Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
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.
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.
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.
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.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.
A family of DNA-binding transcription factors that contain a basic HELIX-LOOP-HELIX MOTIF.
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.
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.
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.
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.
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.
Established cell cultures that have the potential to propagate indefinitely.
A subclass of winged helix DNA-binding proteins that share homology with their founding member fork head protein, Drosophila.
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).
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.
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
The 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.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
A large superfamily of transcription factors that contain a region rich in BASIC AMINO ACID residues followed by a LEUCINE ZIPPER domain.
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.
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.
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)
Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.
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.
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.
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.
A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.
Genes 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.
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.
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.
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.
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.
The major sequence-specific DNA-binding component involved in the activation of transcription of RNA POLYMERASE II. It was originally described as a complex of TATA-BOX BINDING PROTEIN and TATA-BINDING PROTEIN ASSOCIATED FACTORS. It is now know that TATA BOX BINDING PROTEIN-LIKE PROTEINS may take the place of TATA-box binding protein in the complex.
Cells 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.
An activating transcription factor that plays a key role in cellular responses to GENOTOXIC STRESS and OXIDATIVE STRESS.
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.
A specificity protein transcription factor that regulates expression of a variety of genes including VASCULAR ENDOTHELIAL GROWTH FACTOR and CYCLIN-DEPENDENT KINASE INHIBITOR P27.
The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.
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.
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.
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.
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.
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.
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.
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.
Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.
Nucleic acid sequences involved in regulating the expression of genes.
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.
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.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
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.
A family of transcription factors that contain regions rich in basic residues, LEUCINE ZIPPER domains, and HELIX-LOOP-HELIX MOTIFS.
Activating transcription factors of the MADS family which bind a specific sequence element (MEF2 element) in many muscle-specific genes and are involved in skeletal and cardiac myogenesis, neuronal differentiation and survival/apoptosis.
Recombinant 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.
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.
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.
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.
An essential GATA transcription factor that is expressed primarily in HEMATOPOIETIC STEM CELLS.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.
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.
A family of transcription factors that contain two ZINC FINGER MOTIFS and bind to the DNA sequence (A/T)GATA(A/G).
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.
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.
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.
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Activating transcription factors 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.
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.
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.
A cell line derived from cultured tumor cells.
The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.
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.
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.
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.
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.
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.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.
A GATA transcription factor that is expressed predominately in SMOOTH MUSCLE CELLS and regulates vascular smooth muscle CELL DIFFERENTIATION.
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.
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.
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.
An activating transcription factor that regulates expression of a variety of genes including C-JUN GENES and TRANSFORMING GROWTH FACTOR BETA2.
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.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.
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.
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.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
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.
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.
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.
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.
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).
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.
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.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
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.
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.
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.
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.
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)
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.
Proteins containing a region of conserved sequence, about 200 amino acids long, which encodes a particular sequence specific DNA binding domain (the T-box domain). These proteins are transcription factors that control developmental pathways. The prototype of this family is the mouse Brachyury (or T) gene product.
Proteins found in any species of fungus.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
DNA-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.
A ubiquitously expressed octamer transcription factor that regulates GENETIC TRANSCRIPTION of SMALL NUCLEAR RNA; IMMUNOGLOBULIN GENES; and HISTONE H2B genes.
Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.
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.
Proteins prepared by recombinant DNA technology.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.
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.
A group of transcription factors that were originally described as being specific to ERYTHROID CELLS.
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.
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.
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.
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.
The developmental history of specific differentiated cell types as traced back to the original STEM CELLS in the embryo.
Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations.
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.
An early growth response transcription factor that has been implicated in regulation of CELL PROLIFERATION and APOPTOSIS.
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.
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.
Deletion of sequences of nucleic acids from the genetic material of an individual.
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.
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.
A family of low-molecular weight, non-histone proteins found in chromatin.
Proteins found in any species of bacterium.
All of the processes involved in increasing CELL NUMBER including CELL DIVISION.
A transcription factor that takes part in WNT signaling pathway. The activity of the protein is regulated via its interaction with BETA CATENIN. Transcription factor 7-like 2 protein plays an important role in the embryogenesis of the PANCREAS and ISLET CELLS.
An ets proto-oncogene expressed primarily in adult LYMPHOID TISSUE; BRAIN; and VASCULAR ENDOTHELIAL CELLS.
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.
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)
The biosynthesis of DNA carried out on a template of RNA.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
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.
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.
A basic helix-loop-helix transcription factor that was originally identified in DROSOPHILA as essential for proper gastrulation and MESODERM formation. It plays an important role in EMBRYONIC DEVELOPMENT and CELL DIFFERENTIATION of MUSCLE CELLS, and is found in a wide variety of organisms.
A tissue-specific subunit of NF-E2 transcription factor that interacts with small MAF PROTEINS to regulate gene expression. P45 NF-E2 protein is expressed primarily in MEGAKARYOCYTES; ERYTHROID CELLS; and MAST CELLS.
Transport proteins that carry specific substances in the blood or across cell membranes.
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.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
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.
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.
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.
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.
Gated transport mechanisms by which proteins or RNA are moved across the NUCLEAR MEMBRANE.
One of the BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTORS that is synthesized as a membrane-bound protein in the ENDOPLASMIC RETICULUM. In response to endoplasmic reticulum stress it translocates to the GOLGI APPARATUS. It is activated by PROTEASES and then moves to the CELL NUCLEUS to regulate GENETIC TRANSCRIPTION of GENES involved in the unfolded protein response.
A family of mammalian POU domain factors that are expressed predominately in NEURONS.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
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.
A subclass of SOX transcription factors that are expressed in neuronal tissue where they may play a role in the regulation of CELL DIFFERENTIATION. Members of this subclass are generally considered to be transcriptional activators.
Formation of an acetyl derivative. (Stedman, 25th ed)
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.
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).)
A basic-leucine zipper transcription factor that regulates GLOBIN gene expression and is related to TRANSCRIPTION FACTOR AP-1. NF-E2 consists of a small MAF protein subunit and a tissue-restricted 45 kDa subunit.
Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.
A heterotrimeric DNA-binding protein that binds to CCAAT motifs in the promoters of eukaryotic genes. It is composed of three subunits: A, B and C.
Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.
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)
A species of fruit fly much used in genetics because of the large size of its chromosomes.
A subclass of closely-related SOX transcription factors. Members of this subfamily have been implicated in regulating the differentiation of OLIGODENDROCYTES during neural crest formation and in CHONDROGENESIS.
Ubiquitously expressed basic HELIX-LOOP-HELIX MOTIF transcription factors. They bind CANNTG sequences in the promoters of a variety of GENES involved in carbohydrate and lipid metabolism.
Interruption or suppression of the expression of a gene at transcriptional or translational levels.
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.
The entity of a developing mammal (MAMMALS), generally from the cleavage of a ZYGOTE to the end of embryonic differentiation of basic structures. For the human embryo, this represents the first two months of intrauterine development preceding the stages of the FETUS.
Elements of limited time intervals, contributing to particular results or situations.
A family of muscle-specific transcription factors which bind to DNA in control regions and thus regulate myogenesis. All members of this family contain a conserved helix-loop-helix motif which is homologous to the myc family proteins. These factors are only found in skeletal muscle. Members include the myoD protein (MYOD PROTEIN); MYOGENIN; myf-5, and myf-6 (also called MRF4 or herculin).
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.
Histochemical localization of immunoreactive substances using labeled antibodies as reagents.
The developmental entity of a fertilized egg (ZYGOTE) in animal species other than MAMMALS. For chickens, use CHICK EMBRYO.
The process by which two molecules of the same chemical composition form a condensation product or polymer.
Factors that form a preinitiation complex at promoters that are specifically transcribed by RNA POLYMERASE I.
A basic helix-loop-helix transcription factor that plays a role in determining cell fate during embryogenesis. It forms a heterodimer with TWIST TRANSCRIPTION FACTOR and ACHAETE-SCUTE GENE COMPLEX-related TRANSCRIPTION FACTORS.
Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.
Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.
A POU domain factor that regulates expression of GROWTH HORMONE; PROLACTIN; and THYROTROPIN-BETA in the ANTERIOR PITUITARY GLAND.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
A subclass of closely-related SOX transcription factors. Members of the group have been found expressed in developing neuronal tissue, LYMPHOCYTES, and during EMBRYONIC DEVELOPMENT.

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

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

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

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

Separation of shoot and floral identity in Arabidopsis. (3/70946)

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

Novel regulation of the homeotic gene Scr associated with a crustacean leg-to-maxilliped appendage transformation. (4/70946)

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

Apontic binds the translational repressor Bruno and is implicated in regulation of oskar mRNA translation. (5/70946)

