Nucleic acid sequences involved in regulating the expression of genes.
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.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
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.
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 which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
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).
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
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 which complements a specific mRNA or DNA molecule, or fragment thereof; used for hybridization studies in order to identify microorganisms and for genetic studies.
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)
Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template.
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.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
The parts of a macromolecule that directly participate in its specific combination with another molecule.
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.
Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.
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.
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.
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 whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.
A 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.
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.
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.
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 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.
Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
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
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
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.
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.
Genes that are introduced into an organism using GENE TRANSFER TECHNIQUES.
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.
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).
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.
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.
Deoxyribonucleic acid that makes up the genetic material of viruses.
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.
Established cell cultures that have the potential to propagate indefinitely.
Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.
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.
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.
Ribonucleic acid that makes up the genetic material of viruses.
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.
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.
Deletion of sequences of nucleic acids from the genetic material of an individual.
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.
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 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.
Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.
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.
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.
Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO.
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.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
Biologically functional sequences of DNA chemically synthesized in vitro.
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.
The region of DNA which borders the 5' end of a transcription unit and where a variety of regulatory sequences are located.
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.
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)
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.
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.
The functional hereditary units of VIRUSES.
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).
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
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.
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.
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)
The region of DNA which borders the 3' end of a transcription unit and where a variety of regulatory sequences are located.
Sequential operating programs and data which instruct the functioning of a digital computer.
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.
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.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
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.
Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.
ANIMALS whose GENOME has been altered by GENETIC ENGINEERING, or their offspring.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
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).
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.
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).
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
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 used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
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.
The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.
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.
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.
The relationships of groups of organisms as reflected by their genetic makeup.
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.
A form of creatine kinase found in the MITOCHONDRIA.
The functional hereditary units of BACTERIA.
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.
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.
A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.
Any method used for determining the location of and relative distances between genes on a chromosome.
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.
Actual loss of portion of a chromosome.
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.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
A superfamily of proteins containing the globin fold which is composed of 6-8 alpha helices arranged in a characterstic HEME enclosing structure.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
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)
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.
An isoenzyme of creatine kinase found in the MUSCLE.
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.
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.
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.
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.
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.
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.
Proteins found in any species of bacterium.
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.
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.
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)
Nucleotide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.
The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.
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.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
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.
Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.
The systematic study of the complete DNA sequences (GENOME) of organisms.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.
Proteins found in any species of virus.
The rate dynamics in chemical or physical systems.
Biochemical identification of mutational changes in a nucleotide sequence.
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.
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).
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.
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.
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.
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.
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.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
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 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.
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)
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
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.
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.
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.
Color of the iris.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
The functional hereditary units of FUNGI.
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.
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.
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.
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)
Nucleic acid sequences that are involved in the negative regulation of GENETIC TRANSCRIPTION by chromatin silencing.
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.
A group of transcription factors that were originally described as being specific to ERYTHROID CELLS.
Proteins prepared by recombinant DNA technology.
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.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
The parts of the gene sequence that carry out the different functions of the GENES.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
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.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.
The functional hereditary units of INSECTS.
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.
Molecules of DNA that possess enzymatic activity.
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.
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 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.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
A species of POLYOMAVIRUS originally isolated from Rhesus monkey kidney tissue. It produces malignancy in human and newborn hamster kidney cell cultures.
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.
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.
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.
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.
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.
Short fragments of DNA or RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.
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)
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.
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.
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 BIOLOGY techniques used in the diagnosis of disease.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
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.
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
Deoxyribonucleic acid that makes up the genetic material of fungi.
A paired box transcription factor that is essential for ORGANOGENESIS of the CENTRAL NERVOUS SYSTEM and KIDNEY.
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.
A congenital anomaly of the hand or foot, marked by the presence of supernumerary digits.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
Purine or pyrimidine bases attached to a ribose or deoxyribose. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
The functional hereditary units of PLANTS.
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
DNA or RNA bound to a substrate thereby having fixed positions.
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 devoted to knowledge about specific genes and gene products.
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.
