Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Peptide Nucleic Acids: DNA analogs containing neutral amide backbone linkages composed of aminoethyl glycine units instead of the usual phosphodiester linkage of deoxyribose groups. Peptide nucleic acids have high biological stability and higher affinity for complementary DNA or RNA sequences than analogous DNA oligomers.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Genes, Regulator: Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Enhancer Elements, Genetic: Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.Nucleic Acid Probes: Nucleic acid which complements a specific mRNA or DNA molecule, or fragment thereof; used for hybridization studies in order to identify microorganisms and for genetic studies.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Nucleic Acid Amplification Techniques: Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Nucleic Acid Denaturation: Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.Regulatory Elements, Transcriptional: Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)Genes, Reporter: Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Mice, Transgenic: Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Chloramphenicol O-Acetyltransferase: An enzyme that catalyzes the acetylation of chloramphenicol to yield chloramphenicol 3-acetate. Since chloramphenicol 3-acetate does not bind to bacterial ribosomes and is not an inhibitor of peptidyltransferase, the enzyme is responsible for the naturally occurring chloramphenicol resistance in bacteria. The enzyme, for which variants are known, is found in both gram-negative and gram-positive bacteria. EC 2.3.1.28.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.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.Transgenes: Genes that are introduced into an organism using GENE TRANSFER TECHNIQUES.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.beta-Galactosidase: A group of enzymes that catalyzes the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-galactosides. Deficiency of beta-Galactosidase A1 may cause GANGLIOSIDOSIS, GM1.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Regulatory Sequences, Ribonucleic Acid: Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.Transfection: The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.Lac Operon: The genetic unit consisting of three structural genes, an operator and a regulatory gene. The regulatory gene controls the synthesis of the three structural genes: BETA-GALACTOSIDASE and beta-galactoside permease (involved with the metabolism of lactose), and beta-thiogalactoside acetyltransferase.E-Box Elements: DNA locations with the consensus sequence CANNTG. ENHANCER ELEMENTS may contain multiple copies of this element. E-boxes play a regulatory role in the control of transcription. They bind with basic helix-loop-helix (bHLH) type TRANSCRIPTION FACTORS. Binding specificity is determined by the specific bHLH heterodimer or homodimer combination and by the specific nucleotides at the 3rd and 4th position of the E-box sequence.Nucleotide Motifs: Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO.Deoxyribonuclease I: An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. The enzyme has a preference for double-stranded DNA.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Genes, Synthetic: Biologically functional sequences of DNA chemically synthesized in vitro.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.5' Flanking Region: The region of DNA which borders the 5' end of a transcription unit and where a variety of regulatory sequences are located.Oligonucleotide Probes: Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.DNA Footprinting: A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Self-Sustained Sequence Replication: An isothermal in-vitro nucleotide amplification process. The process involves the concomitant action of a RNA-DIRECTED DNA POLYMERASE, a ribonuclease (RIBONUCLEASES), and DNA-DIRECTED RNA POLYMERASES to synthesize large quantities of sequence-specific RNA and DNA molecules.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Genes, Viral: The functional hereditary units of VIRUSES.Homeodomain Proteins: Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL).Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Consensus Sequence: A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.G-Quadruplexes: Higher-order DNA and RNA structures formed from guanine-rich sequences. They are formed around a core of at least 2 stacked tetrads of hydrogen-bonded GUANINE bases. They can be formed from one two or four separate strands of DNA (or RNA) and can display a wide variety of topologies, which are a consequence of various combinations of strand direction, length, and sequence. (From Nucleic Acids Res. 2006;34(19):5402-15)3' Flanking Region: The region of DNA which borders the 3' end of a transcription unit and where a variety of regulatory sequences are located.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.DNA, Recombinant: Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.Animals, Genetically Modified: ANIMALS whose GENOME has been altered by GENETIC ENGINEERING, or their offspring.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Genomic Library: A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Acacia: A plant genus of the family FABACEAE. The gums and tanning agents obtained from Acacia are called GUM ARABIC. The common name of catechu is more often used for Areca catechu (ARECA).RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Genetic Vectors: DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.Transcription Initiation Site: The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.Drosophila: A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.In Situ Hybridization: A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA 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.Creatine Kinase, Mitochondrial Form: A form of creatine kinase found in the MITOCHONDRIA.Genes, Bacterial: The functional hereditary units of BACTERIA.Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.Operon: In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.DNA, Single-Stranded: A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.5' Untranslated Regions: The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.Chromosome Deletion: Actual loss of portion of a chromosome.Tumor Cells, Cultured: Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Globins: A superfamily of proteins containing the globin fold which is composed of 6-8 alpha helices arranged in a characterstic HEME enclosing structure.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)DNA, Intergenic: Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.Creatine Kinase, MM Form: An isoenzyme of creatine kinase found in the MUSCLE.Drosophila Proteins: Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.Luciferases: Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.Electrophoretic Mobility Shift Assay: An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.TATA Box: A conserved A-T rich sequence which is contained in promoters for RNA polymerase II. The segment is seven base pairs long and the nucleotides most commonly found are TATAAAA.Green Fluorescent Proteins: Protein analogs and derivatives of the Aequorea victoria green fluorescent protein that emit light (FLUORESCENCE) when excited with ULTRAVIOLET RAYS. They are used in REPORTER GENES in doing GENETIC TECHNIQUES. Numerous mutants have been made to emit other colors or be sensitive to pH.DNA Probes: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.Bacterial Proteins: Proteins found in any species of bacterium.DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.Sensitivity and Specificity: Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)Aptamers, Nucleotide: Nucleotide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.3' Untranslated Regions: The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.Chromosomes, Artificial, Bacterial: DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Genes, Homeobox: Genes that encode highly conserved TRANSCRIPTION FACTORS that control positional identity of cells (BODY PATTERNING) and MORPHOGENESIS throughout development. Their sequences contain a 180 nucleotide sequence designated the homeobox, so called because mutations of these genes often results in homeotic transformations, in which one body structure replaces another. The proteins encoded by homeobox genes are called HOMEODOMAIN PROTEINS.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Gene Expression Regulation, Enzymologic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.Viral Proteins: Proteins found in any species of virus.Kinetics: The rate dynamics in chemical or physical systems.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Chromatin Immunoprecipitation: A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Chromatin: 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.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Nucleic Acid Heteroduplexes: Double-stranded nucleic acid molecules (DNA-DNA or DNA-RNA) which contain regions of nucleotide mismatches (non-complementary). In vivo, these heteroduplexes can result from mutation or genetic recombination; in vitro, they are formed by nucleic acid hybridization. Electron microscopic analysis of the resulting heteroduplexes facilitates the mapping of regions of base sequence homology of nucleic acids.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Gene Targeting: The integration of exogenous DNA into the genome of an organism at sites where its expression can be suitably controlled. This integration occurs as a result of homologous recombination.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.Untranslated Regions: The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.Eye Color: Color of the iris.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Genes, Fungal: The functional hereditary units of FUNGI.Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.MyoD Protein: A myogenic regulatory factor that controls myogenesis. Though it is not clear how its function differs from the other myogenic regulatory factors, MyoD appears to be related to fusion and terminal differentiation of the muscle cell.Tilapia: A freshwater fish used as an experimental organism and for food. This genus of the family Cichlidae (CICHLIDS) inhabits Central and South America (one species extends north into Texas), West Indies, Africa, Madagascar, Syria, and coastal India.Methylation: Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)Silencer Elements, Transcriptional: Nucleic acid sequences that are involved in the negative regulation of GENETIC TRANSCRIPTION by chromatin silencing.Blotting, Northern: Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Erythroid-Specific DNA-Binding Factors: A group of transcription factors that were originally described as being specific to ERYTHROID CELLS.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Single-Strand Specific DNA and RNA Endonucleases: Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Gene Components: The parts of the gene sequence that carry out the different functions of the GENES.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Transformation, Genetic: Change brought about to an organisms genetic composition by unidirectional transfer (TRANSFECTION; TRANSDUCTION, GENETIC; CONJUGATION, GENETIC, etc.) and incorporation of foreign DNA into prokaryotic or eukaryotic cells by recombination of part or all of that DNA into the cell's genome.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Genes, Insect: The functional hereditary units of INSECTS.Polyribonucleotides: A group of 13 or more ribonucleotides in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.DNA, Catalytic: Molecules of DNA that possess enzymatic activity.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Viruses: Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells.RNA, Untranslated: RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Simian virus 40: A species of POLYOMAVIRUS originally isolated from Rhesus monkey kidney tissue. It produces malignancy in human and newborn hamster kidney cell cultures.Alternative Splicing: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.PolynucleotidesZebrafish: An exotic species of the family CYPRINIDAE, originally from Asia, that has been introduced in North America. They are used in embryological studies and to study the effects of certain chemicals on development.Intercalating Agents: Agents that are capable of inserting themselves between the successive bases in DNA, thus kinking, uncoiling or otherwise deforming it and therefore preventing its proper functioning. They are used in the study of DNA.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.Virus Replication: The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.Oligonucleotides, Antisense: Short fragments of DNA or RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.Nucleotides: The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)GuanineGenome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Histones: Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.Embryo, Mammalian: The entity of a developing mammal (MAMMALS), generally from the cleavage of a ZYGOTE to the end of embryonic differentiation of basic structures. For the human embryo, this represents the first two months of intrauterine development preceding the stages of the FETUS.Molecular Diagnostic Techniques: MOLECULAR BIOLOGY techniques used in the diagnosis of disease.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Fluorescent Dyes: Agents that emit light after excitation by light. The wave length of the emitted light is usually longer than that of the incident light. Fluorochromes are substances that cause fluorescence in other substances, i.e., dyes used to mark or label other compounds with fluorescent tags.RNA Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.PAX2 Transcription Factor: A paired box transcription factor that is essential for ORGANOGENESIS of the CENTRAL NERVOUS SYSTEM and KIDNEY.Mutagenesis, Insertional: Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.Polydactyly: A congenital anomaly of the hand or foot, marked by the presence of supernumerary digits.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Nucleosides: Purine or pyrimidine bases attached to a ribose or deoxyribose. (From King & Stansfield, A Dictionary of Genetics, 4th ed)Genes, Plant: The functional hereditary units of PLANTS.Thymidine Kinase: An enzyme that catalyzes the conversion of ATP and thymidine to ADP and thymidine 5'-phosphate. Deoxyuridine can also act as an acceptor and dGTP as a donor. (From Enzyme Nomenclature, 1992) EC 2.7.1.21.Immobilized Nucleic Acids: DNA or RNA bound to a substrate thereby having fixed positions.Chickens: Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Response Elements: Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.Insect Hormones: Hormones secreted by insects. They influence their growth and development. Also synthetic substances that act like insect hormones.

