Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.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.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.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.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.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.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.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Basic Helix-Loop-Helix Transcription Factors: A family of DNA-binding transcription factors that contain a basic HELIX-LOOP-HELIX MOTIF.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.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.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.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.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.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Forkhead Transcription Factors: A subclass of winged helix DNA-binding proteins that share homology with their founding member fork head protein, Drosophila.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).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.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.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.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).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.Transcription Factor AP-2: A family of DNA binding proteins that regulate expression of a variety of GENES during CELL DIFFERENTIATION and APOPTOSIS. Family members contain a highly conserved carboxy-terminal basic HELIX-TURN-HELIX MOTIF involved in dimerization and sequence-specific DNA binding.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 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)Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.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.Kruppel-Like Transcription Factors: A family of zinc finger transcription factors that share homology with Kruppel protein, Drosophila. They contain a highly conserved seven amino acid spacer sequence in between their ZINC FINGER MOTIFS.Transcription Factors, TFII: The so-called general transcription factors that bind to RNA POLYMERASE II and that are required to initiate transcription. They include TFIIA; TFIIB; TFIID; TFIIE; TFIIF; TFIIH; TFII-I; and TFIIJ. In vivo they apparently bind in an ordered multi-step process and/or may form a large preinitiation complex called RNA polymerase II holoenzyme.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.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.YY1 Transcription Factor: A ubiquitously expressed zinc finger-containing protein that acts both as a repressor and activator of transcription. It interacts with key regulatory proteins such as TATA-BINDING PROTEIN; TFIIB; and ADENOVIRUS E1A PROTEINS.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.STAT3 Transcription Factor: A signal transducer and activator of transcription that mediates cellular responses to INTERLEUKIN-6 family members. STAT3 is constitutively activated in a variety of TUMORS and is a major downstream transducer for the CYTOKINE RECEPTOR GP130.GATA4 Transcription Factor: A GATA transcription factor that is expressed in the MYOCARDIUM of developing heart and has been implicated in the differentiation of CARDIAC MYOCYTES. GATA4 is activated by PHOSPHORYLATION and regulates transcription of cardiac-specific genes.Transcription Factor TFIID: The major sequence-specific DNA-binding component involved in the activation of transcription of RNA POLYMERASE II. It was originally described as a complex of TATA-BOX BINDING PROTEIN and TATA-BINDING PROTEIN ASSOCIATED FACTORS. It is now know that TATA BOX BINDING PROTEIN-LIKE PROTEINS may take the place of TATA-box binding protein in the complex.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.Activating Transcription Factor 3: An activating transcription factor that plays a key role in cellular responses to GENOTOXIC STRESS and OXIDATIVE STRESS.NFATC Transcription Factors: A family of transcription factors characterized by the presence of highly conserved calcineurin- and DNA-binding domains. NFAT proteins are activated in the CYTOPLASM by the calcium-dependent phosphatase CALCINEURIN. They transduce calcium signals to the nucleus where they can interact with TRANSCRIPTION FACTOR AP-1 or NF-KAPPA B and initiate GENETIC TRANSCRIPTION of GENES involved in CELL DIFFERENTIATION and development. NFAT proteins stimulate T-CELL activation through the induction of IMMEDIATE-EARLY GENES such as INTERLEUKIN-2.Sp3 Transcription Factor: A specificity protein transcription factor that regulates expression of a variety of genes including VASCULAR ENDOTHELIAL GROWTH FACTOR and CYCLIN-DEPENDENT KINASE INHIBITOR P27.Transcription Initiation Site: The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.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.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.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.Paired Box Transcription Factors: A family of transcription factors that control EMBRYONIC DEVELOPMENT within a variety of cell lineages. They are characterized by a highly conserved paired DNA-binding domain that was first identified in DROSOPHILA segmentation 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.Activating Transcription Factor 2: An activating transcription factor that regulates expression of a variety of GENES including C-JUN GENES; CYCLIN A; CYCLIN D1; and ACTIVATING TRANSCRIPTION FACTOR 3.Transcription Factor TFIIB: An RNA POLYMERASE II specific transcription factor. It plays a role in assembly of the pol II transcriptional preinitiation complex and has been implicated as a target of gene-specific transcriptional activators.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.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.E2F1 Transcription Factor: An E2F transcription factor that interacts directly with RETINOBLASTOMA PROTEIN and CYCLIN A and activates GENETIC TRANSCRIPTION required for CELL CYCLE entry and DNA synthesis. E2F1 is involved in DNA REPAIR and APOPTOSIS.RNA Polymerase II: A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 2.7.7.6.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.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.Basic Helix-Loop-Helix Leucine Zipper Transcription Factors: A family of transcription factors that contain regions rich in basic residues, LEUCINE ZIPPER domains, and HELIX-LOOP-HELIX MOTIFS.MEF2 Transcription Factors: Activating transcription factors of the MADS family which bind a specific sequence element (MEF2 element) in many muscle-specific genes and are involved in skeletal and cardiac myogenesis, neuronal differentiation and survival/apoptosis.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.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.GATA3 Transcription Factor: A GATA transcription factor that is found predominately in LYMPHOID CELL precursors and has been implicated in the CELL DIFFERENTIATION of HELPER T-CELLS. Haploinsufficiency of GATA3 is associated with HYPOPARATHYROIDISM; SENSORINEURAL HEARING LOSS; and renal anomalies syndrome.GATA1 Transcription Factor: A GATA transcription factor that is specifically expressed in hematopoietic lineages and plays an important role in the CELL DIFFERENTIATION of ERYTHROID CELLS and MEGAKARYOCYTES.GATA2 Transcription Factor: An essential GATA transcription factor that is expressed primarily in HEMATOPOIETIC STEM CELLS.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.TCF Transcription Factors: A family of DNA-binding proteins that are primarily expressed in T-LYMPHOCYTES. They interact with BETA CATENIN and serve as transcriptional activators and repressors in a variety of developmental processes.GATA Transcription Factors: A family of transcription factors that contain two ZINC FINGER MOTIFS and bind to the DNA sequence (A/T)GATA(A/G).Microphthalmia-Associated Transcription Factor: A basic helix-loop-helix leucine zipper transcription factor that regulates the CELL DIFFERENTIATION and development of a variety of cell types including MELANOCYTES; OSTEOCLASTS; and RETINAL PIGMENT EPITHELIUM. Mutations in MITF protein have been associated with OSTEOPETROSIS and WAARDENBURG SYNDROME.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.STAT1 Transcription Factor: A signal transducer and activator of transcription that mediates cellular responses to INTERFERONS. Stat1 interacts with P53 TUMOR SUPPRESSOR PROTEIN and regulates expression of GENES involved in growth control and APOPTOSIS.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.Activating Transcription Factors: Activating transcription factors were originally identified as DNA-BINDING PROTEINS that interact with early promoters from ADENOVIRUSES. They are a family of basic leucine zipper transcription factors that bind to the consensus site TGACGTCA of the cyclic AMP response element, and are closely related to CYCLIC AMP-RESPONSIVE DNA-BINDING PROTEIN.Transcription Factor RelA: A subunit of NF-kappa B that is primarily responsible for its transactivation function. It contains a C-terminal transactivation domain and an N-terminal domain with homology to PROTO-ONCOGENE PROTEINS C-REL.E2F Transcription Factors: A family of basic helix-loop-helix transcription factors that control expression of a variety of GENES involved in CELL CYCLE regulation. E2F transcription factors typically form heterodimeric complexes with TRANSCRIPTION FACTOR DP1 or transcription factor DP2, and they have N-terminal DNA binding and dimerization domains. E2F transcription factors can act as mediators of transcriptional repression or transcriptional activation.Cell Line, Tumor: A cell line derived from cultured tumor cells.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.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.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.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.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.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.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.GATA6 Transcription Factor: A GATA transcription factor that is expressed predominately in SMOOTH MUSCLE CELLS and regulates vascular smooth muscle CELL DIFFERENTIATION.Activating Transcription Factor 4: An activating transcription factor that regulates the expression of a variety of GENES involved in amino acid metabolism and transport. It also interacts with HTLV-I transactivator protein.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.Transcription Factor 7-Like 1 Protein: A transcription factor that takes part in WNT signaling pathway where it may play a role in the differentiation of KERATINOCYTES. The transcriptional activity of this protein is regulated via its interaction with BETA CATENIN.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.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.Transcription Factor TFIIIA: One of several general transcription factors that are specific for RNA POLYMERASE III. It is a zinc finger (ZINC FINGERS) protein and is required for transcription of 5S ribosomal genes.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.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.Mice, Knockout: Strains of mice in which certain GENES of their GENOMES have been disrupted, or "knocked-out". To produce knockouts, using RECOMBINANT DNA technology, the normal DNA sequence of the gene being studied is altered to prevent synthesis of a normal gene product. Cloned cells in which this DNA alteration is successful are then injected into mouse EMBRYOS to produce chimeric mice. The chimeric mice are then bred to yield a strain in which all the cells of the mouse contain the disrupted gene. Knockout mice are used as EXPERIMENTAL ANIMAL MODELS for diseases (DISEASE MODELS, ANIMAL) and to clarify the functions of the genes.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.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.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.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.Down-Regulation: A negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.Proto-Oncogene Proteins c-jun: Cellular DNA-binding proteins encoded by the c-jun genes (GENES, JUN). They are involved in growth-related transcriptional control. There appear to be three distinct functions: dimerization (with c-fos), DNA-binding, and transcriptional activation. Oncogenic transformation can take place by constitutive expression of c-jun.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.Proto-Oncogene Proteins c-ets: A family of transcription factors that share a unique DNA-binding domain. The name derives from viral oncogene-derived protein oncogene protein v-ets of the AVIAN ERYTHROBLASTOSIS VIRUS.Mice, Transgenic: Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.Up-Regulation: A positive regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.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.Transcription Factor TFIIH: A general transcription factor that is involved in basal GENETIC TRANSCRIPTION and NUCLEOTIDE EXCISION REPAIR. It consists of nine subunits including ATP-DEPENDENT DNA HELICASES; CYCLIN H; and XERODERMA PIGMENTOSUM GROUP D PROTEIN.Mice, Inbred C57BLSOX9 Transcription Factor: A SOXE transcription factor that plays a critical role in regulating CHONDROGENESIS; OSTEOGENESIS; and male sex determination. Loss of function of the SOX9 transcription factor due to genetic mutations is a cause of CAMPOMELIC DYSPLASIA.Transcription Factor TFIIA: An RNA POLYMERASE II specific transcription factor. It may play a role in transcriptional activation of gene expression by interacting with the TATA-BOX BINDING PROTEIN component of TRANSCRIPTION FACTOR TFIID.DNA-Directed RNA Polymerases: Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).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.Histones: Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.STAT5 Transcription Factor: A signal transducer and activator of transcription that mediates cellular responses to a variety of CYTOKINES. Stat5 activation is associated with transcription of CELL CYCLE regulators such as CYCLIN KINASE INHIBITOR P21 and anti-apoptotic genes such as BCL-2 GENES. Stat5 is constitutively activated in many patients with acute MYELOID LEUKEMIA.Transcription Factor DP1: A transcription factor that possesses DNA-binding and E2F-binding domains but lacks a transcriptional activation domain. It is a binding partner for E2F TRANSCRIPTION FACTORS and enhances the DNA binding and transactivation function of the DP-E2F complex.In Situ Hybridization: A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.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.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)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.T-Box Domain Proteins: Proteins containing a region of conserved sequence, about 200 amino acids long, which encodes a particular sequence specific DNA binding domain (the T-box domain). These proteins are transcription factors that control developmental pathways. The prototype of this family is the mouse Brachyury (or T) gene product.Fungal Proteins: Proteins found in any species of fungus.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.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.Octamer Transcription Factor-1: A ubiquitously expressed octamer transcription factor that regulates GENETIC TRANSCRIPTION of SMALL NUCLEAR RNA; IMMUNOGLOBULIN GENES; and HISTONE H2B genes.Regulatory Elements, Transcriptional: Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.Gene Expression Regulation, Enzymologic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Gene Expression Regulation, Neoplastic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.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.Erythroid-Specific DNA-Binding Factors: A group of transcription factors that were originally described as being specific to ERYTHROID CELLS.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.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.Transcription Factors, TFIII: Factors that bind to RNA POLYMERASE III and aid in transcription. They include the assembly factors TFIIIA and TFIIIC and the initiation factor TFIIIB. All combine to form a preinitiation complex at the promotor that directs the binding of RNA POLYMERASE III.GA-Binding Protein Transcription Factor: A heterotetrameric transcription factor composed of two distinct proteins. Its name refers to the fact it binds to DNA sequences rich in GUANINE and ADENINE. GA-binding protein integrates a variety of SIGNAL TRANSDUCTION PATHWAYS and regulates expression of GENES involved in CELL CYCLE control, PROTEIN BIOSYNTHESIS, and cellular METABOLISM.Cell Lineage: The developmental history of specific differentiated cell types as traced back to the original STEM CELLS in the embryo.Gene Regulatory Networks: Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations.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.Early Growth Response Protein 1: An early growth response transcription factor that has been implicated in regulation of CELL PROLIFERATION and APOPTOSIS.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.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.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.RNA Interference: A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.RNA, Small Interfering: Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.High Mobility Group Proteins: A family of low-molecular weight, non-histone proteins found in chromatin.Bacterial Proteins: Proteins found in any species of bacterium.Cell Proliferation: All of the processes involved in increasing CELL NUMBER including CELL DIVISION.Transcription Factor 7-Like 2 Protein: A transcription factor that takes part in WNT signaling pathway. The activity of the protein is regulated via its interaction with BETA CATENIN. Transcription factor 7-like 2 protein plays an important role in the embryogenesis of the PANCREAS and ISLET CELLS.Proto-Oncogene Protein c-ets-1: An ets proto-oncogene expressed primarily in adult LYMPHOID TISSUE; BRAIN; and VASCULAR ENDOTHELIAL CELLS.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.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)Reverse Transcription: The biosynthesis of DNA carried out on a template of RNA.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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Apoptosis: One of the mechanisms by which CELL DEATH occurs (compare with NECROSIS and AUTOPHAGOCYTOSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA; (DNA FRAGMENTATION); at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth.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.Twist Transcription Factor: A basic helix-loop-helix transcription factor that was originally identified in DROSOPHILA as essential for proper gastrulation and MESODERM formation. It plays an important role in EMBRYONIC DEVELOPMENT and CELL DIFFERENTIATION of MUSCLE CELLS, and is found in a wide variety of organisms.NF-E2 Transcription Factor, p45 Subunit: A tissue-specific subunit of NF-E2 transcription factor that interacts with small MAF PROTEINS to regulate gene expression. P45 NF-E2 protein is expressed primarily in MEGAKARYOCYTES; ERYTHROID CELLS; and MAST CELLS.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Chloramphenicol O-Acetyltransferase: An enzyme that catalyzes the acetylation of chloramphenicol to yield chloramphenicol 3-acetate. Since chloramphenicol 3-acetate does not bind to bacterial ribosomes and is not an inhibitor of peptidyltransferase, the enzyme is responsible for the naturally occurring chloramphenicol resistance in bacteria. The enzyme, for which variants are known, is found in both gram-negative and gram-positive bacteria. EC 2.3.1.28.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Proto-Oncogene Proteins c-fos: Cellular DNA-binding proteins encoded by the c-fos genes (GENES, FOS). They are involved in growth-related transcriptional control. c-fos combines with c-jun (PROTO-ONCOGENE PROTEINS C-JUN) to form a c-fos/c-jun heterodimer (TRANSCRIPTION FACTOR AP-1) that binds to the TRE (TPA-responsive element) in promoters of certain genes.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.Nerve Tissue ProteinsOligodeoxyribonucleotides: 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.Transcription Factor TFIIIB: One of several general transcription factors that are specific for RNA POLYMERASE III. TFIIIB recruits and positions pol III over the initiation site and remains stably bound to the DNA through multiple rounds of re-initiation by RNA POLYMERASE III.Active Transport, Cell Nucleus: Gated transport mechanisms by which proteins or RNA are moved across the NUCLEAR MEMBRANE.Activating Transcription Factor 6: One of the BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTORS that is synthesized as a membrane-bound protein in the ENDOPLASMIC RETICULUM. In response to endoplasmic reticulum stress it translocates to the GOLGI APPARATUS. It is activated by PROTEASES and then moves to the CELL NUCLEUS to regulate GENETIC TRANSCRIPTION of GENES involved in the unfolded protein response.Transcription Factor Brn-3: A family of mammalian POU domain factors that are expressed predominately in NEURONS.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Cell Cycle: The complex series of phenomena, occurring between the end of one CELL DIVISION and the end of the next, by which cellular material is duplicated and then divided between two daughter cells. The cell cycle includes INTERPHASE, which includes G0 PHASE; G1 PHASE; S PHASE; and G2 PHASE, and CELL DIVISION PHASE.SOXB1 Transcription Factors: A subclass of SOX transcription factors that are expressed in neuronal tissue where they may play a role in the regulation of CELL DIFFERENTIATION. Members of this subclass are generally considered to be transcriptional activators.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.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).)NF-E2 Transcription Factor: A basic-leucine zipper transcription factor that regulates GLOBIN gene expression and is related to TRANSCRIPTION FACTOR AP-1. NF-E2 consists of a small MAF protein subunit and a tissue-restricted 45 kDa subunit.Genes, Regulator: Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.CCAAT-Binding Factor: A heterotrimeric DNA-binding protein that binds to CCAAT motifs in the promoters of eukaryotic genes. It is composed of three subunits: A, B and C.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.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.SOXE Transcription Factors: A subclass of closely-related SOX transcription factors. Members of this subfamily have been implicated in regulating the differentiation of OLIGODENDROCYTES during neural crest formation and in CHONDROGENESIS.Upstream Stimulatory Factors: Ubiquitously expressed basic HELIX-LOOP-HELIX MOTIF transcription factors. They bind CANNTG sequences in the promoters of a variety of GENES involved in carbohydrate and lipid metabolism.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.Cell Cycle Proteins: Proteins that control the CELL DIVISION CYCLE. This family of proteins includes a wide variety of classes, including CYCLIN-DEPENDENT KINASES, mitogen-activated kinases, CYCLINS, and PHOSPHOPROTEIN PHOSPHATASES as well as their putative substrates such as chromatin-associated proteins, CYTOSKELETAL PROTEINS, and TRANSCRIPTION FACTORS.Embryo, Mammalian: The entity of a developing mammal (MAMMALS), generally from the cleavage of a ZYGOTE to the end of embryonic differentiation of basic structures. For the human embryo, this represents the first two months of intrauterine development preceding the stages of the FETUS.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Myogenic Regulatory Factors: A family of muscle-specific transcription factors which bind to DNA in control regions and thus regulate myogenesis. All members of this family contain a conserved helix-loop-helix motif which is homologous to the myc family proteins. These factors are only found in skeletal muscle. Members include the myoD protein (MYOD PROTEIN); MYOGENIN; myf-5, and myf-6 (also called MRF4 or herculin).RNA Polymerase III: A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure where it transcribes DNA into RNA. It has specific requirements for cations and salt and has shown an intermediate sensitivity to alpha-amanitin in comparison to RNA polymerase I and II. EC 2.7.7.6.Immunohistochemistry: Histochemical localization of immunoreactive substances using labeled antibodies as reagents.Embryo, Nonmammalian: The developmental entity of a fertilized egg (ZYGOTE) in animal species other than MAMMALS. For chickens, use CHICK EMBRYO.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.Pol1 Transcription Initiation Complex Proteins: Factors that form a preinitiation complex at promoters that are specifically transcribed by RNA POLYMERASE I.Transcription Factor 3: A basic helix-loop-helix transcription factor that plays a role in determining cell fate during embryogenesis. It forms a heterodimer with TWIST TRANSCRIPTION FACTOR and ACHAETE-SCUTE GENE COMPLEX-related TRANSCRIPTION FACTORS.Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.Amino Acid Motifs: Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.Transcription Factor Pit-1: A POU domain factor that regulates expression of GROWTH HORMONE; PROLACTIN; and THYROTROPIN-BETA in the ANTERIOR PITUITARY GLAND.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.SOXC Transcription Factors: A subclass of closely-related SOX transcription factors. Members of the group have been found expressed in developing neuronal tissue, LYMPHOCYTES, and during EMBRYONIC DEVELOPMENT.POU Domain Factors: A family of transcription factors characterized by the presence of a bipartite DNA-binding domain known as the POU domain. The POU domain contains two subdomains, a POU-specific domain and a POU-homeodomain. The POU domain was originally identified as a region of approximately 150 amino acids shared between the Pit-1, Oct-1, Oct-2, and Unc-86 transcription factors.

Inducible NO synthase: role in cellular signalling. (1/70946)

The discovery of endothelium-derived relaxing factor and its identification as nitric oxide (NO) was one of the most exciting discoveries of biomedical research in the 1980s. Besides its potent vasodilatory effects, NO was found under certain circumstances to be responsible for the killing of microorganisms and tumour cells by activated macrophages and to act as a novel, unconventional type of neurotransmitter. In 1992, Science picked NO as the 'Molecule of the Year', and over the past years NO has become established as a universal intercellular messenger that acutely affects important signalling pathways and, on a more long-term scale, modulates gene expression in target cells. These actions will form the focus of the present review.  (+info)

The surface ectoderm is essential for nephric duct formation in intermediate mesoderm. (2/70946)

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. (3/70946)

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. (4/70946)

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. (5/70946)

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)

The Drosophila kismet gene is related to chromatin-remodeling factors and is required for both segmentation and segment identity. (6/70946)

The Drosophila kismet gene was identified in a screen for dominant suppressors of Polycomb, a repressor of homeotic genes. Here we show that kismet mutations suppress the Polycomb mutant phenotype by blocking the ectopic transcription of homeotic genes. Loss of zygotic kismet function causes homeotic transformations similar to those associated with loss-of-function mutations in the homeotic genes Sex combs reduced and Abdominal-B. kismet is also required for proper larval body segmentation. Loss of maternal kismet function causes segmentation defects similar to those caused by mutations in the pair-rule gene even-skipped. The kismet gene encodes several large nuclear proteins that are ubiquitously expressed along the anterior-posterior axis. The Kismet proteins contain a domain conserved in the trithorax group protein Brahma and related chromatin-remodeling factors, providing further evidence that alterations in chromatin structure are required to maintain the spatially restricted patterns of homeotic gene transcription.  (+info)

The homeobox gene Pitx2: mediator of asymmetric left-right signaling in vertebrate heart and gut looping. (7/70946)

Left-right asymmetry in vertebrates is controlled by activities emanating from the left lateral plate. How these signals get transmitted to the forming organs is not known. A candidate mediator in mouse, frog and zebrafish embryos is the homeobox gene Pitx2. It is asymmetrically expressed in the left lateral plate mesoderm, tubular heart and early gut tube. Localized Pitx2 expression continues when these organs undergo asymmetric looping morphogenesis. Ectopic expression of Xnr1 in the right lateral plate induces Pitx2 transcription in Xenopus. Misexpression of Pitx2 affects situs and morphology of organs. These experiments suggest a role for Pitx2 in promoting looping of the linear heart and gut.  (+info)

A Drosophila doublesex-related gene, terra, is involved in somitogenesis in vertebrates. (8/70946)

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)

Divergence of transcription factor binding sites is considered to be an important source of regulatory evolution. The associations between transcription factor binding sites and phenotypic diversity have been investigated in many model organisms. However, the understanding of other factors that contribute to it is still limited. Recent studies have elucidated the effect of chromatin structure on molecular evolution of genomic DNA. Though the profound impact of nucleosome positions on gene regulation has been reported, their influence on transcriptional evolution is still less explored. With the availability of genome-wide nucleosome map in yeast species, it is thus desirable to investigate their impact on transcription factor binding site evolution. Here, we present a comprehensive analysis of the role of nucleosome positioning in the evolution of transcription factor binding sites. We compared the transcription factor binding site frequency in nucleosome occupied regions and nucleosome depleted regions
Didier Picard, January 2015 Current list of HBD fusion proteins_ Protein X a HBD b regulated as c Refs. transcription factor in Arabidopsis transcription factor Arabidopsis transcription factor in tobacco coactivator transcription factor 1 2 3 transcription factor transcription factor, differentiation factor transcription factor putative transcription factor in arabidposis transcription factor oncoprotein transcription factor transcription factor oncoprotein oncoprotein oncoprotein transcription factor oncoprotein, transcription factor 6 7 transcription factor transcription factor in yeast, tissue culture cells and zebra fish transcriptional repressor transcription factor transcription factor in yeast, in tissue culture cells, transgenic mice, Xenopus, Drosophila and plants transcription factor, promoter of proliferation transcription factor transcription factor 19 20, 21, i Transcription factors APETALA3 ATF6α Athb-1 GR ER e GR Bob1/OBF1 ER e CCAT (from calcium ER e 4 5 channel cav1.2) C/EBP ...
Since the successful isolation of mouse and human embryonic stem cells (ESCs) in the past decades, massive investigations have been conducted to dissect the pluripotency network that governs the ability of these cells to differentiate into all cell types. Beside the core Oct4-Sox2-Nanog circuitry, accumulating regulators, including transcription factors, epigenetic modifiers, microRNA and signaling molecules have also been found to play important roles in preserving pluripotency. Among the various regulations that orchestrate the cellular pluripotency program, transcriptional regulation is situated in the central position and appears to be dominant over other regulatory controls. In this review, we would like to summarize the recent advancements in the accumulating findings of new transcription factors that play a critical role in controlling both pluripotency network and ESC identity.
... is a protein database which contains information on transcription factors (TFs) of silkworm.
The Oxidative Stress Responsive Transcription Factor Pap1 Confers DNA Damage Resistance on Checkpoint-Deficient Fission Yeast Cells. . 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.
This unit describes how to use the Transcription Element Search System (TESS). This Web site predicts transcription factor binding sites (TFBS) in DNA sequence using two different kinds of models of sites, strings and positional weight matrices. The binding of transcription factors to DNA is a major part of the control of gene expression. Transcription factors exhibit sequence-specific binding; they form stronger bonds to some DNA sequences than to others. Identification of a good binding site in the promoter for a gene suggests the possibility that the corresponding factor may play a role in the regulation of that gene. However, the sequences transcription factors recognize are typically short and allow for some amount of mismatch. Because of this, binding sites for a factor can typically be found at random every few hundred to a thousand base pairs. TESS has features to help sort through and evaluate the significance of predicted sites. Curr. Protoc. Bioinform. 21:2.6.1-2.6.15. © 2008 by John ...