Hormones secreted by insects. They influence their growth and development. Also synthetic substances that act like insect hormones.
A family of DNA-binding transcription factors that contain a basic HELIX-LOOP-HELIX MOTIF.

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 ...
The His-1 gene is developmentally expressed in the murine choroid plexus but is silenced in the adult brain. To test the hypothesis that the gene contains cis-acting elements that contribute to this repression, we have analyzed segments of the proximal promoter for negative regulatory sequences by transient transfection analysis. The activity of the proximal promoter was moderately influenced by positively and negatively acting sequences located from 2335 to 2168 and 2617 to 2335, respectively. A strong His-1-positive regulatory element (HPRE, 118 to 129) was essential for maximal promoter activity and could also enhance the activity of the heterologous SV40 promoter in an orientation-dependent manner. The HPRE contains homology to the neuronal restrictive silencer element (NRSE) but interacted with nuclear proteins that were distinct from the NRSE-binding factor (NRSF). By contrast, a potent negative regulatory sequence (HNRE) was identified in the first exon that repressed either the His-1 or ...
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. ...
TY - JOUR. T1 - Use of MCF-7 cell variants to evaluate growth regulatory potential of estrogen-induced products. AU - Davidson, N. E.. AU - Bronzert, D. A.. AU - Chambon, P.. PY - 1985/1/1. Y1 - 1985/1/1. UR - UR - M3 - Article. AN - SCOPUS:17344375640. VL - VOL. 26. SP - No. 777. JO - Proceedings of the American Association for Cancer Research. JF - Proceedings of the American Association for Cancer Research. ER - ...
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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.
Tomás Allen Rush, Virginie Puech-Pagès, Adeline Bascaules, Patricia Jargeat, Fabienne Maillet, Alexandra Haouy, Arthur QuyManh Maës, Cristobal Carrera Carriel, Devanshi Khokhani, Michelle Keller-Pearson, Joanna Tannous, Kevin R. Cope, Kevin Garcia, Junko Maeda, Chad Johnson, Bailey Kleven, Quanita J. Choudhury, Jessy Labbé, Candice Swift, Michelle A. OMalley, Jin Woo Bok, Sylvain Cottaz, Sébastien Fort, Verena Poinsot, Michael R. Sussman, Corinne Lefort, Jeniel Nett, Nancy P. Keller, Guillaume Bécard, Jean-Michel ...
Cells use protein-DNA and protein-protein interactions to regulate transcription. A biophysical understanding of this process has, however, been limited by the lack of methods for quantitatively characterizing the interactions that occur at specific promoters and enhancers in living cells. Here we show how such biophysical information can be revealed by a simple experiment in which a library of partially mutated regulatory sequences are partitioned according to their in vivo transcriptional activities and then sequenced en masse. Computational analysis of the sequence data produced by this experiment can provide precise quantitative information about how the regulatory proteins at a specific arrangement of binding sites work together to regulate transcription. This ability to reliably extract precise information about regulatory biophysics in the face of experimental noise is made possible by a recently identified relationship between likelihood and mutual information. Applying our experimental ...
histone deacetylase complex, nucleoplasm, nucleus, DNA-binding transcription factor activity, DNA-binding transcription factor activity, RNA polymerase II-specific, transcription factor binding, transcription regulatory region sequence-specific DNA binding
Understanding transcription factor (TF) mediated control of gene expression remains a major challenge at the interface of computational and experimental biology. Computational techniques predicting TF-binding site specificity are frequently unreliable. On the other hand, comprehensive experimental validation is difficult and time consuming. We introduce a simple strategy that dramatically improves robustness and accuracy of computational binding site prediction. First, we evaluate the rate of recurrence of computational TFBS predictions by commonly used sampling procedures. We find that the vast majority of results are biologically meaningless. However clustering results based on nucleotide position improves predictive power. Additionally, we find that positional clustering increases robustness to long or imperfectly selected input sequences. Positional clustering can also be used as a mechanism to integrate results from multiple sampling approaches for improvements in accuracy over each one ...
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
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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 ...