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

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

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

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

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

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

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

Divergence of transcription factor binding sites is considered to be an important source of regulatory evolution. The associations between transcription factor binding sites and phenotypic diversity have been investigated in many model organisms. However, the understanding of other factors that contribute to it is still limited. Recent studies have elucidated the effect of chromatin structure on molecular evolution of genomic DNA. Though the profound impact of nucleosome positions on gene regulation has been reported, their influence on transcriptional evolution is still less explored. With the availability of genome-wide nucleosome map in yeast species, it is thus desirable to investigate their impact on transcription factor binding site evolution. Here, we present a comprehensive analysis of the role of nucleosome positioning in the evolution of transcription factor binding sites. We compared the transcription factor binding site frequency in nucleosome occupied regions and nucleosome depleted regions
Didier Picard, January 2015 Current list of HBD fusion proteins_ Protein X a HBD b regulated as c Refs. transcription factor in Arabidopsis transcription factor Arabidopsis transcription factor in tobacco coactivator transcription factor 1 2 3 transcription factor transcription factor, differentiation factor transcription factor putative transcription factor in arabidposis transcription factor oncoprotein transcription factor transcription factor oncoprotein oncoprotein oncoprotein transcription factor oncoprotein, transcription factor 6 7 transcription factor transcription factor in yeast, tissue culture cells and zebra fish transcriptional repressor transcription factor transcription factor in yeast, in tissue culture cells, transgenic mice, Xenopus, Drosophila and plants transcription factor, promoter of proliferation transcription factor transcription factor 19 20, 21, i Transcription factors APETALA3 ATF6α Athb-1 GR ER e GR Bob1/OBF1 ER e CCAT (from calcium ER e 4 5 channel cav1.2) C/EBP ...
Fig 5: regulation of transcription : which evidence code should be used? kct10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA has_regulation_target(Tbx5a) Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA tbx5a has_regulation _target(Tbx5a) Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IGI tbx5a has_regulation _target(Tbx5a) kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IMP has_regulation_target: tbx5b ...
The DNA sequence that a transcription factor binds to is called a transcription factor binding site or response element. Chemically, transcription factors usually interact with their binding sites using a combination of hydrogen bonds and Van der Waals forces. Due to the nature of these chemical interactions, most transcription factors bind DNA in a sequence specific manner. However, not all bases in the transcription factor binding site may actually interact with the transcription factor. In addition some of these interactions may be weaker than others. Thus, transcription factors dont bind just one sequence but are capable of binding a subset of closely related sequences, each with a different strength of interaction. For example, although the consensus binding site for the TATA binding protein (TBP) is: TATAAAA the TBP transcription factor can also bind similar sequences such as: TATATAT or TATATAA Because transcription factors can bind a set of related sequences and the sequences dont tend ...
For decades, it has been hypothesized that gene regulation has had a central role in human evolution, yet much remains unknown about the genome-wide impact of regulatory mutations. Here we use whole-genome sequences and genome-wide chromatin immunoprecipitation and sequencing data to demonstrate that natural selection has profoundly influenced human transcription factor binding sites since the divergence of humans from chimpanzees 4-6 million years ago. Our analysis uses a new probabilistic method, called {INSIGHT}, for measuring the influence of selection on collections of short, interspersed noncoding elements. We find that, on average, transcription factor binding sites have experienced somewhat weaker selection than protein-coding genes. However, the binding sites of several transcription factors show clear evidence of adaptation. Several measures of selection are strongly correlated with predicted binding affinity. Overall, regulatory elements seem to contribute substantially to both ...
The DNA sequence that a transcription factor binds to is called a transcription factor-binding site or response element.[55]. Transcription factors interact with their binding sites using a combination of electrostatic (of which hydrogen bonds are a special case) and Van der Waals forces. Due to the nature of these chemical interactions, most transcription factors bind DNA in a sequence specific manner. However, not all bases in the transcription factor-binding site may actually interact with the transcription factor. In addition, some of these interactions may be weaker than others. Thus, transcription factors do not bind just one sequence but are capable of binding a subset of closely related sequences, each with a different strength of interaction. For example, although the consensus binding site for the TATA-binding protein (TBP) is TATAAAA, the TBP transcription factor can also bind similar sequences such as TATATAT or TATATAA. Because transcription factors can bind a set of related ...
Since the successful isolation of mouse and human embryonic stem cells (ESCs) in the past decades, massive investigations have been conducted to dissect the pluripotency network that governs the ability of these cells to differentiate into all cell types. Beside the core Oct4-Sox2-Nanog circuitry, accumulating regulators, including transcription factors, epigenetic modifiers, microRNA and signaling molecules have also been found to play important roles in preserving pluripotency. Among the various regulations that orchestrate the cellular pluripotency program, transcriptional regulation is situated in the central position and appears to be dominant over other regulatory controls. In this review, we would like to summarize the recent advancements in the accumulating findings of new transcription factors that play a critical role in controlling both pluripotency network and ESC identity.
Silkworm Transcription Factor Database (SilkTF) is a protein database which contains information on transcription factors (TFs) of silkworm.
The Oxidative Stress Responsive Transcription Factor Pap1 Confers DNA Damage Resistance on Checkpoint-Deficient Fission Yeast Cells. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
This unit describes how to use the Transcription Element Search System (TESS). This Web site predicts transcription factor binding sites (TFBS) in DNA sequence using two different kinds of models of sites, strings and positional weight matrices. The binding of transcription factors to DNA is a major part of the control of gene expression. Transcription factors exhibit sequence-specific binding; they form stronger bonds to some DNA sequences than to others. Identification of a good binding site in the promoter for a gene suggests the possibility that the corresponding factor may play a role in the regulation of that gene. However, the sequences transcription factors recognize are typically short and allow for some amount of mismatch. Because of this, binding sites for a factor can typically be found at random every few hundred to a thousand base pairs. TESS has features to help sort through and evaluate the significance of predicted sites. Curr. Protoc. Bioinform. 21:2.6.1-2.6.15. © 2008 by John ...
The transcriptional coactivator peroxisome proliferator-activated receptor-gamma coactivator-1beta (PGC-1beta) has been implicated in important metabolic processes. A mouse lacking PGC-1beta (PGC1betaKO) was generated and phenotyped using physiological, molecular, and bioinformatic approaches. PGC1betaKO mice are generally viable and metabolically healthy. Using systems biology, we identified a general defect in the expression of genes involved in mitochondrial function and, specifically, the electron transport chain. This defect correlated with reduced mitochondrial volume fraction in soleus muscle and heart, but not brown adipose tissue (BAT). Under ambient temperature conditions, PGC-1beta ablation was partially compensated by up-regulation of PGC-1alpha in BAT and white adipose tissue (WAT) that lead to increased thermogenesis, reduced body weight, and reduced fat mass. Despite their decreased fat mass, PGC1betaKO mice had hypertrophic adipocytes in WAT. The thermogenic role of PGC-1beta was
ABSTRACT: One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the gene expression data with transcription factor binding data (based on ChIP-seq and DNase-seq) within 10 kb of the transcription start sites of expressed genes. This ...
ABSTRACT: One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the gene expression data with transcription factor binding data (based on ChIP-seq and DNase-seq) within 10 kb of the transcription start sites of expressed genes. This ...
ABSTRACT: One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the gene expression data with transcription factor binding data (based on ChIP-seq and DNase-seq) within 10 kb of the transcription start sites of expressed genes. This ...
Clinical evidence suggests that antiestrogens inhibit the development of androgen-insensitive prostate cancer. Here, we show that the estrogen receptor β (ERβ) mediates inhibition by the antiestrogen ICI 182,780 (ICI) and its enhancement by estrogen. ERβ associated with gene promoters through the tumor-suppressing transcription factor KLF5 (Krüppel-like zinc finger transcription factor 5). ICI treatment increased the recruitment of the transcription coactivator CBP [CREB (adenosine 3′,5′-monophosphate response element-binding protein)-binding protein] to the promoter of FOXO1 through ERβ and KLF5, which enhanced the transcription of FOXO1. The increase in FOXO1 abundance led to anoikis in prostate cancer cells, thereby suppressing tumor growth. In contrast, estrogen induced the formation of complexes containing ERβ, KLF5, and the ubiquitin ligase WWP1 (WW domain containing E3 ubiquitin protein ligase 1), resulting in the ubiquitination and degradation of KLF5. The combined presence of ...
Isolation of transcriptional activators of CDR1 and CDR2 by mining in the C. albicans genome.In this article, we report the isolation of a transcription factor involved in the regulation of CDR1 and CDR2 by inspection of genome data. We focused on Zn(2)-Cys(6) transcription factors because these factors are able to target 5′-CGG-3′ motifs that are present in the DRE of CDR1 and CDR2 promoters. These transcription factors have in common a Zn(2)-Cys(6) DNA-binding domain which targets sequences with direct, inverted, or everted palindromic repeats containing a 5′-CGG-3′ motif with various numbers of nucleotides in the intervening spacer region. Several examples can be cited from studies performed with S. cerevisiae: Hap1p recognizes the direct repeat 5′-CGGNNNTANCGG-3′; the heterodimer Pip2p/Oaf1p binds to inverted repeats of the consensus sequence 5′-CGGN15-18-CCG-3′; Pdr8p and Yrr1p, which are factors involved in multidrug resistance, target DNA-binding motifs containing the ...
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TY - JOUR. T1 - In Vivo mutational analysis of the DNA binding domain of the tissue-specific transcription factor, Pit-1. AU - Liang, Jie. AU - Moye-Rowley, Scott. AU - Maurer, Richard A.. PY - 1995/10/27. Y1 - 1995/10/27. N2 - Pit-1 is a member of the POU family of transcription factors, which contain a bipartite DNA binding domain. The DNA binding domain consists of a POU-specific domain and a POU homeodomain. Each of the subdomains can interact with DNA independently, but both subdomains are required for high affinity, sequence-specific DNA binding. To examine the contributions of individual amino acids to the function of the DNA binding domain of Pit-1, we developed an approach involving random, in vitro mutagenesis followed by functional screening in Saccharomyces cerevisiae. Using this strategy, we identified a number of point mutations that altered the function of the Pit-1 DNA binding domain. Mutations that altered Pit-1 function were found in both the POU-specific and the POU ...
Transcription factors directly control when, where, and the extent to which genes are expressed. Signal transduction pathways are responsible for either activating or inhibiting many of them. Transcription factors are also regulated by cofactors, forming complexes that can activate or inhibit transcriptional activity. Many transcription factors, such as nuclear receptors, reside in the cytoplasm and enter the nucleus upon activation (e.g., ligand binding). Posttranslational modifications and coregulating proteins provide additional layers of regulation. Transcription factors are involved in a wide variety of processes, such as development, stress responses, and immunity. Activation or inhibition of transcription factors is often dysregulated during oncogenesis. Transcription factors can also be dysregulated during developmental processes, promoting or inhibiting cellular differentiation. Analyzing the expression, regulation, activity, and sequence of transcription factor genes can help determine ...
The human transcription enhancer factor-1 (TEF-1) belongs to a family of evolutionarily conserved proteins that have a DNA binding TEA domain. TEF-1 shares a 98% homology with Drosophila scalloped (sd) in the DNA binding domain and a 50% similarity in the activation domain. We have expressed human TEF-1 in Drosophila under the hsp-70 promoter and find that it can substitute for Sd function. The transformants rescue the wingblade defects as well as the lethality of loss-of-function alleles. Observation of reporter activity in the imaginal wing discs of the enhancer-trap alleles suggests that TEF-1 is capable of promoting sd gene regulation. The functional capability of the TEF-1 product was assessed by comparing the extent of rescue by heat shock (hs)-TEF-1 with that of hs-sd. The finding that TEF-1 can function in vivo during wingblade development offers a potent genetic system for the analysis of its function and in the identification of the molecular partners of TEF-1.. ...
Background TF-TFBS-TFT triplets -Transcription factors(TF) regulate transcription factor target(TFT) through binding to transcription factor DNA binding sites(TFBS).
This paper describes a novel approach to constructing Position-Specific Weight Matrices (PWMs) based on the transcription factor binding site (TFBS) data provide by the TRANSFAC database and comparison of the newly generated PWMs with the original TRANSFAC matrices. Multiple local sequence alignment was performed on the TFBSs of each transcription factor. Several different alignment programs were tested and their matrices were compared to the original TRANSFAC matrices. One of the alignment programs, GLAM, produced comparable matrices in terms of the average ranking of true positive sites across the whole test set of sequences. ...
The mechanisms underlying the development and progression of breast cancer are not fully understood, and this is particularly challenging because of its diverse etiologies [20]. However, it is clear that changes in gene expression are essential to drive different processes that occur during tumourigenesis [21]. Transcription factors control gene expression by binding to specific DNA sequences in gene promoters and often regulate multiple target genes. Because of this ability to control different target genes, deregulation of transcription factors can drive events associated with the initiation and progression of diseases such as cancer [22]. Previous studies have shown that the Brn-3b transcription factor is elevated in ,60% of primary breast cancers [1], and when increased, it significantly enhances proliferation and anchorage-independent growth in vitro and tumour growth in vivo [2, 3]. Elevated Brn-3b also confers resistance to growth-inhibitory stimuli and increases the migratory potential ...
ELF4 is a member of the ETS family of transcription factors (TF) with transcription activating properties (Lacorazza and Nimer, 2003). ELF4 binds to DNA sequences containing the consensus 5-WGGA-3 and transactivates promoters of the hematopoietic growth factor genes CSF2, IL3, IL8, and of the bovine lysozyme gene (Miyazaki et al., 1996; Mao et al., 1999; Hedvat et al., 2004; Suico et al., 2004). ELF4 acts synergistically with RUNX1 to transactivate the IL3 promoter (Mao et al., 1999). It also transactivates the PRF1 promoter in natural killer (NK) cells (Lacorazza et al., 2002). ELF4 has important molecular functions, including protein binding, transcription activator activity, sequence-specific DNA binding, transcription factor activity. ELF4 interacts with multiple proteins, including Cyclin A/CDK2 kinase complex, FBXO4, FBXO7, PML, RUNX1, SKP2 and UBB (Miyazaki et al., 1996; Mao et al., 1999; Miyazaki et al., 2001; Liu et al., 2006; Suico et al., 2006). ELF4 has been implicated in widely ...
This function reads in transcription factor information given the selected transcription factor target gene database. The information is downloaded via the AnnotationHub package and merged, if necessary.
Breast cancer is one of the most common malignant diseases in women. Epithelial-mesenchymal transition (EMT) has been documented to play an important role in proliferation, invasion and metastasis of tumor cells as well as drug resistance. Even though the signal transducer and activator of transcription 3 (STAT3) is not a master transcription factor of EMT, STAT3 is involved in the regulation of EMT-related gene expression. However, it remains unclear whether targeted inhibitors of STAT3 affect EMT-mediated proliferation, migration, invasion and drug resistance of tumor cells. In this paper, we investigated the effects of STAT3 and its interaction with Twist, a master transcription factor, in EMT program and subsequent changes in proliferation, migration and invasion of breast cancer cells by interfering STAT3 signaling pathway with different strategies such as STAT3 inactivation and STAT3 silencing. Furthermore, we explored the role of inhibiting STAT3 phosphorylation in the EMT regulation of ...