The transcriptional coactivator peroxisome proliferator-activated receptor-gamma coactivator-1beta (PGC-1beta) has been implicated in important metabolic processes. A mouse lacking PGC-1beta (PGC1betaKO) was generated and phenotyped using physiological, molecular, and bioinformatic approaches. PGC1betaKO mice are generally viable and metabolically healthy. Using systems biology, we identified a general defect in the expression of genes involved in mitochondrial function and, specifically, the electron transport chain. This defect correlated with reduced mitochondrial volume fraction in soleus muscle and heart, but not brown adipose tissue (BAT). Under ambient temperature conditions, PGC-1beta ablation was partially compensated by up-regulation of PGC-1alpha in BAT and white adipose tissue (WAT) that lead to increased thermogenesis, reduced body weight, and reduced fat mass. Despite their decreased fat mass, PGC1betaKO mice had hypertrophic adipocytes in WAT. The thermogenic role of PGC-1beta was
ABSTRACT: One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the gene expression data with transcription factor binding data (based on ChIP-seq and DNase-seq) within 10 kb of the transcription start sites of expressed genes. This ...
ABSTRACT: One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the gene expression data with transcription factor binding data (based on ChIP-seq and DNase-seq) within 10 kb of the transcription start sites of expressed genes. This ...
ABSTRACT: One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the gene expression data with transcription factor binding data (based on ChIP-seq and DNase-seq) within 10 kb of the transcription start sites of expressed genes. This ...
Gentaur molecular products has all kinds of products like :search , GenWay \ TFIIH basal transcription factor complex p62 subunit - Basic transcription factor 62 kDa subunit; BTF2-p62; General transcription factor IIH polypeptide 1 Polyclonal \ 15-288-22005B for more molecular products just contact us
Transcription factors directly control when, where, and the extent to which genes are expressed. Signal transduction pathways are responsible for either activating or inhibiting many of them. Transcription factors are also regulated by cofactors, forming complexes that can activate or inhibit transcriptional activity. Many transcription factors, such as nuclear receptors, reside in the cytoplasm and enter the nucleus upon activation (e.g., ligand binding). Posttranslational modifications and coregulating proteins provide additional layers of regulation. Transcription factors are involved in a wide variety of processes, such as development, stress responses, and immunity. Activation or inhibition of transcription factors is often dysregulated during oncogenesis. Transcription factors can also be dysregulated during developmental processes, promoting or inhibiting cellular differentiation. Analyzing the expression, regulation, activity, and sequence of transcription factor genes can help determine ...
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.. ...
Background TF-TFBS-TFT triplets -Transcription factors(TF) regulate transcription factor target(TFT) through binding to transcription factor DNA binding sites(TFBS).
This paper describes a novel approach to constructing Position-Specific Weight Matrices (PWMs) based on the transcription factor binding site (TFBS) data provide by the TRANSFAC database and comparison of the newly generated PWMs with the original TRANSFAC matrices. Multiple local sequence alignment was performed on the TFBSs of each transcription factor. Several different alignment programs were tested and their matrices were compared to the original TRANSFAC matrices. One of the alignment programs, GLAM, produced comparable matrices in terms of the average ranking of true positive sites across the whole test set of sequences. ...
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 ...
This function reads in transcription factor information given the selected transcription factor target gene database. The information is downloaded via the AnnotationHub package and merged, if necessary.
Breast cancer is one of the most common malignant diseases in women. Epithelial-mesenchymal transition (EMT) has been documented to play an important role in proliferation, invasion and metastasis of tumor cells as well as drug resistance. Even though the signal transducer and activator of transcription 3 (STAT3) is not a master transcription factor of EMT, STAT3 is involved in the regulation of EMT-related gene expression. However, it remains unclear whether targeted inhibitors of STAT3 affect EMT-mediated proliferation, migration, invasion and drug resistance of tumor cells. In this paper, we investigated the effects of STAT3 and its interaction with Twist, a master transcription factor, in EMT program and subsequent changes in proliferation, migration and invasion of breast cancer cells by interfering STAT3 signaling pathway with different strategies such as STAT3 inactivation and STAT3 silencing. Furthermore, we explored the role of inhibiting STAT3 phosphorylation in the EMT regulation of ...
The Turner lab has focused on the role of transcription factors in the development of peripheral sensory neurons, the spinal cord, midbrain, and habenula. Transcription factors are proteins which bind to DNA in the nucleus to switch on or off the genes which characterize specific cell types. Without the correct complement of transcription factors, cells undergo an "identity crisis" and fail to execute their correct developmental programs. Many genetic disorders in the brain and other organ systems have been linked to defective transcription factor function. Most of the Turner Lab studies have been conducted in transgenic mice in which they either "knockout" the factor of interest, or express a tracer protein in the neurons that express the factor. Studies have focused mainly on the homeodomain transcription factors Brn3a, Islet1, and Hmx1. In recent work, they have shown that without the combinatorial effects of Brn3a and Islet1, developing sensory neurons remain in a "ground state" in which ...
Researchers are only beginning to understand how individual variation in gene regulation can have a lasting impact on ones health and susceptibility to certain diseases. Now, an ambitious survey of the human genome has identified differences in the binding of master regulators called transcription factors to DNA that affect how genes are expressed in different people.. The study, which is published in the March 18, 2010, issue of Science, looked at two common transcription factors. HHMI medical research fellow Maya Kasowski and her colleagues in the laboratory of molecular biologist Michael Snyder at Yale University conducted the work with Jan Korbel at the European Molecular Biology Laboratory. Snyder has since joined the faculty at Stanford University.. Transcription factors account for as much as 10 percent of the coding genome in humans and other organisms. When activated, transcription factors switch on or off hundreds or thousands of genes, a cascade that programs cells to grow or divide. ...
While developmental processes such as axon pathfinding and synapse formation have been characterized in detail, comparatively less is known of the intrinsic developmental mechanisms that regulate transcription of ion channel genes in embryonic neurons. Early decisions, including motoneuron axon targeting, are orchestrated by a cohort of transcription factors that act together in a combinatorial manner. These transcription factors include Even-skipped (Eve), islet and Lim3. The perdurance of these factors in late embryonic neurons is, however, indicative that they might also regulate additional aspects of neuron development, including the acquisition of electrical properties. To test the hypothesis that a combinatorial code transcription factor is also able to influence the acquisition of electrical properties in embryonic neurons we utilized the molecular genetics of Drosophila to manipulate the expression of Eve in identified motoneurons. We show that increasing expression of this transcription factor,
Transcriptional coactivator for steroid receptors and nuclear receptors. Greatly increases the transcriptional activity of PPARG and thyroid hormone receptor on the uncoupling protein promoter. Can regulate key mitochondrial genes that contribute to the program of adaptive thermogenesis. Plays an essential role in metabolic reprogramming in response to dietary availability through coordination of the expression of a wide array of genes involved in glucose and fatty acid metabolism. Induces the expression of PERM1 in the skeletal muscle in an ESRRA-dependent manner. Also involved in the integration of the circadian rhythms and energy metabolism. Required for oscillatory expression of clock genes, such as ARNTL/BMAL1 and NR1D1, through the coactivation of RORA and RORC, and metabolic genes, such as PDK4 and PEPCK. Isoform 4 specifically activates the expression of IGF1 and suppresses myostatin expression in skeletal muscle leading to muscle fiber hypertrophy.
Recent development of methods for genome‐wide identification of transcription factor binding sites by chromatin immunoprecipitation (ChIP) has led to novel insights into transcriptional regulation and greater understanding of the function of individual transcription factors
Transcriptional super-enhancers drive expression of oncogenes in many cancers and are being targeted with novel transcriptional and epigenetic therapeutics (1,2,3,4). Super-enhancers are acquired in cancers through multiple mechanisms, including DNA translocation of an extant super-enhancer and focal amplification. We recently discovered a novel mechanism by which super-enhancers are nucleated in T cell acute lymphoblastic leukemias (T-ALLs) (5). In this case, a small, monoallelic insertion creates a DNA binding site for a master transcription factor protein, which binds and recruits additional factors to nucleate the super-enhancer, which in turn drives high levels of the TAL1 transcription factor. We describe here a method for unbiased identification of similar genomic insertions that nucleate potentially oncogenic regulatory elements in cancers. This approach uses data from genome-wide ChIP-Seq studies that map locations of enhancer-binding proteins to identify sequences missing from ...
It is important to note that even when all experiments are included, the best results produce clusters with only a 28% true positive rate (see Figure E.1.a in Additional data file 1). That is, most of the genes in a given cluster do not share a common, known transcription factor. There are several possible reasons for this. First, with the present state of knowledge, it is possible that genes in the same cluster do in fact share a common transcription factor that is not (yet) represented in the databases used as gold standards (YPD, SCPD and ChIP data). We note for example, that when one compares ChIP data to YPD, the false-negative rate is approximately 80% using the recommended p-value of 0.001. That is, known gene transcription factor interactions from YPD are identified only about 20% of the time by ChIP (see Table F in Additional data file 1). Hence, it is possible that our evaluation criteria all underestimate the number of co-regulated genes in a cluster. Second, gene regulation is more ...
Transcription factor and DNA molecule. Molecular model of glucocorticoid receptor (GR) transcription factor protein (purple and blue) complexed with a molecule of DNA (deoxyribonucleic acid, pink and green). Transcription factors regulate the transcription of DNA to RNA (ribonucleic acid) by the enzyme RNA polymerase. RNA is the intermediate product between a gene and its protein. When glucocorticoid binds to GR, GR enters the cells nucleus and binds to the DNA, causing an increase in the production of the apoptosis (programmed cell death) protein bax. - Stock Image A617/0259
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
Hi: Take a look at TRANSFAC: http://nar.oupjournals.org/cgi/content/full/29/1/281 Good luck! On 8 Jun 2001 12:10:46 +0100, Heather Peto ,hp217 at cam.ac.uk, wrote: ,Hi , ,Does anyone know how I would look up which genes are turned on/off by ,a given transciption factor? Is there a database I can search? I am ,looking to see all the proteins produced / downgraded after CREB and ,a set of other transcription factors are activated. , ,many thanks , ,Heather :) , ...
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
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We present an integrated method called Chromia for the genome-wide identification of functional target loci of transcription factors. Designed to capture the characteristic patterns of transcription factor binding motif occurrences and the histone profiles associated with regulatory elements such as …
I have pursued a breadth of research that explored the functional genomic study of eukaryotic transcriptional regulation. I have utilized two model organisms, many experimental methodologies, and have developed a suite of computational resources to study the interaction of transcription factors with regulated targets. In Saccharomyces cerevisiae I worked with my collaborator Dr. Zhanzhi (Mike) Hu to characterize the whole-genome transcriptional response of 263 individual transcription factor deletions. We utilized a sophisticated error model and directed-weighted graphs to model a network of high-confidence targets for each transcription factor profiled. We then used regulatory epistasis to elucidate the true set of primary KO-regulated targets and construct a functional transcriptional regulatory network. This network was analyzed for ontological and sequence motif enrichment in order to gain insight into the biological functions represented by transcription factors studied. Functional ...
Background: Conventional wisdom holds that, owing to the dominance of features such as chromatin level control, the expression of a gene cannot be readily predicted from knowledge of promoter architecture. This is reflected, for example, in a weak or absent correlation between promoter divergence and expression divergence between paralogs. However, an inability to predict may reflect an inability to accurately measure or employment of the wrong parameters. Here we address this issue through integration of two exceptional resources: ENCODE data on transcription factor binding and the FANTOM5 high-resolution expression atlas. Results: Consistent with the notion that in eukaryotes most transcription factors are activating, the number of transcription factors binding a promoter is a strong predictor of expression breadth. In addition, evolutionarily young duplicates have fewer transcription factor binders and narrower expression. Nonetheless, we find several binders and cooperative sets that are ...
Conventional wisdom holds that, owing to the dominance of features such as chromatin level control, the expression of a gene cannot be readily predicted from knowledge of promoter architecture. This is reflected, for example, in a weak or absent correlation between promoter divergence and expression divergence between paralogs. However, an inability to predict may reflect an inability to accurately measure or employment of the wrong parameters. Here we address this issue through integration of two exceptional resources: ENCODE data on transcription factor binding and the FANTOM5 high-resolution expression atlas. Consistent with the notion that in eukaryotes most transcription factors are activating, the number of transcription factors binding a promoter is a strong predictor of expression breadth. In addition, evolutionarily young duplicates have fewer transcription factor binders and narrower expression. Nonetheless, we find several binders and cooperative sets that are disproportionately associated
Transcription factors are frequently the chief determinants of the composition and stability of large transcription complexes. Transcriptional regulation is mediated through the interactions of transcription factors with specific binding sites. Transcription factors help to recruit RNA polymerases to active genes for the production of RNA transcripts. Detect Transcription factors using Mercks antibodies.
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Transcription factors, in a somewhat simplified definition, are proteins that regulate transcription by binding to specific sequence elements in regulatory genome regions such as promoters, enhancers etc. TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here.. For further information about the latest version, kindly refer to Wingender, E., Schoeps, T., Haubrock, M., Krull, M. and Dönitz, J.: TFClass: expanding the classification of human transcription factors to their mammalian orthologs. Nucleic Acids Res. 46, D343-D347 (2018). ...
Transcription factors mediate gene regulation by site-specific binding to chromosomal operators. It is commonly assumed that the level of repression is determined solely by the equilibrium binding of a repressor to its operator. However, this assumption has not been possible to test in living cells. Here we have developed a single-molecule chase assay to measure how long an individual transcription factor molecule remains bound at a specific chromosomal operator site. We find that the lac repressor dimer stays bound on average 5 min at the native lac operator in Escherichia coli and that a stronger operator results in a slower dissociation rate but a similar association rate. Our findings do not support the simple equilibrium model. The discrepancy with this model can, for example, be accounted for by considering that transcription initiation drives the system out of equilibrium. Such effects need to be considered when predicting gene activity from transcription factor binding strengths.. ...