Predicted to have DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in otic placode formation. Predicted to localize to nucleus. Is expressed in several structures, including fin bud; germ ring; immature eye; median fin fold; and nervous system ...
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?
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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 ...
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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.
Newly developed genome-editing tools, such as the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 system, allow simple and rapid genetic modification in most model organisms and human cell lines. Here, we report the production and analysis of mice carrying the inactivation via deletion of a genomic insulator, a key non-coding regulatory DNA element found 5′ upstream of the mouse tyrosinase (Tyr) gene. Targeting sequences flanking this boundary in mouse fertilized eggs resulted in the efficient deletion or inversion of large intervening DNA fragments delineated by the RNA guides. The resulting genome-edited mice showed a dramatic decrease in Tyr gene expression as inferred from the evident decrease of coat pigmentation, thus supporting the functionality of this boundary sequence in vivo, at the endogenous locus. Several potential off-targets bearing sequence similarity with each of the two RNA guides used were analyzed and found to be largely intact. This study reports ...
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.
TRANSFAC 3.2 is available now at: 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 ( 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 ...
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 ...
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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 temporally and spatially restricted expression of the mouse Engrailed (En) genes is essential for development of the midbrain and cerebellum. The regulation of En-2 expression was studied using in vitro protein-DNA binding assays and in vivo expression analysis in transgenic mice to gain insight into the genetic events that lead to regionalization of the developing brain. A minimum En-2 1.0 kb enhancer fragment was defined and found to contain multiple positive and negative regulatory elements that function in concert to establish the early embryonic mid-hindbrain expression. Furthermore, the mid-hindbrain regulatory sequences were shown to be structurally and functionally conserved in humans. The mouse paired-box-containing genes Pax-2, Pax-5 and Pax-8 show overlapping expression with the En genes in the developing brain. Significantly, two DNA-binding sites for Pax-2, Pax-5 and Pax-8 proteins were identified in the 1.0 kb En-2 regulatory sequences, and mutation of the binding sites ...
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
Ated GCC box in vitro.Prediction of cis-acting Elements of Promoter Region of AaERFPutative cis-acting elements of the promoter were predicted using the
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 ...
Transcriptional networks have been shown to evolve very rapidly, prompting questions as to how such changes arise and are tolerated. Recent comparisons of transcriptional networks across species have implicated variations in the cis-acting DNA sequences near genes as the main cause of divergence. Wh …
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.
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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.. ...
I currently model per-face and per-vertex attributes with a geometry shader and per-face/vertex indexing based on gl_PrimitiveIDIn. The alternative is promoting per-face and per-shared point attributes to per-vertex frequency, which can get very heavy and sluggish for large production models (in the 5M+ polygon range). Using multiple element buffers/indices might improve the performance of this case; at least Id be interested to try ...
Which of the following classes allow elements to be accessed in the order that they were added? Why those options are not included in the answer.
"Nucleic Acids Research. 13 (12): 4401-10. 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 Research. 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 ...
Implications for finding sequence motifs in regulatory regions". Nucleic Acids Research. 29 (12): 2607-18. doi:10.1093/nar/ ... Zhu W, Lomsadze A, Borodovsky M (July 2010). "Ab initio gene identification in metagenomic sequences". Nucleic Acids Research. ... Rho M, Tang H, Ye Y (November 2010). "FragGeneScan: predicting genes in short and error-prone reads". Nucleic Acids Research. ... Nucleic Acids Research. 31 (13): 3738-41. doi:10.1093/nar/gkg610. PMC 169016. PMID 12824407. Keilwagen J, Wenk M, Erickson JL, ...
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. ...
... 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. ...
... a database to aid the analysis of regulatory sequences in mRNAs". Nucleic Acids Research. 37 (Database issue): D72-D76. doi: ... Transterm is a database of mRNA sequences, codon usage, and associated cis-regulatory elements that regulate gene expression. ...