The paired-domain transcription factor Pax8 binds to the upstream enhancer of the rat sodium/iodide symporter gene and participates in both thyroid-specific and cyclic-AMP-dependent transcription. (1/7095)

The gene encoding the Na/I symporter (NIS) is expressed at high levels only in thyroid follicular cells, where its expression is regulated by the thyroid-stimulating hormone via the second messenger, cyclic AMP (cAMP). In this study, we demonstrate the presence of an enhancer that is located between nucleotides -2264 and -2495 in the 5'-flanking region of the NIS gene and that recapitulates the most relevant aspects of NIS regulation. When fused to either its own or a heterologous promoter, the NIS upstream enhancer, which we call NUE, stimulates transcription in a thyroid-specific and cAMP-dependent manner. The activity of NUE depends on the four most relevant sites, identified by mutational analysis. The thyroid-specific transcription factor Pax8 binds at two of these sites. Mutations that interfere with Pax8 binding also decrease transcriptional activity of the NUE. Furthermore, expression of Pax8 in nonthyroid cells results in transcriptional activation of NUE, strongly suggesting that the paired-domain protein Pax8 plays an important role in NUE activity. The NUE responds to cAMP in both protein kinase A-dependent and -independent manners, indicating that this enhancer could represent a novel type of cAMP responsive element. Such a cAMP response requires Pax8 but also depends on the integrity of a cAMP responsive element (CRE)-like sequence, thus suggesting a functional interaction between Pax8 and factors binding at the CRE-like site.  (+info)

High sequence turnover in the regulatory regions of the developmental gene hunchback in insects. (2/7095)

Extensive sequence analysis of the developmental gene hunchback and its 5' and 3' regulatory regions in Drosophila melanogaster, Drosophila virilis, Musca domestica, and Tribolium castaneum, using a variety of computer algorithms, reveals regions of high sequence simplicity probably generated by slippage-like mechanisms of turnover. No regions are entirely refractory to the action of slippage, although the density and composition of simple sequence motifs varies from region to region. Interestingly, the 5' and 3' flanking regions share short repetitive motifs despite their separation by the gene itself, and the motifs are different in composition from those in the exons and introns. Furthermore, there are high levels of conservation of motifs in equivalent orthologous regions. Detailed sequence analysis of the P2 promoter and DNA footprinting assays reveal that the number, orientation, sequence, spacing, and protein-binding affinities of the BICOID-binding sites varies between species and that the 'P2' promoter, the nanos response element in the 3' untranslated region, and several conserved boxes of sequence in the gene (e.g., the two zinc-finger regions) are surrounded by cryptically-simple-sequence DNA. We argue that high sequence turnover and genetic redundancy permit both the general maintenance of promoter functions through the establishment of coevolutionary (compensatory) changes in cis- and trans-acting genetic elements and, at the same time, the possibility of subtle changes in the regulation of hunchback in the different species.  (+info)

Multiple cis-acting regulatory regions are required for restricted spatio-temporal Hoxa5 gene expression. (3/7095)

Genetic analyses have revealed the essential role of the murine Hoxa5 gene for the correct specification of the cervical and upper thoracic region of the skeleton, and for the normal organogenesis and function of the respiratory tract, both structures expressing Hoxa5 during embryogenesis. To understand how the expression domains of the Hoxa5 gene are established during development, we have analyzed the cis-acting control regions mediating Hoxa5 gene expression using a transgenic approach. Four transcripts are derived from the Hoxa5 locus. The shortest and most abundant one displays a specific spatio-temporal profile of expression at earlier stages and in more anterior structures along the embryonic axis than the larger forms. We established that an 11.1 kilobase pair (kb) genomic fragment, extending from position -3.8 kb to +7.3 kb relative to Hoxa5 transcription initiation site, was sufficient to reproduce the temporal expression and substantially reconstitute the spatial pattern of the major Hoxa5 transcript. By deletion analyses, we identified a 2.1 kb fragment located downstream of the Hoxa5 gene that possesses mesodermal enhancer activity. Overall, the findings demonstrate that cis-acting regulatory elements essential for the correct expression of the major Hoxa5 transcript are located both upstream and downstream of the Hoxa5 coding sequences.  (+info)

Activation and repression of p21(WAF1/CIP1) transcription by RB binding proteins. (4/7095)

The Cdk inhibitor p21(WAF1/CIP1) is a negative regulator of the cell cycle, although its expression is induced by a number of mitogens that promote cell proliferation. We have found that E2F1 and E2F3, transcription factors that activate genes required for cell cycle progression, are strong activators of the p21 promoter. In contrast, HBP1 (HMG-box protein-1), a novel retinoblastoma protein-binding protein, can repress the p21 promoter and inhibit induction of p21 expression by E2F. Both E2Fs and HBP1 regulate p21 transcription through cis-acting elements located between nucleotides -119 to +16 of the p21 promoter and the DNA binding domains of each of these proteins are required for activity. Sequences between -119 and -60 basepairs containing four Sp1 consensus elements and two noncanonical E2F binding sites are of major importance for E2F activation, although E2F1 and E2F3 differ in the extent of their ability to activate expression when this segment is deleted. The opposing effects of E2Fs and HBP1 on p21 promoter activity suggest that interplay between these factors may determine the level of p21 transcription in vivo.  (+info)

Transcription of the stationary-phase-associated hspX gene of Mycobacterium tuberculosis is inversely related to synthesis of the 16-kilodalton protein. (5/7095)

The 16-kDa protein, an alpha-crystallin homologue, is one of the most abundant proteins in stationary-phase Mycobacterium tuberculosis. Here, transcription and translation of the hspX gene, which encodes the 16-kDa protein, have been investigated by Northern blotting analysis, primer extension, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis with a microaerophilic stationary-phase model. Two transcripts of about 2.5 and 1.1 kb were demonstrated by Northern blot analysis and hybridized to the hspX gene probe. Primer extension analysis revealed that the transcription start site is located 33 nucleotides upstream of the hspX gene start codon. The cellular level of the hspX mRNA was maximum in log-phase bacilli and was markedly reduced after 20 days in unagitated culture, when the organisms had entered the stationary phase. A third transcript of 0.5 kb was detected 0.6 kb downstream of the hspX gene; this transcript has a transcriptional pattern completely different from that of the 1.1- and 2.5-kb products, suggesting that there may be another gene in this region. In contrast to the high level of hspX mRNA in log-phase bacilli, 16-kDa protein synthesis was low in log-phase bacteria and rose to its maximum after 20 days. In both log-phase and stationary-phase bacteria the mRNA was unstable, with a half-life of 2 min, which indicated that the transcript stability was growth rate independent and not a general means for controlling the gene expression. However, the cellular content of 16-kDa protein, while low in log-phase bacteria, rose to a maximum at 10 days and remained at this high level for up to 50 days, which indicates that this protein is a stable molecule with a low turnover rate. These data suggest that the regulation of hspX expression during entry into and maintenance of stationary phase involves translation initiation efficiency and protein stability as potential mechanisms.  (+info)

Tight correlation between inhibition of DNA repair in vitro and transcription factor IIIA binding in a 5S ribosomal RNA gene. (6/7095)

UV-induced photoproducts (cyclobutane pyrimidine dimers, CPDs) in DNA are removed by nucleotide excision repair (NER), and the presence of transcription factors on DNA can restrict the accessibility of NER enzymes. We have investigatigated the modulation of NER in a gene promoter using the Xenopus transcription factor IIIA (TFIIIA)-5S rDNA complex and Xenopus oocyte nuclear extracts. TFIIIA alters CPD formation primarily in the transcribed strand of the 50 bp internal control region (ICR) of 5S rDNA. During NER in vitro, CPD removal is reduced at most sites in both strands of the ICR when TFIIIA is bound. Efficient repair occurs just outside the TFIIIA-binding site (within 10 bp), and in the absence of 5S rRNA transcription. Interestingly, three CPD sites within the ICR [+56, +75 (transcribed strand) and +73 (non-transcribed strand)] are repaired rapidly when TFIIIA is bound, while CPDs within approximately 5 bases of these sites are repaired much more slowly. CPDs at these three sites may partially displace TFIIIA, thereby enabling rapid repair. However, TFIIIA is not completely displaced during NER, at least at sites outside the ICR, even though the NER complex could be sterically hindered by TFIIIA. Such inefficient repair of transcription factor binding sites could increase mutation frequency in regulatory regions of genes.  (+info)