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TY - JOUR. T1 - Chromatin properties of regulatory DNA probed by manipulation of transcription factors. AU - Sharov, Alexei A.. AU - Nishiyama, Akira. AU - Qian, Yong. AU - Dudekula, Dawood B.. AU - Longo, Dan L.. AU - Schlessinger, David. AU - Ko, Minoru. PY - 2014/8/1. Y1 - 2014/8/1. N2 - Transcription factors (TFs) bind to DNA and regulate the transcription of nearby genes. However, only a small fraction of TF binding sites have such regulatory effects. Here we search for the predictors of functional binding sites by carrying out a systematic computational screening of a variety of contextual factors (histone modifications, nuclear lamin-bindings, and cofactor bindings). We used regression analysis to test if contextual factors are associated with upregulation or downregulation of neighboring genes following the induction or knockdown of the 9 TFs in mouse embryonic stem (ES) cells. Functional TF binding sites appeared to be either active (i.e., bound by P300, CHD7, mediator, cohesin, and ...
Transcription is a process finely regulated by different transcription factors (TFs) which bind regulatory sequences present in gene promoters and allow the precise execution of gene expression programs. Misregulation of such process can lead to different pathologies, including development/differentiation defects, uncontrolled cell growth and cancer. For these reasons it is important to understand the molecular details of the interplay that occurs between different TFs to modulate gene expression. NF-Y, the heterotrimeric complex composed by NF-YA, NF-YB and NF-YC subunits, all required for DNA binding, recognizes the consensus sequence CCAAT, present in about 30% of eukaryotic promoters, at -60/-100 bp from the Transcription Start Site (TSS). One of the most important roles of NF-Y in transcription is to interact synergistically with other TFs to activate, or to repress, gene expression. In this study we focused on the relationship occurring between NF-Y and the TFs MAX, Myc and USF1, which ...
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The three basic DNA-binding domain mutations from the associated transcription factor (Mitf), Mitfmi/mi, Mitfwh/wh and Mitfor/or, influence osteoclast differentiation with adjustable penetrance whilst impairing melanocyte advancement completely. situated on murine chromosome 6p, encodes for a simple helix-loop-helix leucine zipper (bHLH-Zip) transcription element known as Mitf (Hallsson et al., 2000). The human being MITF is definitely mutated in family members with Waardenburg symptoms type II (WS2) (Tassabehji et al., 1994). Mitf relates to its family carefully, Tfe3, TfeB and TfeC bHLH-Zip transcription elements and binds to E-box components on promoters of focus on genes such as for example so that as homodimers or 96574-01-5 manufacture as heterodimers with additional Mitf-family members, to operate a vehicle target gene manifestation (Aksan and Goding, 1998; Luchin et al., 2000; Mansky et al., 2002b; Fisher and Motyckova, 96574-01-5 manufacture 2002). Recent research established that Mitf ...
Transcription factor and ribosomal RNA (rRNA). Molecular model showing the 6 zinc fingers of transcription factor IIIA (yellow) bound to RNA (ribonucleic acid, red and blue) from a 5s ribosome sub-unit. Transcription factors are proteins that bind to specific DNA sequences, and control the movement (transcription) of genetic information from DNA to mRNA (messenger RNA) during gene expression. Ribosomes are responsible for reading the RNA strand and assembling amino acids to form the protein encoded by the gene being transcribed. - Stock Image F006/9530
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The family of repeats (FR) is a major upstream enhancer of the Epstein-Barr virus (EBV) latent C promoter (Cp) that controls transcription of six different latent nuclear proteins following interaction with the EBV nuclear protein EBNA1. Here, it was shown that Cp could also be activated by octamer-binding factor (Oct) proteins. Physical binding to the FR by the cellular transcription factors Oct-1 and Oct-2 was demonstrated by using an electrophoretic mobility-shift assay. Furthermore, Oct-1 in combination with co-regulator Bob.1, or Oct-2 alone, could drive transcription of a heterologous thymidine kinase promoter linked to the FR in both B cells and epithelial cells. Cp controlled by the FR was also activated by binding of Oct-2 to the FR. This may have direct implications for B cell-specific regulation of Cp.
Clustering of TFBSs, singly or in combination, has frequently been used as a method for computational CRM discovery. While false-positive prediction rates remain high for many studies, when CRMs are positively identified by these methods, it is assumed that the TFBSs that were used as input to the prediction algorithm are important functional regulators of the CRMs activity, as are the transcription factors that bind to these sites. Although in some cases this has been shown to be the case [e.g. [11]], more often than not the assumption is allowed to rest unchallenged. Here, we show through extensive empirical testing in vivo that many of these specific TFBSs, and/or their assumed cognate transcription factors, appear to be relatively or completely unimportant for CRM activity. This leads to the somewhat paradoxical result that although consideration of the putative TFBSs led to successful CRM discovery, the sites in many cases do not appear to be functional CRM constituents. What explains this ...
Putative chromatin remodeling complexes, such as the yeast SWI/SNF complex (for a recent review see Burns and Peterson, 1997) and its mammalian homologs (Kwon et al., 1994; Wang et al., 1996), histone acetyltransferases, such as GCN5 (Brownell et al., 1996), CBP (Bannister and Kouzarides, 1996), P300 (Ogryzko et al., 1996), P/CAF (Yang et al., 1996) and TAFII250 (Mizzen et al., 1996), and histone deacetylases (Taunton et al., 1996; Alland et al., 1997; Hassig et al., 1997) are emerging as key players in the processes of cellular differentiation and oncogenesis. These factors appear to act as effectors for a large number of sequence‐specific transcription factors such as members of the nuclear receptor superfamily (Hanstein et al., 1996, Kamei et al., 1996; Heinzel et al., 1997; Nagy et al., 1997), the myb proto‐oncogene (Dai et al., 1996), cAMP response element binding protein (Kwok et al., 1994), the proto‐oncogenes c‐jun and c‐fos (Bannister and Kouzarides, 1995; Kamei et al., 1996), ...
You have isolated a novel transcription factor. How will you determine the genes regulated by transcription factor in the whole genome? How will you determine the transcription factor binding sites in the whole genome?
Previous studies documented that 1,25-vitD treatment suppressed the induction of DC differentiation and maturation markers (CD1A, MHC class II molecules, CD83, costimulatory molecules, etc.) and suppressed the down-regulation of the monocyte marker CD14 (7, 8, 9, 10). If 1,25-vitD mainly acted through the inhibition of the differentiation and the maturation program, it would most likely act through suppressing/antagonizing the effect of transcription factors driving DC differentiation and maturation. In this way, the sets of genes regulated by differentiation and 1,25-vitD would overlap to a very large degree. Our data, however, do not support the scenario that the effect of 1,25-vitD is mostly restricted to the transcriptional regulation of "master transcription factors" or antagonism of transcription factors activated during maturation.. Our comparative analysis of the transcriptomes of monocytes, differentiating DCs, and IDCs differentiated in the presence or absence of 1,25-vitD suggest that ...
Although mutations causing monogenic disorders most frequently lie within the affected gene, sequence variation in complex disorders is more commonly found in noncoding regions. Furthermore, recent genome- wide studies have shown that common DNA sequence variants in noncoding regions are associated with normal variation in gene expression resulting in cell-specific and/or allele-specific differences. The mechanism by which such sequence variation causes changes in gene expression is largely unknown. We have addressed this by studying natural variation in the binding of key transcription factors (TFs) in the well-defined, purified cell system of erythropoiesis. We have shown that common polymorphisms frequently directly perturb the binding sites of key TFs, and detailed analysis shows how this causes considerable (∼10-fold) changes in expression from a single allele in a tissue-specific manner. We also show how a SNP, located at some distance from the recognized TF binding site, may affect ...
Definition of nf-e2 transcription factor, p45 subunit in the Definitions.net dictionary. Meaning of nf-e2 transcription factor, p45 subunit. What does nf-e2 transcription factor, p45 subunit mean? Information and translations of nf-e2 transcription factor, p45 subunit in the most comprehensive dictionary definitions resource on the web.
The researchers identified the hierarchical tree of coherent gene groups and transcription-factor networks that determine the patterns of genes expressed during brain development. They found that some "master transcription factors" at the top level of the hierarchy regulated the expression of a significant number of gene groups.. The scientists findings can be used for selection of transcription factors that could be targeted in the treatment of specific mental disorders.. "We live in the unique time when huge amounts of data related to genes, DNA, RNA, proteins, and other biological objects have been extracted and stored," said lead author Igor Tsigelny, a research scientist with SDSC as well as with UC San Diegos Moores Cancer Center and its Department of Neurosciences.. "I can compare this time to a situation when the iron ore would be extracted from the soil and stored as piles on the ground. All we need is to transform the data to knowledge, as ore to steel. Only the supercomputers and ...
New York University biologists captured highly transient interactions between transcription factors-proteins that control gene expression-and target genes in the genome and showed that these typically missed interactions have important practical implications. In a new study published in Nature Communications, the researchers developed a method to capture transient interactions of NLP7, a master transcription factor involved in nitrogen use in plants, revealing that the majority of a plants response to nitrogen is controlled by these short-lived regulatory interactions.. "Our approaches to capturing transient transcription factor-target interactions genome-wide can be applied to validate dynamic interactions of transcription factors for any pathway of interest in agriculture or medicine," said Gloria Coruzzi, Carroll & Milton Petrie Professor in NYUs Department of Biology and Center for Genomics and Systems Biology and the papers senior author.. Dynamic interactions between regulatory proteins ...
View Notes - Lecture 4 Regulation of Transcription Factor Activity by Extracellular Signals from IPHY 3060 at Colorado. IPHY 2060 Lecture 4: Regulation of Transcription Factor Activity by
Molecular biology is a rapidly evolving field that has led to the development of increasingly sophisticated technologies to improve our capacity to study cellular processes in much finer detail. Transcription is the first step in protein expression and the major point of regulation of the components that determine the characteristics, fate and functions of cells. The study of transcriptional regulation has been greatly facilitated by the development of reporter genes and transcription factor expression vectors, which have become versatile tools for manipulating promoters, as well as transcription factors in order to examine their function. The understanding of promoter complexity and transcription factor structure offers an insight into the mechanisms of transcriptional control and their impact on cell behaviour. This review focuses on some of the many applications of molecular cut-and-paste tools for the manipulation of promoters and transcription factors leading to the understanding of crucial aspects
We present an individual agent-based model of transcription factor binding to DNA. We explicitly represent every single transcription factor and every sing
CD4 T cells can adopt one of two opposing fates: a helper T cell (Th) specialized in supporting pathogen clearance, or a regulatory T cell (Treg) that attenuates immune responses. IL-17A-producing inflammatory Th17 cells stand out among Th cells, possessing a high level of inherent plasticity in response to altered environments. The underlying mechanisms controlling such flexibility are largely unknown. In this regard, we have identified the AP-1 family of transcription factors (TFs) as key regulators of Th17 cell identity. Our previous work revealed the pioneering role of BATF in supporting global enhancer accessibility and flexibility in CD4 T cells, and here, we describe an antagonistic AP-1 TF, JunB, that limits Th17 plasticity. Indeed, we find that CD4 T cells deficient in JunB exhibit dysregulated effector cytokine and TF expression signatures, and lack disease potential in a mouse model of autoimmunity. In particular, JunB serves to restrain inappropriate Treg and Th1 differentiation. ...
There are at least 16 genes within the common overlapping region. A few of these genes are expressed in the central nervous system and/or likely to be dosage sensitive, or reported to be associated with disease by animal studies. These genes could be candidate genes for patients with deletion or duplication in this region.. The transcription factor gene (SP1) is most likely to be dosage sensitive (haploinsufficiency score: 0.81%) [DECIPHER]. The protein encoded by the SP1 gene is a zinc finger transcription factor that binds to GC-rich motifs of many promoters and is then involved in a variety of cellular processes such as cell growth, apoptosis, differentiation and immune responses, DNA damage response, and chromatin remodeling (provided by RefSeq, Nov 2014). The SP7 gene (haploinsufficiency score: 14.4%) encodes a bone specific transcription factor (osterix) which regulates osteogenesis and bone formation during embryonic development [8]. Niger et al. [9] reported that the activity of osterix ...
Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate …
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 ...
Nashun B, Hill PW, Hajkova P, 2015, Reprogramming of cell fate: epigenetic memory and the erasure of memories past., EMBO Journal, Vol: 34, Pages: 1296-1308, ISSN: 0261-4189 Cell identity is a reflection of a cell type-specific gene expression profile, and consequently, cell type-specific transcription factor networks are considered to be at the heart of a given cellular phenotype. Although generally stable, cell identity can be reprogrammed in vitro by forced changes to the transcriptional network, the most dramatic example of which was shown by the induction of pluripotency in somatic cells by the ectopic expression of defined transcription factors alone. Although changes to cell fate can be achieved in this way, the efficiency of such conversion remains very low, in large part due to specific chromatin signatures constituting an epigenetic barrier to the transcription factor-mediated reprogramming processes. Here we discuss the two-way relationship between transcription factor binding and ...
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Inter-individual genetic variation is a major cause of diversity in phenotypes and disease susceptibility. Although sequence variants in gene promoters and protein-coding regions provide obvious prioritization of disease-causing variants, most (88%) genome-wide association study (GWAS) loci are in non-coding DNA, suggesting regulatory functions1. Prioritization of functional intergenic variants remains challenging, owing in part to an incomplete understanding of how regulation is achieved at the nucleotide level in different cell types and environmental contexts2,3,4,5,6,7,8,9,10,11. Recent studies have described important roles for lineage-determining transcription factors (LDTFs), also referred to as pioneer factors or master regulators, in selecting cell-type-specific enhancers12,13,14,15, but the sequence determinants that guide their binding are poorly understood. Previous findings in macrophages and B cells suggest a hierarchical model of regulatory function6, in which a relatively small ...