Mariño-Ramírez L, Lewis KC, Landsman D, Jordan IK (2005). "Transposable elements donate lineage-specific regulatory sequences ... Strand DJ, McDonald JF (June 1985). "Copia is transcriptionally responsive to environmental stress". Nucleic Acids Research. 13 ... A consensus sequence is a sequence that is created based on the repeats that comprise a TE family. A base pair in a consensus ... Insertional mutagenesis uses the features of a TE to insert a sequence. In most cases this is used to remove a DNA sequence or ...
... 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 ...
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 ...
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 ... Bergemann AD, Ma ZW, Johnson EM (December 1992). "Sequence of cDNA comprising the human pur gene and sequence-specific single- ...
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 ...
... 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 ...
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 ...
Those include the following: Heme binds to a short sequence that serve as a regulatory function in diverse proteins; Heme ... Nucleic Acids Research. 46 (1): 215-228. doi:10.1093/nar/gkx1051. ISSN 0305-1048. PMC 5758875. PMID 29126261. Zhang, L.; ... "Heme binds to a short sequence that serves a regulatory function in diverse proteins". The EMBO Journal. 14 (2): 313-320. doi: ...
ORF1 trimers have RNA-binding and nucleic acid chaperone activity that are necessary for retrotransposition. The second ORF of ... "Binding of the ubiquitous nuclear transcription factor YY1 to a cis regulatory sequence in the human LINE-1 transposable ... International Human Genome Sequencing Consortium) (February 2001). "Initial sequencing and analysis of the human genome". ... Nucleic Acids Research. 32 (13): 3846-55. doi:10.1093/nar/gkh698. PMC 506791. PMID 15272086. Li J, Kannan M, Trivett AL, Liao H ...
Nucleic Acids Research. 8 (1): 1-20. ISSN 0305-1048. PMID 6243775. Siu, Francis K Y; Lee, Leo T O; Chow, Billy K C (2007-12-20 ... 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 ...
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 ...
... regulatory sequences, nucleic acid MeSH G06.184.603.080.689.330 - enhancer elements (genetics) MeSH G06.184.603.080.689.330.240 ... amino acid MeSH G06.184.842.200.820 - structural homology, protein MeSH G06.184.842.550 - sequence homology, nucleic acid MeSH ... 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. ...
Presumably, the RNAs function as cis-regulatory elements, however the poor sequence conservation makes it difficult to ... Nucleic Acids Res. 45 (18): 10811-10823. doi:10.1093/nar/gkx699. PMC 5737381. PMID 28977401.. ... The osmY RNA motif exhibits little conserved sequence in comparison to many known RNAs, although its secondary structure is ... It is generally located nearby to the Shine-Dalgarno sequence of the downstream gene. ...
Finder Multiple EM for Motif Elicitation Nucleic acid sequence Protein primary structure Protein I-sites Sequence logo Sequence ... 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 ... A regulatory DNA sequence does not regulate unless it is activated. Different regulatory sequences are activated and then ... About 600 regulatory sequences in promoters and about 800 regulatory sequences in enhancers appear to depend on double strand ... 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 ...
Nucleic Acids Res. 17 (1): 171-183. doi:10.1093/NAR/17.1.171. PMC 331543. Becker, M.M.; Wang, Z.; Grossmann, G.; Becherer, K.A ... 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- ... due to a slower reaction and digestion time.Ultraviolet irradiation can be used to excite nucleic acids and create ...
Sinha S, Liang Y, Siggia E (2006). "Stubb: a program for discovery and analysis of cis-regulatory modules". Nucleic Acids Res. ... An example of a cis-acting regulatory sequence is the operator in the lac operon. This DNA sequence is bound by the lac ... Sharan R, Ben-Hur A, Loots GG, Ovcharenko I (2004). "CREME: Cis-Regulatory Module Explorer for the human genome". Nucleic Acids ... The design of regulatory modules help in producing feedback, feed forward, and cross-regulatory loops. Cis-regulatory modules ...
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 ...
