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.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.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.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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.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.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.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.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.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Transcription Initiation Site: The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.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.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.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.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).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.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.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.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.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)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.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.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.Basic Helix-Loop-Helix Transcription Factors: A family of DNA-binding transcription factors that contain a basic HELIX-LOOP-HELIX MOTIF.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.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.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.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.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).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.Reverse Transcription: The biosynthesis of DNA carried out on a template of RNA.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.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).Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.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.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.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.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.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.Forkhead Transcription Factors: A subclass of winged helix DNA-binding proteins that share homology with their founding member fork head protein, Drosophila.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.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.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.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.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.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.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.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.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.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.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.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.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.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 Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.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.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.Bacterial Proteins: Proteins found in any species of bacterium.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.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.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.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.Operon: In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.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.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.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.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.Cell Line, Tumor: A cell line derived from cultured tumor cells.Activating Transcription Factor 3: An activating transcription factor that plays a key role in cellular responses to GENOTOXIC STRESS and OXIDATIVE STRESS.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.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)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.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.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.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.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.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.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.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.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.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.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.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.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.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.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.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)Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.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.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.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.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.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.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.Templates, Genetic: Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.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.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.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.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.Octamer Transcription Factor-1: A ubiquitously expressed octamer transcription factor that regulates GENETIC TRANSCRIPTION of SMALL NUCLEAR RNA; IMMUNOGLOBULIN GENES; and HISTONE H2B genes.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.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.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.Transcription Initiation, Genetic: The process that starts the transcription of an RNA molecule. It includes the assembly of the initiation complex and establishment of the start site.Pol1 Transcription Initiation Complex Proteins: Factors that form a preinitiation complex at promoters that are specifically transcribed by RNA POLYMERASE I.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).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, 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.Terminator Regions, Genetic: DNA sequences recognized as signals to end GENETIC TRANSCRIPTION.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.Fungal Proteins: Proteins found in any species of fungus.GATA2 Transcription Factor: An essential GATA transcription factor that is expressed primarily in HEMATOPOIETIC STEM CELLS.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.RNA Polymerase I: A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. The enzyme functions in the nucleolar structure and transcribes DNA into RNA. It has different requirements for cations and salts than RNA polymerase II and III and is not inhibited by alpha-amanitin. EC 2.7.7.6.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.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.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.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.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.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.Activating Transcription Factor 1: An activating transcription factor that regulates expression of a variety of genes including C-JUN GENES and TRANSFORMING GROWTH FACTOR BETA2.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.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.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.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.Acetylation: Formation of an acetyl derivative. (Stedman, 25th ed)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.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.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.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.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.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.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.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.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.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Mice, Transgenic: Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.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.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Mice, Inbred C57BLDrosophila: 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.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.GATA6 Transcription Factor: A GATA transcription factor that is expressed predominately in SMOOTH MUSCLE CELLS and regulates vascular smooth muscle CELL DIFFERENTIATION.Genes, Bacterial: The functional hereditary units of BACTERIA.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)Genes, Fungal: The functional hereditary units of FUNGI.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.beta-Galactosidase: A group of enzymes that catalyzes the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-galactosides. Deficiency of beta-Galactosidase A1 may cause GANGLIOSIDOSIS, GM1.Kinetics: The rate dynamics in chemical or physical systems.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.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.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.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.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Regulatory Elements, Transcriptional: Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.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.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.Transcriptional Elongation Factors: Transcription factors whose primary function is to regulate the rate in which RNA is transcribed.Nucleosomes: The repeating structural units of chromatin, each consisting of approximately 200 base pairs of DNA wound around a protein core. This core is composed of the histones H2A, H2B, H3, and H4.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.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)Sigma Factor: A protein which is a subunit of RNA polymerase. It effects initiation of specific RNA chains from DNA.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Histone Deacetylases: Deacetylases that remove N-acetyl groups from amino side chains of the amino acids of HISTONES. The enzyme family can be divided into at least three structurally-defined subclasses. Class I and class II deacetylases utilize a zinc-dependent mechanism. The sirtuin histone deacetylases belong to class III and are NAD-dependent enzymes.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)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).)Time Factors: Elements of limited time intervals, contributing to particular results or situations.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.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.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.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.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.STAT6 Transcription Factor: A signal transducer and activator of transcription that mediates cellular responses to INTERLEUKIN-4. Stat6 has been shown to partner with NF-KAPPA B and CCAAT-ENHANCER-BINDING PROTEINS to regulate GENETIC TRANSCRIPTION of interleukin-4 responsive GENES.TATA-Binding Protein Associated Factors: Factors that associate with TATA-BOX BINDING PROTEIN. Many of them are components of TRANSCRIPTION FACTOR TFIIDRNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.SOX9 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.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.Cell Proliferation: All of the processes involved in increasing CELL NUMBER including CELL DIVISION.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.High Mobility Group Proteins: A family of low-molecular weight, non-histone proteins found in chromatin.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.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.Active Transport, Cell Nucleus: Gated transport mechanisms by which proteins or RNA are moved across the NUCLEAR MEMBRANE.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.Transcription Termination, Genetic: The discontinuation of transcription at the end of a transcription unit, including the recognition of termination sites and release of the newly synthesized RNA molecule.Chromatin Assembly and Disassembly: The mechanisms effecting establishment, maintenance, and modification of that specific physical conformation of CHROMATIN determining the transcriptional accessibility or inaccessibility of the DNA.

The Drosophila kismet gene is related to chromatin-remodeling factors and is required for both segmentation and segment identity. (1/75781)

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)

Transcriptional repression by the Drosophila giant protein: cis element positioning provides an alternative means of interpreting an effector gradient. (2/75781)

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

Activation of systemic acquired silencing by localised introduction of DNA. (3/75781)

BACKGROUND: In plants, post-transcriptional gene silencing results in RNA degradation after transcription. Among tobacco transformants carrying a nitrate reductase (Nia) construct under the control of the cauliflower mosaic virus 35S promoter (35S-Nia2), one class of transformants spontaneously triggers Nia post-transcriptional gene silencing (class II) whereas another class does not (class I). Non-silenced plants of both classes become silenced when grafted onto silenced stocks, indicating the existence of a systemic silencing signal. Graft-transmitted silencing is maintained in class II but not in class I plants when removed from silenced stocks, indicating similar requirements for spontaneous triggering and maintenance. RESULTS: Introduction of 35S-Nia2 DNA by the gene transfer method called biolistics led to localised acquired silencing (LAS) in bombarded leaves of wild-type, class I and class II plants, and to systemic acquired silencing (SAS) in class II plants. SAS occurred even if the targeted leaf was removed 2 days after bombardment, indicating that the systemic signal is produced, transmitted and amplified rapidly. SAS was activated by sense, antisense and promoterless Nia2 DNA constructs, indicating that transcription is not required although it does stimulate SAS. CONCLUSIONS: SAS was activated by biolistic introduction of promoterless constructs, indicating that the DNA itself is a potent activator of post-transcriptional gene silencing. The systemic silencing signal invaded the whole plant by cell-to-cell and long-distance propagation, and reamplification of the signal.  (+info)

Association of snRNA genes with coiled bodies is mediated by nascent snRNA transcripts. (4/75781)

BACKGROUND: Coiled bodies are nuclear organelles that are highly enriched in small nuclear ribonucleoproteins (snRNPs) and certain basal transcription factors. Surprisingly, coiled bodies not only contain mature U snRNPs but also associate with specific chromosomal loci, including gene clusters that encode U snRNAs and histone messenger RNAs. The mechanism(s) by which coiled bodies associate with these genes is completely unknown. RESULTS: Using stable cell lines, we show that artificial tandem arrays of human U1 and U2 snRNA genes colocalize with coiled bodies and that the frequency of the colocalization depends directly on the transcriptional activity of the array. Association of the genes with coiled bodies was abolished when the artificial U2 arrays contained promoter mutations that prevent transcription or when RNA polymerase II transcription was globally inhibited by alpha-amanitin. Remarkably, the association was also abolished when the U2 snRNA coding regions were replaced by heterologous sequences. CONCLUSIONS: The requirement for the U2 snRNA coding region indicates that association of snRNA genes with coiled bodies is mediated by the nascent U2 RNA itself, not by DNA or DNA-bound proteins. Our data provide the first evidence that association of genes with a nuclear organelle can be directed by an RNA and suggest an autogenous feedback regulation model.  (+info)

TIF1gamma, a novel member of the transcriptional intermediary factor 1 family. (5/75781)

We report the cloning and characterization of a novel member of the Transcriptional Intermediary Factor 1 (TIF1) gene family, human TIF1gamma. Similar to TIF1alpha and TIF1beta, the structure of TIF1beta is characterized by multiple domains: RING finger, B boxes, Coiled coil, PHD/TTC, and bromodomain. Although structurally related to TIF1alpha and TIF1beta, TIF1gamma presents several functional differences. In contrast to TIF1alpha, but like TIF1beta, TIF1 does not interact with nuclear receptors in yeast two-hybrid or GST pull-down assays and does not interfere with retinoic acid response in transfected mammalian cells. Whereas TIF1alpha and TIF1beta were previously found to interact with the KRAB silencing domain of KOX1 and with the HP1alpha, MODI (HP1beta) and MOD2 (HP1gamma) heterochromatinic proteins, suggesting that they may participate in a complex involved in heterochromatin-induced gene repression, TIF1gamma does not interact with either the KRAB domain of KOX1 or the HP1 proteins. Nevertheless, TIF1gamma, like TIF1alpha and TIF1beta, exhibits a strong silencing activity when tethered to a promoter. Since deletion of a novel motif unique to the three TIF1 proteins, called TIF1 signature sequence (TSS), abrogates transcriptional repression by TIF1gamma, this motif likely participates in TIF1 dependent repression.  (+info)

Telomerase reverse transcriptase gene is a direct target of c-Myc but is not functionally equivalent in cellular transformation. (6/75781)

The telomerase reverse transcriptase component (TERT) is not expressed in most primary somatic human cells and tissues, but is upregulated in the majority of immortalized cell lines and tumors. Here, we identify the c-Myc transcription factor as a direct mediator of telomerase activation in primary human fibroblasts through its ability to specifically induce TERT gene expression. Through the use of a hormone inducible form of c-Myc (c-Myc-ER), we demonstrate that Myc-induced activation of the hTERT promoter requires an evolutionarily conserved E-box and that c-Myc-ER-induced accumulation of hTERT mRNA takes place in the absence of de novo protein synthesis. These findings demonstrate that the TERT gene is a direct transcriptional target of c-Myc. Since telomerase activation frequently correlates with immortalization and telomerase functions to stabilize telomers in cycling cells, we tested whether Myc-induced activation of TERT gene expression represents an important mechanism through which c-Myc acts to immortalize cells. Employing the rat embryo fibroblast cooperation assay, we show that TERT is unable to substitute for c-Myc in the transformation of primary rodent fibroblasts, suggesting that the transforming activities of Myc extend beyond its ability to activate TERT gene expression and hence telomerase activity.  (+info)

B-MYB transactivates its own promoter through SP1-binding sites. (7/75781)