Active Motif offers a large number of recombinant transcription factor proteins that can be used in a variety of assays to study transcriptional regulation and DNA binding.
CD4(+) T lymphocytes orchestrate adaptive immune responses by differentiating into various subsets of effector T cells such as T-helper 1 (Th1), Th2, Th17, and regulatory T cells. These subsets have been generally described by master transcription factors that dictate the expression of cytokines and receptors, which ultimately define lymphocyte effector functions. However, the view of T-lymphocyte subsets as stable and terminally differentiated lineages has been challenged by increasing evidence of functional plasticity within CD4(+) T-cell subsets, which implies flexible programming of effector functions depending on time and space of T-cell activation. An outstanding question with broad basic and traslational implications relates to the mechanisms, besides transcriptional regulation, which define the plasticity of effector functions. In this study, we discuss the emerging role of regulatory non-coding RNAs in T-cell differentiation and plasticity. Not only microRNAs have been proven to be ...
Lets return to the example of transcription factor binding to DNA. As already noted, if a DNA sequence serves as an enhancer or promoter, it will bind a specific set of transcription factors. If a scientist then observes transcription factors binding to DNA, it is reasonable to conclude that these binding sites play a role in regulating gene expression. Though not certain, this conclusion is probabilistic. Despite the uncertainty associated with it, the conclusion is still reasonable because a vast body of data demonstrates that transcription factors bind to specific DNA sequences that regulate gene expression. Yes, another explanation for why these transcription factors bind to DNA may exist. Confirmatory experiments can reduce this uncertainty ...
Hypoxia-inducible factor-1 (HIF1) is a master transcription factor that orchestrates the adaptation of tumor cells to hypoxia by activating the expression of a broad range of genes promoting neoangiogenesis, tumor growth, glycolysis, metastasis, and resistance to treatments. Accumulating evidence now suggests that this adaptation depends on the stabilization or the increased synthesis of the HIF1A subunit. To have a better understanding of HIF1A regulation, we focused our attention on the environmental carcinogen cadmium (Cd). Our data now challenge these hypotheses and reveal unique and opposing activities of Cd on HIF1A expression and activity. Instead of a mere action on synthesis, Cd increases by itself the stability of HIF1A protein under normoxia; independently of proteasome impairment, oxidative damage or endoplasmic reticulum stress. However, little if any HIF1A is able to translocate to the nucleus of Cd-treated cells where it activates barely HIF1 transcriptional function. ...
The NFkB family of transcription factors regulates multiple cellular processes including inflammation, immunity, and stress responses. The IkB family of inhibitors sequester these transcription factors in the cytosol. A variety of ligands such as inflammatory cytokines, growth factors, and antigens from pathogens activate the NFkB pathway, stimulating IkB protein phosphorylation and subsequent degradation. Newly released NFkB transcription factors form active complexes and translocate into the nucleus to induce expression of their target genes. Hundreds of NFkB target genes have been identified using experimental techniques such as expression studies, chromatin immunoprecipitation, and bioinformatic analyses of predicted transcription factor binding sites. These NFkB target genes include cytokines as well as genes involved in biological processes such as inflammation, immune responses, development and differentiation, and apoptosis. Dysregulation of NFkB signal transduction is associated with ...
The interactions between sequence-specific transcription factors (TFs) and their DNA binding sites are an integral part of the gene regulatory networks within cells. My group developed highly parallel in vivo microarray technology, termed protein
We wanted to test the idea that stress causes a loss of brain synapses in humans," said senior author Ronald Duman, the Elizabeth Mears and House Jameson Professor of Psychiatry and professor of neurobiology and of pharmacology. "We show that circuits normally involved in emotion, as well as cognition, are disrupted when this single transcription factor is activated.". The research team analyzed tissue of depressed and non-depressed patients donated from a brain bank and looked for different patterns of gene activation. The brains of patients who had been depressed exhibited lower levels of expression in genes that are required for the function and structure of brain synapses. Lead author and postdoctoral researcher H.J. Kang discovered that at least five of these genes could be regulated by a single transcription factor called GATA1. When the transcription factor was activated, rodents exhibited depressive-like symptoms, suggesting GATA1 plays a role not only in the loss of connections between ...
These tracks complement each other and together can shed much light on regulatory DNA. The histone marks are informative at a high level, but they have a resolution of just ~200 bases and do not provide much in the way of functional detail. The DNase hypersensitivity assay is higher in resolution at the DNA level and can be done on a large number of cell types since its just a single assay. At the functional level, DNase hypersensitivity suggests that a region is very likely to be regulatory in nature, but provides little information beyond that. The transcription factor ChIP assay has a high resolution at the DNA level and, due to the very specific nature of the transcription factors, is often informative with respect to functional detail. However, since each transcription factor must be assayed separately, the information is only available for a limited number of transcription factors on a limited number of cell lines. Though each assay has its strengths and weaknesses, the fact that all of ...
We demonstrate a computational approach for achieving systematic understanding of transcription factor functions based on gene regulation network.
We demonstrate a computational approach for achieving systematic understanding of transcription factor functions based on gene regulation network.
This gene encodes a member of the GATA family of zinc-finger transcription factors that are named for the consensus nucleotide sequence they bind in the promoter regions of target genes. The encoded protein plays an essential role in regulating transcription of genes involved in the development and proliferation of hematopoietic and endocrine cell lineages. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Mar 2009 ...
TF not in the TRANSFAC database. What now? - posted in Bioinformatics and Biostatistics: Hi, Oddly enough I cannot find the important and highly topical transcription factor in the TRANSFAC database. I want to perform TFBS prediction and want to make sure NANOG is included in the results. I have run a few gene promoters which are experimentally proven to be targeted by NANOG through some of the TRANSFAC prediction programs, but NANOG does not show up. Any suggestions onhow to proceed....
Here, we report that a complex enhancer, encoded by the distant Tce1 activator of transcription factor Gata3, is necessary for T cell development and is critical for the generation of ETP and for CD4 development, as demonstrated by CRISPR/Cas-mediated genome editing. This analysis also illuminated the mechanism of action of Tce1 during T cell development and identified several transcription factors that are responsible for engaging this enhancer activity in T cells.. Many studies have shown that GATA3 is required at multiple stages for normal T cell development (1, 2). Its abundance varies significantly between stages and is tightly controlled (5-11, 74). Although several transcription factors have been proposed as upstream regulators of Gata3 by demonstration that they bind near the Gata3 1a and/or 1b promoters (39, 40, 50, 75, 76), a functional requirement for any of those binding sites has not been confirmed by in vivo mutagenesis. Furthermore, the data shown here and previously clearly ...
The regulation of gene expression is a fundamental process within every cell that often allows exquisite control over a genes activity (for review see [1]). Altering transcription rates is an effective strategy for regulating gene activity. It is well established that transcription of a given gene is dependent upon a promoter sequence located within a few hundred base pairs of the transcriptional start site. Promoter activity is modulated by sequence-specific transcription factors that physically interact either with the protein complexes that make up the core transcriptional machinery or with the promoter sequence itself.. In eukaryotes, the activity of a promoter can be modified by transcription factors binding to DNA sequences (frequently termed cis-regulatory modules or enhancers) that are located from hundreds to hundreds of thousands of base pairs away from the promoter. These regulatory modules can either increase or decrease the rate of transcription for a target gene, depending on the ...
Genes with promoter regions [-2kb,2kb] around transcription start site containing the motif GGGAGGRR which matches annotation for MAZ: MYC-associated zinc finger protein (purine-binding transcription factor). Source Broad Institute. Link http://www.broadi…
basic helix-loop-helix (bHLH) transcription factor belonging to the class A family; acts as a general negative regulator of cell proliferation; binds specifically to oligomers of E-box motifs; forms heterodimers with other bHLH proteins of both class A and class B, e.g. E2A, TAL1, myogenin and MyoD; implicated in myogenesis, hematopoiesis and neurogenesis ...
Thank you very much for your suggestion. It is easy to registrate on gene-regulation.com. But when I browse the TRANSFAC database, it links to http://www.biobase-international.com/. For a free trial, it must finish a registration form. It is hard to pass this registration form. It is like this http://www.biobase-international.com/pages/index.php?id=456. In JARSPAR I can not find the factors which I interested no profiles in JASPAR satisfies search criteria 2008/5/29 lichunjiang ,lichunjiang at sibs.ac.cn,: , , , Really? I registrated for gene-regulation.com a couple of years ago, it is , quite easy.�It does not make sense that you can not register. Or you , should just write to the service to fix the problem. , , Actually, , it is free to use a reduced version. For the full professional version, , you need to pay. , , Besides Transfac, I recommend another , database: JARSPAR available at http://jaspar.genereg.net/.�It is , totally free to use. , Hope this help. , Good luck! , , , ,, It seems ...
Transforming growth factor β (TGF-β) signaling pathway is a major pathway in cellular processes such as cell growth, apoptosis, and cellular homeostasis. The signaling pathway activated by 17β-estadiol (E2) appeared to inhibit the TGF-β signaling pathway by cross-talk with the TGF-β components in estrogen receptor (ER) positive cells. In this study, we examined the inhibitory effects of endocrine disrupting chemicals (EDCs), including 4-nonylphenol (NP), 4-otylphenol (OP), bisphenol A (BPA), and benzophenon-1 (BP-1), in the TGF-β signaling pathway in BG-1 ovarian cancer cells expressing estrogen receptors (ERs). The transcriptional and translational levels of TGF-β related genes were examined by reverse transcription-PCR (RT-PCR), Western blot analysis, and xenograft mouse models of ovarian cancer cells. As a result, treatment with NP, OP, and BPA induced the expressions of SnoN, a TGF-β pathway inhibitor, and c-Fos, a TGF-β target transcription factor. Treatment with NP, BPA, and BP-1 ...
The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks in the evolution ...
NAM, ATAF, and CUC2 (NAC) proteins are encoded by one of the largest plant-specific transcription factor gene families. The functions of many NAC proteins relate to different aspects of lignocellulosi
... is available now at: http://transfac.gbf.de. On the TRANSFAC server, you will find also the sequence analysis programs PatSearch MatInspector SaGa FastM and Thure Etzolds SRS5 with a large collection of databases. TRANSFAC is a database about eukaryotic transcription factors and their binding sites. It consists of six cross-linked tables: SITE CELL FACTOR CLASS MATRIX GENE It is also cross-linked with TRRD (Transcription Regulatory Region Database) and COMPEL from the ICG, Novosibirsk (N. A. Kolchanov, A. E. Kel). It contains numerous cross-references to external databases such EMBL, SWISSPROT, PIR, FLYBASE, EPD, and PROSITE. For further details see Wingender et al., Nucleic Acids Res. 25:265-268, 1997. NEW FEATURES are: - Additional FACTOR and SITE entries, - cross-references to PDB, - comprehensive linkage of FACTOR entries with a proposed transcription factor classification sytem (http://transfac.gbf.de/TRANSFAC/cl/cl.html). The TRANSFAC database comes along with several ...
Motivation: Traditional and high-throughput techniques for determining transcription factor (TF) binding specificities are generating large volumes of data of uneven quality, which are scattered across individual databases. Results: FootprintDB integrates some of the most comprehensive freely available libraries of curated DNA binding sites and systematically annotates the binding interfaces of the corresponding TFs. The first release contains 2422 unique TF sequences, 10 112 DNA binding sites and 3662 DNA motifs. A survey of the included data sources, organisms and TF families was performed together with proprietary database TRANSFAC, finding that footprintDB has a similar coverage of multicellular organisms, while also containing bacterial regulatory data. A search engine has been designed that drives the prediction of DNA motifs for input TFs, or conversely of TF sequences that might recognize input regulatory sequences, by comparison with database entries. Such predictions can also be ...
bHLH transcription factors have common roles in inducing neuronal differentiation, but distinct roles in neuronal subtype specification, functions that are contingent on developmental context (Parras et al., 2002; Nakada et al., 2004a; Powell et al., 2004; Reeves and Posakony, 2005). To determine Atoh1-specific targets, we first identified transcripts specific to the Atoh1 lineage and not common to the neighboring dorsal Neurog1 lineage. Significantly, we identified five new Atoh1-specific targets and their responsive enhancers using a combination of microarray expression data, ChIP-seq experiments, and enhancer-reporter assays.. Previously, known direct targets of Atoh1 in vivo in the developing neural tube or cerebellum included the homeodomain transcription factors, Barhl1 and Barhl2 (Saba et al., 2005; Kawauchi and Saito, 2008), the Sonic hedgehog transcriptional effector, Gli2 (Flora et al., 2009), and Atoh1 itself (Helms et al., 2000). The direct Atoh1 targets identified here have diverse ...
Sensors made from custom DNA molecules could be used to personalize cancer treatments and monitor the quality of stem cells, according to an international team of researchers led by scientists at UC Santa Barbara and the University of Rome Tor Vergata.. The new nanosensors can quickly detect a broad class of proteins called transcription factors, which serve as the master control switches of life. The research is described in an article published in Journal of the American Chemical Society.. "The fate of our cells is controlled by thousands of different proteins, called transcription factors," said Alexis Vallée-Bélisle, a postdoctoral researcher in UCSBs Department of Chemistry and Biochemistry, who led the study. "The role of these proteins is to read the genome and translate it into instructions for the synthesis of the various molecules that compose and control the cell. Transcription factors act a little bit like the settings of our cells, just like the settings on our phones or ...