... an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments". Nucleic Acids ... Sequencing, by contrast, is thought to have less bias, although the sequencing bias of different sequencing technologies is not ... "Impact of sequencing depth in ChIP-seq experiments". Nucleic Acids Research. 42 (9): e74. doi:10.1093/nar/gku178. ISSN 1362- ... There are many new sequencing methods used in this sequencing step. Some technologies that analyze the sequences can use ...
Nucleic Acids Res. 45 (18): 10811-10823. doi:10.1093/nar/gkx699. PMC 5737381. PMID 28977401. Fujiwara-Nagata E, Eguchi Y, ... However, promoter sequences occur upstream of the nqr operon in the distantly related organism Vibrio anguillarum. The fact ... Based on their locations, it is reasonable to hypothesize that nqrA-Marinomonas RNAs function as cis-regulatory elements. ... as nqrA-Marinomonas RNAs raises questions about the putative cis-regulatory function of these RNAs. However, it is possible ...
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 acid sequences of the cDNA and gene predict protein structure and suggest sites of regulatory control". Proc. Natl. ... Wen DZ, Dittman WA, Ye RD, Deaven LL, Majerus PW, Sadler JE (Jul 1987). "Human thrombomodulin: complete cDNA sequence and ... Wen DZ, Dittman WA, Ye RD, Deaven LL, Majerus PW, Sadler JE (Jul 1987). "Human thrombomodulin: complete cDNA sequence and ...
Nucleic Acids Res. 45 (18): 10811-10823. doi:10.1093/nar/gkx699. PMC 5737381. PMID 28977401.. ... Some Mu-gpT-DE RNAs contain a stem that overlaps the Shine-Dalgarno sequence of the downstream gene, which could suggest a cis- ... regulatory function. However, this phenomenon could also be a arise if Mu-gpT-DE RNAs are part of a tightly packed genome, as ... The Mu-gpT-DE motif is only found in metagenomic sequences arising from unknown organisms. Mu-gpT-DE RNAs usually occur ...
... locating transcription-regulating binding sites in mixed aligned and unaligned sequence data". Nucleic Acids Research. 38 (Web ... For locating matches to a user-specified sequence motif for a regulatory binding site, Phyloscan provides a statistically ... Phyloscan is a web service for DNA sequence analysis that is free and open to all users (without login requirement). ... Staden, R (April 1989). "Methods for calculating the probabilities of finding patterns in sequences". Computer Applications in ...
... but can also arise from polyploidisation or nucleic acid hybridization. Over evolutionary time, if the function of the new ... are enzymes that differ in amino acid sequence but catalyze the same chemical reaction. These enzymes usually display different ... Its different regulatory features and lower affinity for glucose (compared to other hexokinases), allows it to serve different ... In particular, amino acid substitutions that change the electric charge of the enzyme (such as replacing aspartic acid with ...
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. ...
... technique that uses fluorescent probes that bind to only those parts of a nucleic acid sequence with a high degree of sequence ... "The lncRNA Malat1 is Dispensable for Mouse Development but Its Transcription Plays a cis-Regulatory Role in the Adult". Cell ... RNA probes can be designed for any gene or any sequence within a gene for visualization of mRNA,[3][4][5] lncRNA[6][7][8] and ... Repetitive DNA sequences must be blocked by adding short fragments of DNA to the sample. The probe is then applied to the ...
"Nucleotide sequences of mouse genomic loci including a gene or pseudogene for U6 (4.8S) nuclear RNA". Nucleic Acids Research ... The TATA box is considered a non-coding DNA sequence (also known as a cis-regulatory element). It was termed the "TATA box" as ... This sequence was originally called Box A, which is now known to be the sequence that interacts with the homologue of the ... In the 1980s, while investigating nucleotide sequences in mouse genome loci, the Hogness box sequence was found and "boxed in" ...
... compared amino acid compositions in the same histone from different organisms, and compared amino acid sequences of the same ... "Nucleic Acids Research. 34 (9): 2653-62. doi:10.1093/nar/gkl338. PMC 1464108. PMID 16714444.. ... Histone gene transcription is controlled by multiple gene regulatory proteins such as transcription factors which bind to ... 3. Complete amino acid sequence of pea seedling histone IV; comparison with the homologous calf thymus histone". The Journal of ...