Post-translational modifications (PTMs) of transcription factors alter interactions with co-regulators and epigenetic modifiers. For example, members of the C/EBP transcription factor family are extensively methylated on arginine and lysine residues in short, conserved, modular domains, implying modification-dependent cofactor docking. Here we describe array peptide screening (APS), a systematic and differential approach to detect PTM-dependent interactions in the human proteome using chemically synthesized, biotinylated peptides coupled to fluorophore-labeled streptavidin. Peptides with and without a modified residue are applied in parallel to bacterial expression libraries in an arrayed format. Interactions are detected and quantified by laser scanning to reveal proteins that differentially bind to nonmodified or modified peptides. We have previously used this method to investigate the effect of arginine methylation of C/EBPβ peptides. The method enables determination of PTM-dependent transcription
The Turner lab has focused on the role of transcription factors in the development of peripheral sensory neurons, the spinal cord, midbrain, and habenula. Transcription factors are proteins which bind to DNA in the nucleus to switch on or off the genes which characterize specific cell types. Without the correct complement of transcription factors, cells undergo an identity crisis and fail to execute their correct developmental programs. Many genetic disorders in the brain and other organ systems have been linked to defective transcription factor function. Most of the Turner Lab studies have been conducted in transgenic mice in which they either knockout the factor of interest, or express a tracer protein in the neurons that express the factor. Studies have focused mainly on the homeodomain transcription factors Brn3a, Islet1, and Hmx1. In recent work, they have shown that without the combinatorial effects of Brn3a and Islet1, developing sensory neurons remain in a ground state in which ...
The analysis of regulatory regions in genome sequences is strongly based on the detection of potential transcription factor binding sites. The preferred models for representation of transcription factor binding specificity have been termed position-specific scoring matrices. JASPAR is an open-access …
Researchers are only beginning to understand how individual variation in gene regulation can have a lasting impact on ones health and susceptibility to certain diseases. Now, an ambitious survey of the human genome has identified differences in the binding of master regulators called transcription factors to DNA that affect how genes are expressed in different people.. The study, which is published in the March 18, 2010, issue of Science, looked at two common transcription factors. HHMI medical research fellow Maya Kasowski and her colleagues in the laboratory of molecular biologist Michael Snyder at Yale University conducted the work with Jan Korbel at the European Molecular Biology Laboratory. Snyder has since joined the faculty at Stanford University.. Transcription factors account for as much as 10 percent of the coding genome in humans and other organisms. When activated, transcription factors switch on or off hundreds or thousands of genes, a cascade that programs cells to grow or divide. ...
While developmental processes such as axon pathfinding and synapse formation have been characterized in detail, comparatively less is known of the intrinsic developmental mechanisms that regulate transcription of ion channel genes in embryonic neurons. Early decisions, including motoneuron axon targeting, are orchestrated by a cohort of transcription factors that act together in a combinatorial manner. These transcription factors include Even-skipped (Eve), islet and Lim3. The perdurance of these factors in late embryonic neurons is, however, indicative that they might also regulate additional aspects of neuron development, including the acquisition of electrical properties. To test the hypothesis that a combinatorial code transcription factor is also able to influence the acquisition of electrical properties in embryonic neurons we utilized the molecular genetics of Drosophila to manipulate the expression of Eve in identified motoneurons. We show that increasing expression of this transcription factor,
While developmental processes such as axon pathfinding and synapse formation have been characterized in detail, comparatively less is known of the intrinsic developmental mechanisms that regulate transcription of ion channel genes in embryonic neurons. Early decisions, including motoneuron axon targeting, are orchestrated by a cohort of transcription factors that act together in a combinatorial manner. These transcription factors include Even-skipped (Eve), islet and Lim3. The perdurance of these factors in late embryonic neurons is, however, indicative that they might also regulate additional aspects of neuron development, including the acquisition of electrical properties. To test the hypothesis that a combinatorial code transcription factor is also able to influence the acquisition of electrical properties in embryonic neurons we utilized the molecular genetics of Drosophila to manipulate the expression of Eve in identified motoneurons. We show that increasing expression of this transcription factor,
Transcriptional coactivator for steroid receptors and nuclear receptors. Greatly increases the transcriptional activity of PPARG and thyroid hormone receptor on the uncoupling protein promoter. Can regulate key mitochondrial genes that contribute to the program of adaptive thermogenesis. Plays an essential role in metabolic reprogramming in response to dietary availability through coordination of the expression of a wide array of genes involved in glucose and fatty acid metabolism. Induces the expression of PERM1 in the skeletal muscle in an ESRRA-dependent manner. Also involved in the integration of the circadian rhythms and energy metabolism. Required for oscillatory expression of clock genes, such as ARNTL/BMAL1 and NR1D1, through the coactivation of RORA and RORC, and metabolic genes, such as PDK4 and PEPCK. Isoform 4 specifically activates the expression of IGF1 and suppresses myostatin expression in skeletal muscle leading to muscle fiber hypertrophy.
Recent development of methods for genome‐wide identification of transcription factor binding sites by chromatin immunoprecipitation (ChIP) has led to novel insights into transcriptional regulation and greater understanding of the function of individual transcription factors
Background: Variants in transcription factor binding sites (TFBSs) may have important regulatory effects, as they have the potential to alter transcription factor (TF) binding affinities and thereby affecting gene expression. With recent advances in sequencing technologies the number of variants identified in TFBSs has increased, hence understanding their role is of significant interest when interpreting next generation sequencing data. Current methods have two major limitations: they are limited to predicting the functional impact of single nucleotide variants (SNVs) and often rely on additional experimental data, laborious and expensive to acquire. We propose a purely bioinformatic method that addresses these two limitations while providing comparable results. Results: Our method uses position weight matrices and a sliding window approach, in order to account for the sequence context of variants, and scores the consequences of both SNVs and INDELs in TFBSs. We tested the accuracy of our method ...
Transcriptional super-enhancers drive expression of oncogenes in many cancers and are being targeted with novel transcriptional and epigenetic therapeutics (1,2,3,4). Super-enhancers are acquired in cancers through multiple mechanisms, including DNA translocation of an extant super-enhancer and focal amplification. We recently discovered a novel mechanism by which super-enhancers are nucleated in T cell acute lymphoblastic leukemias (T-ALLs) (5). In this case, a small, monoallelic insertion creates a DNA binding site for a master transcription factor protein, which binds and recruits additional factors to nucleate the super-enhancer, which in turn drives high levels of the TAL1 transcription factor. We describe here a method for unbiased identification of similar genomic insertions that nucleate potentially oncogenic regulatory elements in cancers. This approach uses data from genome-wide ChIP-Seq studies that map locations of enhancer-binding proteins to identify sequences missing from ...
sequence-specific DNA binding transcription factors;sequence-specific DNA binding; FUNCTIONS IN: sequence-specific DNA binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: regulation of transcription, DNA-dependent; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Homeobox (InterPro:IPR001356); BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT1G15215.2); Has 91 Blast hits to 88 proteins in 16 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 91; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink ...
It is important to note that even when all experiments are included, the best results produce clusters with only a 28% true positive rate (see Figure E.1.a in Additional data file 1). That is, most of the genes in a given cluster do not share a common, known transcription factor. There are several possible reasons for this. First, with the present state of knowledge, it is possible that genes in the same cluster do in fact share a common transcription factor that is not (yet) represented in the databases used as gold standards (YPD, SCPD and ChIP data). We note for example, that when one compares ChIP data to YPD, the false-negative rate is approximately 80% using the recommended p-value of 0.001. That is, known gene transcription factor interactions from YPD are identified only about 20% of the time by ChIP (see Table F in Additional data file 1). Hence, it is possible that our evaluation criteria all underestimate the number of co-regulated genes in a cluster. Second, gene regulation is more ...
Aplha, transcription related growth factors and stimulating factors or repressing nuclear factors are complex subunits of proteins involved in cell differentiation. Complex subunit associated factors are involved in hybridoma growth, Eosinohils, eritroid proliferation and derived from promotor binding stimulating subunits on the DNA binding complex. NFKB 105 subunit for example is a polypetide gene enhancer of genes in B cells.The activation of transcription factor subunits is the first step of gene expression, in which a particular segment of DNA is copied into RNA (mRNA) by the enzyme RNA polymerases. Transcription factors, unites and elongations can be RNA and DNA nucleic acids, base pairs of nucleotides . Converting from DNA to RNA is made by enzymatic reactions. During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, anti-parallel RNA strand called a primary transcript. Transcriptions are key functions in signal transduction pathways. Signaling ...
T helper 17 (Th17) cells have crucial functions in mucosal immunity and the pathogenesis of several chronic inflammatory diseases. The lineage-specific transcription factor, RORγt, encoded by the RORC gene modulates Th17 polarization and function, as well as thymocyte development. Here we define several regulatory elements at the human RORC locus in thymocytes and peripheral CD4+ T lymphocytes, with CRISPR/Cas9-guided deletion of these genomic segments supporting their role in RORγt expression. Mechanistically, T cell receptor stimulation induces cyclosporine A-sensitive histone modifications and P300/CBP acetylase recruitment at these elements in activated CD4+ T cells. Meanwhile, NFAT proteins bind to these regulatory elements and activate RORγt transcription in cooperation with NF-kB. Our data thus demonstrate that NFAT specifically regulate RORγt expression by binding to the RORC locus and promoting its permissive conformation. The master transcription factor RORγt, encoded by the RORC gene,
Transcription factor and DNA molecule. Molecular model of glucocorticoid receptor (GR) transcription factor protein (purple and blue) complexed with a molecule of DNA (deoxyribonucleic acid, pink and green). Transcription factors regulate the transcription of DNA to RNA (ribonucleic acid) by the enzyme RNA polymerase. RNA is the intermediate product between a gene and its protein. When glucocorticoid binds to GR, GR enters the cells nucleus and binds to the DNA, causing an increase in the production of the apoptosis (programmed cell death) protein bax. - Stock Image A617/0259
Author Summary The main role of transcription factors is to modulate the expression levels of functionally related genes in response to environmental and cellular cues. For this process to be precise, the transcription factor needs to locate and bind specific DNA sequences in the genome and needs to bind these sites with a strength that appropriately adjusts the amount of gene expressed. Both specific protein-DNA interactions and transcription factor activity are intimately coupled, because they are both dependent upon the biochemical properties of the DNA-binding domain. Here we experimentally probe how variable these properties are using a novel in vivo selection assay. We observed that the specific binding preferences for the transcription factor MarA and its transcriptional activity can be altered over a large range with a few mutations and that selection on one function will impact the other. This work helps us to better understand the mechanism of transcriptional regulation and its evolution, and
1. JolmaA, YanJ, WhitingtonT, ToivonenJ, NittaKR, et al. (2013) DNA-binding specificities of human transcription factors. Cell 152: 327-339 doi:10.1016/j.cell.2012.12.009. 2. NobregaMA, OvcharenkoI, AfzalV, RubinEM (2003) Scanning human gene deserts for long-range enhancers. Science 302: 413 doi:10.1126/science.1088328. 3. BernsteinBE, BirneyE, DunhamI, GreenED, GunterC, et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74 doi:10.1038/nature11247. 4. Pique-RegiR, DegnerJF, PaiAA, GaffneyDJ, GiladY, et al. (2011) Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res 21: 447-455 doi:10.1101/gr.112623.110. 5. SongL, CrawfordGE (2010) DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb Protoc 2010: pdb.prot5384 doi:10.1101/pdb.prot5384. 6. YanJ, EngeM, WhitingtonT, DaveK, LiuJ, et al. (2013) Transcription factor ...
The oxygen distribution in skin is highly heterogeneous. Oxygen tension at the dermal-epithelial junction where melanocytes reside is about 5%, whereas it is about 0.5% around hair follicles (36). Oxygen availability has important physiological consequences, including the mediation of cellular transformation, especially during the melanocyte-melanoma transition (14). Cellular adaptation to hypoxia is facilitated by the expression of HIFα subunits, mainly HIF1α and HIF2α. HIF proteins are transcription factors that, under hypoxia, enable the activation of target genes involved in metabolism regulation, stress adaptation, growth, migration and invasion, drug resistance, and apoptotic cell death (37).. Protein function is frequently regulated by assembly into complexes. This aspect is particularly important for transcription factors, which interact with co-activators or repressors and with the transcription machinery to regulate gene expression. Indeed, transcription factor functions are ...
Hi: Take a look at TRANSFAC: http://nar.oupjournals.org/cgi/content/full/29/1/281 Good luck! On 8 Jun 2001 12:10:46 +0100, Heather Peto ,hp217 at cam.ac.uk, wrote: ,Hi , ,Does anyone know how I would look up which genes are turned on/off by ,a given transciption factor? Is there a database I can search? I am ,looking to see all the proteins produced / downgraded after CREB and ,a set of other transcription factors are activated. , ,many thanks , ,Heather :) , ...
View Notes - Lec20 from BCH 110 at UC Riverside. Lecture 20 Eukaryotic Gene Regulation 2 REGULATORY TRANSCRIPTION FACTORS & ACTIVATION MECHANISMS Lodish 6th edition Chapter 7 Lodish 5th edition
...Munich (Germany) August 8 2006 -- Genomatix Software GmbH a pionee...It contains genomic TF binding sites and protein binding domains rela... We have developed our in-house TF database now for more than a decade...,MatBase,--,A,new,transcription,factor,knowledge,base,released,by,Genomatix,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
The assignment of biological function to the large number of genes that have now been sequenced, with new sequence data being compiled rapidly, is currently one of the most challenging goals in biology. Genetic analysis, particularly the effects of loss-of-function mutations, is of central importance to achieving this goal. In plants, unlike yeast, targeted gene disruption is laborious and inefficient (Kempin et al., 1997). Gene silencing by antisense or sense suppression is also a common approach to studying plant gene function (Kooter and Mol, 1993; Baulcombe, 1996), but the specificity and extent of gene disruption through such methods have not been extensively tested, so the analysis and interpretation of suppression sometimes have proved difficult (van der Krol et al., 1990; Höfgen et al., 1994).. T-DNA and transposable elements can alter gene function upon insertion into coding or regulatory sequences (Feldmann, 1991; Martienssen, 1998). Many lines of Arabidopsis harboring either T-DNA or ...
We present an integrated method called Chromia for the genome-wide identification of functional target loci of transcription factors. Designed to capture the characteristic patterns of transcription factor binding motif occurrences and the histone profiles associated with regulatory elements such as …