Transcription factors CCAAT/enhancer-binding protein beta and nuclear factor-Y bind to discrete regulatory elements in the very low density lipoprotein receptor promoter. (7/7095)

Expression of the very low density lipoprotein receptor (VLDL-R) is barely detectable in liver, but occurs in adipose tissue, skeletal muscle, heart, and placenta, where it is postulated to supply triglyceride to tissues that utilize fatty acids. To investigate its tissue-specific expression, cell lines were transfected with luciferase reporter gene constructs driven by the 5'-flanking region of the VLDL-R gene. Transcriptional activity of a 4.2-kb promoter fragment was 5-fold higher in BeWo placental cells than in Huh-7 hepatoma cells, consistent with relative endogenous expression of the VLDL-R. By deletion analysis, DNase I protection assays and site-directed mutagenesis, two regulatory elements were essential for maximal promoter activity in BeWo cells: footprint site D (-856 to -830) and an inverted CCAAT box (-703 to -707). Mutation of either element reduced promoter activity by 60% in BeWo cells, but had little effect in Huh-7 cells, suggesting that these elements direct cell-type specific transcription. Electrophoretic mobility-shift assays with BeWo nuclear extracts revealed that the inverted CCAAT box binds transcription factor NF-Y, and site D binds CCAAT/enhancer-binding protein b (C/EBPbeta) and minor amounts of C/EBPalpha and C/EBPdelta. Overexpression of a dominant negative NF-YA vector confirmed involvement of NF-Y in the regulation of the VLDL-receptor gene through the CCAAT box. However overexpression of C/EBP could not stimulate transcription from the VLDL-receptor promoter nor from site D fused to a heterologous promoter, suggesting that the simultaneous binding of an accessory factor(s) may be necessary for C/EBP transactivation via the D site.  (+info)

Structural and functional characterization of the mouse Sox9 promoter: implications for campomelic dysplasia. (8/7095)

Mutations in SOX9 cause campomelic dysplasia (CD), a dominant skeletal dysmorphology and XY sex reversal syndrome. The CD phenotype is sensitive to dosage and expression levels of SOX9. Sox9 is expressed during chondrocyte differentiation and is up-regulated in male and down-regulated in female genital ridges during sex differentiation. In order to study the sex- and tissue-specific regulation of Sox9, we have defined the transcription start site and characterized the mouse Sox9 promoter region. The Sox9 proximal promoter shows moderately high nucleotide similarity between mouse and human. Transient transfection experiments using various deletion constructs of the 6.8 kb upstream region of mouse Sox9 fused to a luciferase reporter showed that the interval between 193 and 73 bp from the transcription start site is essential for maximal promoter activity in cell lines and in primary male and female gonadal somatic cells and liver cells isolated from 13.5 d.p.c. mouse embryos. This minimal promoter region was shown by DNase I hypersensitive site assay to be in an 'open' state of chromatin structure in gonads of both sexes, but not in the liver. Promoter activity was higher in testis than in ovary and liver, but deletion of the region from -193 to -73 bp abolished this difference. We conclude that the proximal promoter region is in part responsible for the sex- and tissue-specific expression of the Sox9 gene and that more distal positive and negative elements contribute to its regulation in vivo, consistent with the observation that translocations upstream from SOX9 can result in campomelic dysplasia.  (+info)