B-MYB is an ubiquitous protein required for mammalian cell growth. In this report we show that B-MYB transactivates its own promoter through a 120 bp segment proximal to the transcription start site. The B-MYB-responsive element does not contain myb-binding sites and gel-shift analysis shows that SP1, but not B-MYB, protein contained in SAOS2 cell extracts binds to the 120 bp B-myb promoter fragment. B-MYB-dependent transactivation is cooperatively increased in the presence of SP1, but not SP3 overexpression. When the SP1 elements of the B-myb promoter are transferred in front of a heterologous promoter, an increased response to B-MYB results. In contrast, c-MYB, the prototype member of the Myb family, is not able to activate the luciferase construct containing the SP1 elements. With the use of an SP1-GAL4 fusion protein, we have determined that the cooperative activation occurs through the domain A of SP1. These observations suggest that B-MYB functions as a coactivator of SP1, and that diverse combinations of myb and SP1 sites may dictate the responsiveness of myb-target genes to the various members of the myb family.  (+info)

Differential stability of the DNA-activated protein kinase catalytic subunit mRNA in human glioma cells. (8/75781)

DNA-dependent protein kinase (DNA-PK) functions in double-strand break repair and immunoglobulin [V(D)J] recombination. We previously established a radiation-sensitive human cell line, M059J, derived from a malignant glioma, which lacks the catalytic subunit (DNA-PKcs) of the DNA-PK multiprotein complex. Although previous Northern blot analysis failed to detect the DNA-PKcs transcript in these cells, we show here through quantitative studies that the transcript is present, albeit at greatly reduced (approximately 20x) levels. Sequencing revealed no genetic alteration in either the promoter region, the kinase domain, or the 3' untranslated region of the DNA-PKcs gene to account for the reduced transcript levels. Nuclear run-on transcription assays indicated that the rate of DNA-PKcs transcription in M059J and DNA-PKcs proficient cell lines was similar, but the stability of the DNA-PKcs message in the M059J cell line was drastically (approximately 20x) reduced. Furthermore, M059J cells lack an alternately spliced DNA-PKcs transcript that accounts for a minor (5-20%) proportion of the DNA-PKcs message in all other cell lines tested. Thus, alterations in DNA-PKcs mRNA stability and/or the lack of the alternate mRNA may result in the loss of DNA-PKcs activity. This finding has important implications as DNA-PKcs activity is essential to cells repairing damage induced by radiation or radiomimetric agents.  (+info)