I have pursued a breadth of research that explored the functional genomic study of eukaryotic transcriptional regulation. I have utilized two model organisms, many experimental methodologies, and have developed a suite of computational resources to study the interaction of transcription factors with regulated targets. In Saccharomyces cerevisiae I worked with my collaborator Dr. Zhanzhi (Mike) Hu to characterize the whole-genome transcriptional response of 263 individual transcription factor deletions. We utilized a sophisticated error model and directed-weighted graphs to model a network of high-confidence targets for each transcription factor profiled. We then used regulatory epistasis to elucidate the true set of primary KO-regulated targets and construct a functional transcriptional regulatory network. This network was analyzed for ontological and sequence motif enrichment in order to gain insight into the biological functions represented by transcription factors studied. Functional ...
"Transcription Factors". Retrieved 27 March 2014.[permanent dead link] Weiner CP, Mason CW, Dong Y, Buhimschi IA, Swaan PW, ... The table below shows some transcription factors that have been predicted by Genomatix that binds to the regulatory sequence of ...
S2CID 205134793.CS1 maint: multiple names: authors list (link) Kaveri Sidhu, Vijay Kumar (2015). "c-ETS transcription factors ... Manfred Gossen; Jörg Kaufmann; Steven J. Triezenberg (6 December 2012). Transcription Factors. Springer Science & Business ... "Combinatorial action of transcription factors orchestrates cell cycle-dependent expression of the ribosomal protein genes and ... B virus potentiates cell transformation by inducing c-Myc-dependent expression of the RNA polymerase I transcription factor UBF ...
CS1 maint: discouraged parameter (link)[permanent dead link] "Protein One". Transcription Factors. Archived from the original ... PAR b ZIP family and Sp4 Transcription Factor. NRF1 encodes a protein which homodimerizes and activates expression of key ... CREB binds to cAMP response elements thereby increasing or decreasing the transcription of downstream genes while PAR b ZIP ... Conserved binding sites in mammals which are located on this promoter include Nuclear Respiratory Factor 1 (NFR1), cAMP- ...
... a transcription factor that is induced during cellular stress. Smad3 and ATF3 then coordinate to repress Id1 transcription, ... When there is no TGF-β present, a repressor complex composed of Smad3, and the transcription factors E2F4 and p107 exist in the ... IDs are transcription factors that regulate genes involved in cell differentiation, maintaining multi-potency in stem cells, ... Trimers of two receptor-regulated SMADs and one co-SMAD act as transcription factors that regulate the expression of certain ...
Plant Transcription Factor Database and Plant Transcriptional Regulation Data and Analysis Platform Open source web service for ... Some proteins though serve only to activate other genes, and these are the transcription factors that are the main players in ... Genes can be viewed as nodes in the network, with input being proteins such as transcription factors, and outputs being the ... Next, each direct input is assigned to an operator site and different transcription factors can be allowed, or not, to compete ...
"TEAD Transcription Factors Mediate the Function of TAZ in Cell Growth and Epithelial-Mesenchymal Transition". Journal of ... Plant Transcription Factors. Methods in Molecular Biology. 754. pp. 195-218. doi:10.1007/978-1-61779-154-3_11. ISBN 978-1-61779 ... "Isolation of Transcription Factor Complexes from Arabidopsis Cell Suspension Cultures by Tandem Affinity Purification". In Yuan ... for interaction proteomics and transcription factor complexes with the SBP-Tag and Protein G, for proteins that interact with ...
Latchman DS (2004). "Methods for Studying Transcription Factors". Eukaryotic Transcription Factors. The Biochemical Journal. ... Transcription factors (TFs) bind to the promoter region of SLC46A3 and modulate the transcription of the gene. The table below ... "SLC46A3 Transcription Factor Binding Sites". Genomatix: MatInspector. Miller DM, Thomas SD, Islam A, Muench D, Sedoris K ( ... CCAAT-displacement protein (CDP) and nuclear transcription factor Y (NF-Y) have multiple binding sites within the promoter ...
Along with general growth there are also transcription factors that directly effect the production of additional lateral shoots ... Nicolas, Michael; Cubas, Pilar (2016). "The Role of TCP Transcription Factors in Shaping Flower Structure, Leaf Morphology, and ... Plant Transcription Factors. pp. 249-267. doi:10.1016/b978-0-12-800854-6.00016-6. ISBN 9780128008546. Breuninger, Holger; ... like the TCP family (also known as Teosinte branched 1/cycloidea/proliferating cell factor) which are plant specific proteins ...
A transcription factor or promoter factor is a protein that controls the rate of transcription of genetic information from DNA ... Karin M (Feb 1990). "Too many transcription factors: positive and negative interactions". The New Biologist. 2 (2): 126-31. ... ISBN 978-1-4160-2255-8. Latchman DS (Dec 1997). "Transcription factors: an overview". The International Journal of Biochemistry ...
... & Pax Transcription Factors. 44: 33-38. doi:10.1016/j.semcdb.2015.08.010. PMID 26325077. de Vanssay, Augustin; ... Paramutation & Pax Transcription Factors. 44: 47-50. doi:10.1016/j.semcdb.2015.08.007. PMID 26335266.. ... The gene at this locus, when actively transcribed, codes for a transcription factor that promotes anthocyanin production, ... which encodes a transcription factor that confers red pigment to corn kernels, can heritably change specific strongly expressed ...
April 8, 1994). "SREBP-1, a membrane-bound transcription factor released by sterol-regulated proteolysis.". Cell. Retrieved ... Espenshade, Peter J. (2006). "SREBPs: sterolregulated transcription factors.". Journal of Cell Science. Retrieved December 6, ... a family of membrane-bound transcription factors. Since 1993, Goldstein, Brown, and their colleagues have described the ...
... is a comprehensive database of transcription factors. transcription factors Zhang, Hong-Mei; Chen Hu; Liu Wei; Liu ... a comprehensive animal transcription factor database". Nucleic Acids Res. England. 40 (1): D144-9. doi:10.1093/nar/gkr965. PMC ...
Kadauke S, Blobel GA (April 2013). "Mitotic bookmarking by transcription factors". Epigenetics & Chromatin. 6 (1): 6. doi: ... Gene transcription ceases during prophase and does not resume until late anaphase to early G1 phase. The nucleolus also ... Aneuploidy Binary fission Chromosome abnormality Cytoskeleton Meiosis Mitogen Mitosis Promoting Factor Mitotic bookmarking ...
While both the conventionally-bred and the engineered varieties exhibit altered expression of the same transcription factor of ... "MYB transcription factors in Arabidopsis". Trends in Plant Science. 15 (10): 573-581. doi:10.1016/j.tplants.2010.06.005. PMID ... "Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors". Nature ...
CREs typically regulate gene transcription by binding to transcription factors. A single transcription factor may bind to many ... This design occurs when the signal ligand is absent while the transcription factor is present; this transcription factor ends ... In order to initiate transcription of the downstream gene, a host of DNA-binding proteins called transcription factors (TFs) ... Cis-regulatory modules carry out their function by integrating the active transcription factors and the associated co-factors ...
... transcription factor brn-3b MeSH D12.776.930.632.625.875 - transcription factor brn-3c MeSH D12.776.930.635.600.100 - ets- ... mafg transcription factor MeSH D12.776.930.127.656.750.750 - mafk transcription factor MeSH D12.776.930.127.656.770 - nf-e2 ... mafg transcription factor MeSH D12.776.930.316.750.750.750 - mafk transcription factor MeSH D12.776.930.316.750.770 - nf-e2 ... coup transcription factor i MeSH D12.776.930.682.074.500 - coup transcription factor ii MeSH D12.776.930.682.350.174 - estrogen ...
There are several important transcription factors that are predicted to bind to the promoter sequence of VXN. The most common ... transcription factors include; HMG box-containing protein 1, repressive glucocorticoid receptor, cAMP-responsive binding ... protein and Homeo domain factor Pbx-1. VXN has been associated with breast cancer in humans. The gene has been researched in ...
Some transcription factors bind as dimers. Therefore, their binding sites may consist of two conserved regions, separated by a ... These transcription factor binding sites (TFBS), or regulatory motifs, have proven hard to identify, primarily because they are ... Phylogenetic footprinting is a technique used to identify transcription factor binding sites (TFBS) within a non-coding region ... Phylogenetic footprinting relies upon two major concepts: The function and DNA binding preferences of transcription factors are ...
Transcription factors Category:Transcription coregulators; Transcription coregulators like PELP-1; Coactivator (genetics) "The ... may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor." Category: ... nuclear transport factor 2 (NTF2), Ran, exportin "Enables the directed movement of charged atoms or small charged molecules ...
These factors include: The transcription factor p63, which prevents epidermal stem cells from differentiating into ... Cathepsin E. TALE homeodomain transcription factors. Hydrocortisone. Since keratinocyte differentiation inhibits keratinocyte ... Epidermal growth factor. Transforming growth factor alpha. Cholera toxin. Within the epidermis keratinocytes are associated ... The roles of transforming growth factor-alpha and epidermal growth factor". Cell. 50 (7): 1131-7. doi:10.1016/0092-8674(87) ...
Beerli RR, Barbas CF (2002). "Engineering polydactyl zinc-finger transcription factors". Nat. Biotechnol. 20 (2): 135-41. doi: ... family DNA sequences and their use in the construction of artificial transcription factors". J. Biol. Chem. 280 (42): 35588-97 ...
... product portfolio contains solutions[buzzword] for: • Literature and pathway mining • Transcription factor analysis ... transcription factor binding site (TFBS) analysis ( identification, over-representation, binding partner analysis, framework ...
ATF6 (activating transcription factor 6) is a basic leucine zipper transcription factor. Upon Grp78 dissociation, the entire ... is upregulated downstream of the bZIP transcription factor ATF4 (activating transcription factor 4) and uniquely responsive to ... The activated transcription factor upregulates UPR 'stress genes' by directly binding to stress element promoters in the ... These transcription factors then proceed to alter the expression of exercise-regulated muscle genes. PGC-1alpha, a ...
ISBN 978-0-471-58651-7. Koh JT, Zheng J (September 2007). "The new biomimetic chemistry: artificial transcription factors". ACS ... There is also interest in creating small molecule artificial transcription factors to regulate gene expression, examples ... "Sonic hedgehog and other soluble factors from differentiating embryoid bodies inhibit pancreas development". Stem Cells. 25 (5 ...
Therefore, transcription factors are crucial for adipogenesis. Transcription factors, peroxis proliferator-activated receptor γ ... other transcription factors function in the progression of differentiation. Adipocyte determination and differentiation factor ... C/EBPs, transcription factors, are members of the basic-leucine zipper class. cAMP, an inducer of adipogenesis, can promote ... The second phase of growth arrest is the expression of two key transcription factors PPARγ and C/EBPα which promote expression ...
C1q and tumor necrosis factor related protein 2 and DYNLT1. Based on the transcription factor binding sites listed in the ... The transcription factor binding sites associated with this promoter and confirmed with a ChIP signal include HNF4A, CEBPB, ... Trimarchi, Jeffrey M.; Fairchild, Brian; Wen, Jessica; Lees, Jacqueline A. (13 February 2001). "The E2F6 transcription factor ... Gallant S, Gilkeson G (2006). "ETS transcription factors and regulation of immunity". Archivum Immunologiae et Therapiae ...
Sterner DE, Berger SL (June 2000). "Acetylation of histones and transcription-related factors". Microbiol. Mol. Biol. Rev. 64 ( ... of the eukaryotic genome into highly condensed chromatin makes it inaccessible to the factors required for gene transcription, ... For a detailed example of histone modifications in transcription regulation see RNA polymerase control by chromatin structure ... Zhang Y, Reinberg D (2001). "Transcription regulation by histone methylation: interplay between different covalent ...
Huang, C; Chan, JA; Schuurmans, C (2014). "Proneural bHLH Genes in Development and Disease". BHLH Transcription Factors in ... are principally determined by molecular and genetic factors. These factors notably include the Notch signaling pathway, and ... Many environmental factors, such as exercise, stress, and antidepressants have been reported to change the rate of neurogenesis ...
Plant Transcription Factor Database MIKC type MADS family at PlantTFDB: Plant Transcription Factor Database. ... Gramzow L, Ritz MS, Theissen G (April 2010). "On the origin of MADS-domain transcription factors". Trends in Genetics. 26 (4): ... West AG, Shore P, Sharrocks AD (May 1997). "DNA binding by MADS-box transcription factors: a molecular mechanism for ... MADS-domain proteins are generally transcription factors. The length of the MADS-box reported by various researchers varies ...
... transcription factors such as grainyhead-like protein 2 homologue (GRHL2), and ETS-related transcription factors ELF3 and ELF5 ... Kruppel-like factor 8) can bind to the E-cadherin promoter and repress its transcription, whereas factors such as Twist, ... nuclear factor-kappaB and Activating Transcription Factor 2 have also been implicated to be involved in EMT. Wnt signaling ... Many transcription factors (TFs) that can repress E-cadherin directly or indirectly can be considered as EMT-TF (EMT inducing ...
The transcription factor gene TWIST is thought to decrease the function of FGFR, thus also indirectly regulating fetal bone ... These last two are both important factors influencing bone development.[27]. Environmental factorsEdit. Environmental factors ... Biomechanical factorsEdit. Biomechanical factors include fetal head constraint during pregnancy.[27] It has been found by Jacob ... Fibroblast growth factor and fibroblast growth factor receptors regulate fetal bone growth and are expressed in cranial sutures ...
Differentiation of mature B cells into plasma cells is dependent upon the transcription factors Blimp-1/PRDM1 and IRF4. ... This is a type of safeguard to the system, almost like a two-factor authentication method. First, the B cells have to encounter ...
transcription factor activity, sequence-specific DNA binding. • RNA polymerase II regulatory region sequence-specific DNA ... The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in ... regulation of transcription, DNA-templated. • negative regulation of transcription from RNA polymerase II promoter. • positive ... "The thyroid transcription factor-1 gene is a candidate target for regulation by Hox proteins". EMBO J. 13 (14): 3339-47. PMC ...
Dreuillet C, Tillit J, Kress M, Ernoult-Lange M. In vivo and in vitro interaction between human transcription factor MOK2 and ... Emerin interacts in vitro with the splicing-associated factor, YT521-B. Eur. J. Biochem. June 2003, 270 (11): 2459-66. PMID ...
Palmer, H. E. (1917). The Scientific Study and Teaching of Languages: A Review of the Factors and Problems Connected with the ... Palmer, H. E. (1922). Everyday Sentences in Spoken English, with Phonetic Transcription and Intonation Marks (for the Use of ... Palmer, H. E. and F. G. Blandford (1927). Everyday Sentences in Spoken English, with Phonetic Transcription and Intonation ... Palmer, H. E. and F. G. Blandford (1935). Everyday Sentences in Spoken English, with Phonetic Transcription and Intonation ...
Zinc finger protein transcription factor. Failed agents. *Aplaviroc. *Atevirdine. *Brecanavir. *Capravirine. *Dexelvucitabine ...
On the other hand, a lack of α-catenin can promote aberrant transcription, which can lead to cancer. As a result, it can be ... Yi ZY, Feng LJ, Xiang Z, Yao H (2011). "Vascular endothelial growth factor receptor-1 activation mediates epithelial to ... There are other physiological factors that are associated with cancer development through their interactions with catenins. For ... β-catenin becomes a coactivator for TCF and LEF to activate Wnt genes by displacing Groucho and HDAC transcription repressors. ...
positive regulation of transcription from RNA polymerase II promoter. • حمل أنثوي. • positive regulation of cell proliferation ... transforming growth factor beta receptor signaling pathway. • positive regulation of cell migration. • ...
2D3-regulated transcription factor MN1 stimulates vitamin D receptor-mediated transcription and inhibits osteoblastic cell ... MN1 is a transcription coregulator that enhances or represses RAR/RXR-mediated gene transcription through interaction with RAC3 ... 2007). "The MN1 oncoprotein activates transcription of the IGFBP5 promoter through a CACCC-rich consensus sequence". J. Mol. ... "The MN1 oncoprotein synergizes with coactivators RAC3 and p300 in RAR-RXR-mediated transcription". Oncogene. 22 (5): 699-709. ...
... proteins including interferon regulatory factor 3 and interferon regulatory factor 7 trigger a signalling cascade that leads to ... whose concentration in the host cell determines when L switches from gene transcription to genome replication. Replication of ... Education of the general public about the risk factors for Ebola infection and of the protective measures individuals may take ... When EVD is suspected, travel, work history, and exposure to wildlife are important factors with respect to further diagnostic ...
... probably with the help of an unknown GDP exchange factor. A domain of Toc159 might be the exchange factor that carry out the ... See also: Transcription and translation. Protein synthesis within chloroplasts relies on an RNA polymerase coded by the ... The highly oxidative environment inside chloroplasts increases the rate of mutation so post-transcription repairs are needed to ...
SP can induce the cytokines that are capable of inducing NK-1 transcription factors.[14] ... Koon HW, Zhao D, Na X, Moyer MP, Pothoulakis C (Oct 2004). "Metalloproteinases and transforming growth factor-alpha mediate ... the role of brain-derived neurotrophic factor and substance P". The British Journal of Dermatology. 157 (5): 922-5. doi:10.1111 ... "Neurotrophic and anhidrotic keratopathy treated with substance P and insulinlike growth factor 1". Archives of Ophthalmology. ...