RATIONALE: Regulatory DNA elements in the human genome play important roles in determining the transcriptional abundance and spatiotemporal gene expression during embryonic heart development and somatic cell reprogramming. It is not well known how chromatin marks in regulatory DNA elements are modulated to establish cell type-specific gene expression in the human heart. OBJECTIVE: We aimed to decipher the cell type-specific epigenetic signatures in regulatory DNA elements and how they modulate heart-specific gene expression. METHODS AND RESULTS: We profiled genome-wide transcriptional activity and a variety of epigenetic marks in the regulatory DNA elements using massive RNA-seq (n=12) and ChIP-seq (chromatin immunoprecipitation combined with high-throughput sequencing; n=84) in human endothelial cells (CD31(+)CD144(+)), cardiac progenitor cells (Sca-1(+)), fibroblasts (DDR2(+)), and their respective induced pluripotent stem cells. We uncovered 2 classes of regulatory DNA elements: class I was ...
MOTIVATION Presently available programs for the recognition of potential transcription factor binding sites in genomic sequences generally yield a huge amount of output. These output lists have to be filtered to obtain biologically significant elements, which is highly laborious work to be done manually. RESULTS We developed a strategy for systematic verification and improvement of the underlying profiles, and for their contextual analysis by a fuzzy clustering approach using non-redundant libraries of search profiles as a prerequisite. AVAILABILITY The tools mentioned in the paper are available upon request. CONTACT [email protected]
Fingerprint Dive into the research topics of Multiple positive and negative 5 regulatory elements control the cell-type-specific expression of the embryonic skeletal myosin heavy-chain gene.. Together they form a unique fingerprint. ...
A number of interactive questions are embedded within the short film The Making of the Fittest: Evolving Switches, Evolving Bodies, which illustrates how mutations in gene regulatory regions can result in the evolution of major anatomical features.. ...
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The regulation of transcription requires complex interactions between proteins bound to DNA sequences that are often separated by hundreds of base pairs. As demonstrated by a nuclear ligation assay, the distal enhancer and the proximal promoter regions of the rat prolactin gene were found to be juxtaposed. By acting through its receptor bound to the distal enhancer, estrogen stimulated the interaction between the distal and proximal regulatory regions two- to threefold compared to control values. Thus, the chromatin structure of the prolactin gene may facilitate the occurrence of protein-protein interactions between transcription factors bound to widely separated regulatory elements. ...
Transcriptional repressor required to restrict transcription of ECB-dependent genes to the G1/M phase by repressing their transcription during the interval from late G1 to M phases. Genes that contain a ECB (early cell box) element in their transcription regulatory region are transcribed only during G1/M phases. In vitro, is capable of binding to the DNA of the leucine tRNA gene.
Multiple cis-acting sequences contribute to evolved regulatory variation forDrosophila Adh genes. Delineation of cis-acting sequences required for expression of Drosophila mojavensis Adh-1
Cis-regulatory modules (CRM) are segments of DNA responsible for tissue- and time- specific regulation of gene expression (1). The length of CRMs is difficult to estimate directly but it is believed to vary from several hundreds to several thousands of ba
Science 8 May 2015: Vol. 348 no. 6235 pp. 618-619 New database links regulatory DNA to its target genes. Elizabeth Pennisi. [paraphrase]. Several major research consortia have delivered what amount to users manuals for the genome, mapping the locations of thousands of regulatory genomic switches, the specific genes they control, and where in the body they are turned on or off. The latest and arguably boldest of the big biology efforts has yielded preliminary results. By analyzing genetic material gleaned from more than 100 people who had died just hours before, the Genotype-Tissue Expression (GTEx) project portrays gene regulation in action, identifying the genes switched on or off by subtle changes in DNA within 2 million bases of any gene. By evaluating multiple tissues from each body, it also charts the reach of those regulatory sequences across cell types some affect a gene in all tissues; others are influential in a few tissues or just one. Earlier efforts took other approaches to mapping ...
1. MEET.5.1:Motif Element Estimation Tools - MEET 5.1 is an R-package that includes a set of models, aprox. 550, and tools for the detection of cis-regulatory sequences ...
Predicted to have DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription, DNA-templated; response to cold; and sleep. Predicted to localize to nucleus. Is expressed in several structures, including brain; cardinal system; pleuroperitoneal region; shield; and swim bladder bud. Orthologous to human BHLHE41 (basic helix-loop-helix family member e41 ...
nucleus, DNA-binding transcription factor activity, sequence-specific DNA binding, transcription regulatory region DNA binding, cell differentiation, regulation of transcription, DNA-templated, seed trichome elongation
The hINV basal promoter, which encodes forty one nucleotides upstream of the transcription commence web site and no AP1 web sites, is not controlled by TAM67
Looking for online definition of Regulatory elements in the Medical Dictionary? Regulatory elements explanation free. What is Regulatory elements? Meaning of Regulatory elements medical term. What does Regulatory elements mean?
The Details by cell line view is the default view, where you get the generic MultiCell regulatory feature and cell-specific classifications, as well as part of their supporting evidence displayed as tracks. To display more evidence tracks, you can go to the Configure this page link and select tracks within the Regulation subsection. DNA Methylation and external sources (Other regulatory regions) are not used as evidence for regulatory regions ...
The information on this website is issued and approved by Martin Currie Investment Management Ltd (MCIM), the investment manager to Securities Trust of Scotland (the Trust). MCIM is authorised and regulated by the Financial Conduct Authority (FCA).
Since the sequencing of the human genome in 2001, all our genes - around 20,000 in total - have been identified. But much is still unknown - for instance where and when each is active. Next to each gene sits a short ...
A Consumer Guide discusses the basic technical, economic and regulatory information you should know before buying a photovoltaic (PV) solar electric generation system.
Previous work has suggested that the promoter regions of the human embryonic zeta 2 and epsilon globin genes contain negative regulatory regions that could play a role in the repression of these genes in postembryonic erythroblasts. We have examined this possibility by studying the expression of these genes in mouse erythroleukemia cells, an adult erythroid cell line that might be expected to contain repressor molecules that would bind to the putative negative regulatory regions. When attached to appropriate upstream regulatory elements (alpha HS-40 and beta HS1,2) both the zeta and epsilon genes were expressed in these cells at a low level, but no increase in expression was observed when similar constructs lacking the proposed negative regulatory sequences were introduced into these cells. These results cast doubt on the possibility that these sequences play a major role in the developmental repression of the embryonic globin genes, unless they function only in a normal chromosomal organization.
... is available now at: http://transfac.gbf.de. On the TRANSFAC server, you will find also the sequence analysis programs PatSearch MatInspector SaGa FastM and Thure Etzolds SRS5 with a large collection of databases. TRANSFAC is a database about eukaryotic transcription factors and their binding sites. It consists of six cross-linked tables: SITE CELL FACTOR CLASS MATRIX GENE It is also cross-linked with TRRD (Transcription Regulatory Region Database) and COMPEL from the ICG, Novosibirsk (N. A. Kolchanov, A. E. Kel). It contains numerous cross-references to external databases such EMBL, SWISSPROT, PIR, FLYBASE, EPD, and PROSITE. For further details see Wingender et al., Nucleic Acids Res. 25:265-268, 1997. NEW FEATURES are: - Additional FACTOR and SITE entries, - cross-references to PDB, - comprehensive linkage of FACTOR entries with a proposed transcription factor classification sytem (http://transfac.gbf.de/TRANSFAC/cl/cl.html). The TRANSFAC database comes along with several ...
Enhancers and promoters are cis-acting regulatory elements associated with lineage-specific gene expression. Previous studies showed that different categories of active regulatory elements are in regions of open chromatin, and each category is associated with a specific subset of post-translationally marked histones. These regulatory elements are systematically activated and repressed to promote commitment of hematopoietic stem cells along separate differentiation paths, including the closely related erythrocyte (ERY) and megakaryocyte (MK) lineages. However, the order in which these decisions are made remains unclear. To characterize the order of cell fate decisions during hematopoiesis, we collected primary cells from mouse bone marrow and isolated 10 hematopoietic populations to generate transcriptomes and genome-wide maps of chromatin accessibility and histone H3 acetylated at lysine 27 binding (H3K27ac). Principle component analysis of transcriptional and open chromatin profiles demonstrated that
Mammalian transcription is controlled by a complex interplay of regulatory events. Together, these events determine the correct spatio-temporal initiation and rate of RNA polymerase II (RNAPII) gene transcription. Several decades of research on transcriptional regulation have identified different modes of regulation that have been ascribed to distinct regulatory elements - stretches of DNA with specific…
Ng, C. [伍志祥。]. (1999). Identification of cis-regulatory sequence for the expression of epidermal growth factor (EGF) gene. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_ ...
IDT facilitates a unique, scalable method for analyzing hundreds of enhancer:promoter interactions in a single assay Advancing the development of novel methods for understanding gene expression, Integrated DNA Technologies (IDT) has enabled Dr Jim Hughes, Associate Professor at the Weatherall Institute of Molecular Medicine, Oxford, UK, to optimize his unique Capture-C method, based on Chromosomal Conformational Capture (3C). As outlined in the recent DECODED Online article, Understanding How Distal Regulatory Elements Control Gene...
The systematic prediction and categorisation of promoters, repressors, enhancers, etc., is not only essential to unravel the inner workings of biochemical networks, but also to engineer novel synthetic ones. Each putative regulatory region, however, has to be validated experimentally in order to be categorized as a fully defined functional element, which constitutes a significant bottleneck. In most studies, the promoter activity is illustrated as the amount of fluorescence divided by the optical density. These values are obtained from a coupled time-series experiment. With relatively simple mathematical reasoning, a tool that describes promoter activity in each time point has been implemented. The protein expression and the protein maturation process are modelled as a first order differential equations taking into account the degradation and the maturation rates which are to be known in advance. The promoter activity is then expressed based on the measured quantities of optical density and ...