Has anyone ever worked with tagetitoxin, a selective transcription inhibitor of chloroplast with arabidopsis? I would like to know who sells tagetitoxin, and at which concentrations it is recommendable to work with on Arabidopsis. I would appriciate very much any info on this subject. Diana ,http://bgumail.bgu.ac.il/agent/[email protected], leicaj at bgumail.bgu.ac.il ...
The wheat bZip transcription factor TaABF1 mediates both abscisic acid (ABA)-induced and ABA-suppressed gene expression. As levels of TaABF1 protein do not change in response to ABA, and TaABF1 is in a phosphorylated state in vivo, we investigated whether TaABF1 could be regulated at the post-translational level. In bombarded aleurone cells, a TaABF1 protein carrying phosphomimetic mutations (serine to aspartate) at four sites (S36D, S37D, S113D, S115D) was three to five times more potent than wild-type TaABF1 in activating HVA1, an ABA-responsive gene. The phosphomimetic mutations also increased the ability of TaABF1 to downregulate the ABA-suppressed gene Amy32b. These findings strongly suggest that phosphorylation at these sites increases the transcriptional regulatory activity of TaABF1. In contrast to the activation observed by the quadruple serine to aspartate mutation, a single S113D mutation completely eliminated the ability of TaABF1 to upregulate HVA1 or downregulate Amy32b. Thus ...
Transcription begins with the binding of RNA polymerase, together with one or more general transcription factor, to a specific DNA sequence referred to as a "promoter" to form an RNA polymerase-promoter "closed complex". In the "closed complex" the promoter DNA is still fully double-stranded.[5]. RNA polymerase, assisted by one or more general transcription factors, then unwinds approximately 14 base pairs of DNA to form an RNA polymerase-promoter "open complex". In the "open complex" the promoter DNA is partly unwound and single-stranded. The exposed, single-stranded DNA is referred to as the "transcription bubble."[5]. RNA polymerase, assisted by one or more general transcription factors, then selects a transcription start site in the transcription bubble, binds to an initiating NTP and an extending NTP (or a short RNA primer and an extending NTP) complementary to the transcription start site sequence, and catalyzes bond formation to yield an initial RNA product.[5]. In bacteria, RNA ...
Transcription begins with the binding of RNA polymerase, together with one or more general transcription factor, to a specific DNA sequence referred to as a "promoter" to form an RNA polymerase-promoter "closed complex". In the "closed complex" the promoter DNA is still fully double-stranded.[5]. RNA polymerase, assisted by one or more general transcription factors, then unwinds approximately 14 base pairs of DNA to form an RNA polymerase-promoter "open complex". In the "open complex" the promoter DNA is partly unwound and single-stranded. The exposed, single-stranded DNA is referred to as the "transcription bubble."[5]. RNA polymerase, assisted by one or more general transcription factors, then selects a transcription start site in the transcription bubble, binds to an initiating NTP and an extending NTP (or a short RNA primer and an extending NTP) complementary to the transcription start site sequence, and catalyzes bond formation to yield an initial RNA product.[5]. In bacteria, RNA ...
Embryonic differentiation depends upon tissue-specific gene expression programs, created by temporally and spatially regulated transcription. Production of specific mRNAs can be stimulated or repressed via regulation of transcription initiation. Transcript production can also be controlled through a rate-limiting step of transcription elongation (Lis, 1998). For example, heat shock response genes, such as hsp70, are constitutively occupied by a RNA polymerase II (Pol II) complex that is paused proximal to the promoter after transcription initiation (Rougvie and Lis, 1988; Rasmussen and Lis, 1993). Transcription elongation is inhibited until heat shock stimulation occurs, at which time the paused Pol II becomes hyperphosphorylated and transcript synthesis proceeds. Several factors have been implicated in the stimulation or repression of transcription elongation (Conaway et al., 2000; Winston, 2001; Yamaguchi et al., 2001; Zorio and Bentley, 2001), but their precise regulatory roles during ...
Focused transcription typically initiates within the Inr, and the A nucleotide in the Inr consensus is usually designed as the "+ 1" position, whether or not transcription actually initiates at that particular nucleotide. This convention is useful because other core promoter motifs, such as the MTE and DPE, function with the Inr in a manner that exhibits a strict spacing dependence with the Inr consensus sequence (and hence, the A + 1 nucleotide) rather than the actual transcription start site (Burke and Kadonaga, 1997, Kutach and Kadonaga, 2000 and Lim et al., 2004)."[2]. "NC2 (negative cofactor 2; also known as Dr1-Drap1) [...] was identified as repressor of TATA-dependent transcription [...]."[2]. "Several core promoter elements have been previously identified in eukaryotes, but those cannot account for transcription from most RNA polymerase II-transcribed genes."[1]. ...
Faithful transcription initiation is critical for accurate gene expression, yet the mechanisms underlying specific transcription start site (TSS) selection in mammals remain unclear. Here, we show that the histone-fold domain protein NF-Y, a ubiquitously expressed transcription factor, controls the fidelity of transcription initiation at gene promoters in mouse embryonic stem cells. We report that NF-Y maintains the region upstream of TSSs in a nucleosome-depleted state while simultaneously protecting this accessible region against aberrant and/or ectopic transcription initiation. We find that loss of NF-Y binding in mammalian cells disrupts the promoter chromatin landscape, leading to nucleosomal encroachment over the canonical TSS. Importantly, this chromatin rearrangement is accompanied by upstream relocation of the transcription pre-initiation complex and ectopic transcription initiation. Further, this phenomenon generates aberrant extended transcripts that undergo translation, disrupting gene
A retroviral vector-rescue system in which co-packaging of the two co-expressed vectors is required for transduction of one of the vectors has been established previously. By using this rescue system, two distinct packaging-cell populations have been generated. One cell population expressed retroviral RNA from co-localized transcription sites, resulting in local and overlapping accumulation of both RNA transcripts. In the other cell population, the two transcription cassettes were introduced separately, leading to distinct transcription sites of the two RNAs and no significant co-localization of the RNAs. Titre measurements from the two distinct cell populations showed large differences in rescue titre, which is an indirect measure of co-packaging efficiency. Thus, the cell populations with overlapping RNA accumulation gave rise to 15-80-fold-higher rescue titres than cell populations with non-overlapping RNA accumulation. These data show that the spatial position of proviral transcription sites affects
Transcription elongation elements in the NusG family members are ubiquitous from bacterias to human beings and play diverse assignments in the legislation of gene appearance. than facilitates transcript elongation by its cognate RNAP. Alternatively much like the regulators Tth NusG evidently binds close to the upstream end from the transcription bubble competes with σA Cdh13 and mementos forwards translocation by RNAP. Our data claim that the system of NusG recruitment to RNAP is normally universally conserved despite the fact that the regulatory final results among its homologs can happen distinct. Launch The transcription elongation aspect NusG continues to be identified in based on its requirement of phage λ N-dependent gene appearance and thus called N utilization product G (1). Following studies showed that (Eco) NusG impacts Rho-dependent termination (2) transcriptional arrest by HK022 Nun proteins (3) RNA string elongation (4) and translation (5) and can be an essential component from ...
Detects differential transcription between pairs of samples or between groups of replicates. FDM is based on a statistical method for performing a permutation test on ACT-Graphs that does not depend on annotations or an underlying transcripts inference. The application first align RNA-seq reads to a reference genome and determines the regions of differential RNA transcript expression between pairs of splice graphs for finally assess the significance of differential transcription.
Dehydroepiandrosterone (DHEA) is a peroxisome proliferating agent when administered in pharmacological dosages, but it has not been shown to function through the peroxisome proliferator-activated receptor in cell-based assays. Because members of the thyroid hormone/vitamins A and D nuclear receptor subfamily, including PPAR, are known to modulate each others function in gene expression by heterodimerization, we sought to establish whether DHEA and thyroid hormone interact to regulate several of the hepatic and renal enzymes associated with peroxisome proliferation, i.e., peroxisomal beta-oxidation and microsomal NADPH:cytochrome P450 oxidoreductase and the cytochromes P450 4A. In rats administered exogenous T3 to attain a hyperthyroid state, induction of the three isozymes of CYP4A (4A1, 4A2, and 4A3) by DHEA was suppressed , 60-80% at the mRNA level, with induction of CYP4A2 mRNA being completely inhibited. Nuclear run-on transcription assays indicated that this inhibitory effect was regulated ...
It recently has been established that adenine-containing cofactors, including nicotinamide adenine dinucleotide (NAD+), reduced nicotinamide adenine dinucleotide (NADH), and 3-desphospho-coenzyme A (dpCoA), can serve as non-canonical initiating nucleotides (NCINs) for transcription initiation by bacterial and eukaryotic cellular RNA polymerases (RNAPs) and that the efficiency of the reaction is determined by promoter sequence (Bird et al., 2016). Here we describe a protocol to quantify the relative efficiencies of transcription initiation using an NCIN vs. transcription initiation using a nucleoside triphosphate (NTP) for a given promoter sequence.
Transcriptome Sequencing analyses provide information to detect novel transcribed regions, splice events and additional promoters and exons. Transcript annotation studies also help to analyze the impact of transcriptional complexity on current models of key signaling pathways. Next Generation Sequencing can also provide information on aberrant transcription events, like pseudogenes, fusion genes, and genome rearrangements. However, the greatest advantage is to decipher quantitative gene expression profile.. ...
Renaud Dumas. Significance: In most biological processes, genes have to be activated and/or repressed. In plants, the TOPLESS protein is essential for gene repression through its action as a corepressor bridging transcription factor with chromatin remodeling complexes. Here we combine biochemical and structural studies to describe the structure of TOPLESS, how it tetramerizes, and how it interacts with its protein partners. We show that both the tetramerization interface and the binding site for protein partners have been conserved since algae, highlighting the ancestrality of TOPLESS function. Comparison of this plant protein with one of its animal counterparts also shows how corepressors can use a common domain differently to achieve similar properties, illustrating the tinkering of evolution in transcriptional repression.. Abstract: Transcriptional repression involves a class of proteins called corepressors that link transcription factors to chromatin remodeling complexes. In plants such as ...
Precise patterns of gene expression during development are regulated predominantly at the level of transcription. In transcription-driven gene regulation, transcriptional activators bind to enhancer elements and orchestrate the colocalization of proteins at the gene promoter to activate transcription. The transcriptional status of a particular gene in a cell or developing tissue is therefore determined primarily by the precise combination of transcription factors that can bind to the enhancer sequence in that specific cell.. There are, however, well-known exceptions to transcription-driven gene regulation. Most notably, in newly fertilized embryos of chicken, fish, frog, flies and worms, early cell divisions and fate specification are primarily controlled by proteins and RNAs deposited into the egg by the mother (Newport and Kirschner, 1982; Edgar and Schubiger, 1986; Powell-Coffman et al., 1996). Even in mammals, maternally contributed factors play an essential role early in preimplantation ...
One of the simplest ways to model GFP transcription is to use an ODE:. $\frac{d [GFP_{mRNA}]}{dt} = a - b{\cdot}[GFP_{mRNA}]$. where $a$ is GFP transcription rate and $b$ is GFP mRNA degradation rate (both constants). Normally, we assume $a,,b$.. Suppose we wish to account for plasmid concentration with the value of transcription rate $a$ - e.g. with higher plasmid concentration, the ratio $a/b$ should increase as the mRNA saturation levels are expected to be reached faster. In other words, suppose we transfect 2 individual constructs depicted above, 10 ng of one and 30 ng of the other - how should this difference in concentration impact the rate constants values, assuming the constructs are otherwise identical?. Assuming this, approximately how does gene transcription rate $a$ change as a function of the amount of transfected plasmid containing the above construct? Ideally, Id be interested in knowing this for HEK 293 cells, but any other decent estimation is acceptable. One simple option is ...
The recently determined three-dimensional (3D) structure of a bacterial class II transcription complex helps to reveal how it binds to specific DNA sequences, thus driving transcription of downstream genes. This X-ray-based structural analysis provides the first atomic structure for such an intact class II transcription activation complex, according to Richard H. Ebright at Rutgers University in Piscataway, N.J. He and his colleagues reported their findings on 10 June 2016 in Science (doi:10.1126/science.aaf4417).
Once transcription is initiated at the transcription start site (TSS), Pol II pauses at the site just downstream of TSS and requires elongation factors to allow it to proceed. Switching of the RNA Pol II complex from the initiation to the elongation complexes is important for functional transcription, which is mediated by P-TEFb kinase phosphorylating Ser2 position in CTD (Fig. 3A) (Jonkers and Lis, 2015). As assumed, most of the mRNA processing complexes are assembled during the elongation step of transcription (Perales and Bentley, 2009) So chromatin-associated and pol II-interacting mRNA processing proteins are likely to function in regulating transcription elongation (Allemand et al., 2008).. A direct role for SR proteins in transcriptional regulation has been shown for SRSF2. In contrast to shuttling SR proteins (such as SRSF1, SRSF3, and SRSF7), SRSF2 is a non-shuttling protein located in the nucleus. Interestingly, SRSF2 associates with DNA only, but not with cytoplasmic mRNA, suggesting ...
It has been shown that the overall transcription of ribosomal RNA genes can be stimulated by many signals (41); however, increased transcription is not due to an increased number of actively transcribed rDNA units but instead is due to changes in the rate of transcription, especially of elongation (42, 43). B-WICH is an ATP-dependent chromatin remodeling complex containing SNF2h, a human ISWI ATPase, and it was shown to associate with Pol I facilitating its transcription (30). The SIRT7 interaction with components of the B-WICH complex supports a hypothesis where SIRT7 regulates the rate of elongation of Pol I through the ATP-dependent remodeling activities of B-WICH.. SIRT7 knockdown is known to inhibit rDNA transcription (9, 10), and our results show for the first time that SIRT7 knockdown also leads to a reduction in the large subunit of Pol I at the protein level but not at the mRNA level. A question to be addressed in future studies is whether this regulation of Pol I protein level occurs ...
Cyclin-dependent kinase 7 (CDK7) is an important constituent of the cellular transcriptional machinery, where it phosphorylates the C-terminal domain (CTD) of RNAP polymerase II (RNAPII). Because many tumor types are critically dependent on transcription for maintenance of their oncogenic state, pharmacological modulation of CDK7 kinase activity is considered as an approach to treat cancer. Multiple series of CDK7 inhibitors were identified by iterative medicinal chemistry efforts and SAR based approach. Early compounds were optimized towards attaining good physicochemical properties, high potency, good selectivity and desirable pharmacokinetic profile to achieve anti-tumor activity. We have identified compounds from two distinct chemical series that are highly potent in inhibiting CDK7 in biochemical assays. These inhibitors demonstrate time-dependent inhibition of CDK7 indicating covalent nature of binding. The compounds showed potent anti-proliferative activity in cell lines derived from ...
Transcription. Molecular model of DNA (deoxyribonucleic acid, upper right) transcription. During transcription, a complementary messenger ribonucleic acid (mRNA) strand (bottom left) is synthesised. The enzyme RNA polymerase (not shown) recognises a start sign on the DNA strand and moves along the strand building the mRNA. mRNA is the intermediary between DNA and its protein product. - Stock Image C015/4455
Transcription and translation are fundamental molecular mechanisms of gene activity regulation with profound implications for human health. The ligand-dependent transcriptional regulation by nuclear receptors bound to DNA response elements involves the transient assembly of large co-regulator complexes. These trigger chromatin remodeling and facilitate the assembly of the general transcription machinery on the promoter of the target gene. Gene expression is also regulated at the level of protein synthesis, for example, by protein factors that bind to the ribosome during the translation initiation, elongation and termination phase. The initiation phase is strongly regulated by factors and also by the mRNA itself and well-characterized reaction intermediates of the initiating ribosomal nano-machinery are potential targets for antibiotics. Both transcription and translation complexes represent large, transient macromolecular assemblies that we investigate by using an integrative structural biology ...
In vitro analysis of transcription and the factors that play a role in transcription require preparation of an extract that faithfully reproduces in vivo transcription
Mice lacking the lymphocyte-specific transcription factor Bob1 (also called OBF-1 or OCA-B) fail to generate germinal centers and a robust Ig response. We show that peripheral B cells in Bob1−/− mice bear characteristics of chronically activated or anergic-like B cells and identify the immunosuppressive microRNA-146a, together with other microRNAs, as novel transcriptional targets of Bob1. The inability to restrict B cell signaling could contribute to the immunodeficient phenotype of these mice and is consistent with an important role for Bob1 in suppressing B cell activation in vivo. ...
