ligated streptavidin magnetic particles. (bio.net)
  • The DNA tumor virus simian virus 40 produces the Large T antigen which. (bio-medicine.org)
  • The DNA tumor virus simian virus 40 produces the Large T antigen which inactivates two of the cell's most important cancer-preventing proteins, p53 and pRb. (bio-medicine.org)
  • In a study published in the Journal of Biological Chemistry, researchers at the Fred Hutchinson Cancer Research Center report the discovery of an additional target for T antigen--a protein called Fbw7. (bio-medicine.org)
  • SV40 T antigen contains a motif that mimics the destruction signal found in these proteins. (bio-medicine.org)
  • All TGFβ family members use this mechanism, and MAD-related proteins (the SMAD family) are found in many species. (biologists.org)
  • Odintsova, M. 2004-10-10 00:00:00 A comparative analysis of proteins from chloroplast nucleoids was performed in two higher-plant species (Pisum sativumL. (deepdyve.com)