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Define transcription factor: any of various proteins that bind to DNA and play a role in the regulation of gene expression by promoting transcription
You describe your approach to mapping transcription regulatory networks as gene-centered. What does that mean?. Most people trying to understand transcription at a global scale are doing ChIP-chromatin-immunoprecipitation. Thats a transcription factor-centered approach, or protein-to-gene: you pull down a factor, and identify a bunch of DNA fragments by PCR sequencing or microarray (ChIP-chip). Its beautiful, but it does have its limitations. If you have a transcription factor with a restricted expression pattern-maybe its expressed at very low levels or only in one or two cells of the worm-then ChIP isnt technically feasible yet. And there arent enough good antibodies to do this on a genome-wide scale, which partly explains the paucity of data for 99% of transcription factors in the human genome.. So we go the other away around. We start with a piece of DNA, and identify the transcription factors that can bind to it- what we call a transcription factor binding profile-using the yeast ...
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 ...
Transcription factors (TFs) are a class of proteins that are essential for the regulation of gene expression and for the control of protein expression in normal physiological conditions
The long-term goal of our group is to understand how a single transcription factor can regulate vastly different sets of genes depending on the cell type and to identify and study processes that influence the expression level of individual genes.. We study transcriptional regulation using the glucocorticoid receptor (GR), a member of the steroid hormone receptor family. Upon hormone stimulation, GR binds to specific DNA sequences to regulate the expression of target genes. Although GR is expressed throughout the body, the genes regulated and the genomic loci bound by GR show little overlap between cell-types. Current efforts are aimed to investigate the role of sequence motifs and chromatin in cell-type-specific genomic binding and transcriptional regulation. Further, we study signals involved in fine-tuning expression levels of individual target genes, specifically the role of DNA as a ligand that allosterically modulates the activity of GR.. ...
Looking for the meaning of e2f1 transcription factor? Find out what is the meaning of e2f1 transcription factor on Phrases.net! The Webs largest and most authoritative phrases and idioms resource.
Based on their evolutionary origin, MADS box transcription factor genes have been divided into two classes, namely, type I and II. The plant-specific type II MIKC MADS box genes have been most intensively studied and shown to be key regulators of developmental processes, such as meristem identity, flowering time, and fruit and seed development. By contrast, very little is known about type I MADS domain transcription factors, and they have not attracted interest for a long time. A number of recent studies have now indicated a key regulatory role for type I MADS box factors in plant reproduction, in particular in specifying female gametophyte, embryo, and endosperm development. These analyses have also suggested that type I MADS box factors are decisive for setting reproductive boundaries between species. ...
Transcription factors are proteins that bind to DNA to promote or suppress protein production. Since almost all diseases involve disruption of the protein-production process, transcription factors are promising biological ...
Author Summary An enhanceosome is a functional unit that consists of DNA segment called enhancer; its transcription factors (TFs); and their interacting cofactors. To function, the TFs must assemble on their corresponding response elements (REs) cooperatively. Understanding how TFs assemble is important because the TF combination on the enhancer spells gene-specific activation (or repression). Traditional studies focused mainly on the derivation of consensus DNA sequences, and the TF interaction with its respective RE. This yielded limited success in deciphering the mechanism of selective TF binding. Here, in addition to the conventional roles of protein and DNA, we studied the organization of REs. The IFN-β enhanceosome is a good example because there are limited protein-protein interactions between consecutive TFs. Our molecular dynamics simulations revealed that cooperativity is achieved via overlap of REs, in addition to sparse protein-protein interactions. That is, because the REs overlap, binding
General questions of interest: • So just what the bloody hell is a small RNA? (Fig. 1) • Hare and Frankel both use Drosophila as the study organism - not an uncommon choice, but how representative is Drosophila as a model of genetic evolution? How broadly can the results be generalized? Lynch: - Is this paper something which could ever be made accessible to the public? (eg. "As a consequence of the modular structure of cis-regulatory regions, the effect of mutations that alter a single cis-regulatory element will be restricted to particular places and times and not globally affect gene expression, that is, not alter expression in every tissue in which a particular gene is expressed.") - What is the ultimate point of this paper? (e.g. is it that last sentence, "Thus, the evolution of transcription factor proteins themselves, and not just their binding sites, plays an active role in the evolution of development.") Frankel: - How does this paper disagree with previous literature (eg. ...
General questions of interest: • So just what the bloody hell is a small RNA? (Fig. 1) • Hare and Frankel both use Drosophila as the study organism - not an uncommon choice, but how representative is Drosophila as a model of genetic evolution? How broadly can the results be generalized? Lynch: - Is this paper something which could ever be made accessible to the public? (eg. "As a consequence of the modular structure of cis-regulatory regions, the effect of mutations that alter a single cis-regulatory element will be restricted to particular places and times and not globally affect gene expression, that is, not alter expression in every tissue in which a particular gene is expressed.") - What is the ultimate point of this paper? (e.g. is it that last sentence, "Thus, the evolution of transcription factor proteins themselves, and not just their binding sites, plays an active role in the evolution of development.") Frankel: - How does this paper disagree with previous literature (eg. ...
The single spanning INM protein emerin is encoded by the EMD gene, which, when mutated, produces the X‐linked form of Emery-Dreifuss muscular dystrophy (EDMD; Gruenbaum et al, 2005). The lamin‐associated protein LAP2β was originally identified as a single spanning INM protein with a nucleoplasmic binding region for lamin B and chromatin (Foisner & Gerace, 1993). Both emerin and LAP2β associate with several transcriptional regulators, and this association invariably coincides with repression of the transcription factor target genes. In most instances, the mechanism of repression is not clear because it is uncertain whether the transcription factor acts as an activator or repressor of transcription-often transcription factors can do both. If the transcription factor acts as an activator, sequestering the transcription factor away from its target gene is a possible mechanism. If the transcription factor acts as a repressor, a model would be created of a repressive environment for the target ...
Looking for online definition of winged-helix transcription factor RFX4 in the Medical Dictionary? winged-helix transcription factor RFX4 explanation free. What is winged-helix transcription factor RFX4? Meaning of winged-helix transcription factor RFX4 medical term. What does winged-helix transcription factor RFX4 mean?
Antibodies for proteins involved in RNA polymerase II transcription factor binding pathways, according to their Panther/Gene Ontology Classification
Looking for online definition of ETS-related transcription factor Elf-4 in the Medical Dictionary? ETS-related transcription factor Elf-4 explanation free. What is ETS-related transcription factor Elf-4? Meaning of ETS-related transcription factor Elf-4 medical term. What does ETS-related transcription factor Elf-4 mean?
The chicken ovalbumin upstream promoter transcription factors (COUP-TFs) are members from the steroid/thyroid hormone receptor superfamily and function in transcriptional regulation of a multitude of genes. of the ovalbumin gene (Bagchi et al., 1987; Pastorcic et al., 1986; Wang et Procyanidin B3 inhibitor Mouse monoclonal to Human Albumin al., 1987). It was found to bind an element (COUP) between C90 and C70 within the ovalbumin promoter that is much like thyroid and estrogen response elements (Pastorcic et al., 1986). The COUP-TF has also been shown to bind cis-elements involved in positive transcription rules in the rat insulin II (Hwung et al., 1988; Hwung et al., 1988b), chicken VLDL II (Wijnholds et Procyanidin B3 inhibitor al., 1988), and human being apolipoprotein AI and CIII genes (Ladias and Karathanasis, 1991). It was also reported to bind to bad regulatory elements in the proopiomelanocortin (Drouin et al., 1989a; Drouin et al., 1989b) and HIV-1 (Cooney et al., 1991) promoters. The ...
Developmental and Growth Hormone Regulation of the Expression of Liver-Enriched Transcription Factors in the Bovine Liver Satyanarayana Eleswarapu ABSTRACT Liver gene expression changes during development and is affected by growth hormone (GH). These changes in gene expression may be due to the differential expression of the liver-enriched transcription factors (LETFs). To study the potential involvement of LETFs in the regulation of gene expression in the bovine liver, we cloned the cDNA fragments of nine bovine LETFs, including hepatocyte nuclear factor (HNF)-1Æ Ã , 1Æ Ã , 3Æ Ã , 3Æ Ã , 3Æ Ã , 6, albumin D-element binding protein (DBP), and CCAAT/enhancer-binding proteins (C/EBP) -Æ Ã and Æ Ã , and compared the expression levels of them between adult and fetal bovine liver and between GH-treated and untreated adult bovine liver. The mRNA abundance of the LETFs was determined by ribonuclease protection assay (RPA). The cloned bovine LETF cDNA sequences showed high degrees of ...
5-R(*UP*AP*GP*AP*UP)-3, 5-R(*UP*AP*GP*AP*UP)-3, 5-R(*UP*AP*GP*AP*UP)-3, 5-R(*UP*AP*GP*AP*UP)-3, 5-R(*UP*AP*GP*AP*UP)-3, 5-R(*UP*AP*GP*AP*UP)-3, 5-R(*UP*AP*GP*AP*UP)-3, 5-R(*UP*AP*GP*AP*UP)-3, 5-R(*UP*AP*GP*AP*UP)-3, 5-R(*UP*AP*GP*AP*UP)-3, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION ...
WRKY transcription factors are known to play important roles in plant responses to biotic stresses. We previously showed that the expression of the WRKY gene, VqWRKY52, from Chinese wild Vitis quinquangularis was strongly induced 24 h post inoculation with powdery mildew. In this study, we analyzed the expression levels of VqWRKY52 following treatment with the defense related hormones salicylic acid (SA) and methyl jasmonate (MeJA), revealing that VqWRKY52 was strongly induced by SA but not JA. We characterized the VqWRKY52 gene, which encodes a WRKY III gene family member, and found that ectopic expression in Arabidopsis thaliana enhanced resistance to powdery mildew and Pseudomonas syringae pv. tomato DC3000, but increased susceptibility to Botrytis cinerea, compared with wild type plants. The transgenic A. thaliana lines displayed strong cell death induced by the biotrophic powdery mildew pathogen, the hemibiotrophic Pseudomonas syringe pathogen and the necrotrophic pathogen B. cinerea. In addition,
Purpose : The peroxisome proliferator-activated receptor alpha agonist fenofibrate prevents progression of diabetic retinopathy, yet its mechanism of protective action is not known. Here, we tested the hypothesis that peroxisome proliferator-activated receptor alpha agonists promote retinal health in the setting of diabetes by inducing a unique transcriptional signature in the eye. Methods : First, we induced peroxisome proliferator-activated receptor alpha activity in the retina using systemically- or locally-introduced agonists and measured changes in canonical transcriptional targets. Second, we investigated retinal peroxisome proliferator-activated receptor responsiveness using a transgenic reporter system. Third, we performed a microarray analysis of transcript changes in whole retina after intravitreous delivery of several peroxisome proliferator-activated receptor alpha agonists and validated putative targets. Results : Canonical genes involved in lipid metabolism and beta-oxidation are ...
Consisting of about 110 amino acids, the domain in winged-helix transcription factors (see Regulation of gene expression) has ... Winged-Helix+Transcription+Factors at the US National Library of Medicine Medical Subject Headings (MeSH) ... Retrieved from "https://en.wikipedia.org/w/index.php?title=Winged-helix_transcription_factors&oldid=730546101" ...
Transcription factors[edit]. NFAT transcription factors are implicated in breast cancer, more specifically in the process of ... Prognostic factors[edit]. Prognostic factors are reflected in the classification scheme for breast cancer including stage, (i.e ... Jauliac S, López-Rodriguez C, Shaw LM, Brown LF, Rao A, Toker A (July 2002). "The role of NFAT transcription factors in ... The primary risk factors for breast cancer are being female and older age.[29] Other potential risk factors include genetics,[ ...
Transcription factors[edit]. Zinc finger. The zinc ion (green) is coordinated by two histidine residues and two cysteine ... Many transcription factors contain a structure known as a zinc finger, this is a structural module where a region of protein ... Rodríguez E, Díaz C (December 1995). "Iron, copper and zinc levels in urine: relationship to various individual factors". ...
General transcription factor. General transcription factors (GTFs) or basal transcription factors are protein transcription ... Transcription initiation[edit]. The completed assembly of the holoenzyme with transcription factors and RNA polymerase II bound ... The transcription factor TFIIH is involved in transcription initiation and DNA repair. MAT1 (for 'ménage à trois-1') is ... It also is a subunit of basal transcription factor 2 (TFIIH) and, thus, functions in class II transcription. XPG (ERCC5) forms ...
Transcription factors[edit]. The first targets of DELLA proteins identified were PHYTOCHROME INTERACTING FACTORs (PIFs). PIFs ... "Large-scale identification of gibberellin-related transcription factors defines group VII ETHYLENE RESPONSE FACTORS as ... GA-GID1-DELLA signal pathway: In the absence of GA, DELLA proteins bind to and inhibit transcription factors (TFs) and ... In addition to repressing transcription factors, DELLAs also bind to prefoldins (PFDs). PFDs are molecular chaperones, meaning ...
transcription factor activity, sequence-specific DNA binding. • RNA polymerase II regulatory region sequence-specific DNA ... The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in ... regulation of transcription, DNA-templated. • negative regulation of transcription from RNA polymerase II promoter. • positive ... "The thyroid transcription factor-1 gene is a candidate target for regulation by Hox proteins". EMBO J. 13 (14): 3339-47. PMC ...