Assume we have a set of sequences upstream of genes that are involved in a pathway with a common function. Since these genes are to be regulated more or less simultaneously, common regulatory factors or CIS-acting elements are likely to be involved. We want to investigate if, among the set of sequences, certain motifs are responsible for the regulation. An indication for this would be if we can find motifs that are present very frequently.
ENCODES a protein that exhibits dynein complex binding (ortholog); transcription regulatory region DNA binding (ortholog); INVOLVED IN motile cilium assembly (ortholog); positive regulation of gene expression (ortholog); positive regulation of non-motile cilium assembly (ortholog); ASSOCIATED WITH Giant Axonal Neuropathy (ortholog); FOUND IN nuclear body (ortholog); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; cobalt dichloride
The valve acts similar to one on a Basketball or Volleyball! On TV she won an Emmy for her 1975 TV Special Gypsy in My Soul and gave a well-publicized star turn on the 2012/2013 season of PBS Downton Abby. Three review authors independently extracted data using a standard form and assessed study quality! The level of expression of a gene encoding a particular revTetR protein may be manipulated by the choice of promoters with different transcription rates to which the revTetR coding sequence is operably associated, the inclusion of one or more positive and/or negative regulatory sequences which control the rate of transcription from that promoter, and the copy number of the vector carrying the revTetR coding sequence. Im using the same blog platform as yours and Im having difficulty finding one? Niel uptown differin gel over the counter canada has broken his arm, but all he cares about is the beauty of the Forresters house and the smell of Mrs. You can also explore some of this yourself ...
Corine Bertolotto, Roser Buscà, Patricia Abbe, Karine Bille, Edith Aberdam, et al.. Different cis -Acting Elements Are Involved in the Regulation of TRP1 and TRP2 Promoter Activities by Cyclic AMP: Pivotal Role of M Boxes (GTCATGTGCT) and of Microphthalmia. Molecular and Cellular Biology, American Society for Microbiology, 1998, 18 (2), pp.694-702. ⟨10.1128/mcb.18.2.694⟩. ⟨inserm-02533084⟩ ...
It is known that lamin A interacts with a variety of nuclear factors, including transcriptional regulators, chromatin, and nuclear membrane associated proteins. However it still remains unclear which proteins, genes, or regulatory DNA elements interact with lamin A in normal cells,or with progerin and lamin A in HGPS cells. We hypothesize that perturbations of chromatin structure and nuclear organization by progerin result in genome-wide defects in gene transcription, ultimatelyleading to HGPS. To test this idea, our approach combines chromatin immunoprecipitation, Hi-C approach of mapping of high-order nuclear organization, with next-generation sequencing and/or mass spectrometry techniques. Our goal is to identify differentially modified chromatin regions and differentially associated protein/DNA elements with lamin A and progerin in HGPS cells. Combined with gene expression analysis, we also aim to develop novel methods to integrate those multi-dimensional genomic data with gene expression ...
The site provides both general and detailed State OSHA safety information including those states with approved State Occupational Safety and Health Plans - Complete contact and regulatory information - Free
One of the primary goals in the field of genetics is to identify genetic variants that contribute to disease heritability. Elucidating the functional consequence of genetic variants associated with disease provides essential insights into the molecular mechanisms that define human traits. However, this is complicated by the fact that a preponderance of disease-associated genetic variation lies outside of protein-coding genes. Rather than modify protein structure and function, these noncoding variants frequently impact regulatory elements and thereby alter the quantitative and spatiotemporal regulation of gene expression.. The regulation of gene expression is critical for establishing and maintaining the diverse cell types of the human body. Genes with critical cellular functions are frequently regulated through a circuit involving multiple regulatory elements that are brought within physical proximity by DNA folding. These complex regulatory circuits are hotspots for genetic predisposition to ...
Gene expression is orchestrated by distinct regulatory regions to ensure a wide variety of cell types and functions. A challenge is to identify which regulatory regions are active, what are their associated features and how they work together in each cell type. Several approaches have tackled this problem by modeling gene expression based on epigenetic marks, with the ultimate goal of identifying driving regions and associated genomic variations that are clinically relevant in particular in precision medicine. However, these models rely on experimental data, which are limited to specific samples (even often to cell lines) and cannot be generated for all regulators and all patients. In addition, we show here that, although these approaches are accurate in predicting gene expression, inference of TF combinations from this type of models is not straightforward. Furthermore these methods are not designed to capture regulation instructions present at the sequence level, before the binding of regulators or
aacggccaca agttcagcgt 3660gtccggcgag ggcgagggcg atgccaccta cggcaagctg accctgaagt tcatctgcac 3720caccggcaag ctgcccgtgc cctggcccac cctcgtgacc accctgacct acggcgtgca 3780gtgcttcagc cgctaccccg accacatgaa gcagcacgac ttcttcaagt ccgccatgcc 3840cgaaggctac gtccaggagc gcaccatctt cttcaaggac gacggcaact acaagacccg 3900cgccgaggtg aagttcgagg gcgacaccct ggtgaaccgc atcgagctga agggcatcga 3960cttcaaggag gacggcaaca tcctggggca caagctggag tacaactaca acagccacaa 4020cgtctatatc atggccgaca agcagaagaa cggcatcaag gtgaacttca agatccgcca 4080caacatcgag gacggcagcg tgcagctcgc cgaccactac cagcagaaca cccccatcgg 4140cgacggcccc gtgctgctgc ccgacaacca ctacctgagc acccagtccg ccctgagcaa 4200agaccccaac gagaagcgcg atcacatggt cctgctggag ttcgtgaccg ccgccgggat 4260cactctcggc atggacgagc tgtacaagta aagcggccgc gactctagat cataatcagc 4320cataccacat ttgtagaggt tttacttgct ttaaaaaacc tcccacacct ccccctgaac 4380ctgaaacata aaatgaatgc aattgttgtt gttaacttgt ttattgcagc ttataatggt 4440tacaaataaa gcaatagcat cacaaatttc acaaataaag catttttttc actgcattct ...
The xmlToEdit element is an optional element of the editing element.. xmlToEdit elements are used to define the editing components that can be used in a form. The xmlToEdit elements can contain multiple editWith elements that specify the editing components that will be used to edit various types of XML DOM nodes.. ...
Author Summary The spatial-temporal expression pattern of a gene, which is crucial to its function, is controlled by cis-regulatory DNA sequences. Forming the basic units of regulatory sequences are transcription factor binding sites, often organized into larger modules that determine gene expression in response to combinatorial environmental signals. Understanding the conservation and change of regulatory sequences is critical to our knowledge of the unity as well as diversity of animal development and phenotypes. In this paper, we study the evolution of sequences involved in the regulation of body patterning in the Drosophila embryo. We find that mutations of nucleotides within a binding site are constrained by evolutionary forces to preserve the sites binding affinity to the cognate transcription factor. Functional binding sites are frequently destroyed during evolution and the rate of loss across evolutionary spans is roughly constant. We also find that the evolutionary fate of a site strongly
Predicted to have activating transcription factor binding activity; protein C-terminus binding activity; and transcription regulatory region DNA binding activity. Involved in negative regulation of transcription, DNA-templated and response to interferon-gamma. Predicted to localize to the PML body; cell surface; and cytosol. Used to study MHC class II deficiency and osteoporosis. Human ortholog(s) of this gene implicated in Addisons disease; MHC class II deficiency; autoimmune hypersensitivity disease (multiple); myocardial infarction; and rheumatoid arthritis (multiple). Is expressed in bladder; central nervous system; and retina. Orthologous to human CIITA (class II major histocompatibility complex transactivator ...
While combinatorial models of transcriptional regulation can be inferred for metazoan systems from a priori biological knowledge, validation requires extensive and time-consuming experimental work. Thus, there is a need for computational methods that can evaluate hypothesized cis regulatory codes before the difficult task of experimental verification is undertaken. We have developed a novel computational framework (termed
The genome has intricate controls of its function, usually in a highly quantitative, coordinated and dynamic manner. Studies of genetics usually focused on how bases (A/T/C/G) lead to a function, or binary presence of absence of genes or regulatory elements for controlling its function, rather than seeking for a comprehensive dynamic and quantitative picture. For example, it remains major questions how quantitative gene expression leads to different functions, or how multiple regulatory elements (e.g., enhancers) work together to control diverse outcomes of the genome (considering it is the same DNA sequence). Driven by curiosity and availability of new tools, we aim to apply genetic engineering and other high-throughput perturbation and measure methods to study how genes and regulatory elements quantitatively contributes to the overall function fo the genome. We are also very interested in exploring how epigenetics (chemical modifcations of the DNA or nucleosomes) modulate and affect the ...
For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown that the minimum number of genes from each species that need to be compared to produce a reliable phylogeny is about 20. Yeast has also become an attractive model to study speciation in eukaryotes, especially to understand molecular mechanisms behind the establishment of reproductive isolation. Comparison of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because they are short and degenerate and occupy different positions. Comparative genomics helps to ...
Data on 6,500 pesticides, insecticides and herbicides including toxicity, water pollution, ecological toxicity, uses and regulatory status.
Data on 6,500 pesticides, insecticides and herbicides including toxicity, water pollution, ecological toxicity, uses and regulatory status.
Sulphate is a macro element known to be beneficial to calcification of the coral skeletal matrix and health of SPS/LPS coral, when used in conjunction with Triton Lab ICP testing for appropriate dosing
Expression of GSDMB (GSDML, PRO2521) in human tissue. Overview of the antibody staining with HPA023925, HPA052407 and CAB013681 in immunohistochemistry