Transcription factor. Τ. *Template:Single strand DNA discovery. Retrieved from "https://simple.wikipedia.org/w/index.php?title= ...
T3 bind to thyroid receptor proteins in the cell nucleus and cause metabolic effects through the control of DNA transcription ...
"An essential transcription factor, SciP, enhances robustness of Caulobacter cell cycle regulation". Proceedings of the National ... in addition to many extracytoplasmic function sigma factors, providing the organism with the ability to respond to a wide range ...
The key events mediating rod versus S cone versus M cone differentiation are induced by several transcription factors, ... If any of the previously mentioned factors' functions are ablated, the default photoreceptor is a S cone. These events take ... Photoreceptor precursors come about through inhibition of Notch signaling and increased activity of various factors including ...
The transcription factor Sox9 can be found in multiple sites in the body (pancreas, central nervous system, intestines) and it ... Runx2 (which may also be known as Cbfa1), and Osx (a zinc finger containing transcription factor) are necessary for ... These factors also have a role in hypertrophic chondrocyte maturation.[3] [5] ... Main article: Transforming growth factor beta. During mandible development, most of it is formed through intramembranous ...
Molecular biology is the study of molecular underpinnings of the process of replication, transcription and translation of the ... The father of modern medicine: the first research of the physical factor of tetanus Archived 18 November 2011 at the Wayback ... Transparency of information is another factor defining a delivery system. Access to information on conditions, treatments, ...
One group added a transcription factor for the production of anthocyanin from Arabidopsis thaliana[33] whereas another used ... A gene from rice (Osmyb4), which codes for a transcription factor, that was shown to increase cold and drought tolerance in ... "Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors". Nature ... transcription factors from snapdragon (Antirrhinum).[34] When the snapdragon genes were used, the fruits had similar ...
... containing factor Pax8 and the homeodomain-containing factor TTF-1 directly interact and synergistically activate transcription ... containing factor Pax8 and the homeodomain-containing factor TTF-1 directly interact and synergistically activate transcription ... Paramutation & Pax Transcription Factors. 44: 97-106. doi:10.1016/j.semcdb.2015.09.016. PMID 26410163.. ... This gene is a member of the paired box (PAX) family of transcription factors. Members of this gene family typically encode ...
transcription factor complex. • cell-cell adherens junction. • Z disc. • stress fiber. • filamentous actin. ... "Ubiquitination-dependent cofactor exchange on LIM homeodomain transcription factors.". Nature. 416 (6876): 99-103. PMID ... transcription coactivator activity. • ربط أيون فلزي. • cadherin binding involved in cell-cell adhesion. • actin binding. • ... regulation of transcription, DNA-templated. • response to oxidative stress. • cell-cell adhesion. • positive regulation of ...
... with beta-catenin and T-cell factor 4 may bypass canonical Wnt signaling to down-regulate adipogenic transcription factors". ... "Recruitment of the androgen receptor via serum response factor facilitates expression of a myogenic gene". The Journal of ...
transcription factor activity, sequence-specific DNA binding. • ATPase binding. • zinc ion binding. • transcriptional activator ... RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding. • identical protein binding. • ... RNA polymerase II transcription factor activity, sequence-specific DNA binding. • transcriptional activator activity, RNA ... regulation of transcription, DNA-templated. • cell-cell signaling. • negative regulation of gene expression. • transcription, ...
Selectional pleiotropy occurs when the resulting phenotype has many effects on fitness (depending on factors such as age and ... "CACNA1C as a risk factor for schizotypal personality disorder and schizotypy in healthy individuals". Psychiatry Research. 206 ...
Fluorescent signal strength depends on many factors such as probe labeling efficiency, the type of probe, and the type of dye. ... "The lncRNA Malat1 is Dispensable for Mouse Development but Its Transcription Plays a cis-Regulatory Role in the Adult". Cell ... "Microfluidics-assisted fluorescence in situ hybridization for advantageous human epidermal growth factor receptor 2 assessment ...
... transcription factors, and the sigma factor subunits of RNA polymerase. ... The heat resistance of endospores is due to a variety of factors: *Calcium dipicolinate, abundant within the endospore, may ...
Barker ME, Blumsohn A (November 2003). "Is vitamin A consumption a risk factor for osteoporotic fracture?". The Proceedings of ... members of the retinoic acid receptor or retinoid X receptor nuclear transcription family) which are found in every cell ( ...
It needs a range of transcription factors to bind it to promoters. ... Genes, factors and transcriptional specificity". Eur J Biochem. 212 (1): 1-11. doi:10.1111/j.1432-1033.1993.tb17626.x. PMID ... Wierzbicki A.T. et al (2009). "RNA Polymerase V transcription guides ARGONAUTE4 to chromatin". Nat. Genet. 41 (5): 630-4. doi: ... Grummt I. (1999). "Regulation of mammalian ribosomal gene transcription by RNA polymerase I.". Prog Nucleic Acid Res Mol Biol. ...
negative regulation of transcription from RNA polymerase II promoter. • proteolysis. • regulation of synaptic plasticity. • ... regulation of epidermal growth factor-activated receptor activity. • regulation of resting membrane potential. • regulation of ... positive regulation of transcription, DNA-templated. • heart development. • negative regulation of axonogenesis. • embryonic ... negative regulation of epidermal growth factor-activated receptor activity. • cell adhesion. • hematopoietic progenitor cell ...
This gene is a transcription factor that regulates the cell cycle and hence functions as a tumor suppressor. By inducing G ( ... This process increases transcription of certain genes, notably CYP1A1, followed by increased CYP1A1 protein production.[28] ...
Putative ETS transcription factor binding sites within the PTEN promoter were determined by searching for GGAA or TTCC ... ERG is a member of the ETS family of transcription factors that share a DNA-binding domain termed the ETS-binding domain (EBD ... In the current study we sought to look into the possibility that the transcription factor ERG affects the expression of PTEN ... Birdsey GM, Dryden NH, Amsellem V, Gebhardt F, Sahnan K, Haskard DO, Dejana E, Mason JC and Randi AM: Transcription factor Erg ...
Consisting of about 110 amino acids, the domain in winged-helix transcription factors (see Regulation of gene expression) has ... Winged-Helix+Transcription+Factors at the US National Library of Medicine Medical Subject Headings (MeSH) ... Retrieved from "https://en.wikipedia.org/w/index.php?title=Winged-helix_transcription_factors&oldid=730546101" ...
FOX proteins Winged-Helix+Transcription+Factors at the US National Library of Medicine Medical Subject Headings (MeSH) v t e. ... Consisting of about 110 amino acids, the domain in winged-helix transcription factors (see Regulation of gene expression) has ...
This list of manually curated human transcription factors is taken from Lambert, Jolma, Campitelli et al. It was assembled by ... More detailed information is found in the manuscript and the web site accompanying the paper (Human Transcription Factors) ... "The Human Transcription Factors". Cell. 172 (4): 650-665. doi:10.1016/j.cell.2018.01.029. PMID 29425488.. ...
Misexpression of transcription factors in myeloid leukaemia, with Cancer Research UK Manchester Institute. Apply Today. ... Indeed, the great majority of patients with AML have one or more mutations targeting a transcription factor, chromatin modifier ... Project Title: Misexpression of transcription factors in myeloid leukaemia. This 4 year PhD studentship offered in Professor ... In recent years the Somervaille lab has uncovered new and unexpected transcription factor genes which make a frequent and ...
A viral toolkit for recording transcription factor-DNA interactions in live mouse tissues Alexander J. Cammack, Arnav Moudgil, ... A strategy for designing allosteric modulators of transcription factor dimerization Sho Oasa, Vladana Vukojević, Rudolf Rigler ... A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors Riccardo ...
Zinc finger transcription factors or ZF-TFs, are transcription factors composed of a zinc finger-binding domain and any of a ... Zinc finger transcription factor. From Wikipedia, the free encyclopedia. (Redirected from Zinc finger protein transcription ... genes in order to control the transcription of all these genes with a single transcription factor. Also, it is possible to ... Zinc finger protein transcription factors can be encoded by genes small enough to fit a number of such genes into a single ...
Transcription factors bind to the human genome within areas of the genome still viewed as a black box""vast stretches of DNA ... "The activity of transcription factors determines what a cell is doing at any given moment," says Kasowski, who was a medical ... Hence, variation in transcription factor binding can help explain why one person may make more of a certain gene product than ... When activated, transcription factors switch on or off hundreds or thousands of genes, a cascade that programs cells to grow or ...
Hypoxia-responsive transcription factors.. Cummins EP1, Taylor CT.. Author information. 1. Department of Medicine and ... In this review, we comprehensively discuss the transcription factors that have been reported to be hypoxia-responsive and the ... it is clear that a number of other transcription factors are also activated either directly or indirectly. ... While the hypoxia-inducible factor (HIF-1) plays a major role in controlling the ubiquitous transcriptional response to hypoxia ...
Here we discuss the roles of EMT-inducing transcription factors in creating a pro-tumorigenic setting characterized by an ... inducing transcription factors in tumorigenesis. They explore how EMT contributes not only to tumour progression through its ... The transcription factor ZEB1 is aberrantly expressed in aggressive uterine cancers. Cancer Res. 66, 3893-3902 (2006). ... Puisieux, A., Brabletz, T. & Caramel, J. Oncogenic roles of EMT-inducing transcription factors. Nat Cell Biol 16, 488-494 (2014 ...
2001) Malignant transformation of primary chicken spleen cells by human transcription factor c-Rel. Oncogene 20: 7098-7103 ...
B) Factor X could be recruited to a sequence via protein-protein interactions with another transcription factor (TF) in a ... allowing the binding of another factor (diamond) that stimulates transcription of a gene. In this case, loss of a single factor ... A) The transcription factor regulates a gene that is distal to the binding site; therefore, the nearest gene will not show a ... A) Transcription factor X could bind to its consensus motif (black box) and loop via protein-protein interactions to another ...
In Transcription Factors: Methods and Protocols, experts in the field describe state-of-the-art approaches that ... significant breakthroughs in transcription research expanded our appreciation for the complexity of molecular controls on gene ... Transcription Factors: Methods and Protocols compiles the latest techniques for elucidating controls on transcription factor ... Post-translational Control of ETS Transcription Factors: Detection of Modified Factors at Target Gene Promoters ...
A limited list of transcription factors are overactive in most human cancer cells, which makes them targets for the development ... Transcription factors as targets for cancer therapy Nat Rev Cancer. 2002 Oct;2(10):740-9. doi: 10.1038/nrc906. ... A limited list of transcription factors are overactive in most human cancer cells, which makes them targets for the development ... by the fact that there are many more human oncogenes in signalling pathways than there are oncogenic transcription factors. But ...
Transcription Factors RT2 Profiler PCR Array The Human Transcription Factors RT² Profiler PCR Array profiles the expression of ... Transcription Factors RT2 Profiler PCR Array The Mouse Transcription Factors RT² Profiler PCR Array profiles the expression of ... Transcription Factors RT2 Profiler PCR Array The Rat Transcription Factors RT² Profiler PCR Array profiles the expression of 84 ... Stem Cell Transcription Factors EpiTect Methyl II PCR Array The Human Stem Cell Transcription Factors EpiTect Methyl II ...
... the transcription factor that binds the DNA target interacts with a different type of transcription factor (e.g., a factor that ... These prebound transcription factors facilitate activated transcription when auxin levels are elevated or when ARF activators ... ARF transcription factors presumably are present in cells and bound to TGTCTC AuxREs regardless of the auxin status, and auxin ... ARFs May Activate Transcription by Binding Directly to AuxREs or by Associating with Factors That Occupy AuxREs.. Protoplasts ...
Formation of Treg requires FOXO transcription factors that regulate expression of the transcription factor FOXp3 [94]. FOXO1- ... α with FoxO1a and hepatocyte nuclear factor 42α transcription factors," Hepatology, vol. 48, no. 6, pp. 1998-2006, 2008. View ... FOXO Transcription Factors: Their Clinical Significance and Regulation. Yu Wang,1,2 Yanmin Zhou,1 and Dana T. Graves2 ... The forkhead transcription factor family is characterized by a winged-helix DNA binding motif and the forkhead domain [1]. The ...
Transcription factor TFDP3 (IPR028315). Short name: TFDP3 Overlapping homologous superfamilies *E2F-DP heterodimerization ... Transcription factor DP family member 3 (TFDP3) is also known as DP4, which can induce confusion. TFDP3 represents a ... It forms heterodimers with E2F family members and inhibits E2F-dependent transcription and E2F-mediated cell-cycle progression ... Transcription factor DP, C-terminal domain superfamily (IPR038168). Family relationships *Transcription factor DP (IPR015648) * ...
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool.
In transcription factors with a signal sensing domain, the signal sensing domain is the part of the transcription factor that ... Like all proteins, transcription factors are composed of discrete functional modules called "domains". Transcription factors ... transcription factors play a role in all cell processes. Depending on the transcription factor, this can range from regulation ... varies widely between transcription factors. The regulatory effect (and sometimes mechanism) of a specific transcription factor ...
... Tongxiang Lin1,2 and Shouhai Wu1 ... Y. Zhao, X. Yin, H. Qin et al., "Two supporting factors greatly improve the efficiency of human iPSC generation," Cell Stem ... R. Zhao and G. Q. Daley, "From fibroblasts to iPS cells: induced pluripotency by defined factors," Journal of Cellular ... R. Sridharan, J. Tchieu, M. J. Mason et al., "Role of the murine reprogramming factors in the induction of pluripotency," Cell ...
NAC transcription factors 26Imported. ,p>Information which has been imported from another database using automatic procedures ... tr,A0A0M4FKX7,A0A0M4FKX7_MANES NAC transcription factors 26 OS=Manihot esculenta OX=3983 PE=2 SV=1 ...
general transcription factor - a transcription factor that activates gene transcription • gene transcription - copying of DNA ... General transcription factors[edit]. Main articles: Gene transcriptions/General factors and General transcription factors ... "General transcription factors (GTFs), also known as basal transcriptional factors, are a class of protein transcription factors ... GATA transcription factor (GATA), hepatocyte nuclear factors (HNF), PIT-1, MyoD, Myf5, Hox, winged-helix transcription factors ...
... indicated that plants use transcription factors that are structurally related to those of animals in their control of gene ... The cloning of the first transcription factor from plants, the C1 gene of maize, ... The cloning of the first transcription factor from plants, the C1 gene of maize, indicated that plants use transcription ... MYB transcription factors in plants Trends Genet. 1997 Feb;13(2):67-73. doi: 10.1016/s0168-9525(96)10049-4. ...
Rohwer N., Cramer T. (2011) Role of Hypoxia-Inducible Transcription Factors in TAM Function. In: Lawrence T., Hagemann T. (eds ... Belaiba RS, Bonello S, Zahringer C et al (2007) Hypoxia up-regulates hypoxia-inducible factor-1alpha transcription by involving ... Jung Y, Isaacs JS, Lee S et al (2003a) Hypoxia-inducible factor induction by tumour necrosis factor in normoxic cells requires ... Harris AL (2002) Hypoxia - a key regulatory factor in tumour growth. Nat Rev Cancer 2:38-47PubMedCrossRefGoogle Scholar ...
Computational Biology of Transcription Factor Binding. Editors. * Istvan Ladunga Series Title. Methods in Molecular Biology. ... The methods are very up-to-date and clearly presented by authors … . The use of tools for predicting transcription factors ... Identification of Transcription Factor Binding Sites Derived from Transposable Element Sequences Using ChIP-seq ... Authoritative and easy to use, Computational Biology of Transcription Factor Binding guides scientists working in this area and ...
A JCB study shows how a transcription factor called STAT3 remains in the axon of nerve cells to help prevent neurodegeneration ... Newswise - A study in The Journal of Cell Biology shows how a transcription factor called STAT3 remains in the axon of nerve ... It is known that CNTF indirectly turns on the transcription factor STAT3, so the researchers wanted to determine if STAT3 is ...
BHLH transcription factorImported. ,p>Information which has been imported from another database using automatic procedures.,/p ... tr,A0A0U2RCR8,A0A0U2RCR8_9ROSA BHLH transcription factor OS=Prunus pseudocerasus OX=151439 PE=2 SV=1 ...