Solving structures of complexes is inherently more difficult than solving those for individual proteins. As a result, significantly fewer structures of protein complexes than individual proteins have been determined experimentally [1]. In recent years, homology modeling [2, 3] proved to be successful when the target protein has a similar sequence to proteins with known structures. However, the lack of a sufficiently large database of reference complexes makes the method unsuitable for structural modeling of protein complexes. A conceptually simple and straightforwardly applicable approach for modeling structures of bio-molecular complexes is highly desirable. When proposing new protein complexes, the models developed should be checked against the following attributes: stereo-chemically sound, having sufficient interfacial Solvent Excluded Surface Areas [4] (SESAs) to provide adequate binding strengths, physically meaningful for transcription regulation and consistency with the known experimental ...
Although recent studies have revealed that the majority of human genes are subjected to regulation of alternative promoters (APs), the biological relevance of this phenomenon remains unclear. In order to understand biological significance of the presence of diverg .. [more]ent transcription initiation events in the respective cell types, it is indispensable to obtain bird-view of the transcriptome figures at every step of the gene expression; namely, i) how the genomic structure change to transcriptionally active form, ii) where the transcription initiation complex is recruited, iii) to what extent the transcription is activated, iv) what transcripts formed and sorted to what subcellular fractions. We have recently started multi-faceted use of the Illumina GA to answer these questions. Integrative analysis produced for respective aspects of the gene expression regulations revealed the comprehensive figures of the complex human gene transcriptome for the first time. [less] ...
First, 5-prime specificity. In bacteria, translation is co-transcriptional, which means that when mRNA is transcribed, it is translated immediately, before finishing off the transcription. There is even a physical link between the polymease and the ribosome via NusG. And when mRNA is translated, it is cleaved by RelE. Translation and transcription are starting from the 5-prime... and so is the RelE cleavage, one would guess. Moreover, if you cleave the mRNA once, translation downstream of the cleavage site stops - and the initial cleavage is likely to happen co-transcriptionally at the 5-prime and render cleavage at the 3-prime impossible. Is there any need to involve "a conformation or component of the translation complex that is unique to initiation or early elongation"? I think not ...
The image shows the cellular organization of chromosomes in the nucleus; you can observe that in the interchromatin space there is a transcription factory (in the picture: RNA transcripts) ,while around this region there are more than one active locus( of different chromosomes).Then,since the chromosomes are so close ,could happen that a traslocation appear between these active loci ...
MIT initially used a unit of measurement called TIPS (Transcription Initiations per Second) for measure rates of transcription at the ends of its parts; however, this was insufficient because there are places on the DNA (e.g. terminators) where transcription initiations are not taking place. PoPS is a relatively new unit developed during construction of standardized "ends" of DNA pieces that measures the inputs and outputs of BioBrick™ parts. PoPS measure the rate at which RNA polymerase moves past a point in the DNA, similar to measuring the current flow across a specific point in a wire. Devices that have an input and output in PoPS are composable - that is, they can be arbitrarily joined together to create complex devices and systems. Creation of devices allows us to characterize devices and eventually more complex systems, thus PoPS is important as a common signal carrier. PoPS differs from transcription rate in that it can also be measured at terminator sites; upstream, they are ...
EMBL scientists show that close interaction of influenza and host cell transcription machineries is essential for the survival of the virus
A Possible Mechanism of DNA to DNA Transcription in Eukaryotic Cells: Endonuclease Dependent Transcript Cutout. . 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.
BioAssay record AID 660672 submitted by ChEMBL: Inhibition of viral transcription in X4 tropic HIV1 pNL4.3-Luc transfected human MT2 cells at 20 uM dosed post transfection and measured 24 hrs post compound dose by luciferase reporter gene assay.
Ch/Bi 231. Advanced Topics in Biochemistry. 6 units (2-0-4); third term. Transcriptional regulation in eukaryotes. Topics: the subunit structure of eukaryotic RNA polymerases and their role in transcriptional reactions; the composition of eukaryotic promoters, including regulatory units; general and specific transcription factors; developmental regulatory circuits and factors; structural motifs involved in DNA binding and transcriptional initiation and control. Not offered 2016-17. ...
Researchers at the University of Tokyo and their collaborators have revealed genetic transcription systems from about 3 billion years ago
Many genetic variants associated with human disease have been found to be associated with alterations in mRNA expression. Although it is commonly a...
RT-PCR for fimA transcription. RT-PCR assays were used to monitor fimA and 16S rRNA transcription in the parental strain LB5010, ubiB mutant, and ubiB (pUbiB) s
MRNA is synthesized in transcription. During transcription, the DNA molecule unzips, and only one side serves as the template for the synthesis of the mRNA strand. Once synthesized, the mRNA molecule...
Unfortunately, much of the discussion surrounding the publication of ENCODE failed to focus on the usefulness of the catalogue and the techniques that built it. Instead, much of the debate centered on the failure to understand that transcription does not necessarily imply meaningful biological function. Cells are messy biological entities, with lots of gunk and goo floating around, so mistakes happen all the time. Many DNA sequences get translated into RNA, only to have the cell degrade that RNA. Much, perhaps most, of the DNA in our genomes-despite being occasionally transcribed, and thus recorded in ENCODE-is still functionless "junk DNA." That is actually not surprising; it is in fact expected from evolutionary theory. Thanks to ENCODE, though, we should eventually learn which sequences are the junk and which are the gems of cell activity. ...
Are All DNA Binding and Transcription Regulation by an Activator Physiologically Relevant?: Understanding how a regulatory protein occupies its sites in vivo is
... : Produce high yields of RNA with trusted, optimized in vitro transcription reagents.
Signal amplification is an effective way to achieve sensitive analysis of biomarkers, exhibiting great promise in biomedical research and clinical diagnosis. Inspired by the transcription process, we here present a versatile strategy that enables to effectively amplify proteolysis into nucleic acid signal ou
(Phys.org)-An international team of researchers has found that gene transcription in an organism that has died continues for several days. In their paper published in the journal Royal Society Open Biology, the team describes ...
Learning Objectives Explain how RNA is synthesized using DNA as a template Distinguish between transcription in prokaryotes and eukaryotes Dur
Well first, the DNA strands unzip to allow the mRNA to copy a single gene. Then an enzyme builds the mRNA strand by bringing in nitrogen bases and matching
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Modulation of Prrxl1 transcriptional activity by phosphorylation. . 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.
Just read this Abstract from PLoS: Mammalian genes are highly heterogeneous with respect to their nucleotide composition, but the functional consequences of this heterogeneity are not clear. In the previous studies, weak positive or negative correlations have been found between the silent-site guanine and cytosine (GC) content and expression of mammalian genes. However, previous studies…. ...
Control system structure of a pseudo-integral or an ideal integral control problem. hTrsc(·) denotes the transcription process. gTrnl(·) denotes the rate of p
Braidwood Nuclear Generating Station Units 1 and 2 automatically shut down early this morning. Plant technical experts are working to determine the cause.
I ll try to make this short. After a PCT went wrong I ve been shut down for two years. These have been the worst years of my life and I tried
READ THIS Farewell Letter from a Blogger who was forced to shut down his site... Well as you know all good things must come to an end. Tod ...
I have had a rather back to front start to my day today, I dont know why but I found myself doing things in all the wrong order but for some reason, it felt right and did it really matter? I know I have said so many times that routine is so important, but I…
As I was installing new zone, My machine died. It had been running about 20 minutes and the thing just shut down. I think it is electrical as there is...
387448814 - EP 0851912 A4 2000-01-05 - NOVEL FACTORS WHICH MODIFY GENE TRANSCRIPTION AND METHODS OF USE THEREFOR - [origin: WO9708301A1] Eukaryotic RNA polymerase II holoenzymes that contain RNA polymerase II and one or more regulatory proteins are described. These holoenzymes selectively initiate transcription in vitro when supplemented with general transcription factors. The regulatory proteins act positively and negatively to regulate transcription initiation, at least in part, via functional interactions with RNA polymerase II.[origin: WO9708301A1] Eukaryotic RNA polymerase II holoenzymes that contain RNA polymerase II and one or more regulatory proteins are described. These holoenzymes selectively initiate transcription in vitro when supplemented with general transcription factors. The regulatory proteins act positively and negatively to regulate transcription initiation, at least in part, via functional interactions with RNA polymerase II.
Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.
Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. May play a role as a target recruitment subunit in E3 ubiquitin-protein ligase complexes and thus in ubiquitination and subsequent proteasomal degradation of target proteins.
Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. May be part of a complex containing NF2/merlin that participates in cellular signaling to the actin cytoskeleton downstream of tyrosine kinase signaling pathways.
Yeast RNA polymerase II initiation factor b copurifies with three polypeptides of 85, 73, and 50 kilodaltons and with a protein kinase that phosphorylates the carboxyl-terminal repeat domain (CTD) of the largest polymerase subunit. The gene that encodes the 73-kilodalton polypeptide, designated TFB1, was cloned and found to be essential for cell growth. The deduced protein sequence exhibits no similarity to those of protein kinases. However, the sequence is similar to that of the 62-kilodalton subunit of the HeLa transcription factor BFT2, suggesting that this factor is the human counterpart of yeast factor b. Immunoprecipitation experiments using antibodies to the TFB1 gene product demonstrate that the transcriptional and CTD kinase activities of factor b are closely associated with an oligomer of the three polypeptides. Photoaffinity labeling with 3-O-(4-benzoyl)benzoyl-ATP (adenosine triphosphate) identified an ATP-binding site in the 85-kilodalton polypeptide, suggesting that the ...
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 ...
In vitro studies using highly purified calf thymus RNA polymerase II and a fragment spanning the first intron of H3.3 as template DNA have demonstrated the existence of a strong transcription termination site consisting of thymidine stretches. In this study, nuclear run-on experiments have been performed to assess the extent to which transcription elongation is blocked in vivo using DNA probes corresponding to region 5 and 3 of the in vitro termination sites. These studies suggest that H3.3 expression is stimulated following the inhibition of DNA synthesis through the elimination of the transcription elongation block. Interestingly, both the in vivo and in vitro experiments have revealed that the transcriptional block/termination sites are positioned immediately downstream of a 73 bp region that has been over 90% conserved between the chicken and human H3.3 genes. The extreme conservation of this intronic region suggests a possible role in maintaining cis-acting function. Electrophoretic ...
TY - JOUR. T1 - Phosphorylation of the carboxy-terminal repeat domain in RNA polymerase II by cyclin-dependent kinases is sufficient to inhibit transcription. AU - Gebara, Maha M.. AU - Sayre, Michael H.. AU - Corden, Jeffry L.. PY - 1997/3/1. Y1 - 1997/3/1. N2 - Cdc2 kinase triggers the entry of mammalian cells into mitosis, the only cell phase in which transcription is globally repressed. We show here that Cdc2 kinase phosphorylates components of the RNA polymerase II transcription machinery including the RNA polymerase II carboxy-terminal repeat domain (CTD). To test specifically the effect of CTD phosphorylation by Cdc2 kinase, we used a yeast in vitro transcription extract that is dependent on exogenous RNA polymerase II that contains a CTD. Phosphorylation was carried out using immobilized Cdc2 so that the kinase could be removed from the phosphorylated polymerase. ATPγS and Cdc2 kinase were used to produce an RNA polymerase 110 that was not detectably dephosphorylated in the ...
Transcription steps are marked by different modifications of the C-terminal domain of RNA polymerase II (RNAPII). Phosphorylation of Ser5 and Ser7 by cyclin-dependent kinase 7 (CDK7) as part of TFIIH marks initiation, whereas phosphorylation of Ser2 by CDK9 marks elongation. These processes are thought to take place in localized transcription foci in the nucleus, known as transcription factories, but it has been argued that the observed clusters/foci are mere fixation or labeling artifacts. We show that transcription factories exist in living cells as distinct foci by live-imaging fluorescently labeled CDK9, a kinase known to associate with active RNAPII. These foci were observed in different cell types derived from CDK9-mCherry knock-in mice. We show that these foci are very stable while highly dynamic in exchanging CDK9. Chromatin immunoprecipitation (ChIP) coupled with deep sequencing (ChIP-seq) data show that the genome-wide binding sites of CDK9 and initiating RNAPII overlap on transcribed genes.
Transition from the closed to the open promoter complex happens by separation of the DNA strands to form an unwound DNA region. Once the transcription bubble forms the template single strand DNA gets positioned in the active center of Pol II. RNA synthesis then can initiate from the transcription start site. The initially transcribing complex (ITC) is unstable and releases short RNAs during abortive initiation (not shown in the movie). When the RNA reaches a certain length, initiation factors are released, and a stable elongation complex (EC) is formed. Elongation complex contains a DNA-RNA hybrid of eight to nine base pairs. During transcription elongation, the EC repeatedly performs the nucleotide addition cycle (NAC) to attach a nucleotide to the growing messenger RNA (mRNA) chain by catalyzing DNA template-directed formation of an RNA phosphodiester bond. Errors do occur during RNA transcription and must be corrected to prevent synthesis of mutated, nonfunctional proteins that possibly ...
Author Summary The transcription of eukaryotic genes involves a highly ordered series of events, including the recruitment of RNA polymerase to promoters, the production of the RNA transcript, and termination. These events are coordinated with changes in chromatin structure that allow regulatory proteins and RNA polymerase to access the DNA template. The recruitment of RNA polymerase II to promoters is rate-limiting for the expression of most eukaryotic genes. However, RNA polymerase often pauses or stalls a short distance downstream of promoters, providing an additional step at which transcription can be regulated. In this study, we present evidence suggesting that a chromatin-remodeling factor, KIS-L, activates transcription by counteracting promoter-proximal pausing in Drosophila. KIS-L also counteracts histone H3 lysine 27 methylation-a covalent modification of chromatin involved in hereditable gene silencing. Our findings provide a plausible explanation for the developmental abnormalities
On specific signals, segments of DNA corresponding to one or more cistrons become de-repressed and ready to transcribe. Each such DNA transcription segment has a promoter region, initiation site, coding region and a terminator region. Transcription begins at the initiation site and ends at the terminator region. A promoter region has RNA polymerase recognition site and RNA polymerase binding site.. Chain opening occurs in the region occupied by TATAATG nucleotides (TATA box) in most procaryotes. Enzymes required for chain separation are unwindases, gyrases and single stranded binding proteins. Terminator region has either poly A base sequence or palindromic sequence (iden-tical base sequence running in opposite directions in the two DNA chains).. RNA polymerase (common in procaryotes and specific in eucaryotes) binds itself to the promoter region. The two strands of DNA uncoil progressively from the site of polymerase binding. One of the two strands of DNA (3-» 5′) functions as a template ...
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 ...
Antibodies for proteins involved in negative regulation of transcription elongation from RNA polymerase I promoter pathways, according to their Panther/Gene Ontology Classification
Transcriptional repression is a general mechanism for regulating transcriptional initiation in organisms ranging from yeast to humans. Accurate initiation of transcription from eukaryotic protein-encoding genes requires the assembly of a large multiprotein complex consisting of RNA polymerase II and general transcription factors such as TFIIA, TFIIB, and TFIID. DR1 is a repressor that interacts with the TATA-binding protein (TBP) of TFIID and prevents the formation of an active transcription complex by precluding the entry of TFIIA and/or TFIIB into the preinitiation complex. The protein encoded by this gene is a corepressor of transcription that interacts with DR1 to enhance DR1-mediated repression. The interaction between this corepressor and DR1 is required for corepressor function and appears to stabilize the TBP-DR1-DNA complex. [provided by RefSeq, Jul 2008 ...
The Arabidopsis genome contains a large number of gene pairs that encode sense and antisense transcripts with overlapping 3′ regions, indicative for a potential role of natural antisense transcription in regulating sense gene expression or transcript processing. When we mapped poly(A) transcripts of three plant gene pairs with long overlapping antisense transcripts, we identified an unusual transcript composition for two of the three gene pairs. Both genes pairs encoded a class of long sense transcripts and a class of short sense transcripts that terminate within the same polyadenylation region as the antisense transcripts encoded by the opposite strand. We find that the presence of the short sense transcript was not dependent on the expression of an antisense transcript. This argues against the assumption that the common termination region for sense and antisense poly(A) transcripts is the result of antisense-specific regulation. We speculate that for some genes evolution may have especially ...