Transcription factor deficiencies. *IUIS-PID table 3 immunodeficiencies. *Noninfectious immunodeficiency-related cutaneous ...
transcription factor binding. • protein domain specific binding. • RNA polymerase II transcription factor activity, sequence- ... Hepatocyte nuclear factor 3-gamma (HNF-3G), also known as forkhead box protein A3 (FOXA3) or transcription factor 3G (TCF-3G) ... transcription factor activity, sequence-specific DNA binding. • transcription regulatory region DNA binding. • sequence- ... transcription, DNA-templated. • spermatogenesis. • positive regulation of transcription from RNA polymerase II promoter. • ...
... s (SREBPs) are transcription factors that bind to the sterol regulatory element DNA ... SREBPs belong to the basic-helix-loop-helix leucine zipper class of transcription factors.[2] Unactivated SREBPs are attached ... Sterol regulatory element-binding transcription factor 1. X-ray crystallography of Sterol Regulatory Element Binding Protein 1A ... The precursor has a hairpin orientation in the membrane, so that both the amino-terminal transcription factor domain and the ...
transcription corepressor activity. • transcription factor activity, sequence-specific DNA binding. • transcription coactivator ... RNA polymerase II transcription factor activity, sequence-specific DNA binding. Cellular component. • nuclear euchromatin. • ... transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding. • chenodeoxycholic acid binding. • ... RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding. • bile acid receptor activity ...
... transcription factor regulating cell cycle progression),[25] TAL1 (a transcription factor),[26] FOG2 (a transcription factor ... also termed Erythroid transcription factor) is the founding member of the GATA family of transcription factors. This protein is ... "Entrez Gene: GATA1 GATA binding protein 1 (globin transcription factor 1)".. *^ a b c Da Costa L, O'Donohue MF, van Dooijeweert ... transcription factor complex. • protein-DNA complex. Biological process. • negative regulation of cell proliferation. • ...
transcription factor activity, RNA polymerase II transcription factor recruiting. • RNA polymerase II transcription factor ... Arabidospsis thaliana MYB family at Database of Arabidopsis Transcription Factors (DATF). This article incorporates text from ... Myb proto-oncogene protein is a member of the MYB (myeloblastosis) family of transcription factors. The protein contains three ... regulation of transcription, DNA-templated. • negative regulation of transcription from RNA polymerase II promoter. • positive ...
transcription factor activity, sequence-specific DNA binding. • transcription factor binding. • RNA polymerase II core promoter ... Hepatocyte nuclear factor 3-beta (HNF-3B), also known as forkhead box protein A2 (FOXA2) or transcription factor 3B (TCF-3B) is ... transcription regulatory region DNA binding. • RNA polymerase II transcription factor activity, sequence-specific DNA binding. ... negative regulation of sequence-specific DNA binding transcription factor activity. • transcription, DNA-templated. • positive ...
transcription factor binding. • activating transcription factor binding. • E-box binding. • protein binding. • protein ... transcription regulatory region DNA binding. Cellular component. • transcription factor complex. • protein complex. • nuclear ... In addition, this transcription factor plays an important role in limb and branchial arch development.[6] In one study, it was ... Shen L, Li XF, Shen AD, Wang Q, Liu CX, Guo YJ, Song ZJ, Li ZZ (July 2010). "Transcription factor HAND2 mutations in sporadic ...
Genetic disorder, protein biosynthesis: Transcription factor/coregulator deficiencies. (1) Basic domains. 1.2. *Feingold ...
transcription factor activity, sequence-specific DNA binding. • sequence-specific DNA binding. • transcription factor binding. ... repressing transcription factor binding. • RNA polymerase II transcription factor activity, sequence-specific DNA binding. ... transcription factor complex. • cytoplasm. • cell nucleus. • nucleoplasm. • transcriptional repressor complex. Biological ... RNA polymerase II repressing transcription factor binding. • protein binding. • recombinase activity. • chromatin binding. • ...
... , ODD, odd-skipped related transcription factor 1, odd-skipped related transciption factor 1. ... Protein odd-skipped-related 1 is a transcription factor that in humans is encoded by the OSR1 gene.[5][6][7] The OSR1 and OSR2 ... OSR1 and OSR2 are homologous to the Odd-skipped class transcription factors in Drosophila, encoded by odd,[5] bowl, sob[9] and ... RNA polymerase II transcription factor activity, sequence-specific DNA binding. • RNA polymerase II regulatory region sequence- ...
RNA polymerase II transcription factor binding. • transcription factor activity, sequence-specific DNA binding. • transcription ... negative regulation of sequence-specific DNA binding transcription factor activity. • regulation of transcription, DNA- ... negative regulation of transcription, DNA-templated. • transcription, DNA-templated. • negative regulation of transcription ... Members of the ID family inhibit the functions of basic helix-loop-helix transcription factors in a dominant-negative manner by ...
... , MTF-1, ZRF, metal-regulatory transcription factor 1, metal regulatory transcription factor 1. ... transcription factor activity, sequence-specific DNA binding. • transcription coactivator activity. • transcriptional activator ... transcription, DNA-templated. • positive regulation of transcription, DNA-templated. • positive regulation of transcription ... Metal regulatory transcription factor 1 is a protein that in humans is encoded by the MTF1 gene.[5][6] ...
transcription corepressor activity. • metal ion binding. • nucleic acid binding. • RNA polymerase II transcription factor ... DC-SCRIPT is able to repress ER and PR mediated transcription, whereas it can activate transcription mediated by RAR and PPAR. ... negative regulation of transcription from RNA polymerase II promoter. • negative regulation of intracellular estrogen receptor ... than normal breast tissue from the same patient and that DC-SCRIPT mRNA expression is an independent prognostic factor for good ...
see also transcription factor/coregulator deficiencies. This article on a gene on the human X chromosome and/or its associated ... regulation of transcription, DNA-templated. • transcription, DNA-templated. • DNA geometric change. • negative regulation of B ...
Interferon regulatory factor 7, also known as IRF7, is a member of the interferon regulatory factor family of transcription ... transcription regulatory region DNA binding. • RNA polymerase II transcription factor activity, sequence-specific DNA binding. ... IRF7 encodes interferon regulatory factor 7, a member of the interferon regulatory transcription factor (IRF) family. IRF7 has ... "Interferon regulatory factor-7 synergizes with other transcription factors through multiple interactions with p300/CBP ...
RNA polymerase II transcription factor activity, sequence-specific DNA binding. Cellular component. • cell nucleus. ... regulation of transcription, DNA-templated. • transcription, DNA-templated. • oogenesis. • regulation of transcription from RNA ...
... and transcription factor 1, TCF1, respectively) and of the hepatocyte growth factor/scatter factor gene (HGF)". Genomics. 13 (2 ... and transcription factor 1, TCF1, respectively) and of the hepatocyte growth factor/scatter factor gene (HGF)". Genomics. 13 (2 ... regulation of transcription, DNA-templated. • transcription, DNA-templated. • positive regulation of transcription from RNA ... DBP is a member of the PAR bZIP (Proline and Acidic amino acid-Rich basic leucine ZIPper) transcription factor family.[5][7] ...
A sigma factorfactor) is a protein needed only for initiation of transcription.[1] It is a bacterial transcription ... Sigma factors in E. coli:. *σ70(RpoD) - σA - the "housekeeping" sigma factor or also called as primary sigma factor, ... It is homologous to archaeal transcription factor B and to eukaryotic TFIIB.[2] The specific sigma factor used to initiate ... The number of sigma factors varies between bacterial species.[1][4] E. coli has seven sigma factors. Sigma factors are ...
transcription factor activity, sequence-specific DNA binding. • transcription coactivator activity. • transcriptional activator ... positive regulation of sequence-specific DNA binding transcription factor activity. • negative regulation of transcription from ... transcription from RNA polymerase II promoter. • transcription, DNA-templated. • nervous system development. • regulation of ... Sommer L, Ma Q, Anderson DJ (1996). "neurogenins, a novel family of atonal-related bHLH transcription factors, are putative ...
Differentiation of mature B cells into plasma cells is dependent upon the transcription factors Blimp-1/PRDM1 and IRF4. ... This is a type of safeguard to the system, almost like a two-factor authentication method. First, the B cells have to encounter ...
M type MADS family at PlantTFDB: Plant Transcription Factor Database. *MIKC type MADS family at PlantTFDB: Plant Transcription ... Gramzow L, Ritz MS, Theissen G (April 2010). "On the origin of MADS-domain transcription factors". Trends in Genetics. 26 (4): ... Shore P, Sharrocks AD (April 1995). "The MADS-box family of transcription factors". European Journal of Biochemistry. 229 (1): ... the protein shows homology to transcription factors". The EMBO Journal. 9 (3): 605-13. PMC 551713 . PMID 1968830.. ...
A list of famous quotations and authors that contain the term ga-binding protein transcription factor - from the Quotes.net ... We couldnt find any quotes or authors matching ga-binding protein transcription factor.. Maybe you were looking for one of ...
... Head, B ; Aballay, A ... Name: Head, Aballay_Recovery from an Acute Infection in C. elegans Requires the GATA Transcription.pdf ... that genes altered during recovery from infection were transcriptionally regulated by conserved transcription factors, ...
Myc Proto Oncogene Protein (Transcription Factor p64 or Class E... ... Transcription Factor p64 or Class E Basic Helix Loop Helix Protein 39 or MYC) - Pipeline Review, H2 2017 report by Global ... Myc Proto Oncogene Protein (Transcription Factor p64 or Class E Basic Helix Loop Helix Protein 39 or MYC) - Myc (c-Myc) protein ... Myc Proto Oncogene Protein (Transcription Factor p64 or Class E Basic Helix Loop Helix Protein 39 or MYC) - Drug Profiles. BGA- ...
... we present data arguing that the forkhead transcription factor Foxp3 acts as the regulatory T cell lineage specification factor ... Regulatory T Cell Lineage Specification by the Forkhead Transcription Factor Foxp3,/a,,/em, (2005) ... Regulatory T Cell Lineage Specification by the Forkhead Transcription Factor Foxp3 (2005) ... cite web , title=Regulatory T Cell Lineage Specification by the Forkhead Transcription Factor Foxp3 , year=2005 , url=http:// ...
These deletions rendered pRL-SV40 unresponsive to GATA transcription factor stimulation and reduced the response of pRL-TK. A ... We report here that plasmids expressing GATA-4 or GATA-6 transcription factor increased Renilla luciferase gene expression by 2 ... the latter can potentially be transactivated by GATA transcription factors. Taken together, these findings highlight the ... Members of the GATA transcription factor family have been used in many transfection studies to investigate their roles in the ...
The effect of gamma radiation on the zinc finger motifs in transcription factor IIIA (TFIIIA), a zinc finger protein, was ... Gamma Radiation-Induced Damage in the Zinc Finger of the Transcription Factor IIIA ...
Putative ETS transcription factor binding sites within the PTEN promoter were determined by searching for GGAA or TTCC ... ERG is a member of the ETS family of transcription factors that share a DNA-binding domain termed the ETS-binding domain (EBD ... In the current study we sought to look into the possibility that the transcription factor ERG affects the expression of PTEN ... Birdsey GM, Dryden NH, Amsellem V, Gebhardt F, Sahnan K, Haskard DO, Dejana E, Mason JC and Randi AM: Transcription factor Erg ...
Network-Guided Discovery of Extensive Epistasis between Transcription Factors Involved in Aliphatic Glucosinolate Biosynthesis ... Network-Guided Discovery of Extensive Epistasis between Transcription Factors Involved in Aliphatic Glucosinolate Biosynthesis ... Network-Guided Discovery of Extensive Epistasis between Transcription Factors Involved in Aliphatic Glucosinolate Biosynthesis ... Network-Guided Discovery of Extensive Epistasis between Transcription Factors Involved in Aliphatic Glucosinolate Biosynthesis ...
Consisting of about 110 amino acids, the domain in winged-helix transcription factors (see Regulation of gene expression) has ... Winged-Helix+Transcription+Factors at the US National Library of Medicine Medical Subject Headings (MeSH) ... Retrieved from "https://en.wikipedia.org/w/index.php?title=Winged-helix_transcription_factors&oldid=730546101" ...
Misexpression of transcription factors in myeloid leukaemia, with Cancer Research UK Manchester Institute. Apply Today. ... Indeed, the great majority of patients with AML have one or more mutations targeting a transcription factor, chromatin modifier ... Project Title: Misexpression of transcription factors in myeloid leukaemia. This 4 year PhD studentship offered in Professor ... In recent years the Somervaille lab has uncovered new and unexpected transcription factor genes which make a frequent and ...
A viral toolkit for recording transcription factor-DNA interactions in live mouse tissues Alexander J. Cammack, Arnav Moudgil, ... A strategy for designing allosteric modulators of transcription factor dimerization Sho Oasa, Vladana Vukojević, Rudolf Rigler ... A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors Riccardo ...
Zinc finger transcription factors or ZF-TFs, are transcription factors composed of a zinc finger-binding domain and any of a ... Zinc finger transcription factor. From Wikipedia, the free encyclopedia. (Redirected from Zinc finger protein transcription ... genes in order to control the transcription of all these genes with a single transcription factor. Also, it is possible to ... Zinc finger protein transcription factors can be encoded by genes small enough to fit a number of such genes into a single ...
Transcription factors bind to the human genome within areas of the genome still viewed as a black box""vast stretches of DNA ... "The activity of transcription factors determines what a cell is doing at any given moment," says Kasowski, who was a medical ... Hence, variation in transcription factor binding can help explain why one person may make more of a certain gene product than ... When activated, transcription factors switch on or off hundreds or thousands of genes, a cascade that programs cells to grow or ...