This is also true with transcription factors: Not only do transcription factors control the rates of transcription to regulate ... DNA within nucleosomes is inaccessible to many transcription factors. Some transcription factors, so-called pioneering factors ... an important class of transcription factors called general transcription factors (GTFs) are necessary for transcription to ... But, for many transcription factors, this is a key point in their regulation.[38] Important classes of transcription factors ...
DNA structure influences the function of transcription factors. Spatial arrangement of the binding site and neighbouring ... Other factors must also be involved in determining how strongly a transcription factor activates a gene. ... Transcription factors bind to a section of DNA and control how strongly a gene in that section is activated. Scientists had ... Substances known as transcription factors often determine how a cell develops as well as which proteins it produces and in what ...
  • Researchers at the Max Planck Institute for Molecular Genetics in Berlin have analysed proteins for such modifications that control gene activity, so-called transcription factors. (innovations-report.com)
  • Transcription factors are responsible for transcribing the correct genes and therefore for producing the right quantity of proteins. (innovations-report.com)
  • Transcription factors are proteins that bind to specific DNA sequences in order to regulate gene expression . (conservapedia.com)
  • however, the majority of transcription factors function through interaction with one or more adapter proteins . (conservapedia.com)
  • Transcription factors comprise several protein families (groups of closely related proteins), many of which are found in every lineage of organism. (conservapedia.com)
  • The trans-activating domain is the part of the transcription factor that interacts with and binds to other proteins. (conservapedia.com)
  • There are approximately 2600 proteins in the human genome that contain DNA-binding domains, and most of these are presumed to function as transcription factors, [7] though other studies indicate it to be a smaller number. (wikiversity.org)
  • [8] Therefore, approximately 10% of genes in the genome code for transcription factors, which makes this family the single largest family of human proteins. (wikiversity.org)
  • Transcription factors (TFs) are a class of proteins that are essential for the regulation of gene expression and for the control of protein expression in normal physiological conditions. (els.net)
  • TFs work alone or with other proteins in a complex, by promoting (as an activator ), or blocking (as a repressor ) the recruitment of RNA polymerase (the enzyme that performs the transcription of genetic information from DNA to RNA) to specific genes. (wikipedia.org)
  • The transcription factor can either do this directly or recruit other proteins with this catalytic activity. (wikipedia.org)
  • Substances known as transcription factors often determine how a cell develops as well as which proteins it produces and in what quantities. (mpg.de)
  • These proteins, known as transcription factors, control the activity of genes. (mpg.de)
  • In molecular biology, the GCM transcription factors are a family of proteins which contain a GCM motif. (wikipedia.org)
  • Transcription factors (TFs) are proteins that regulate the transcription of genes, which is the first step in making a protein. (phys.org)
  • Transcription factors are proteins that regulate the transcription of genes, or the production of mRNA from DNA. (biolegend.com)
  • To characterize the entire complement of transcription factors encoded by the genomes of Arabidopsis , Drosophila , C. elegans , and S. cerevisiae , we used a comprehensive list of proteins, domains, and motifs to query the corresponding sequence databases. (sciencemag.org)
  • Transcription factors are usually defined as proteins that show sequence-specific DNA binding and are capable of activating and/or repressing transcription. (sciencemag.org)
  • Transcription factors are proteins that bind to specific regions of the DNA to promote or repress the activity of many genes. (innovations-report.com)
  • A single transcription factor can spur the transcription of dozens of genes into messenger RNA (mRNA), which is then translated into proteins that do the work of the cell. (innovations-report.com)
  • Transcription factors (TFs) are proteins that bind to specific DNA sequences in order to direct which genes should be turned on or off in a tissue. (ucsd.edu)
  • Between 2,000 and 3,000 transcription factor proteins are encoded by the human genome, potentially creating more than 4 million potential protein pairings. (ucsd.edu)
  • We have generated a series of fusion proteins carrying portions of subunit lie, the second largest subunit of Drosophila RNA polymerase I, and have used them in a domain interference assay to identify a fragment of the lie subunit that carries the binding site for a basal transcription factor. (ingentaconnect.com)
  • Fusion proteins carrying a subunit lie fragment spanning residues Ala 519 -Gly 992 strongly inhibit promoter-driven transcription in both unfractionated nuclear extracts and in reconstituted systems. (ingentaconnect.com)
  • The same fusion proteins similarly inhibit dTFIIF stimulation of Pol II elongation on dC-tailed templates, suggesting that the IIc(A519-G992) fragment, which carries conserved regions D-H, interferes with transcription by binding to dTFIIF. (ingentaconnect.com)
  • Transcription factors are involved in the process of transcribing DNA into RNA, which is then translated into proteins. (nationwidechildrens.org)
  • From the original setting of mouse ESC culture, scientists identified the active components leukaemia inhibitory factor (LIF) and bone morphogenic proteins (BMP), which maintain the pluripotency in ESCs through activating the Jak/Stat3 signaling pathway and inducing the inhibitors of differentiation (Id) genes, respectively [ 4 , 5 , 6 ]. (mdpi.com)
  • Transcription factors are proteins that interact with DNA to turn genes on or off. (eurekalert.org)
  • Since it is known that 13 different members of the fibroblast growth factor, or Fgf, family act as signaling proteins between the two different tissues -- dental mesenchyme and oral epithelium -- during murine tooth development, Javed and colleagues looked for changes in Fgf ligands in the mice lacking Sp7. (eurekalert.org)
  • Transcription factors perform this function alone, or by using other proteins in a complex, by increasing (as an activator ), or preventing (as a repressor ) the presence of RNA polymerase , a protein which transcribes genetic information. (wikidoc.org)
  • Transcription factors are one of the groups of proteins that read and interpret the genetic "blueprint" in the DNA. (wikidoc.org)
  • Transcription factor synthesis Transcription factors (like all proteins) are transcribed from a gene on a chromosome into RNA, and then the RNA is translated into protein. (wikidoc.org)
  • Class I bHLH proteins are important transcription factors whose binding sites are frequently clustered throughout the β-globin gene locus, suggesting their role in globin gene regulation. (umontreal.ca)
  • I will first briefly introduce what transcription factors are and discuss why polymorphisms in these proteins play an important role in the development of disease. (hstalks.com)
  • As their name indicates, transcription factors are a class of DNA-binding proteins that are responsible for the transcription of genes, which is the conversion of a double-stranded sequence of DNA into a copy of single-stranded RNA, thereby regulating the expression of genes. (hstalks.com)
  • Transcription factors are just one of the diverse groups of proteins that are crucial for the successful transcription by Pol II in eukaryotic cells. (hstalks.com)
  • These proteins include general transcription factors, or GTFs, cofactors, and histone-modifying enzymes. (hstalks.com)
  • LIM-homeodomain proteins direct cellular differentiation by activating transcription of cell-type-specific genes, but this activation requires cooperation with other nuclear factors. (worldwidescience.org)
  • Zinc finger transcription factors or ZF-TFs , are transcription factors composed of a zinc finger - binding domain and any of a variety of transcription-factor effector-domains that exert their modulatory effect in the vicinity of any sequence to which the protein domain binds. (wikipedia.org)
  • In transcription factors with a signal sensing domain, the signal sensing domain is the part of the transcription factor that binds to chemical signals (e.g. a steroid hormone or cAMP), allowing the transcription factor to function in response to a particular chemical signal. (conservapedia.com)
  • Once the DNA double helix and its associated epigenome have been melted so that the template strand is available for binding, a transcription factor binds to a specific nucleotide sequence to biochemically influence gene transcription . (wikiversity.org)
  • a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to mRNA is called a transcription factor . (wikiversity.org)
  • Researchers at the Max Planck Institute for Molecular Genetics in Berlin have now discovered that the DNA segment to which a transcription factor binds can assume various spatial arrangements. (mpg.de)
  • In the field of molecular biology, a transcription factor (sometimes called a sequence-specific DNA binding factor) is a protein that binds to specific DNA sequences and thereby controls the transfer (or transcription) of genetic information from DNA to mRNA. (phys.org)
  • Once the transcription factor binds to an enhancer region, this can cause stimulation or repression of gene transcription. (biolegend.com)
  • [1] Before the start of transcription, the transcription factor II D (TFIID) complex, binds to the core promoter of the gene. (wikiversity.org)
  • We report the identification of a Ca 2+ -responsive E-box element, CaRE2, within BDNF promoter III that binds upstream stimulatory factors 1 and 2 (USF1/2) and show that USFs are required for the activation of CaRE2-dependent transcription from BDNF promoter III. (jneurosci.org)
  • ERG was demonstrated to bind to the PTEN promoter and repress its transcription. (spandidos-publications.com)
  • They also have the advantage that the targeted sequence need not be symmetrical unlike with most other DNA-binding motifs based on natural transcription factors that bind as dimers. (wikipedia.org)
  • Transcription factors bind to the human genome within areas of the genome still viewed as a black box""vast stretches of DNA sequence between known genes. (redorbit.com)
  • To do so, they deployed a new technology that uses chemicals to freeze transcription factors as they bind to the genome. (redorbit.com)
  • That is, in some of individuals, a single letter change at a certain binding region influenced the likelihood that the transcription factor would bind there. (redorbit.com)
  • Auxin-response factors (ARFs) bind with specificity to TGTCTC auxin-response elements (AuxREs), which are found in promoters of primary/early auxin-response genes. (pnas.org)
  • Transcription factors bind to either enhancer or promoter regions of DNA adjacent to the genes that they regulate. (wikipedia.org)
  • Transcription factors bind to a section of DNA and control how strongly a gene in that section is activated. (mpg.de)
  • A team of scientists headed by Sebastiaan Meijsing at the Max Planck Institute for Molecular Genetics have now come to a different conclusion: The researchers discovered that transcription factors can assume various shapes depending on which DNA segment they bind to. (mpg.de)
  • Consequently, transcription factors can bind to DNA segments without affecting a nearby gene. (mpg.de)
  • A family of transcription factors that contain two ZINC FINGER MOTIFS and bind to the DNA sequence (A/T)GATA(A/G). (abbreviations.com)
  • TFIID is the first protein to bind to DNA during the formation of the pre-initiation transcription complex of RNA polymerase II (RNA Pol II). (wikiversity.org)
  • General transcription factors (GTFs), also known as basal transcriptional factors, are a class of protein transcription factors that bind to specific sites on DNA to activate transcription. (wikiversity.org)
  • Now each Mig1p can bind DNA and drag the other transcription factors with them. (yeastgenome.org)
  • To perform an assay, add nuclear or cell extract from mammalian cells to the wells and incubate to allow the transcription factor to bind to its sequence. (clontech.com)
  • The TFs bind, attract other TFs and create a complex that eventually facilitates binding by RNA polymerase, thus beginning the process of transcription. (thebalance.com)
  • Together these studies establish that DNA-binding domains from heterologous factors can bind to synthetic promoters containing appropriate binding sites on naked DNA templates introduced into plant cells, and nonplant activation domains can productively interact with the transcription machinery of the plant when covalently linked to a DNA-binding domain. (genetics.org)
  • Kageyama R, Sasai Y, Nakanishi S. Molecular characterization of transcription factors that bind to the cAMP responsive region of the substance P precursor gene. (labome.org)
  • Transcription factors that form transcription initiation complexes on DNA, bind to specific DNA-DIRECTED RNA POLYMERASES and are required to initiate transcription. (curehunter.com)
  • They bind DNA and help initiate a program of increased or decreased gene transcription. (wikidoc.org)
  • Many of these GTFs don't actually bind DNA but are part of the large transcription preinitiation complex that interacts with RNA polymerase directly. (wikidoc.org)
  • General transcription factors bind to sequence elements, for instance, a TATA box located in the core promoter. (hstalks.com)
  • Given these and other observations that transcription and epigenetic factor dysfunction is of central importance in AML , understanding how epigenetic dysfunction arises and contributes to the differentiation block holds rich promise for the identification of new therapeutic targets for patient benefit. (nature.com)
  • Through analysis of the AML chromatin landscape this project will make use of leading edge technologies and experimental approaches to discover how transcription factor genes FOXC1 and IRX3 are derepressed in AML to confer a differentiation block. (nature.com)
  • Derepression of the Iroquois homeodomain transcription factor IRX3 confers differentiation block in acute leukemia. (nature.com)
  • Transcription factors can also be dysregulated during developmental processes, promoting or inhibiting cellular differentiation. (qiagen.com)
  • In complex organisms, specific transcription factors regulate developmental processes and cell differentiation . (conservapedia.com)
  • It is the action of transcription factors that determines the differentiation fate of cells. (biolegend.com)
  • In the last century, Golden2 was proposed as a second golden producing factor and identified as controlling cellular differentiation in maize leaves. (frontiersin.org)
  • The availability of this large combinatorial network of transcription factors will provide scientists with many opportunities to study gene regulation, tissue differentiation and evolution in mammals," said Ideker, professor in the Department of Medicine and at UCSD's Jacobs School of Engineering. (ucsd.edu)
  • two reports illustrate how the same transcription factor, MEF2, which functions in the differentiation of skeletal muscle, can play different roles in the survival of neurons and T cells. (sciencemag.org)
  • Five redundant PLETHORA AP2-domain transcription factors play a major role in specifying the stem cell niche, and in controlling the rate of differentiation in the meristem. (wur.nl)
  • 2) how the many target genes of these transcription factors orchestrate division and differentiation. (wur.nl)
  • Transcription factors are only one of the means by which our cells express different combinations of genes, allowing for differentiation into the various types of cells, tissues, and organs that make up our bodies. (thebalance.com)
  • microRNA-9-2 and microRNA-9-3 double-mutant mice demonstrate that microRNA-9 ( miR-9 ) controls neural progenitor proliferation and differentiation in the developing telencephalon by regulating the expression of multiple transcription factors. (jneurosci.org)
  • Several transcription factors control the proliferation/differentiation of these cells. (jneurosci.org)
  • Many SOX transcription factors play important roles in regulating CELL DIFFERENTIATION. (harvard.edu)
  • Responding to cues (stimuli), these transcription factors turn on/off the transcription of the appropriate genes which in turn allows for changes in cell morphology or activities needed for cell fate determination and cellular differentiation . (wikidoc.org)
  • Current approaches to regulate T-cell differentiation have focused on manipulating cell culture conditions and using transcription factors to differentiate T cells away from the exhausted condition. (seattlechildrens.org)
  • TCF1 is a transcription factor that plays a key role in the differentiation of memory T cells and can sustain T cell activity even after prolonged antigen exposure. (seattlechildrens.org)
  • Indeed, the great majority of patients with AML have one or more mutations targeting a transcription factor, chromatin modifier or regulator of DNA methylation and this emphasises the absolute centrality of epigenetic and transcription factor dysfunction to the disease. (nature.com)
  • They also modify transcription factors and CHROMATIN through ACETYLATION. (nih.gov)
  • 3) how these transcription factors influence and are influenced by chromatin domains and modifications during the progression from stem cell to differentiated cell. (wur.nl)
  • For the first time, we found that in other hematopoietic lineages, human β-globin locus is in active chromatin and interacts with transcription factors involved in repression. (umontreal.ca)
  • Strikingly and consistent with the expression of globin genes, we characterized transcription factors involved in open chromatin configuration and basal level of globin gene expression in lymphoid progenitor cells. (umontreal.ca)
  • These enzymes, by modifying the acetylation of histones or methylation of histones or DNA, are going to mediate changes in the accessibility of the chromatin to the transcription factors. (hstalks.com)