Transcription is a crucial step in gene expression, orchestrated by RNA polymerase (RNAP), a molecular machine that transfers genetic information from DNA to RNA . Bacterial transcription provides a tractable model system which provides mechanistic insights on its more complex eukaryotic counterpart. Bacterial transcription is initiated after an RNAP holoenzyme (core RNAP bound to a σ initiation factor) melts the double-stranded DNA (dsDNA) around the transcription start to form a transcription bubble in the RNAP-promoter DNA open complex (RPo). Subsequently, RNAP performs cycles of RNA synthesis and dissociation (abortive initiation) and at a certain point, escapes from the promoter and enters elongation. RNAP has been studied extensively using genetic, biochemical and structural methods. Recent X-ray structures 3,4 vastly improved our understanding of transcription, leading to mechanistic proposals, and experiments that tested these proposals and further examined RNAP function. However, crystal
Cells are subjected to dramatic changes of gene expression upon environmental changes. Stresscauses a general down-regulation of gene expression together with the induction of a set of stress-responsivegenes. The p38-related stress-activated protein kinase Hog1 is an important regulator of transcription uponosmostress in yeast. Genome-wide localization studies of RNA polymerase II (RNA Pol II) and Hog1 showed that stress induced major changes in RNA Pol II localization, with a shift toward stress-responsive genes relative to housekeeping genes. RNA Pol II relocalization required Hog1, which was also localized to stress-responsive loci. In addition to RNA Pol II-bound genes, Hog1 also localized to RNA polymerase III-bound genes, pointing to a wider role for Hog1 in transcriptional control than initially expected. Interestingly, an increasing association of Hog1 with stressresponsive genes was strongly correlated with chromatin remodeling and increased gene expression. Remarkably, MNase-Seq ...
Injury-elicited differential transcriptional regulation of phospholipid growth factor receptors in the cornea.: The phospholipid growth factors (PLGFs), includi
There are three major forms of life on Earth, bacteria, archaea and eukaryotes (Figure 3). RNA polymerase in bacteria is less complex than RNA polymerase in eukaryotes. Some of the increased complexity of RNA polymerase in eukaryotes reflects differences between DNA in eukaryotes and DNA in bacteria. Two important differences are that eukaryotes organize their DNA into nucleosomes and have more complex mechanisms for regulation of gene transcription.[5] Nucleosomes are a complex of DNA and histone proteins (Figure 4). In order for transcription to occur, DNA must be released from being tightly coiled in nucleosomes. Bacteria do not have nucleosomes. Another complication of eukaryotic gene expression regulation is that gene sequences controlling transcription are often distant from the DNA site where transcription starts. The RNA polymerase of bacteria is relatively small with a core of five protein subunits and one additional protein that recognizes the start points for transcription[6]. In ...
A promoter is a region of DNA that facilitates the transcription of a particular gene. "Promoters can be about 100-1000 [nucleotides] long.[1]. A promoter is on the template strand for the gene and near the gene in numbers of nucleotides (nts) along the DNA template strand. Usually, the promoter lies within the string of nucleotides between genes. Some promoters are called constitutive as they are active in all circumstances in the cell, while others are regulated becoming active in response to specific stimuli. These specific stimuli for a gene find a receptive portion within that genes promoter. In the case of genes that are used to produce proteins, the RNA polymerase II holoenzyme that actually performs the transcription from the template strand needs to find chemical cues for attachment to the DNA and where to begin transcription. Preceding this are chemical cues for which DNA strand is the template strand and in what direction transcription is to be performed. A promoter contains cues for ...
Recent work suggests a role for multiple host factors in facilitating HIV-1 reverse transcription. Previously, we identified a cellular activity which increases the efficiency of HIV-1 reverse transcription in vitro. Here, we describe aspects of the activity which shed light on its function. The cellular factor did not affect synthesis of strong-stop DNA but did improve downstream DNA synthesis. The stimulatory activity was isolated by gel filtration in a single fraction of the exclusion volume. Velocity-gradient purified HIV-1, which was free of detectable RNase activity, showed poor reverse transcription efficiency but was strongly stimulated by partially purified cell proteins. Hence, the cell factor(s) did not inactivate an RNase activity that might degrade the viral genomic RNA and block completion of reverse transcription. Instead, the cell factor(s) enhanced first strand transfer and synthesis of late reverse transcription suggesting it stabilized the reverse transcription complex. The ...
How does RNA polymerase II coordinate the synthesis of messenger RNA, resulting in proper cellular regulation and organismic development? The sessions will cover new findings in transcriptional initiation, elongation and termination and the role of RNA polymerase II, its C-terminal domain and the associated factors in this process. New findings on the roles of chromatin, their interacting proteins and post-translational modifications, their numerous transcriptional properties and their role in development also will be addressed. The plenary lecture will be presented by Ramin Shiekhattar, who will describe his work on the functions of long noncoding RNAs in transcriptional regulation, development and disease pathogenesis. This years meeting represents the 10th anniversary of this important and influential conference. ...
During RNA Polymerase II transcription, the C-terminal domain (CTD) of Rpb1 has been proposed to act as a scaffold to coordinate transcription initiation, elongation, termination, histone modification, and mRNA processing events. These events have been shown to correlate with distinct changes in the pattern of CTD phosphorylation across open reading frames. The major focus of our research is to study the role of the CTD phosphatase Rtr1 during the transcription cycle and to understand how alterations in the phosphorylation state of the CTD influence gene expression and mRNA processing.. ...
Free CAK and rCAK complexes show a stronger preference for the cdk2 substrate versus the ctd oligopeptide. CAK is thus most likely involved in regulation of the cell cycle through cdk phosphorylation (Morgan, 1995). Although free CAK is able to use the ctd oligopeptide as a substrate, it cannot phosphorylate the CTD of RNA pol II alone or when added to an in vitro transcription system lacking TFIIH. On the contrary, TFIIH which contains CAK, is able to phosphorylate the CTD of RNA pol II, in addition to TBP and TFIIEα, two polypeptides absolutely required for basal transcription of protein‐coding genes.. Free CAK and rCAK are not able to substitute for TFIIH in transcription. TFIIH lacking CAK complex allows RNA synthesis when added to an in vitro transcription system that contains all the components of the basal transcription machinery. However, when a CAK subcomplex (free CAK or rCAK) is added, the level of RNA synthesis is significantly increased. TFIIH may thus incorporate CAK to become ...
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.
The second session will delve into fundamental mechanisms in gene regulation. Joan Conaway (Stowers Institute for Medical Research) will focus on the Mediator complex, which bridges interactions between transcription activators and RNA polymerase II, helping to recruit polymerase to a genes promoter. New results from the Conaway lab reveal that Mediator also can enhance transcription elongation through stimulating the release of paused Pol II.. Dylan Taatjes (University of Colorado at Boulder) will provide additional insights into Mediator and its interactions with the transcription machinery. Structural analyses of Mediator in complex with various transcription activators shed light on how Mediator translates activator binding to Pol II and the general transcription factors to influence transcription. In addition to protein factors, RNA species are emerging as important regulators of gene expression. Ramin Shiekhettar (Wistar Institute) will present his recent findings on the roles of long ...
A central, yet unresolved question related to cytokine‐regulated gene transcription is the mechanism by which STATs are connected to activation of basal transcription machinery. Here, we show that the TAD of STAT6 is interacting with p100. p100 was found to enhance the STAT6‐mediated transcription, and to bind to the large subunit of RNA pol II, thus providing a link between STAT6 and the general transcription apparatus.. p100 is a ubiquitously expressed protein that was initially identified as a protein interacting with the acidic TAD of EBNA2 (Tong et al., 1995). p100 enhanced transcriptional activity of EBNA2, but did not affect the function of another acidic TAD of VP16. Thus, p100 is not a general coactivator of transcription but its function requires specific protein interactions with transcription factors. Based on hydrophobic cluster analysis, the p100 protein is predicted to consist of four similar domains with homology to the SN domain, followed by a C‐terminal TD (Callebaut and ...
DNA transcription control. Computer model showing a molecule of the FP50 homodimer (green) from NF-kB (nuclear factor kappa-light-chain-enhancer of activated B cells) bound to the DNA interferon regulatory factor (IRF) recognition sequence on a strand of DNA (deoxyribonucleic acid, orange). NF-kB is a protein complex that controls the transcription of DNA. IRFs are proteins that regulate the transcription of interferons, which are released in response to the presence of pathogens. - Stock Image C010/4990
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 ...
Nutrients regulate gene transcription by the dynamic cycling of O-linked N-acetylglucosamine (O-GlcNAc) on proteins that constitute the transcriptional machinery. A study shows that O-GlcNAcylation of the nuclear factor κB (NF-κB) subunit c-Rel is required for its binding to the promoters of some, but not all, key T cell receptor-dependent genes; however, O-GlcNAcylation is dispensable for the binding of c-Rel to the promoters of tumor necrosis factor-α-dependent genes. This study not only illustrates how specific stimuli that act on the same transcription factor can elicit the expression of particular sets of genes, it also suggests a possible mechanism for autoimmunity in diabetes.. ...
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article{2983518, abstract = {Tyrosine phosphorylation is a hallmark for activation of STAT proteins, but their transcriptional activity also depends on other secondary modifications. Type I IFNs can activate both the ISGF3 (STAT1:STAT2:IRF9) complex and STAT3, but with cell-specific, selective triggering of only the ISGF3 transcriptional program. Following a genome-wide RNAi screen, we identified the SIN3 transcription regulator homolog A (Sin3a) as an important mediator of this STAT3-targeted transcriptional repression. Sin3a directly interacts with STAT3 and promotes its deacetylation. SIN3A silencing results in a prolonged nuclear retention of activated STAT3 and enhances its recruitment to the SOCS3 promoter, concomitant with histone hyperacetylation and enhanced STAT3-dependent transcription. Conversely, Sin3a is required for ISGF3-dependent gene transcription and for an efficient IFN-mediated antiviral protection against influenza A and hepatitis C viruses. The Sin3a complex therefore acts ...
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Author Summary The regulation of mRNA levels in the cell is important to ensure, for instance, timely cellular responses to changes in the environment. mRNA transcription and mRNA degradation directly affect mRNA levels and it would make sense to have a system in place that would coordinate these opposing processes. Previous studies suggested that regulation of transcription in the nucleus may be linked to regulation of mRNA degradation in the cytoplasm, yet the details of this connection are poorly understood. In this study, we took an evolutionary approach to address this question by comparing both transcription and mRNA degradation between two yeast species. We found that evolution of these distinct processes is coordinated, as genes that diverged in mRNA degradation tend to also diverge in transcription. Interestingly, the coordination is counterproductive, as increased transcription is linked to increased mRNA degradation. We analyzed a hybrid between the two yeast species to classify evolutionary
Reactome is pathway database which provides intuitive bioinformatics tools for the visualisation, interpretation and analysis of pathway knowledge.
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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
Studies on the human myometrium have reported on different microarrays containing different sets of genes or ESTs. However each study profiled only a small number of patients due to various constraints. More profiling information would be an addition to our knowledge base of parturition. We compiled from five human studies, transcriptional differences between the non pregnant myometrium (NP), preterm myometrium (PTNIL), term myometrium not in labor (TNIL) and term myometrium in labor (TIL). Software modules developed by the Draghicis group at Wayne State University (Detroit, MI, USA) were used to propose a hierarchical list of several KEGG pathways most likely adjusted to changes observed in microarray experiments. The differential expression of 118 genes could be dispatched in 14 main KEGG pathways that were the most representative of the changes seen in NP and PTNIL, versus TNIL or TIL. Despite the potential of multiple pitfalls inherent to the use of the microarray technology, gene module analysis
Definition of transcription-based chain reaction. Provided by Stedmans medical dictionary and Drugs.com. Includes medical terms and definitions.
Glucose is an essential regulator of insulin gene expression from β-cells, and it is likely that glucose is required during any physiological scenario when increased insulin production is needed (2,11,29-31). In the present study, we identify signaling mechanisms by which GLP-1 synergistically enhances insulin gene transcription in the presence of glucose. Glucose and GLP-1 have similar effects on β-cells, arising from distinct and overlapping signaling pathways. For example, glucose elevates intracellular calcium, but also provides factors to enhance insulin gene transcription by pathways distinct of calcium (10,32,33). GLP-1 increases cAMP and activates PKA, factors both involved in calcium-dependent and -independent pathways in pancreatic β-cells (34-36). Thus, both glucose factors and GLP-1 factors exert multiple effects on the β-cell, and the points of convergence that synergistically upregulate insulin gene transcription are not well understood.. The obvious common effect produced 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
in Breast Cancer Research [=BCR] (2008), 10(1), 9. INTRODUCTION: Overexpression of the ERBB2 oncogene is observed in about 20% of human breast tumors and is the consequence of increased transcription rates frequently associated with gene amplification ... [more ▼]. INTRODUCTION: Overexpression of the ERBB2 oncogene is observed in about 20% of human breast tumors and is the consequence of increased transcription rates frequently associated with gene amplification. Several studies have shown a link between activator protein 2 (AP-2) transcription factors and ERBB2 gene expression in breast cancer cell lines. Moreover, the Yin Yang 1 (YY1) transcription factor has been shown to stimulate AP-2 transcriptional activity on the ERBB2 promoter in vitro. In this report, we examined the relationships between ERBB2, AP-2alpha, and YY1 both in breast cancer tissue specimens and in a mammary cancer cell line. METHODS: ERBB2, AP-2alpha, and YY1 protein levels were analyzed by immunohistochemistry in a panel ...
RNA polymerase III is important for the transcription of non-protein coding RNAs which are important for protein synthesis, RNA processing and protein trafficking. In recent studies, enhanced RNA polymerase III-dependent transcription was shown to be important for cell transformation and tumorigenesis. Early studies also showed that hypoxia is a common feature in developing tumors, particularly in solid tumors. Under hypoxic conditions, protein synthesis is decreased. As RNA pol III transcribed products, tRNAs and 5S rRNA are important for translation, we were interested in whether RNA pol III transcription is affected under hypoxic conditions. Our studies determined that tRNA, but not U6 RNA gene transcription, was decreased under prolonged hypoxic conditions in cancer cells. We further examined potential change in the transcription factors that might account for the reduction of RNA pol III transcription. These studies revealed that the expression of Brf1, one of the three TFIIIB components ...
GO Terms Descrition:, periodic partitioning by pair rule gene, central nervous system development, RNA polymerase II distal enhancer sequence-specific DNA binding, positive regulation of transcription from RNA polymerase II promoter, trunk segmentation, cell fate specification, RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription, regulation of transcription from RNA polymerase II promoter, blastoderm segmentation, negative regulation of transcription from RNA polymerase II promoter, regulation of transcription, DNA-templated, sequence-specific DNA binding transcription factor activity, nucleus, sequence-specific DNA binding, gonadal mesoderm development, segmentation, posterior head segmentation, germ cell migration ...
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 ...
Looking for online definition of subunit of positive elongation transcription factor b in the Medical Dictionary? subunit of positive elongation transcription factor b explanation free. What is subunit of positive elongation transcription factor b? Meaning of subunit of positive elongation transcription factor b medical term. What does subunit of positive elongation transcription factor b mean?
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
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Transcription activation at two semi-synthetic Escherichia coli promoters, CC(-41.5) and CC(-72.5), is dependent on the cyclic AMP receptor protein (CRP) that binds to sites centred 41.5 and 72.5 bp upstream from the respective transcription startpoints. An UP-element that can bind the C-terminal domain of the RNA polymerase (RNAP) alpha-subunit was cloned upstream of the DNA site for CRP at CC(-41.5) and downstream of the DNA site for CRP at CC(-72.5). In both cases CRP-dependent promoter activity was increased by the UP-element, but CRP-independent activity was not increased. DNase I footprinting was exploited to investigate the juxtaposition of bound CRP and RNAP alpha-subunits. In both cases, CRP and RNAP alpha-subunits occupy their cognate binding sites in ternary CRP-RNAP promoter complexes. RNAP alpha-subunits can occupy the UP-element in the absence of CRP, but this is not sufficient for open complex formation. The positive effects of binding RNAP alpha-subunits upstream of the DNA site ...
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*Human mitochondrial genetics