51900DNAZea mays 1atcgtaatcg gttttcaccg tataccgaac cgaaaaaacc gaataccaaa ctttatcaat 60tcccaaattt gactattcga ttatgtgaac taattgtgtg atacaattaa attgttattc 120acttatttgt atgtgatgta tgatgtatat ctaaatattt gtacctatat aatttttact 180ttttaaaatt atatgtaatc tatcatgtaa acttgttgta tgtattgtct tgattataag 240tttggtattc ggtttttacc gaaaaatcga agtaaaaaac cgaaaccgaa cttctcggtt 300tttcattttc tagaaaaccg aacggtttct aatgtttgaa aaaccgaagt tttttaaaac 360cgaaaaaccg aaccgaagtt tagaaaaaaa ccgaatgccc agccctaaaa attagtaccc 420cataagaact aaaaaaagat aaaatgacta aaaattaatc agttgaaacc aaacctattt 480tcccccacac ctcacggtat tgtttcgcat tccaagtttg aaacacgact ggaaacaaaa 540cccaaaacga ctggagggac cgagcttgtg ctgagcagca gagatggcgg gaaatgctgc 600gtctcccgcc tcagtttcgg atgccccgcc ctttcccaaa ccggccaccg ccgccgcccg 660tgtctcccca ccgacaggtg ggtccaatcc ttaaccacgg accagggccc ccacctgtca 720ggtggacctt ccgaagcaag gatcggccag gcgggaaaac atttcgcggc aggtggcggt 780tgcgccaaat ttctccctcc cttttccgtt cggcgtcccc aaacgcctcc ctattaatct 840ccccgcgttc cccttccctc ...
The Schizosaccharomyces pombe inv1+ regulatory region is unusually large and contains redundant cis-acting elements that function in a SAGA- and Swi/Snf-dependent fashion ...
J:74490 Degenhardt K, Rentschler S, Fishman G, Sassoon DA, Cellular and cis-regulation of En-2 expression in the mandibular arch. Mech Dev. 2002 Feb;111(1-2):125-36 ...
The N attribute of this Cell element must be one of a limited set of values that correspond to ShapeSheet cells. Refer to the table below to determine the values of the N attribute that are permitted for this Cell element.. ...
"Nucleic Acids Research. 13 (12): 4401-4410. doi:10.1093/nar/13.12.4401. PMC 321795. PMID 2409535.. ... "Transposable elements donate lineage-specific regulatory sequences to host genomes". Cytogenetic and Genome Research. 110 (1-4 ... "Nucleic Acids Res. 36 (7): 2284-94. doi:10.1093/nar/gkn064. PMC 2367713. PMID 18287116.. ... A consensus sequence is a sequence that is created based on the repeats that comprise a TE family. A base pair in a consensus ...
... mining cis-regulatory regions in genomes". Nucleic Acids Res. 38 (Web Server issue): W286-92. doi:10.1093/nar/gkq473. PMC ... A tool for searching transcription factor binding sites in DNA sequences". Nucleic Acids Res. 31 (13): 3576-9. doi:10.1093/nar/ ... "Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms". Nucleic Acids Res. 27 (1): 318-22 ... Visualisation and analysis of transcription factor binding sites in nucleotide sequences". Nucleic Acids Res. 31 (13): 3572-5. ...
Implications for finding sequence motifs in regulatory regions." Nucleic Acids Research (2001) 29 (12): 2607-2618. doi:10.1093/ ... doi:10.1093/nar/26.4.1107 Besemer J. and Borodovsky M. "Heuristic approach to deriving models for gene finding." Nucleic Acids ... doi:10.1093/nar/gki937 Zhu W., Lomsadze A. and Borodovsky M. "Ab initio gene identification in metagenomic sequences." Nucleic ... Lukashin A. and Borodovsky M. "GeneMark.hmm: new solutions for gene finding." Nucleic Acids Research (1998) 26 (4): 1107-1115. ...
These short nucleic acid sequences are commonly found in nature and have regulatory functions such as gene silencing.[1] ... Regulatory functions[edit]. Complementarity can be found between short nucleic acid stretches and a coding region or an ... "The practical and pedagogical advantages of an ambigraphic nucleic acid notation". Nucleosides Nucleotides Nucleic Acids. 25 (7 ... Ambigraphic notations readily visualize complementary nucleic acid stretches such as palindromic sequences.[18] This feature is ...
... a database to aid the analysis of regulatory sequences in mRNAs". Nucleic Acids Research. 37: D72-D76. doi:10.1093/nar/gkn763. ... Transterm is a database of mRNA sequences, codon usage, and associated cis-regulatory elements that regulate gene expression. ...
... a database of regulatory sequences and interactions in a wide range of prokaryotic genomes". Nucleic Acids Res. England. 35 ( ... RegTransBase is database of regulatory interactions and transcription factor binding sites in prokaryotes Transcription factors ...
... a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs". Nucleic Acids Res. 38 (Suppl_ ... UTRdb is a database of 5' and 3' untranslated sequences of eukaryotic mRNAs Five prime untranslated region Three prime ...
Rather, it is a regulatory nucleic acid sequence to which Pur-alpha binds that is altered. GRCh38: Ensembl release 89: ... in all organisms are united by Pur-alpha's ability to bind nucleic acids coupled to its ability to interact with regulatory and ... There is a documented interaction between Pur-alpha, the HIV-1 protein, Tat, and a Pur-alpha-binding regulatory sequence in JCV ... Pur protein sequences from bacteria through humans contain an amino acid segment that is strongly conserved (see NCBI ...
This motif consists of two amphipathic α-helices, separated by a small sequence of amino acids, that form one or more β-turns. ... Nucleic Acids Res. 35 (21): 7087-7095. doi:10.1093/nar/gkm746. PMC 2175354 . PMID 17942416. Mädge B.: E-Box. In: Schwab M. (Ed ... "MyoD uses overlapping but distinct elements to bind E-box and tetraplex structures of regulatory sequences of muscle-specific ... The consensus sequence of the E-box is usually CANNTG; however, there exist other E-boxes of similar sequences called ...
Implications for finding sequence motifs in regulatory regions". Nucleic Acids Res. 29 (12): 2607-18. doi:10.1093/nar/29.12. ... "Ab initio gene identification in metagenomic sequences". Nucleic Acids Res. 38 (12): e132. doi:10.1093/nar/gkq275. PMC 2896542 ... Nucleic Acids Res. 2003 Jul 1;31(13):3738-41 Keilwagen J, Wenk M, Erickson J L, Schattat M H, Grau J, Hartung F. Using intron ... Nucleic Acids Res. 2016; 44 (9): e89 Lukashin A. and Borodovsky M. (1998). "GeneMark.hmm: new solutions for gene finding". ...
These short nucleic acid sequences are commonly found in nature and have regulatory functions such as gene silencing. Antisense ... "The practical and pedagogical advantages of an ambigraphic nucleic acid notation". Nucleosides Nucleotides Nucleic Acids. 25 (7 ... "Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences". Retrieved 2008-02-04. Rozak DA (2006). " ... Nucleic acids strands may also form hybrids in which single stranded DNA may readily anneal with complementary DNA or RNA. This ...
Dennis J. Strand; John F. McDonald (1985). "Copia is transcriptionally responsive to environmental stress". Nucleic Acids ... "Transposable elements donate lineage-specific regulatory sequences to host genomes". Cytogenetic and Genome Research. 110 (1-4 ... A consensus sequence is a sequence that is created based on the repeats that comprise a TE family. A base pair in a consensus ... Sequence self-comparison programs use databases such as AB-BLAST to conduct an initial sequence alignment. As these programs ...
Nucleic Acids Res. 8 (1): 1-20. doi:10.1093/nar/8.1.1. PMC 327239 . PMID 6243775. Southwestern Blot at the US National Library ... of the corresponding selectively bound DNA fragments and may improve protein-mediated cloning of DNA regulatory sequences. ... Moreover, their sequence-specific binding allows the purification ...
... regulatory sequences, nucleic acid MeSH G06.184.603.080.689.330 --- enhancer elements (genetics) MeSH G06.184.603.080.689.330. ... amino acid MeSH G06.184.842.200.820 --- structural homology, protein MeSH G06.184.842.550 --- sequence homology, nucleic acid ... repetitive sequences, nucleic acid MeSH G06.184.603.080.708.330 --- interspersed repetitive sequences MeSH G06.184.603.080. ... regulatory sequences, ribonucleic acid MeSH G06.184.603.080.689.687.249 --- rna 3' polyadenylation signals MeSH G06.184.603.080 ...
Implications for finding sequence motifs in regulatory regions, Nucleic Acids Research Heuristic approach to deriving models ... Nucleic Acids Research GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses Nucleic Acids Research ... Nucleic Acids Research GeneMark.hmm: new solutions for gene finding, Nucleic Acids Research GenMark: Parallel Gene recognition ... These algorithms are currently in use in many research labs in the US and abroad as well as at the major sequencing and ...
Sinha S, Liang Y, Siggia E (2006). "Stubb: a program for discovery and analysis of cis-regulatory modules". Nucleic Acids Res. ... However, this definition has changed to define cis-regulatory modules as a DNA sequence with transcription factor binding sites ... Sharan R, Ben-Hur A, Loots GG, Ovcharenko I (2004). "CREME: Cis-Regulatory Module Explorer for the human genome". Nucleic Acids ... Cis-regulatory modules are one of several types of functional regulatory elements. Regulatory elements are binding sites for ...
Nucleic Acids Res. England. 31 (1): 55-7. doi:10.1093/nar/gkg007. PMC 165454 . PMID 12519946. http://corg.molgen.mpg.de. ... Comparative regulatory genomics database (CORG) is a catalogue of conserved non-coding sequence blocks. Non-coding DNA ... Dieterich, C; Wang H; Rateitschak K; Luz H; Vingron M (Jan 2003). "CORG: a database for COmparative Regulatory Genomics". ...
... factors bind Multiple EM for Motif Elicitation Nucleic acid sequence Protein primary structure Sequence logo Sequence mining ... there exist regulatory sequence motifs and motifs within the "junk", such as satellite DNA. Some of these are believed to ... a sequence of elements of the pattern notation matches a sequence of amino acids if and only if the latter sequence can be ... "Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical ...
A regulatory sequence is a segment of a nucleic acid molecule which is capable of increasing or decreasing the expression of ... mRNA A-box Z-box C-box E-box G-box Regulatory sequences for the insulin gene are: A5 Z negative regulatory element (NRE) C2 E2 ... Conserved non-coding sequences often contain regulatory regions, and so they are often the subject of these analyses. CAAT box ... Regulatory sequences are frequently associated with messenger RNA (mRNA) molecules, where they are used to control mRNA ...
Nucleic Acids Res suppl. 3 (2003) 199-200. 4. M. Oda, N. Kobayashi, A. Ito, Y. Kurusu, K. Taira, cis-acting regulatory ... the Bacillus subtilis hut operon and histidine-dependent binding of HutP to the transcript containing the regulatory sequences ... Nucleic Acids Res. 33 (2005) 5494-5502. 6. T. S. Kumarevel, S. C. B. Gopinath, S. Nishikawa, H. Mizuno, P. K. R. Kumar, ... HutP is a 16.2 kDa protein consisting of 148 amino acid residues. HutP also exists in five other Bacillus species, including B ...
Ultraviolet irradiation can be used to excite nucleic acids and create photoreactions, which results in damaged bases in the ... regulatory regions predicted using DNA-protein sequence information (encoded in structures such as Position weight matrix). ... Nucleic Acids Research. 5 (9): 3157-70. doi:10.1093/nar/5.9.3157. PMC 342238 . PMID 212715. Hampshire, A; Rusling, D; Broughton ... Thus is more likely to have its action blocked by a bound protein on a DNA sequence. In addition, the DNase I enzyme is easily ...
... which are usually instructions specifying the order of amino acids in a protein along with regulatory sequences, splicing sites ... peptide nucleic acid (PNA), locked nucleic acid (LNA), and Morpholino oligomers. Antisense therapy Directionality (molecular ... nucleic acid units' roles in specifying amino acids. Depending on the context within molecular biology, sense may have slightly ... Antisense nucleic acid molecules have been used experimentally to bind to mRNA and prevent expression of specific genes. ...
Regulatory analysis of interferon regulated genes; BLAST (Basic Local Alignment Search Tool) analysis and orthologue sequence ... Nucleic Acids Res. England. 37 (Database issue): D852-7. doi:10.1093/nar/gkn732. PMC 2686605 . PMID 18996892. http://www.isicr. ...