... and ProteinsProteinsTranscription Factorsp300-CBP Transcription FactorsCREB-Binding ProteinE1A-Associated p300 Protein ... They function as transcriptional coactivators by bridging between DNA-binding TRANSCRIPTION FACTORS and the basal transcription ... p300-CBP Transcription Factors. A family of histone acetyltransferases that is structurally-related to CREB-BINDING PROTEIN and ... TransferasesAcyltransferasesAcetyltransferasesLysine AcetyltransferasesHistone Acetyltransferasesp300-CBP Transcription Factors ...
Hypoxia-responsive transcription factors.. Cummins EP1, Taylor CT.. Author information. 1. Department of Medicine and ... In this review, we comprehensively discuss the transcription factors that have been reported to be hypoxia-responsive and the ... it is clear that a number of other transcription factors are also activated either directly or indirectly. ... While the hypoxia-inducible factor (HIF-1) plays a major role in controlling the ubiquitous transcriptional response to hypoxia ...
2001) Malignant transformation of primary chicken spleen cells by human transcription factor c-Rel. Oncogene 20: 7098-7103 ...
... Jonathan Schug jschug at www.cbil.upenn.edu Tue Mar 26 10:50:10 EST 1996 *Previous message ... DNA sequence and analyze it for transcription factor binding sites? , , Thanks. , , Jon We have one based on the Transfac ...
However, the transcription factors do not function simply as an on/off switch but rather like a volume control, which allows ... "Transcription factors are like chameleons in the way they can change their appearance. It allows them to respond to different ... Transcription factors are responsible for transcribing the correct genes and therefore for producing the right quantity of ... The glucocorticoid receptor is a transcription factor, which, for example, is activated by the hormone cortisol during fasting ...
Transcription Factors RT2 Profiler PCR Array The Human Transcription Factors RT² Profiler PCR Array profiles the expression of ... Transcription Factors RT2 Profiler PCR Array The Mouse Transcription Factors RT² Profiler PCR Array profiles the expression of ... Transcription Factors RT2 Profiler PCR Array The Rat Transcription Factors RT² Profiler PCR Array profiles the expression of 84 ... Stem Cell Transcription Factors EpiTect Methyl II PCR Array The Human Stem Cell Transcription Factors EpiTect Methyl II ...
... the transcription factor that binds the DNA target interacts with a different type of transcription factor (e.g., a factor that ... These prebound transcription factors facilitate activated transcription when auxin levels are elevated or when ARF activators ... ARF transcription factors presumably are present in cells and bound to TGTCTC AuxREs regardless of the auxin status, and auxin ... ARFs May Activate Transcription by Binding Directly to AuxREs or by Associating with Factors That Occupy AuxREs.. Protoplasts ...
Formation of Treg requires FOXO transcription factors that regulate expression of the transcription factor FOXp3 [94]. FOXO1- ... α with FoxO1a and hepatocyte nuclear factor 42α transcription factors," Hepatology, vol. 48, no. 6, pp. 1998-2006, 2008. View ... FOXO Transcription Factors: Their Clinical Significance and Regulation. Yu Wang,1,2 Yanmin Zhou,1 and Dana T. Graves2 ... The forkhead transcription factor family is characterized by a winged-helix DNA binding motif and the forkhead domain [1]. The ...
Transcription factor TFDP3 (IPR028315). Short name: TFDP3 Overlapping homologous superfamilies *E2F-DP heterodimerization ... Transcription factor DP family member 3 (TFDP3) is also known as DP4, which can induce confusion. TFDP3 represents a ... It forms heterodimers with E2F family members and inhibits E2F-dependent transcription and E2F-mediated cell-cycle progression ... Transcription factor DP, C-terminal domain superfamily (IPR038168). Family relationships *Transcription factor DP (IPR015648) * ...
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool.
In transcription factors with a signal sensing domain, the signal sensing domain is the part of the transcription factor that ... Like all proteins, transcription factors are composed of discrete functional modules called "domains". Transcription factors ... transcription factors play a role in all cell processes. Depending on the transcription factor, this can range from regulation ... varies widely between transcription factors. The regulatory effect (and sometimes mechanism) of a specific transcription factor ...
... Tongxiang Lin1,2 and Shouhai Wu1 ... Y. Zhao, X. Yin, H. Qin et al., "Two supporting factors greatly improve the efficiency of human iPSC generation," Cell Stem ... R. Zhao and G. Q. Daley, "From fibroblasts to iPS cells: induced pluripotency by defined factors," Journal of Cellular ... R. Sridharan, J. Tchieu, M. J. Mason et al., "Role of the murine reprogramming factors in the induction of pluripotency," Cell ...
  • In silico analyses demonstrated that genes altered during recovery from infection were transcriptionally regulated by conserved transcription factors, including GATA/ELT-2, FOXO/DAF-16, and Nrf/SKN-1. (duke.edu)
  • As major regulators of gene expression , transcription factors play a role in all cell processes. (conservapedia.com)
  • We report here on overlapping and nonoverlapping expression patterns of transcription factors in these cells and thus provide novel insights into the dynamic networks of transcriptional regulators in embryonic and adult stem cells. (mendeley.com)
  • Beside the core Oct4-Sox2-Nanog circuitry, accumulating regulators, including transcription factors, epigenetic modifiers, microRNA and signaling molecules have also been found to play important roles in preserving pluripotency. (mdpi.com)
  • MicroRNAs (miRNAs) and transcription factors are master regulators of the cellular system. (intechopen.com)
  • Transcription factors, the key regulators of plant growth and development, are the targets of the miRNAs families. (intechopen.com)
  • Transcription factors are also regulated by cofactors, forming complexes that can activate or inhibit transcriptional activity. (qiagen.com)
  • Cellular functions regulated by FOXO transcription factors. (hindawi.com)
  • Insulin resistance and type 2 diabetes are associated with low levels of high-density lipoprotein-cholesterol (HDL-C). The insulin-repressible FoxO transcription factors are potential mediators of insulin's effect on HDL-C. FoxOs mediate a substantial portion of insulin-regulated transcription, and poor FoxO repression is thought to contribute to the excessive glucose production in diabetes. (jci.org)
  • Authoritative and cutting-edge FOXO Transcription Factors: Methods and Protocols aims to ensure successful results in the further study of this vital field. (springer.com)
  • Our results suggest that ARFs can activate or repress transcription by binding to AuxREs directly and that selected ARFs, when overexpressed, may potentiate activation further by associating with an endogenous transcription factor(s) (e.g., an ARF) that is bound to AuxREs. (pnas.org)
  • Its gene resides at the mi locus in mice, and its protumorogenic targets include factors involved in cell death, DNA replication , repair, mitosis, microRNA production, membrane trafficking, mitochondrial metabolism, and much more. (wikipedia.org)
  • distant structural relatives of the conserved cyclin core or "box" can also function as general transcription factors (like TFIIB) or survive embedded in the chain of the tumor suppressor, retinoblastoma protein. (curehunter.com)
  • FOXA1 Promotes Tumor Progression in Prostate Cancer via the Insulin-Like Growth Factor Binding Protein 3 Pathway. (psu.edu)
  • Without the correct complement of transcription factors, cells undergo an "identity crisis" and fail to execute their correct developmental programs. (washington.edu)
  • These prebound transcription factors facilitate activated transcription when auxin levels are elevated or when ARF activators are overexpressed in transfected protoplasts. (pnas.org)
  • They can act as activators or repressors , respectively increasing or decreasing the transcription of a target gene . (conservapedia.com)
  • A palindromic TGTCTC AuxRE was used as bait in a yeast one-hybrid system to isolate a transcription factor, referred to as auxin-response factor 1 (ARF1) ( 2 ). (pnas.org)
  • They function as transcriptional coactivators by bridging between DNA-binding TRANSCRIPTION FACTORS and the basal transcription machinery. (nih.gov)
  • To identify additional factors necessary for the inhibition of the Cdk1/Cdc28 kinase in G1, we isolated mutants that can replicate DNA in the absence of Cdc4 function. (mendeley.com)
  • These results suggest a new function for the USFs in the regulation of activity-dependent transcription in neurons. (jneurosci.org)
  • The best understood of these genes encode transcription factors, such as GATA-2, RUNX1, ETV6, and C/EBPα, which establish and maintain genetic networks governing the genesis and function of blood stem and progenitor cells. (jci.org)
  • therefore, a better understanding of factors that drive SAN development and function is crucial to generation of potential therapies, such as biological pacemakers, for sinus arrhythmias. (jci.org)
  • RNA-sequencing (RNA-seq) analyses of FACS-purified cells from ISL1-deficient SANs revealed that a number of genes critical for SAN function, including those encoding transcription factors and ion channels, were downstream of ISL1. (jci.org)
  • Fusing combinations of these elements, derived from different kingdoms, has resulted in production of diverse hybrid factors having defined DNA-binding specificity and transcriptional activation function for the target organism in question. (genetics.org)
  • Thus, it is concluded that ref1 possesses transcription repressor activity in addition to its function as a transcriptional auxiliary protein. (labome.org)
  • Overall, this study suggests that specific alternate transcripts of "activator" E2F, dE2F1, may have a dual function on cell cycle progression and cannot simply be viewed as a pro-proliferative transcription factor. (sdbonline.org)
  • We avoid most of this complexity in this demonstration workflow in order to examine transcription factor binding sites in a small set of seven broadly co-expressed Saccharomyces cerevisiae genes of related function. (bioconductor.org)
  • Many genetic disorders in the brain and other organ systems have been linked to defective transcription factor function. (washington.edu)
  • Until now, no one had looked at whether there was any variability in the targets of transcription factors from one person to the next. (redorbit.com)
  • Classifying transcription factor targets and discovering relevant biological features. (openwetware.org)
  • The team mapped every binding region for these two factors inside the genomes of 10 individuals. (redorbit.com)
  • It is known that CNTF indirectly turns on the transcription factor STAT3, so the researchers wanted to determine if STAT3 is behind CNTF's protective powers. (newswise.com)
  • Researchers led by Mustafa Khammash have developed a new method that uses blue light to control the transcription of DNA into RNA in single cells. (phys.org)
  • In a series of experiments, the researchers demonstrated that a transcription factor known as TCF1 (for T cell factor-1) is essential for the creation and persistence of disease-fighting antibodies in the bloodstream. (genome.gov)
  • In the current issue of Proceedings of the National Academy of Sciences , researchers from Nationwide Children's Hospital describe a new paradigm for treating transcription factor-driven cancers. (nationwidechildrens.org)
  • Understanding how such signalling molecules interact with bHLH-PAS transcription factors should inform future drug development for a variety of unmet human conditions including cancer. (wellcome.ac.uk)
  • This is accomplished by the upregulation of a vast array of regeneration-associated genes (RAGs) including the rapid induction of transcription factors and enhanced synthesis of adhesion molecules, cytoskeletal elements, growth factors, cytokines, neuropeptides, and other molecules involved in regeneration. (frontiersin.org)
  • These molecules are composed of programmable DNA-binding ligands flexibly tethered to a small molecule that engages the transcription elongation machinery. (curefa.org)
  • Furthermore, the modular design of Syn-TEF1 defines a general framework for developing a class of molecules that license transcription elongation at targeted genomic loci. (curefa.org)
  • The activity of transcription factors determines what a cell is doing at any given moment," says Kasowski, who was a medical student at Yale when she received her HHMI medical research fellowship. (redorbit.com)
  • As a result, it alters the structure of the transcription factor itself and controls its activity. (mpg.de)
  • Neighbouring DNA segments have a significant impact on transcription factor shape, thus modulating the activity of the gene. (mpg.de)
  • In addition, adjacent DNA segments influence the activity of the bound transcription factors. (mpg.de)
  • Scientists had previously assumed that these segments exert an effect by inhibiting the binding of transcription factors, thus impeding the activity of neighbouring genes," Meijsing says. (mpg.de)
  • Reduced FoxO1 activity is therefore an important factor in the development of pulmonary hypertension. (eurekalert.org)
  • In further experiments it was found that certain growth factors and chemical messengers are responsible for reduced FoxO1 activity. (eurekalert.org)
  • The study, in Proceedings of the National Academy of Sciences, found that broad differences in the gene activity of humans and of chimpanzees, affecting nearly 1,000 genes, appear to be linked to the action of about 90 transcription factors. (innovations-report.com)
  • The analysis revealed a broad pattern of activity in 90 transcription factors that paralleled the activity of about 1,000 genes in humans and chimps. (innovations-report.com)
  • Investigating the regulatory mechanisms that control the transcription of these genes in neurons may provide important insights into activity-dependent neural development and synaptic plasticity. (jneurosci.org)
  • However, activation of CREB alone is not sufficient to mediate the activity-dependent transcription of BDNF exon III. (jneurosci.org)
  • By limiting activity to targeted loci, Syn-TEFs convert constituent modules from broad-spectrum inhibitors of transcription into gene-specific stimulators. (curefa.org)
  • We demonstrate that the activity of CRISPR-based transcription factors (crisprTFs) can be tuned by directing multiple crisprTFs to different positions in natural promoters and by arraying multiple crisprTF-binding sites in the context of synthetic promoters in yeast and human cells. (harvard.edu)
  • Consistent with the predicted loss of ETS transcription factor binding, we observed that recurrent hotspot mutations resulted in decreased luciferase activity in reporter assays. (aacrjournals.org)
  • A large family of structurally-related transcription factors that were originally discovered based upon their close sequence homology to an HMG-box domain found in SEX-DETERMINING REGION Y PROTEIN. (harvard.edu)