4 Genetic code variants. *5 Replication, repair, transcription, and translation *5.1 Mitochondrial DNA polymerase ... Genetic code variants[edit]. The genetic code is, for the most part, universal, with few exceptions: mitochondrial genetics ... mitochondrial transcription factor A (TFAM), and mitochondrial transcription factors B1 and B2 (TFB1M, TFB2M). POLRMT, TFAM, ... The requirement of transcription to produce primers links the process of transcription to mtDNA replication. Full length ...

*Genetic use restriction technology

For DNA transcription terminators, see Terminator (genetics).. This article has multiple issues. Please help improve it or ... Genetic use restriction technology (GURT), colloquially known as terminator technology or suicide seeds, is the name given to ... "Genetic Use Restriction Technologies (Bangalore, June 2003)" (PDF).. (Position Paper Supporting V-GURT development) ... Variety-level genetic use restriction technologies (V-GURTs): This type of GURT produces sterile seeds, so the seed from this ...

*R-loop

"Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability". Molecular Cell. 67 (4): 608-621.e6. doi: ... R-loops as genetic damage[edit]. When unscheduled R-loops form, they can cause damage by a number of different mechanisms.[20] ... Roles of R-loops in genetic regulation[edit]. R-loop formation is a key step in immunoglobulin class switching, a process that ... 2017)[22] speculated that the function of introns in maintaining genetic stability may explain their evolutionary maintenance ...

*PAX6

Freund C, Horsford DJ, McInnes RR (1996). "Transcription factor genes and the developing eye: a genetic perspective". Human ... transcription factor activity, sequence-specific DNA binding. • transcription factor binding. • protein kinase binding. • ... regulation of transcription, DNA-templated. • glucose homeostasis. • transcription, DNA-templated. • central nervous system ... regulation of transcription from RNA polymerase II promoter. • transcription from RNA polymerase II promoter. • smoothened ...

*Transkripsi (genetik) bahasa Indonesia, ensiklopedia bebas

Transcription and RNA polymerase. ISBN 0-7167-3520-2. Diakses tanggal 2010-08-17.. Pemeliharaan CS1: Banyak nama: authors list ... An Introduction to Genetic Analysis. University of British Columbia, University of California, Harvard University (edisi ke-7 ... Transcription: an overview of gene regulation in eukaryotes. ISBN 0-7167-3520-2. Diakses tanggal 2010-08-17.. Pemeliharaan CS1 ... Dalam genetika, transkripsi (bahasa Inggris: transcription) adalah pembuatan RNA terutama mRNA dengan menyalin sebagian berkas ...

*Birendra Bijoy Biswas

Plant Genetic Engineering, Control of Transcription, and Biology of Inositols and Phosphoinositides are some of the notable ... His researches assisted in advancing the studies of transcription process in higher organisms. In order to further his studies ... While in the US, he was successful in identifying the RNA polymerase associated with the transcription and methylation ... ISBN 978-1-4899-1727-0. B.B. Biswas; J. Robin Harris (11 November 2013). Plant Genetic Engineering. Springer Science & Business ...

*Carcinogenesis

Genetic and epigenetic[edit]. There is a diverse classification scheme for the various genomic changes that may contribute to ... One example for rewiring of tissue function in cancer is the activity of transcription factor NF-κB.[78] NF-κB activates the ... Knudson AG (November 2001). "Two genetic hits (more or less) to cancer". Nature Reviews. Cancer. 1 (2): 157-62. doi:10.1038/ ... Often, the multiple genetic changes that result in cancer may take many years to accumulate. During this time, the biological ...

*Transfer RNA

Crick FH (December 1968). "The origin of the genetic code". Journal of Molecular Biology. 38 (3): 367-79. doi:10.1016/0022-2836 ... The transcription terminates after a stretch of four or more thymidines.[2][55] ... Because the genetic code contains multiple codons that specify the same amino acid, there are several tRNA molecules bearing ... One end of the tRNA matches the genetic code in a three-nucleotide sequence called the anticodon. The anticodon forms three ...