Nucleic Acids Res 36(16) 5221-5231. Bernstein, BE; et al. (2005). "Genomic maps and comparative analysis of histone ... "ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments". Nucleic ... Sequencing, by contrast, is thought to have less bias, although the sequencing bias of different sequencing technologies is not ... There are many new sequencing methods used in this sequencing step. Some technologies that analyze the sequences can use ...
"Sequence of the cDNA encoding ITF-1, a positive-acting transcription factor". Nucleic Acids Research. 18 (3): 677. doi:10.1093/ ... E proteins activate transcription by binding to regulatory E-box sequences on target genes as heterodimers or homodimers, and ... They initiate transcription by binding to regulatory E-box sequences on target genes. Deletion of this gene or diminished ... "Nine-amino-acid transactivation domain: Establishment and prediction utilities". Genomics. 89: 756-768. doi:10.1016/j.ygeno. ...
Nucleic Acids Res. November 2002, 30 (21): 4634-42. PMC 135794. PMID 12409453. doi:10.1093/nar/gkf587.. ... sterol regulatory element binding protein import into nucleus. · regulation of apoptotic process. · cellular protein metabolic ... Lamin A/C gene and a related sequence map to human chromosomes 1q12.1-q23 and 10. Somat. Cell Mol. Genet. March 1993, 19 (2): ... a 50-amino acid deletion in prelamin A (amino acids 607-656) removes the site for the second endoproteolytic cleavage. ...
Nucleic Acids Res 22(7):1287-1295.. OpenUrlAbstract/FREE Full Text ... 2010) Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc Natl Acad ... Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Sriram Kosuri, Daniel B. ... Composability of regulatory sequences controlling transcription and translation in Escherichia coli Message Subject (Your Name ...
The nucleotide (nt) sequence of a 1.3-kb region upstream from the ATG was determined. Comparison with promoter regions of other ... Molecular Sequence Data * Oligonucleotide Probes * Promoter Regions, Genetic* * Regulatory Sequences, Nucleic Acid ... The nucleotide (nt) sequence of a 1.3-kb region upstream from the ATG was determined. Comparison with promoter regions of other ... beta-Galactosidase assays and primer extension experiments were used to identify sequence elements involved in transcription ...
... were isolated and sequenced from five gram negative proteobacteria (gamma or alpha subgroup): Enterobacter cloacae (gamma), ... Regulatory Sequences, Nucleic Acid * Sequence Analysis, DNA * Sequence Homology, Amino Acid * Sequence Homology, Nucleic Acid ... despite considerable divergence in nucleotide sequence. Moreover, a stretch of nine amino acid residues Q(R/K)(K/R)LFFNLR, ... Both the sequence complementary to part of 16S rRNA (the downstream box) and a predicted mRNA secondary structure similar to ...
Down-regulation of DNA replication genes and up-regulation of abscisic acid pathway genes were observed. Study further reveals ... 3540 putative Simple Sequence Repeat-Functional Domain Marker (SSR-FDM), 13778 genic Single Nucleotide Polymorphism (SNP) ... Nucleic Acids Res. 35(Web Server issue), W182-W185. doi: 10.1093/nar/gkm321 ... Discovery of Putative Herbicide Resistance Genes and Its Regulatory Network in Chickpea Using Transcriptome Sequencing. Mir A. ...
Nucleic Acid Regulatory Sequences *Young Adult. *Cancer DNA. *Molecular Sequence Data. *Chromosome 3 ... sequence-specific DNA binding - sequence-specific DNA binding transcription factor activity - transcription factor binding - ... regulation of sequence-specific DNA binding transcription factor activity - RNA polymerase II distal enhancer sequence-specific ... We show here that a novel seleno-α-keto acid triggers global histone acetylation in human colon cancer cells and activates ...
Towards a map of cis-regulatory sequences in the human genome. Nucleic Acids Research, Vol. 46, Issue. 11, p. 5395. ... Towards a map of cis-regulatory sequences in the human genome. Nucleic Acids Research, Vol. 46, Issue. 11, p. 5395. ... of cis-regulatory sequences or render them blind to cell communication cues. Cis-regulatory sequences also act as major ... Nucleic Acids Research 9, 6251-6264 17 Veldman, G.M., Lupton, S. and Kamen, R. (1985) Polyomavirus enhancer contains multiple ...
Van Helden, J. (2003) Regulatory sequence analysis tools. Nucleic Acids Res 31: 3593-3596. *CrossRef , ... nitrogen regulatory protein; Marzluf, 1997), PacC (pH regulatory protein; Espeso and Arst, 2000), WC (light regulatory proteins ... Manipulation of nucleic acids. All plasmids were propagated in Escherichia coli DH5α bacterial cells and purified using a ... Nucleotide sequences. Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under Accession ...
In the present study using β-globin regulatory sequences, the transgene arrays consist of copies of a 15 kbp vector. However, ... Nucleic Acids Res. 24, 1465-1471.. OpenUrlAbstract/FREE Full Text. *↵ Robinett, C. C., Straight, A., Li, G., Willhelm, C., ... Here, we extend these results by showing that endogenous factors acting on mammalian regulatory sequences can produce similar ... Here, we address whether endogenous gene regulatory sequences can produce similar changes in large-scale chromatin structure ...
We isolated a cowpox virus from the lesions and sequenced its whole genome. The patient reported that he had been previously ... Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 2001;29:2607-18. DOIPubMed ... MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059-66 ... Gao J, Gigante C, Khmaladze E, Liu P, Tang S, Wilkins K, et al. Genome sequences of Akhmeta virus, an early divergent Old World ...
RSAT 2011 : regulatory sequence analysis tools THOMAS-CHOLLIER M. Nucleic Acids Res. 39, W86-W91, 2011 ... Initial sequence of the chimpanzee genome and comparison with the human genome Chimpanzee Sequencing and Analysis Consortium ... Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome XIE W. ... Allele-specific DNA methylation in mouse strains is mainly determined by cis-acting sequences SCHILLING E. ...
2008). RSAT: regulatory sequence analysis tools. Nucleic Acids Res. 36, 119-127. doi: 10.1093/nar/gkn304 ... 2003). AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements ... A 349-bp splicing factor sequence (AW828516) was amplified from M. incognita and cloned in pBC06 RNAi vector in sense and anti- ... Conserved Cis-Regulatory Elements in the Promoters of Nematode-Responsive and NRRS Gene. The six candidate NRRS genes were ...
RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Res 2011;39:W86-W91. Web Server issue. ... Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res 2004;32(4):1372-1381. ... We used the Regulatory Sequence Analysis Toolkit36 to count the number of instances of each motif within our set of 682 AAMφ- ... Illumina RNA sequencing (RNA-Seq) provided , 5 orders of magnitude dynamic range between the most abundant and lowly expressed ...
The present invention provides methods and probe nucleic acids for detecting mutant forms of target nucleic acids that comprise ... repetitive nucleotide sequences. In certain embodiments, for example, these approaches and reagents can be used to detect ... Thus, genes include coding sequences and optionally, the regulatory sequences required for their expression. Genes also ... The probe nucleic acids, target nucleic acids, and/or amplicons of the target nucleic acids (e.g., via primer nucleic acids ...
Nucleic Acids Res. 2016 Jun 2;44(10):e97. doi: 10.1093/nar/gkw157. Epub 2016 Mar 14. ... Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites. ... Nucleic Acids Res. 2011 Sep 1;39(16):7092-102. doi: 10.1093/nar/gkr404. Epub 2011 May 26. ... Nucleic Acids Res. 2012 Sep;40(16):7858-69. doi: 10.1093/nar/gks477. Epub 2012 Jun 8. ...
Their idea that a single regulatory sequence, the operon, controlled and co-ordinated the expression of several structural... ... A regulatory sequence near the 3′ end of sea urchin histone genes. Nucleic Acids Res., 9, 2997.CrossRefGoogle Scholar ... The leader sequences of simian virus 40 mRNA are not transcribed adjacent to the coding sequences. Proc. Natl. Acad. Sci. USA, ... Their idea that a single regulatory sequence, the operon, controlled and co-ordinated the expression of several structural ...
Base Sequence [G05.360.080]. *Regulatory Sequences, Nucleic Acid [G05.360.080.689]. *Gene Regulatory Networks [G05.360.080.689. ... Regulatory Education and Events Talks focused on regulatory issues and emerging topics in research. ... Regulatory Atlas A directory of institutional regulatory offices, forms, policies, & training for research. ... Regulatory Foundations, Ethics, and Law Program Helping researchers navigate clinical & translational research regulatory ...
Base Sequence [G02.111.570.080]. *Regulatory Sequences, Nucleic Acid [G02.111.570.080.689]. *Promoter Regions, Genetic [G02.111 ... Regulatory Education and Events Talks focused on regulatory issues and emerging topics in research. ... Regulatory Atlas A directory of institutional regulatory offices, forms, policies, & training for research. ... Regulatory Foundations, Ethics, and Law Program Helping researchers navigate clinical & translational research regulatory ...
Regulatory sequence analysis tools. Nucleic Acids Res 31: 3593-3596. (*)STUBB Sinha, S., E. Van Nimwegen, and E.D. Siggia. 2003 ... Nucleic Acids Res. 22(22):4673-80. (*)Conreal Berezikov, E., V. Guryev, R.H. Plasterk, and E. Cuppen. 2004. CONREAL: conserved ... Nucleic Acids Res. 2003 Jul 1;31(13):3580-5. MEME Bailey TL, and C. Elkan. 1994. Fitting a mixture model by expectation ... CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific ...
Regulatory sequence analysis tools. Nucleic Acids Res 31: 3593-3596. (*)STUBB Sinha, S., E. Van Nimwegen, and E.D. Siggia. 2003 ... Nucleic Acids Res. 22(22):4673-80. (*)Conreal Berezikov, E., V. Guryev, R.H. Plasterk, and E. Cuppen. 2004. CONREAL: conserved ... Nucleic Acids Res. 2003 Jul 1;31(13):3580-5. MEME Bailey TL, and C. Elkan. 1994. Fitting a mixture model by expectation ... Multi-species Conserved Sequences. MCS Analysis E.H. Margulies, M. Blanchette, NISC Comparative Sequencing Program, D. Haussler ...
Regulatory Sequences, Nucleic Acid Response Elements Sequence Homology, Nucleic Acid Transcription Factors Transcription, ... Base Sequence Binding Sites Circadian Clocks Circadian Rhythm Conserved Sequence DNA-Binding Proteins Evolution, Molecular Gene ... Molecular Sequence Data Mutation Nucleotide Motifs Plants, Genetically Modified Promoter Regions, Genetic Protein Binding ... We used phylogenetic shadowing to identify three evolutionarily constrained regions (conserved regulatory modules [CRMs]) ...
Categories: Regulatory Sequences, Nucleic Acid Image Types: Photo, Illustrations, Video, Color, Black&White, PublicDomain, ...
These short nucleic acid sequences are commonly found in nature and have regulatory functions such as gene silencing.[1] ... Regulatory functions[edit]. Complementarity can be found between short nucleic acid stretches and a coding region or an ... "The practical and pedagogical advantages of an ambigraphic nucleic acid notation". Nucleosides Nucleotides Nucleic Acids. 25 (7 ... Ambigraphic notations readily visualize complementary nucleic acid stretches such as palindromic sequences.[18] This feature is ...
1992 cDNA nucleotide sequence of Sn, a regulatory gene in maize. Nucleic Acids Res. 20: 373. ... 1989 Nucleotide sequence of the maize R-S gene. Nucleic Acids Res. 17: 8003. ... A 700-amino acid open reading frame bearing strong amino acid sequence similarity to TnpD of the related En/Spm element (Masson ... The overall sequence similarity of the 2166-bp Lcm1 and 2170-bp Lcm2 sequenced regions is 95%. The sequences of the upstream ...