  • For the current study, Kasowski, Snyder, and their colleagues examined two important transcription factors: RNA polymerase II and NFkappaB. (redorbit.com)
  • Transcription factors work by recruiting RNA polymerase to the promoter region of a gene, or by blocking the access of RNA polymerase to a promoter. (conservapedia.com)
  • The general transcription factor II D (TF II D) is one of several general transcription factors that make up the RNA polymerase II preinitiation complex. (wikiversity.org)
  • A vast network of regulatory factors that contribute to the initiation of transcription by RNA polymerase ultimately target any specific gene's core promoter. (wikiversity.org)
  • From these data, the functional significance of domain structure of TFIIF is discussed in terms of its sigma homology sequences and complex formation with RNA polymerase II in the initiation and elongation of transcription. (labome.org)
  • Transcription factors are also regulated by cofactors, forming complexes that can activate or inhibit transcriptional activity. (qiagen.com)
  • The receptors simultaneously act as transcription factors and regulate gene activity in the cells. (mpg.de)
  • A defining feature of transcription factors is that they contain one or more DNA binding domains (DBDs) which attach to specific sequences of DNA adjacent to the genes that they regulate. (phys.org)
  • The new findings indicate that certain transcription factors are working together in a coordinated way to regulate the changes in seen in gene expression between humans and chimps, the researchers said. (innovations-report.com)
  • Cell cycle control Many transcription factors, especially some that are oncogenes or tumor suppressors , help regulate the cell cycle and as such determine how large a cell will get and when it can divide into two daughter cells. (wikidoc.org)
  • This is just as true with transcription: not only do rates of transcription regulate the amounts of gene products (RNA and protein) available to the cell, but the process of transcription itself is regulated. (wikidoc.org)
  • WT1 is also a transcription factor, controlling the rate of transcription of genetic information from DNA to messenger RNA and therefore helping to regulate the expression of genes. (ed.ac.uk)
  • Lineage-specification and -commitment is tightly dependent on lineage-specific transcription factors to regulate the expression of target genes. (umontreal.ca)
  • The TMPRRSS2 portion of the fusion contains an androgen-responsive promoter which drives the aberrant expression of the oncogenic transcription factor ERG ( 10 ). (spandidos-publications.com)
  • The Human Stem Cell Transcription Factors EpiTect Methyl II Signature PCR Array profiles the promoter methylation status of a panel of 22 transcription factors whose association with stem cell. (qiagen.com)
  • Promoter sequences are found at the beginning of the gene and serve as the transcription start site where the transcription initiation complex is formed. (biolegend.com)
  • Binding of TFIID to the TATA box in the promoter region of the gene initiates the recruitment of other factors required for RNA Pol II to begin transcription. (wikiversity.org)
  • The core promoter is the minimal portion of the promoter required to properly initiate gene transcription. (wikiversity.org)
  • The core promoter includes the transcription start site (s) (TSS). (wikiversity.org)
  • To identify molecular mechanisms that control activity-dependent gene expression in the CNS, we have characterized the factors that mediate activity-dependent transcription of BDNF promoter III. (jneurosci.org)
  • Identification of IFN regulatory factor-1 binding site in IL-12 p40 gene promoter. (labome.org)
  • The catalysis of each RNA representation from the template DNA is a transcription, specifically a gene transcription. (wikiversity.org)
  • The overall process is also referred to as gene transcription. (wikiversity.org)
  • Takeba Y, Nagafuchi H, Takeno M, Kashiwakura J, Suzuki N. Txk, a member of nonreceptor tyrosine kinase of Tec family, acts as a Th1 cell-specific transcription factor and regulates IFN-gamma gene transcription. (labome.org)
  • Now, an ambitious survey of the human genome has identified differences in the binding of master regulators called transcription factors to DNA that affect how genes are expressed in different people. (redorbit.com)
  • Transcription factors account for as much as 10 percent of the coding genome in humans and other organisms. (redorbit.com)
  • Closer examination of these variable binding regions showed that single-letter differences in the genome""called SNPs""accounted for some of the difference in transcription factor binding. (redorbit.com)
  • Other, larger differences in the genome, called structural variation, also accounted for a number of the differences in transcription factor binding. (redorbit.com)
  • Genes encoding for transcription factors make up a significant portion of every organism's genome. (conservapedia.com)
  • There are estimated to be well over 2000 genes (some estimates are as high as 3000) encoding for transcription factors in the human genome (~10% of all human genes). (conservapedia.com)
  • Hence, the combinatorial use of a subset of the approximately 2000 human transcription factors easily accounts for the unique regulation of each gene in the human genome during development. (wikiversity.org)
  • The number of transcription factors found within an organism increases with genome size, and larger genomes tend to have more transcription factors per gene. (wikipedia.org)
  • The structure of the interface between the transcription factor and genome segments must therefore play a key role in determining gene activity. (mpg.de)
  • Arabidopsis dedicates over 5% of its genome to code for more than 1500 transcription factors, about 45% of which are from families specific to plants. (sciencemag.org)
  • The genome-wide comparison reveals the evolutionary generation of diversity in the regulation of transcription. (sciencemag.org)
  • With the completion of the Arabidopsis thaliana genome sequence, the entire complement of genes coding for transcription factors from a plant can be identified and described. (sciencemag.org)
  • Protein domains that are sometimes present in transcription factors, but not necessarily associated with them, have not been included in this genome survey, for example, some zinc coordinating motifs that either are involved in protein-protein interactions or have not yet been functionally characterized. (sciencemag.org)
  • Humans share at least 97 percent of their genes with chimpanzees, but, as a new study of transcription factors makes clear, what you have in your genome may be less important than how you use it. (innovations-report.com)
  • Stubbs has had a longtime interest in the evolutionary role of transcription factors and other regulatory agents in the genome. (innovations-report.com)
  • I will cover both variance of transcription factors identified by traditional gene candidate approaches, as well as variance identified by more contemporary genome-wide approaches. (hstalks.com)
  • This talk will focus on the role of transcription factors in the development of complex diseases. (hstalks.com)
  • In Transcription Factors: Methods and Protocols , experts in the field describe state-of-the-art approaches that investigators can use to probe critical mechanisms underlying transcription factor nuclear-cytoplasmic trafficking as well as to assess the functional impact of post-translational modifications on transcription factor function. (springer.com)
  • Many transcription factors, such as nuclear receptors, reside in the cytoplasm and enter the nucleus upon activation (e.g., ligand binding). (qiagen.com)
  • Furthermore, genes are often flanked by several binding sites for distinct transcription factors, and efficient expression of each of these genes requires the cooperative action of several different transcription factors (see, for example, hepatocyte nuclear factors). (wikiversity.org)
  • These events lead to transcription factor aberrant expression and abnormal activity and activate an intra‐cellular signalling cascade resulting in the nuclear translocation and transcriptional activation of target genes involved in many aspects of tumorigenesis, inflammation and proliferation survival of cancer cells and resistance to therapeutic agents. (els.net)
  • Belaiba RS, Bonello S, Zahringer C et al (2007) Hypoxia up-regulates hypoxia-inducible factor-1alpha transcription by involving phosphatidylinositol 3-kinase and nuclear factor kappaB in pulmonary artery smooth muscle cells. (springer.com)
  • For nuclear protein flow cytometry staining, BioLegend's True-Nuclear™ Transcription Factor Buffer Set has been specially formulated for intracellular staining with minimum effect on the surface fluorochrome staining. (biolegend.com)
  • Our data suggest that cell cycle-regulated nuclear accumulation of Swi5 is responsible for the burst of SIC1 transcription at the end of anaphase. (mendeley.com)
  • Recent studies have demonstrated that the production of these inflammatory mediators is altered as a result of the activation of nuclear factor-kB (NF-kB). (cdc.gov)
  • Increasing the amount of nuclear extract containing the transcription factor added to the well will increase the signal. (clontech.com)
  • Exportin 4 mediates a novel nuclear import pathway for Sox family transcription factors. (harvard.edu)
  • The transcription factor ZEB1 (deltaEF1) promotes tumour cell dedifferentiation by repressing master regulators of epithelial polarity. (nature.com)
  • As major regulators of gene expression , transcription factors play a role in all cell processes. (conservapedia.com)
  • We report here on overlapping and nonoverlapping expression patterns of transcription factors in these cells and thus provide novel insights into the dynamic networks of transcriptional regulators in embryonic and adult stem cells. (mendeley.com)
  • Beside the core Oct4-Sox2-Nanog circuitry, accumulating regulators, including transcription factors, epigenetic modifiers, microRNA and signaling molecules have also been found to play important roles in preserving pluripotency. (mdpi.com)
  • Sarkar A, Hochedlinger K. The sox family of transcription factors: versatile regulators of stem and progenitor cell fate. (harvard.edu)
  • MicroRNAs (miRNAs) and transcription factors are master regulators of the cellular system. (intechopen.com)
  • Transcription factors, the key regulators of plant growth and development, are the targets of the miRNAs families. (intechopen.com)
  • The E2F family of transcription factors are evolutionarily conserved regulators of the cell cycle that can be divided into two groups based on their ability to either activate or repress transcription. (sdbonline.org)
  • The present study aimed to determine whether or not ERG regulates PTEN transcription directly. (spandidos-publications.com)
  • Scientists at the Max Planck Institute for Heart and Lung Research in Bad Nauheim and Giessen University have discovered that transcription factor FoxO1 regulates the division of cells and plays a key role in the development of pulmonary hypertension. (eurekalert.org)
  • Together, our results demonstrate that ISL1 regulates approximately one-third of SAN-specific genes, indicate that a combination of ISL1 and other SAN transcription factors could be utilized to generate pacemaker cells, and suggest ISL1 mutations may underlie sick sinus syndrome. (jci.org)
  • They function as transcriptional coactivators by bridging between DNA-binding TRANSCRIPTION FACTORS and the basal transcription machinery. (nih.gov)
  • Basal transcription regulation In eukaryotes , an important class of transcription factors called general transcription factors (GTFs) are necessary for transcription to occur. (wikidoc.org)
  • Some of the regulatory regions, known as binding regions, serve as handholds for transcription factors. (redorbit.com)
  • The mechanism through which a transcription factor functions, and its regulatory effect (up-regulation or down-regulation) on a target gene, varies widely between transcription factors. (conservapedia.com)
  • The regulatory effect (and sometimes mechanism) of a specific transcription factor often varies depending on the target gene, and can sometimes even vary in response to other factors within the cell. (conservapedia.com)
  • For example, the expression of T-bet and FOXP3 transcription factors (along with specific cytokines) will differentiate T cells into T regulatory cells. (biolegend.com)
  • Development is based on the cellular capacity for differential gene expression and is often controlled by transcription factors acting as switches of regulatory cascades ( 1 ). (sciencemag.org)
  • Eivind Almaas, a researcher at the Norwegian University of Science and Technology and a co-author on the study, developed a gene regulatory network diagram of the transcription factors in relation to the genes that rise or fall with them. (innovations-report.com)
  • Investigating the regulatory mechanisms that control the transcription of these genes in neurons may provide important insights into activity-dependent neural development and synaptic plasticity. (jneurosci.org)
  • Examples include heat shock factor (HSF) which upregulates genes necessary for survival at higher temperatures, hypoxia inducible factor (HIF) which upregulates genes necessary for cell survival in low oxygen environments, and sterol regulatory element binding protein (SREBP) which helps maintain proper lipid levels in the cell. (wikidoc.org)
  • A comprehensive knowledge of transcription factor binding sites (TFBS) is important for a mechanistic understanding of transcriptional regulation as well as for inferring gene regulatory networks. (umd.edu)
  • Complex regulatory networks that are controlled by transcription factors and microRNAs, which coordinate gene expression. (intechopen.com)
  • The resources on the regulatory cascades of transcription factors and miRNAs are available in the context of human diseases, but these resources are meager in case of plant diseases. (intechopen.com)
  • In molecular biology , a transcription factor ( TF ) (or sequence-specific DNA-binding factor ) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA , by binding to a specific DNA sequence . (wikipedia.org)
  • In addition, I will describe how the functionality of these transcription factor variants is assessed using various molecular biology techniques. (hstalks.com)
  • In molecular biology , Activating Transcription Factor , ATF , is a class of AP-1 transcription factor dimers. (wikidoc.org)
  • She is particularly interested in the largest family of transcription factors in mammals, the KRAB zinc finger (KRAB-ZNF) genes, which on average have accumulated more differences in sequence between humans and chimps than other genes. (innovations-report.com)
  • In this respect, it is also possible to target a sequence that is common to multiple (usually functionally related) genes in order to control the transcription of all these genes with a single transcription factor. (wikipedia.org)
  • We found that differences in DNA sequence contributed to differences in transcription factor binding," Kasowski says. (redorbit.com)
  • Analyzing the expression, regulation, activity, and sequence of transcription factor genes can help determine their relative importance to the biology of the cellular or disease processes under study. (qiagen.com)
  • The ARF1 protein contains an amino-terminal DNA-binding domain (DBD), which has some sequence similarity to a carboxyl-terminal B3 domain found in the maize transcription factor VIVIPAROUS 1 (VP1) and its relatives ( 2 , 6 - 8 ). (pnas.org)
  • a substance that contains one or more DNA-binding domains that are nucleotide-sequence specific is called a transcription factor . (wikiversity.org)
  • Interacting selectively and non-covalently with a DNA or RNA sequence in order to modulate transcription. (yeastgenome.org)
  • A large family of structurally-related transcription factors that were originally discovered based upon their close sequence homology to an HMG-box domain found in SEX-DETERMINING REGION Y PROTEIN. (harvard.edu)
  • Because the DNA motif recognized by a transcription factor is typically short and degenerate, computational approaches for identifying binding sites based only on the sequence motif inevitably suffer from high error rates. (umd.edu)
  • The chapters are written by prominent scientists, many of whom developed these methods, and highlight protocols that focus on specific transcription factor family members with particular relevance to human disease. (springer.com)
  • But how could specific transcription-factor activity be inhibited? (nih.gov)
  • Thus, Txk is expressed on Th1/Th0 cells with the IFN-gamma production and acts as a Th1 cell-specific transcription factor. (labome.org)
  • Cellular functions regulated by FOXO transcription factors. (hindawi.com)
  • Authoritative and cutting-edge FOXO Transcription Factors: Methods and Protocols aims to ensure successful results in the further study of this vital field. (springer.com)
  • WRKY transcription factors are known to function in a number of plant processes. (mdpi.com)
  • 2014. "Phylogenetic and Transcription Analysis of Chrysanthemum WRKY Transcription Factors. (mdpi.com)
  • Here, we determined that the LIM homeodomain transcription factor ISL1 plays a key role in survival, proliferation, and function of pacemaker cells throughout development. (jci.org)
  • The cloning of the first transcription factor from plants, the C1 gene of maize, indicated that plants use transcription factors that are structurally related to those of animals in their control of gene expression, because C1 showed significant structural homology to the vertebrate cellular proto-oncogene c-MYB. (nih.gov)
  • Depending on the transcription factor, these sequences can be as short as 4 base pairs or as long as 30 base pairs (in a few rare instances, they can be even longer). (conservapedia.com)
  • Many DNA variants associated with diseases belong to sequences that evidently control the activity of transcription factors. (mpg.de)
  • BiO BB] How to get the special Transcription Factor target sequences? (bioinformatics.org)
  • I want to get the Transcription Factor target sequences. (bioinformatics.org)