*Blaschko's lines

They include genetic, congenital and acquired (i.e. non-genetic) conditions. Examples include: Pigmentary disorders Naevus ... Transcription. CRC Press. p. 38. ISBN 978-0-415-27200-1. Harper, John. Textbook of Pediatric Dermatology. p. 691. ISBN 0-86542- ... The stripes are a type of genetic mosaicism. They do not correspond to nervous, muscular, or lymphatic systems. The lines can ... X-linked genetic skin disorder Incontinentia pigmenti CHILD syndrome XLPDR syndrome Acquired inflammatory skin rashes Lichen ...

*Promoter (genetics)

Some cases of many genetic diseases are associated with variations in promoters or transcription factors. ... Divergent transcription could shift nucleosomes to upregulate transcription of one gene, or remove bound transcription factors ... Core promoter - the minimal portion of the promoter required to properly initiate transcription[4] *Includes the transcription ... Main article: Regulation of transcription in cancer. In humans, about 70% of promoters located near the transcription start ...

*KLF4

... can activate transcription by interacting via it N-terminus with specific transcriptional co-activators, such as p300-CBP ... El-Karim EA, Hagos EG, Ghaleb AM, Yu B, Yang VW (August 2013). "Krüppel-like factor 4 regulates genetic stability in mouse ... Kruppel-like factor 4 (KLF4; gut-enriched Krüppel-like factor or GKLF) is a zinc-finger transcription factor, and it was first ... KLF4 is a member of the KLF family of transcription factors, which belongs to the relatively large family of SP1-like ...

*Superfamily database

The general categories of function are: Information: storage, maintenance of genetic code; DNA replication and repair; general ... transcription and translation. Regulation: Regulation of gene expression and protein activity; information processing in ...

*Circadian clock

... there was no transcription or genetic circuits, and therefore no feedback loop. Similar observations were made in a marine alga ... While RORs activate transcription of Bmal1, REV-ERBs repress the same transcription process. Hence, the circadian oscillation ... Evidence for a genetic basis of circadian rhythms in higher eukaryotes began with the discovery of the period (per) locus in ... More recently, however, it was reported that only 22% of messenger RNA cycling genes are driven by de novo transcription.[29] ...

*Nucleic acid test

Ligase chain reaction Transcription mediated amplification (TMA). It uses a slightly different molecular method than PCR but ... The term includes any test that directly detects the genetic material of the infecting organism or virus, such as polymerase ... Branched DNA (quantiplex bDNA) tests use a molecule that links to the specific genetic material. ... These tests use a primer to rapidly make copies of the genetic material. A reverse transcriptase PCR (RT-PCR) is used for HIV ...

*Multiple sequence alignment

Genetic algorithms and simulated annealing[edit]. Standard optimization techniques in computer science - both of which were ... alignment of binding site sequences for the same transcription factor cannot rely on evolutionary related mutation operations. ... "Genetic analysis software". National Center for Biotechnology Information. Retrieved March 3, 2010.. ... Like the genetic algorithm method, simulated annealing maximizes an objective function like the sum-of-pairs function. ...

*Stem cell

Using genetic reprogramming with protein transcription factors, pluripotent stem cells with ESC-like capabilities have been ... "Genetic Engineering & Biotechnology News. Mary Ann Liebert, Inc. p. 13. Retrieved 2008-07-06. (subtitle) Procymal is being ... The transcription factors Oct-4, Nanog, and Sox2 form the core regulatory network that ensures the suppression of genes that ... A human embryonic stem cell is also defined by the expression of several transcription factors and cell surface proteins. ...

*Cell (biology)

Transcription is the process where genetic information in DNA is used to produce a complementary RNA strand. This RNA strand is ... Genetic material. Two different kinds of genetic material exist: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Cells ... Prokaryotic genetic material is organized in a simple circular bacterial chromosome in the nucleoid region of the cytoplasm. ... Eukaryotic genetic material is divided into different,[4] linear molecules called chromosomes inside a discrete nucleus, ...

*Intron

"Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability". Mol. Cell. 67 (4): 608-621.e6. doi: ... As mobile genetic elementsEdit. Introns may be lost or gained over evolutionary time, as shown by many comparative studies of ... "The notion of the cistron ... must be replaced by that of a transcription unit containing regions which will be lost from the ... 2017)[31] speculated that the function of introns in maintaining genetic stability may explain their evolutionary maintenance ...

*Lambda phage

Ptashne, M. "A Genetic Switch: Phage Lambda Revisited", 3rd edition 2003 Ptashne, M. (2005). "Regulation of transcription: from ... causing A-T-rich regions to unwind and drive transcription. Transcription starts from the constitutive PL, PR and PR' promoters ... It regulates the transcription of the cI protein and the Cro protein. The life cycle of lambda phages is controlled by cI and ... This activates transcription in the other direction from PRM, as the N terminal domain of cI on OR2 tightens the binding of RNA ...

*CDH1 (gene)

Genetic and epigenetic control of CDH1[edit]. Several proteins such as SNAI1/SNAIL,[58][59] ZFHX1B/SIP1,[60] SNAI2/SLUG,[61][62 ... positive regulation of transcription, DNA-templated. • cellular response to lithium ion. • cell adhesion. • extracellular ... positive regulation of transcription factor import into nucleus. • pituitary gland development. • response to toxic substance. ... De Craene B, Gilbert B, Stove C, Bruyneel E, van Roy F, Berx G (July 2005). "The transcription factor snail induces tumor cell ...

*Long non-coding RNA

June 2003). "Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease ... NcRNAs also target general transcription factors required for the RNAP II transcription of all genes. These general factors ... Sonic hedgehog induces transcription of Evf-2 from an ultra-conserved element located between the Dlx5 and Dlx6 genes during ... Indeed, the transcription and expression of similar non-coding ultraconserved elements was shown to be abnormal in human ...

*Hypopituitarism

Each transcription factor acts in particular groups of cells. Therefore, various genetic mutations are associated with specific ... This requires particular transcription factors that induce the expression of particular genes. Some of these transcription ... If a genetic cause is suspected, genetic testing may be performed. Treatment of hypopituitarism is threefold: removing the ... In addition to the pituitary, some of the transcription factors are also required for the development of other organs; some of ...

*Intron

"Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability". Mol. Cell. 67 (4): 608-621.e6. doi: ... Lynch M (April 2002). "Intron evolution as a population-genetic process". Proceedings of the National Academy of Sciences. 99 ( ... 2017) speculated that the function of introns in maintaining genetic stability may explain their evolutionary maintenance at ... together with genetic and biochemical analysis of RNA splicing reactions. At least four distinct classes of introns have been ...

*Primary transcript

"Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability". Mol. Cell. 67 (4): 608-621.e6. doi: ... Transcription factors, proteins that bind to DNA elements to either activate or repress transcription, bind to enhancers and ... Activation of transcription depends on whether or not the transcription elongation complex, itself consisting of a variety of ... Histone modification by transcription factors is another key regulatory factor for transcription by RNA polymerase. In general ...

*Mitosis

Gene transcription ceases during prophase and does not resume until late anaphase to early G1 phase.[31][32][33] The nucleolus ... During interphase, the genetic material in the nucleus consists of loosely packed chromatin. At the onset of prophase, ... The genome is composed of a number of chromosomes-complexes of tightly coiled DNA that contain genetic information vital for ... "Mitotic bookmarking by transcription factors". Epigenetics & Chromatin. 6 (1): 6. doi:10.1186/1756-8935-6-6. PMC 3621617. PMID ...

*Trichome

The genetic control of patterning of trichomes and roots hairs shares similar control mechanisms. Both processes involve a core ... The development pathway is regulated by three transcription factors: R2R3 MYB, basic helix-loop-helix, and WD40 repeat. The ... Activation of genes that encode specific protein transcription factors (named GLABRA1 (GL1), GLABRA3 (GL3) and TRANSPARENT ... trichomes in Arabidopsis as a genetic model system". International Review of Cytology. 186: 147-178. doi:10.1016/S0074-7696(08) ...

*人類基因組 - 维基百科,自由的百科全

基因組圖譜主要可以分成兩種,一種是遺傳圖譜(genetic map),另一種則是物理圖譜(physical map)。遺傳圖譜是利用基因的重組率來做分析,單位是分莫甘(centimorgan)。這種圖譜表現出來的是基因或特定DNA片段之間的相對位置,而不 ... a