1992 cDNA nucleotide sequence of Sn, a regulatory gene in maize. Nucleic Acids Res. 20: 373. ... 1995 Sequences required for paramutation of the maize b gene map to a region containing the promoter and upstream sequences. ... The σ region contains sequences derived from a doppia transposable element, some of which could potentially bind regulatory ... These results do not rule out the possibility that both repeated sequences and doppia sequences must be present to cause ...
2008) RSAT: regulatory sequence analysis tools. Nucleic Acids Res 36: W119-W127. ... 2012) The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res 40: D54-D56. ... 2011) AGRIS: the Arabidopsis Gene Regulatory Information Server, an update. Nucleic Acids Res 39: D1118-D1122. ... 1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27: 297-300. ...
  • Mouse sequences were subtracted from the sequence pool and the remaining sequences were de novo assembled at 50x coverage into a 1.82 Mbp complete closed circular Deltaproteobacterial genome containing 2250 putative protein-coding sequences. (g3journal.org)
  • The reversed querying process and the program IdentiCS allow a fast and adequate prediction protein coding sequences and reconstruction of the potential metabolic network from low coverage genome sequences of bacteria. (biomedcentral.com)
  • Despite seemingly large phenotypic differences between species across the primate lineage, protein-coding sequences remain highly conserved. (biomedcentral.com)
  • We sequenced the full genome and characterised the genetic diversity of two Brucella melitensis isolates from Malaysia and the Philippines. (biomedcentral.com)
  • A transposable element ( TE or transposon ) is a DNA sequence that can change its position within a genome , sometimes creating or reversing mutations and altering the cell's genetic identity and genome size . (wikipedia.org)
  • Functional contributions of cis- regulatory sequence variations to human genetic disease are numerous. (biomedcentral.com)
  • Yeast repressor activator protein 1 (RAP1) binds in vitro to specific DNA sequences that are found in diverse genetic elements. (hku.hk)
  • The whole genome sequencing method has become the gold standard for understanding the genetic diversity of bacteria [ 8 ]. (biomedcentral.com)
  • Furthermore, while efforts have been made to create predictors that seek to identify variants in noncoding sequence that might influence expression or have higher chance of causing disease [ 10 - 13 ], no framework has been introduced that focuses on standing variation in the human population to estimate the relative intolerance of a gene's noncoding exome sequence to genetic variation. (prolekare.cz)
  • To capture regulatory function that might be human-specific we formulate a novel human population genetic approach (ncRVIS). (prolekare.cz)
  • Largely based on these and similar findings, a current view of evolution of development emerged that emphasizes the conservation of the genetic "toolkit" within animals and the relative importance of regulatory changes in driving morphological change [ 6 ]. (prolekare.cz)
  • For the sake of simplicity, many of these early population genetic models analyzed these processes without considering the complications imposed by including genotype-phenotype mappings, such as descriptions of the genetic regulatory networks (GRNs) involved in development. (biomedcentral.com)
  • We have supported integrative concepts such as regulatory phrases and, more recently, the genetic-metabolic sensory-response units (GENSOR Units), which pose a lot of new questions. (unam.mx)
  • An example is the N-glycosylation site motif: Asn, followed by anything but Pro, followed by either Ser or Thr, followed by anything but Pro where the three-letter abbreviations are the conventional designations for amino acids (see genetic code). (wikipedia.org)
  • Although the CRP of Y. pestis shows a very high homology to that of E. coli , and the consensus DNA sequence recognized by CRP is shared by the two bacteria, the Y. pestis CRP can recognize the promoters of ompC , F , and X directly rather than that of its own gene, which is different from the relevant regulatory circuit of E. coli . (biomedcentral.com)
  • All of the Asian B. melitensis strains clustered into genotype II with the SEA strains, including the two isolates sequenced in this study, forming a distinct clade denoted here as genotype II d . (biomedcentral.com)
  • Determining the evolutionary and functional importance of regulatory sequence composition is impeded without a detailed knowledge of the genotype-phenotype map. (biomedcentral.com)
  • Aims Exome sequencing was used to genotype comprehensively a Takotsubo (stress) cardiomyopathy (TC) cohort, enabling investigation of a vast 486 gene network for adrenergic signalling. (elsevier.com)
  • abstract = "Aims Exome sequencing was used to genotype comprehensively a Takotsubo (stress) cardiomyopathy (TC) cohort, enabling investigation of a vast 486 gene network for adrenergic signalling.Methods and results Twenty-eight TC subjects, including a mother-daughter pair and five recurrent cases, underwent whole-exome sequencing. (elsevier.com)
  • In this release, we complement HOCOMOCO by MoLoTool (Motif Location Toolbox, http://molotool.autosome.ru) that applies HOCOMOCO models for visualization of binding sites in short DNA sequences. (nsc.ru)
  • Our analyses show that Matlign can reliably discover the most similar analogue from a collection of characterised regulatory elements such that the method is also useful for the annotation of motif predictions by PFM library searches. (biomedcentral.com)
  • Distal intraexon (iE) regulatory elements in 4.1R pre-mRNA govern 32 splice site choice at exon 2 (E2) via nested splicing events, ultimately modulating expression of N-terminal isoforms of cytoskeletal 4.1R protein. (zfin.org)
  • This response addresses your January 3, 2017 request for a regulatory interpretation of whether synthetically created DNA sequences would be considered a select agent or toxin as defined by sections 3(c)(3) and 4 (c)(3) of the select agent regulations, which specifically states that "…select agents and toxins that have been genetically modified" are select agents and toxins. (selectagents.gov)
  • The Federal Select Agent Program (FSAP) guidance document titled Guidance on the Regulation of Select Agent and Toxin Nucleic Acids addresses genetically modified select agents and toxins: "Depending upon the extent of the modification genetically modified select agents or toxins may be regulated. (selectagents.gov)
  • Nace así la bioinformática de la regulación genómica microbiana, con predicciones y análisis del genoma completo de Escherichia coli , con la publicación en Science en 1997 del genoma de dicha bacteria. (unam.mx)
  • En colaboración con colegas experimentalistas, se conforma un equipo de trabajo que publica el primer genoma completo secuenciado en nuestro país, el de la bacteria Rhizobium etli fijadora de nitrógeno. (unam.mx)
  • Deoxyribonucleic acid (DNA) double‐strand breaks, which are caused by many factors such as chemical treatments, radiations and, often, biological factors, are lethal events in organisms carrying DNA as their genome, which include bacteria. (els.net)
  • 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. (bcgsc.ca)
  • En el 2000 logra el reconocimiento de su laboratorio como el Nodo Nacional de Bioinformática dentro de la agrupación internacional EMBNET. (unam.mx)
  • Contrasting evolutionary dynamics of the developmental regulator PAX9, among bats, with evidence for a novel post-transcriptional regulatory mechanism. (nih.gov)
  • No transcriptional regulatory association between CRP and its own gene can be detected in Y. pestis , which is also in contrast to the fact that CRP acts as both repressor and activator for its own gene in E. coli . (biomedcentral.com)
  • As confidence in regulatory annotation and prediction advances, researchers will increasingly draw on such knowledge to design sequences capable of directing targeted gene expression in molecular applications such as gene therapy. (biomedcentral.com)
  • Although many studies associate cis- regulatory variations with phenotype, it is rare for researchers to conclusively demonstrate causality. (biomedcentral.com)
  • Researchers in Australia are sequencing the Wollemi pine tree to try to protect it from extinction, Australia's ABC News reports. (genomeweb.com)
  • Iron-rich Microbial Mats' Main Players: Marsarchaeota Through a combination of sequencing tools and techniques applied to samples collected from acidic iron-oxide microbial mats in Yellowstone National Park over time, researchers have discovered and characterized a novel phylum-level lineage of archaea with at least two major subgroups dubbed Marsarchaeota. (doe.gov)
  • New Software Tools Streamline DNA Sequence Design-and-Build Process Researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI) have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows. (doe.gov)
  • Benchmark Study for Improving Microbial Community Profiling Researchers used synthetic and natural microbial lake communities to compare the microbial community profiles generated from high throughput short-read sequencing and high throughput long-read sequencing approaches. (doe.gov)
  • The resulting pattern of gene expression can be compared to the pattern driven by the endogenous regulatory element, with the similarities and differences giving evidence of conservation and divergence in the gene regulatory network. (prolekare.cz)
  • These questions include how and when the inactive and active alleles are differentiated, what sequences designate that a gene is to be imprinted, and what factors function to imprint the gene. (upenn.edu)
  • Our results suggest that gene regulatory networks are broadly conserved in the phylum Nematoda, but this conservation persists despite substantial reorganization of regulatory elements and could not be detected using naïve comparisons of sequence similarity. (prolekare.cz)
  • One possibility is that ancestral gene regulatory programs are strictly retained. (prolekare.cz)
  • We wanted to assess the conservation of gene regulatory programs among distantly-related members of the phylum Nematoda, a group of morphologically similar worms with mostly small, vermiform bodies. (prolekare.cz)
  • These analyses provide a more complete overview of the gene regulatory networks that define this cell type, and demonstrate the usefulness of the large-scale production efforts of the ENCODE Consortium. (nature.com)
  • Despite different sources, all isolates were identical regarding 16S rRNA gene sequences and were categorized as Geobacillus thermodenitrificans . (springer.com)
  • A subset of NDM-1-positive E. coli isolates was identified as dominant sequence type 101 (ST101) while two strains belonging to ST167 and ST405 harbored NDM-5. (asm.org)
  • You will learn cutting edge approaches including next-generation sequencing, non-coding RNA biology, single molecule FRET and biochemical approaches to study chromatin modifications. (findaphd.com)
  • The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples. (umassmed.edu)
  • The presence of Musashi-binding elements within PAX9 of all mammals examined, chicken, zebrafish, and the fly homolog of PAX9, indicates this regulatory mechanism is ancient, originating basal to much of the animal phylogeny. (nih.gov)