  • Members of the Hey transcriptional factor family are Notch target genes [1], and they have unique and redundant functions in cardiovascular development. (springer.com)
  • Its gene resides at the mi locus in mice, [7] and its protumorogenic targets include factors involved in cell death, DNA replication , repair, mitosis, microRNA production, membrane trafficking, mitochondrial metabolism, and much more. (wikipedia.org)
  • Chapters guide readers through biochemical and molecular methods, imaging approaches to monitor the subcellular localization of FOXO factors, omics and bioinformatics approaches, different animal models used in FOXO research, and human studies to investigate the role of FOXO factors in human disease and longevity. (springer.com)
  • What does gata transcription factors stand for? (abbreviations.com)
  • Couldn't find the full form or full meaning of gata transcription factors? (abbreviations.com)
  • Know what is gata transcription factors ? (abbreviations.com)
  • Got another good explanation for gata transcription factors ? (abbreviations.com)
  • The best understood of these genes encode transcription factors, such as GATA-2, RUNX1, ETV6, and C/EBPα, which establish and maintain genetic networks governing the genesis and function of blood stem and progenitor cells. (jci.org)
  • Specific and dynamic gene expression strongly depends on transcription factor (TF) activity and most plant TFs function in a combinatorial fashion. (wur.nl)
  • The combinatorial regulation of transcription factors and miRNAs guides the appropriate implementation of biological events and developmental processes. (intechopen.com)
  • Our results also suggest that ARF CTDs facilitate interactions between ARF activators that are not bound to DNA and transcription factors (e.g. (pnas.org)
  • In a significant leap forward in the understanding of how specific types of tissue are determined to develop in mammals, an international team of scientists has succeeded in mapping the entire network of DNA-binding transcription factors and their interactions. (ucsd.edu)
  • Further research is still needed to bring applications of this discovery to the clinic, but the implications of understanding the interactions between transcription factors and microsatellites extends beyond Ewing sarcoma. (nationwidechildrens.org)
  • TFs are also usually found working in groups or complexes , forming multiple interactions that allow for varying degrees of control over rates of transcription. (thebalance.com)
  • The relationship between transcription factors and miRNA in different plant species described in this chapter will be of great interest to plant scientists, providing better insights into the mechanism of action and interactions among transcription factors (TFs) and miRNA networks culminating in improving key agronomic traits for crop improvement to meet the future global food demands. (intechopen.com)
  • Similarly, the deficiency of upstream and downstream transcription factors of Tbx1, such as Foxc2, Gbx2 and Hes1, results in abnormal great arteries. (springer.com)
  • RNA-sequencing (RNA-seq) analyses of FACS-purified cells from ISL1-deficient SANs revealed that a number of genes critical for SAN function, including those encoding transcription factors and ion channels, were downstream of ISL1. (jci.org)
  • Transcription factors form a vital link in the chain of regeneration, converting injury-induced stress signals into downstream protein expression via gene regulation. (frontiersin.org)
  • If the signal requires upregulation or downregulation of genes in the recipient cell, often transcription factors will be downstream in the signaling cascade. (wikidoc.org)
  • Response to environment Not only do transcription factors act downstream of signaling cascades related to biological stimuli, but they can also be downstream of signaling cascades involved in environmental stimuli. (wikidoc.org)
  • Zinc finger protein transcription factors can be encoded by genes small enough to fit a number of such genes into a single vector , allowing the medical intervention and control of expression of multiple genes and the initiation of an elaborate cascade of events. (wikipedia.org)
  • Domain structure of a human general transcription initiation factor, TFIIF. (labome.org)
  • These factors are involved in the formation of the transcription of the pre-initiation complex and in the subsequent recruitment of Pol II. (hstalks.com)
  • Nine different ARFs have been analyzed for their capacity to activate or repress transcription in transient expression assays employing auxin-responsive GUS reporter genes. (pnas.org)
  • Our results suggest that ARFs can activate or repress transcription by binding to AuxREs directly and that selected ARFs, when overexpressed, may potentiate activation further by associating with an endogenous transcription factor(s) (e.g., an ARF) that is bound to AuxREs. (pnas.org)
  • Also, it is possible to target a family of related genes by targeting and modulating the expression of the endogenous transcription factor(s) that control(s) them. (wikipedia.org)
  • In the last few years, significant breakthroughs in transcription research expanded our appreciation for the complexity of molecular controls on gene expression in mammalian cells. (springer.com)
  • The mammalian forkhead transcription factors of the O class (FOXOs) have four members: FOXO1, FOXO3, FOXO4, and FOXO6. (hindawi.com)
  • In addition, current and future research can lead to potential avenues to target this transcription factor mechanism for cancer prevention [ citation needed ] . (wikipedia.org)
  • Darnell JE (2002) Transcription factors as targets for cancer therapy. (els.net)
  • Beasley NJ, Leek R, Alam M et al (2002) Hypoxia-inducible factors HIF-1alpha and HIF-2alpha in head and neck cancer: relationship to tumor biology and treatment outcome in surgically resected patients. (springer.com)
  • Here we discuss the roles of EMT-inducing transcription factors in creating a pro-tumorigenic setting characterized by an intrinsic ability to withstand oncogenic insults through the mitigation of p53-dependent oncosuppressive functions and the gain of stemness-related properties. (nature.com)
  • That they are the most direct and hopeful targets for treating cancer is proposed, and this is supported by the fact that there are many more human oncogenes in signalling pathways than there are oncogenic transcription factors. (nih.gov)
  • In the new study, Nowick and computer scientist Tim Gernat, a co-author, took a new look at data from that study, which tracked gene expression - including genes coding for transcription factors - in tissues from six humans and five chimpanzees. (innovations-report.com)
  • Until now, no one had looked at whether there was any variability in the targets of transcription factors from one person to the next. (redorbit.com)
  • A limited list of transcription factors are overactive in most human cancer cells, which makes them targets for the development of anticancer drugs. (nih.gov)
  • As the majority of the RNA targets that depend on WT1 for their expression are not transcription targets, this research proposes that WT1 influences key developmental processes, in part through regulating mRNA turnover. (ed.ac.uk)
  • To test for epistasis within an adaptive trait genetic network, we generated and tested 47 Arabidopsis thaliana double mutant combinations for 20 transcription factors, which all influence the accumulation of aliphatic glucosinolates, the defense metabolites that control fitness. (plantcell.org)
  • Since 1987, the catalogue of MYB-related transcription factors has increased considerably in size due, primarily, to the ever-expanding number of MYB genes identified in higher plants (Arabidopsis thaliana is estimated to contain more than a hundred MYB genes). (nih.gov)
  • Arabidopsis transcription factors that belong to families common to all eukaryotes do not share significant similarity with those of the other kingdoms beyond the conserved DNA binding domains, many of which have been arranged in combinations specific to each lineage. (sciencemag.org)
  • A hybrid transcription factor comprising a fusion of the DNA-binding domain of Saccharomyces cerevisiae GAL4 and the transcription activation domain of maize C1 was expressed in stably transformed Arabidopsis. (genetics.org)
  • A palindromic TGTCTC AuxRE was used as bait in a yeast one-hybrid system to isolate a transcription factor, referred to as auxin-response factor 1 (ARF1) ( 2 ). (pnas.org)
  • i want to isolate a transcription factore which is responsible for a special phenotype so what should i do? (scientistsolutions.com)
  • The activity of transcription factors determines what a cell is doing at any given moment," says Kasowski, who was a medical student at Yale when she received her HHMI medical research fellowship. (redorbit.com)
  • Comprehensive and current, Transcription Factors: Methods and Protocols compiles the latest techniques for elucidating controls on transcription factor intracellular localization and activity, and consequently is unlike any other methods-based text on transcriptional regulation today. (springer.com)
  • As a result, it alters the structure of the transcription factor itself and controls its activity. (mpg.de)
  • Neighbouring DNA segments have a significant impact on transcription factor shape, thus modulating the activity of the gene. (mpg.de)
  • In addition, adjacent DNA segments influence the activity of the bound transcription factors. (mpg.de)
  • Scientists had previously assumed that these segments exert an effect by inhibiting the binding of transcription factors, thus impeding the activity of neighbouring genes," Meijsing says. (mpg.de)
  • Reduced FoxO1 activity is therefore an important factor in the development of pulmonary hypertension. (eurekalert.org)
  • In further experiments it was found that certain growth factors and chemical messengers are responsible for reduced FoxO1 activity. (eurekalert.org)
  • The study, in Proceedings of the National Academy of Sciences, found that broad differences in the gene activity of humans and of chimpanzees, affecting nearly 1,000 genes, appear to be linked to the action of about 90 transcription factors. (innovations-report.com)
  • The analysis revealed a broad pattern of activity in 90 transcription factors that paralleled the activity of about 1,000 genes in humans and chimps. (innovations-report.com)
  • M.E. (1999) Neuronal activity-dependent cell survival dediated by transcription factor MEF2. (sciencemag.org)
  • These results suggest a new function for the USFs in the regulation of activity-dependent transcription in neurons. (jneurosci.org)
  • However, activation of CREB alone is not sufficient to mediate the activity-dependent transcription of BDNF exon III. (jneurosci.org)
  • Thus, it is concluded that ref1 possesses transcription repressor activity in addition to its function as a transcriptional auxiliary protein. (labome.org)
  • Cofactors are also important layers in this process as they modulate the activity of the transcription factor. (hstalks.com)
  • Members of the class O of forkhead box transcription factors (FOXO) have important roles in metabolism, cellular proliferation, stress resistance, and apoptosis. (hindawi.com)
  • It is thought that expression of the Nur77 orphan steroid receptor (whose transcription is dependent on Ca 2+ ), the phosphatase calcineurin, and the transcription factor MEF2, mediates this apoptosis. (sciencemag.org)
  • These prebound transcription factors facilitate activated transcription when auxin levels are elevated or when ARF activators are overexpressed in transfected protoplasts. (pnas.org)
  • They can act as activators or repressors , respectively increasing or decreasing the transcription of a target gene . (conservapedia.com)
  • BIRMINGHAM, Ala. - Amjad Javed, Ph.D., and University of Alabama at Birmingham colleagues have found a key role in tooth development for the transcription factor Specificity protein 7, or Sp7. (eurekalert.org)
  • The name, Golden2 , follows nomenclature used for the first golden producing factor, golden1 , found in maize by Jenkins (1926) . (frontiersin.org)
  • However, the transcription factors do not function simply as an on/off switch but rather like a volume control, which allows gene expression to be precisely controlled. (innovations-report.com)
  • Doedens AL, Stockmann C, Rubinstein MP et al (2010) Macrophage expression of hypoxia-inducible factor-1 alpha suppresses T-cell function and promotes tumor progression. (springer.com)
  • To identify additional factors necessary for the inhibition of the Cdk1/Cdc28 kinase in G1, we isolated mutants that can replicate DNA in the absence of Cdc4 function. (mendeley.com)
  • therefore, a better understanding of factors that drive SAN development and function is crucial to generation of potential therapies, such as biological pacemakers, for sinus arrhythmias. (jci.org)
  • Fusing combinations of these elements, derived from different kingdoms, has resulted in production of diverse hybrid factors having defined DNA-binding specificity and transcriptional activation function for the target organism in question. (genetics.org)
  • distant structural relatives of the conserved cyclin core or "box" can also function as general transcription factors (like TFIIB) or survive embedded in the chain of the tumor suppressor, retinoblastoma protein. (curehunter.com)
  • Overall, this study suggests that specific alternate transcripts of "activator" E2F, dE2F1, may have a dual function on cell cycle progression and cannot simply be viewed as a pro-proliferative transcription factor. (sdbonline.org)
  • Following axotomy, the activation of multiple intracellular signaling cascades causes the expression of a cocktail of regeneration-associated transcription factors which interact with each other to determine the fate of the injured neurons. (frontiersin.org)
  • 2004). "Attenuation of HIV-1 replication in primary human cells with a designed zinc finger transcription factor" . (wikipedia.org)
  • 2001) Malignant transformation of primary chicken spleen cells by human transcription factor c-Rel. (bu.edu)
  • The Human Transcription Factors RT² Profiler PCR Array profiles the expression of 84 genes that directly control when, where, and the extent to which genes are expressed. (qiagen.com)
  • Induction of pluripotent stem cells from adult human fibroblasts by defined factors," Cell , vol. 131, no. 5, pp. 861-872, 2007. (hindawi.com)
  • The chimp network looks very much like the human one except there are a few transcription factors in different positions and with different connectivity," Stubbs said. (innovations-report.com)
  • Recombinant fragment corresponding to Human SP2 transcription factor aa 66-189. (abcam.com)
  • reprogrammed human and mouse somatic cells into ESC-like pluripotent cells (termed induced pluripotent stem cells or iPSC), simply by direct transduction of ESC transcription factors Oct4, Sox2, Klf4, and c-Myc [ 2 , 3 ]. (mdpi.com)
  • Other factors must also be involved in determining how strongly a transcription factor activates a gene. (mpg.de)
  • Your search returned 21 E74 like ETS transcription factor 2 Biomolecules across 8 suppliers. (biocompare.com)
  • Your search returned 102 Spi-B Transcription Factor Antibodies across 25 suppliers. (biocompare.com)
  • In Computational Biology of Transcription Factor Binding, experts in the field examine the basic principles and provide detailed guidance for the computational analyses and biological interpretations of transcription factor binding, while disclosing critical practical information and caveats that are missing from many research publications. (springer.com)
  • Regulation of gene expression at the level of transcription influences or controls many of the biological processes in a cell or organism, such as progression through the cell cycle, metabolic and physiological balance, and responses to the environment. (sciencemag.org)
  • Some of the other recruited transcription factors include TFIIA, TFIIB, and TFIIF. (wikiversity.org)
  • The oncogene ETS‑related gene (ERG) encodes a transcription factor with roles in the regulation of haematopoiesis, angiogenesis, vasculogenesis, inflammation, migration and invasion. (spandidos-publications.com)
  • Here we illustrate mechanistic advances in our understanding of familial MDS/AML syndromes caused by germline mutations of hematopoietic transcription factors. (jci.org)
  • Plant Transcription Factors: Methods and Protocols offers a comprehensive approach by covering the basic concepts as well as the detailed protocols of a series of commonly used tools for investigating plant TFs. (springer.com)
  • Authoritative and accessible, Plant Transcription Factors: Methods and Protocols serves as an ideal guide to seasoned plant molecular biologists as well as scientists new to the field of TFs and provides many necessary methods to all scientists who are interested in exploring the functions of transcription factors. (springer.com)
  • The team mapped every binding region for these two factors inside the genomes of 10 individuals. (redorbit.com)
  • In this review, we comprehensively discuss the transcription factors that have been reported to be hypoxia-responsive and the signalling mechanisms leading to their activation. (nih.gov)
  • Transcription factors use a variety of mechanisms for the regulation of gene expression. (wikipedia.org)
  • This review summarizes the molecular mechanisms involved in silica-induced NF-kB activation and discusses the importance of NF-kB as a critical transcription factor in mediating silica-induced lung diseases. (cdc.gov)
  • It is known that CNTF indirectly turns on the transcription factor STAT3, so the researchers wanted to determine if STAT3 is behind CNTF's protective powers. (newswise.com)
  • Researchers led by Mustafa Khammash have developed a new method that uses blue light to control the transcription of DNA into RNA in single cells. (phys.org)
  • In a series of experiments, the researchers demonstrated that a transcription factor known as TCF1 (for T cell factor-1) is essential for the creation and persistence of disease-fighting antibodies in the bloodstream. (genome.gov)
  • In the current issue of Proceedings of the National Academy of Sciences , researchers from Nationwide Children's Hospital describe a new paradigm for treating transcription factor-driven cancers. (nationwidechildrens.org)