*Glucose-6-phosphate dehydrogenase

Regulation can also occur through genetic pathways. The isoform, G6PDH, is regulated by transcription and posttranscription ... Clinically, an X-linked genetic deficiency of G6PD predisposes a person to non-immune hemolytic anemia . G6PD is widely ... Some scientists have proposed that some of the genetic variation in human G6PD resulted from generations of adaptation to ... Moreover, G6PD is one of a number of glycolytic enzymes activated by the transcription factor hypoxia-inducible factor 1 (HIF1 ...
Genetic and Physical Interactions between Microphthalmia Transcription Factor and PU.1 Are Necessary for Osteoclast Gene ... The microphthalmia transcription factor (MITF), a basic-helix-loop-helix zipper factor, regulates distinct target genes in ... of how lineage-specific gene regulation can be achieved by the combinatorial action of two broadly expressed transcription ...
Scurfy mice have dysfunctional Tregs due to a genetic defect in the transcription factor Forkhead box protein 3 (Foxp3). We ... Scurfy mice have dysfunctional Tregs due to a genetic defect in the transcription factor Forkhead box protein 3 (Foxp3). We ... Development of pulmonary fibrosis through a pathway involving the transcription factor Fra-2/AP-1. Proc Natl Acad Sci U S A. ... Scurfy mice have a missense mutation in the transcription factor Forkhead box protein 3 (Foxp3) gene and therefore lack ...
A well-known transcription factor in the yeast pheromone pathway is used as an example, and the underlying genetic loci ... By mapping differences in transcription factor binding among individuals, here we present the genetic basis of such variation ... studied the variability of transcription factor binding among individuals on a genome-wide scale, using transcription-binding ... and thus the extent and underlying genetic basis of transcription factor binding diversity is unknown. ...
Genetic engineering using transcription factors (TFs) represents an alternative approach that may help overcome this difficulty ... Ueda Y., Yanagisawa S. (2018) Transcription Factor-Based Genetic Engineering to Increase Nitrogen Use Efficiency. In: Shrawat A ... Qu B, He X, Wang J, Zhao Y, Teng W, Shao A, Zhao X, Ma W, Wang J, Li B et al (2015) A wheat CCAAT box-binding transcription ... He X, Qu B, Li W, Zhao X, Teng W, Ma W, Ren Y, Li B, Li Z, Tong Y (2015) The nitrate inducible NAC transcription factor TaNAC2- ...
... transcription genetic include Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms, Using Click ... Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template ... Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms. Clark Fritsch1,2, Jean-Francois Pierre Gout3,4, Marc ...
Runt-related transcription factor 1 (RUNX1) is generally considered to function as a tumor suppressor in the development of ...
DNA is the genetic material of a cell and is copied in the form of pre-mRNA through transcription in eukaryotes. RNA polymerase ... Stochastic modeling of eukaryotic transcription at the single nucleotide level  Vashishtha, Saurabh (Lethbridge, Alta. : ... II is responsible for the transcription of all genes that express proteins. Transcription ... ...
Accessing the druggable genetic programmes governed by mammalian bHLH-PAS transcription factors. Investigator Awards in Science ... We will explore a family of human gene regulating proteins, known as the bHLH-PAS transcription factors, whose 3D structure ... Understanding how such signalling molecules interact with bHLH-PAS transcription factors should inform future drug development ...
We identified Pea3 family transcription factors as the key effectors of FGF signaling in reprograming the epithelia ...
... Abstract A central goal of ... Characterizing and Prototyping Genetic Networks with Cell-Free Transcription-Translation Reactions + Title ... Cell-free transcription-translation (TX-TL) systems offer a simple and fast alternative to performing these characterizations ... As a way to demonstrate the utility of cell-free TX-TL, we illustrate the characterization of two genetic networks: an RNA ...
The transcription is the initial step of gene expression which involves the particular segment of DNA which is copied to RNA ... Transcription Peer-review Journals. The transcription is the initial step of gene expression which involves the particular ... The band of DNA transcribed into RNA is called a transcription unit and encodes at least one gene. Peer review refers to the ...
The kinetics of cessation of transcription give information on both meassenger RNA decay and rate of transcription. Arrhenius ... If cells are irradiated shortly after induction, the transcription of the DNA ceases, and the enzyme produced by the messenger ... and the activation energies mtieasured are 11,000 calories per mole for decay and 22,000 calories per mole for transcription. ...
Genetic" by people in Harvard Catalyst Profiles by year, and whether "Transcription, Genetic" was a major or minor topic of ... "Transcription, Genetic" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH (Medical ... Below are the most recent publications written about "Transcription, Genetic" by people in Profiles. ... Below are MeSH descriptors whose meaning is more general than "Transcription, Genetic". ...
No other data source has: the depth of longitudinal social, behavioral, environmental, genetic, and biological data; the ... Analyses of these data could inform therapeutic interventions; identify new genetic mechanisms for GxE research; inform ... the genetic regulation of the immune system, biomarkers, and very common forms of inflammatory morbidity and morbidity-specific ...
At the same time, current evidence indicates that these regions are particularly stressed by transcription-related mutagenic ... The regions surrounding transcription start sites (TSSs) of genes play a critical role in the regulation of gene expression. ...
Genetic and genomic analyses of RNA polymerase II-pausing factor in regulation of mammalian transcription and cell growth. J. ... Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation ... Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation ... Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation ...
Genetic variations in the transcription factors GATA4 and GATA6 and bleeding complications in patients receiving warfarin ... Genetic variations in the transcription factors GATA4 and GATA6 and bleeding complications in patients receiving warfarin ...
Genetic networks controlled by the bacterial replication initiator and transcription factor DnaA in Bacillus subtilis. Download ... Genetic networks controlled by the bacterial replication initiator and transcription factor DnaA in Bacillus subtilis. Research ... In B. subtilis, DnaA has previously been shown to repress its own transcription and has also been implicated in directing part ... DnaA is the bacterial replication initiator, which also functions as a transcription factor to regulate gene expression. ...
Previous reports demonstrated that the MFNLP could lead to the duplication of transcription factor binding sites (TFBS) ... Genetic Diversity in HIV-1 Subtype C LTR from Brazil and Mozambique Generates New Transcription Factor-Binding Sites. José ... "Genetic Diversity in HIV-1 Subtype C LTR from Brazil and Mozambique Generates New Transcription Factor-Binding Sites." Viruses ... Genetic Diversity in HIV-1 Subtype C LTR from Brazil and Mozambique Generates New Transcription Factor-Binding Sites. Viruses ...
Association of the Genetic Polymorphisms in Transcription Factor 7-Like 2 and Peroxisome Proliferator-Activated Receptors-γ2 ... Transcription factor 7-like 2 gene (TCF7L2) and peroxisome proliferator-activated receptors-γ2 (PPAR-γ2) have a profound effect ... In this investigation, we carried out genetic association study of the SNPs in PPAR-γ2 and TCF7L2 with T2DM susceptibility and ... L. S. H. Wu, C. H. Hsieh, D. Pei, Y. J. Hung, S.-W. Kuo, and E. Lin, "Association and interaction analyses of genetic variants ...
Convergent transcription and stalling of transcription are enriched at DNA breakpoints found in acute lymphoblastic leukemia ... and associate with DNA structures and sequences that mediate genetic instability. ... Indication of transcription-coupled genetic instability at leukemia SV hotspots lacking RSS motifs.. (A) Overlap between RLFS ... These mechanisms of transcription-coupled genetic instability, earlier implicated in lymphomas (Pavri et al., 2010; Meng et al ...
sar Genetic determinants necessary for transcription of RNAII and RNAIII in the agr locus of Staphylococcus aureus.. A L Cheung ... sar Genetic determinants necessary for transcription of RNAII and RNAIII in the agr locus of Staphylococcus aureus. ... sar Genetic determinants necessary for transcription of RNAII and RNAIII in the agr locus of Staphylococcus aureus. ... sar Genetic determinants necessary for transcription of RNAII and RNAIII in the agr locus of Staphylococcus aureus. ...
Identification of a Genetic Signature of Activated Signal Transducer and Activator of Transcription 3 in Human Tumors. James V. ... Identification of a Genetic Signature of Activated Signal Transducer and Activator of Transcription 3 in Human Tumors ... Identification of a Genetic Signature of Activated Signal Transducer and Activator of Transcription 3 in Human Tumors ... Identification of a Genetic Signature of Activated Signal Transducer and Activator of Transcription 3 in Human Tumors ...
... Kalantarian, Maryam ... AGAMOUS-LIKE 36 (AGL36), a member of the MADS-box transcription factor type I Mγ family, has been identified as an imprinted ... In a series of phenotypic and genetic analysis, a 10% transmission reduction of the agl36;agl62 double mutant combination ...
In a new study published in Nature Genetic , Genetics And Genomics ... Ilsley likens the interaction between transcription factors and their enhancers to the tuning of a radio. "Some transcription ... ability to accept different kinds of transcription factors in different ways.. You can bring in foreign transcription factors ... Transcription factors bind to specific sections of DNA called enhancers, either inhibiting or activating expression of the ...
  • Evidence from various studies has shown that genetic susceptibility to T2DM is polygenic [ 5 , 6 ], and Genome Wide Association Studies (GWAS) have reported more than 20 genetic loci associated with the risk of T2DM [ 7 , 8 ]. (hindawi.com)
  • Although a DNA fragment encompassing the sarA transcript plus a 189-bp upstream region was sufficient for agr expression, complementation analysis revealed that the sarB transcript was the most effective in augmenting agr transcription as determined by RNAII and RNAIII transcription and gel retardation assays with the P2 and P3 promoters of agr. (asm.org)
  • Transcription is initiated at regions of DNA called promoters, which are typically 20 to 150 base pairs long, depending on the organism. (encyclopedia.com)
  • Activation-induced deaminase (AID) can drive lymphomagenesis by generating off-target DNA breaks at loci that harbor highly active enhancers and display convergent transcription. (elifesciences.org)
  • Typical approaches to GWAS exploit linkage disequilibrium (LD) between genetic variants such as SNPs and loci that directly affect traits of interest. (biomedcentral.com)
  • Microphthalmia-associated transcription factor (MITF), is thought to be a central player in melanoma biology, and it controls many aspects of the phenotypic expression of the melanocytic lineage. (frontiersin.org)
  • However, recently the paired box transcription factor PAX3 was shown to transcriptionally activate POU3F2/BRN2, leading to direct repression of MITF expression. (frontiersin.org)
  • While these data support the notion of independent roles for MITF and PAX3, additional experiments are required to provide robust examination of the proposed genetic switch theory. (frontiersin.org)
  • Microphthalmia-associated transcription factor also known as class E basic helix-loop-helix protein 32 or bHLHe32 is a protein that in humans is encoded by the MITF gene. (wikipedia.org)
  • MITF is a basic helix-loop-helix leucine zipper transcription factor involved in lineage-specific pathway regulation of many types of cells including melanocytes, osteoclasts, and mast cells. (wikipedia.org)
  • Scientists at Johns Hopkins say they are one step closer to understanding the genetic mechanism of a rare, complex, multiple-gene disorder called Hirschsprung's disease. (medicalxpress.com)
  • In addition, current and future research can lead to potential avenues to target this transcription factor mechanism for cancer prevention. (wikipedia.org)
  • Many genetic variants associated with human disease have been found to be associated with alterations in mRNA expression. (diagenode.com)
  • Our results suggest that protein-based mechanisms might functionally buffer genetic alterations that influence mRNA expression levels and that pQTLs might contribute phenotypic diversity to a human population independently of influences on mRNA expression. (diagenode.com)
  • To achieve this, one of the important strategies is to genetically engineer the ruling peanut varieties using transcription factor regulating the expression of several downstream, abiotic-stress responsive gene(s). (frontiersin.org)
  • To determine the extent of genetic variations and the nature of swine HEV infections in U.S. pigs, we developed a universal reverse transcription-PCR (RT-PCR) assay that is capable of detecting genetically divergent strains of HEV. (pubmedcentralcanada.ca)
  • Further genetic evidence for involvement of PGC-1 alpha in HD pathogenesis was generated by the findings that sequence variations in the PPARGC1A gene encoding PGC-1 alpha exert modifying effects on the AO in HD. (biomedcentral.com)
  • Interestingly, average additive genetic effects for gene transcription were smaller than those reported for traditional phenotypic traits in salmonids, suggesting that the evolutionary potential of gene transcription is lower than that of traditional traits. (uwindsor.ca)
  • In a series of phenotypic and genetic analysis, a 10% transmission reduction of the agl36;agl62 double mutant combination through the female gametophyte was observed, suggesting a role in the female gametophyte. (uio.no)
  • We also provide guidelines for designing TX-TL experiments to characterize new genetic networks. (caltech.edu)
  • In this study, we used a 5 × 5 full-factorial breeding design within each of two Atlantic salmon (Salmo salar) populations to characterize the genetic architecture of gene transcription. (uwindsor.ca)
  • Results of preclinical studies by MUSC investigators reported in the July 2016 issue of PLOS One, demonstrate for the first time that the transcription factor KLF12 promotes CRC cell growth, in part, by activating EGR1. (medicalxpress.com)
  • Boullosa J, Bachu M, Bila D, Ranga U, Süffert T, Sasazawa T, Tanuri A. Genetic Diversity in HIV-1 Subtype C LTR from Brazil and Mozambique Generates New Transcription Factor-Binding Sites. (mdpi.com)
  • Our results support the existence of different components within the basic transcription complexes that antagonistically interact with the NC2 repressor and suggest that the correct balance between the activities of specific positive and negative components is essential for cell growth. (genetics.org)
  • Transcription factor 7-like 2 gene ( TCF7L2 ) and peroxisome proliferator-activated receptors- γ 2 ( PPAR- γ 2 ) have a profound effect on the incidence of type 2 diabetes mellitus (T2DM) and had previously been found to be associated with T2DM risk in various ppopulations. (hindawi.com)
  • So those are all ways in which genetic modification can be used in plants. (sophia.org)