"for their contributions concerning the determination of base sequences in nucleic acids"[۲۹] ... "for his discoveries concerning reversible پروتئین فسفرگیری as a biological regulatory mechanism"[۷۲] ... "for his fundamental studies of the biochemistry of nucleic acids, with particular regard to recombinant-DNA"[۲۹] ... "for his work on ribonuclease, especially concerning the connection between the amino acid sequence and the biologically active ...
... nucleic acid - nucleic acid test - nucleocapsid - nucleoli - nucleoside - nucleoside analog - nucleoside reverse transcriptase ... regulatory genes - regulatory T cells - remission - renal - rescue therapy - resistance - retina - retinal detachment - ... long terminal repeat sequence (LTR) - long-term nonprogressors - LTR - lumbar - lumbar puncture - lymph - lymph nodes - ... amino acids - anaphylactic shock - anemia - anergy - angiogenesis - angiomatosis - anorexia - antenatal - antibiotic - ...
... be transferred from nucleic acid to nucleic acid but cannot be transferred back from protein to either protein or nucleic acid ... Ribosome units are used to transcribe the mRNA of the virus into the amino acid sequences which can be made into proteins in ... The promoter of the provirus DNA can also cause over expression of regulatory genes. ... U3 is a sequence between PPT and R, which serves as a signal that the provirus can use in transcription. R is the terminal ...
Other emerging biomarkers include MicroRNA (miRNA), Circulating nucleic acids, and Exosome/micro-vesicles biomarkers. ... Regulatory validationEdit. Proof of concept Previously used to identify the specific characteristics of the biomarker, this ... In genetics, a biomarker (identified as genetic marker) is a DNA sequence that causes disease or is associated with ...
Watson, J. D.; Crick, FH (1953). "Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid" (PDF). Nature ... International Human Genome Sequencing Consortium (October 2004). "Finishing the euchromatic sequence of the human genome". ... Maston, G. A.; Evans, S. K.; Green, M. R. (2006). "Transcriptional Regulatory Elements in the Human Genome". Annual Review of ... Hershey, AD; Chase, M (1952). "Independent functions of viral protein and nucleic acid in growth of bacteriophage". The Journal ...
"Nucleic Acids Research》 41 (Database issue): D764-72. doi:10.1093/nar/gks1049. PMC 3531171. PMID 23203881.. ... 참고](Biochemistry Chapter10 Regulatory Strategies: Enzymes and Hemoglobin P403L1 ,Jeremy M. Berg,John L. Tymoczko,Lubert Stryer ... Petsko GA, Ringe D (2003). 》Chapter 1: From sequence to structure》. 》Protein structure and function》. London: New Science. 27쪽 ... Smith S (December 1994). "The animal fatty acid synthase: one gene, one polypeptide, seven enzymes". 》FASEB Journal》 8 (15): ...
"Nucleic Acids Res. 13 (17): 6361-73. doi:10.1093/nar/13.17.6361. PMC 321958. PMID 2995927.. ... transcription regulatory region DNA binding. • protein binding. • protease binding. • tumor necrosis factor receptor binding. • ... positive regulation of sequence-specific DNA binding transcription factor activity. • cellular response to nicotine. • positive ... TNF is primarily produced as a 233-amino acid-long type II transmembrane protein arranged in stable homotrimers.[24][25] From ...
RNA is an acronym for ribonucleic acid, a nucleic acid. Many different kinds are now known.[1] ... The mRNA translates the sequence of base pairs into a sequence of amino acids to form proteins. This process is called ... Regulatory RNAs[change , change source]. There are a number of RNAs which regulate genes, that is, they regulate the rate at ... The main function of RNA is to carry information of amino acid sequence from the genes to where proteins are assembled on ...
"Nucleic Acids Res. 27 (11): 2291-8. PMC 148793 . PMID 10325416. doi:10.1093/nar/27.11.2291.. ... The SET domain is a 130-amino acid sequence involved in modulating gene activities. This domain has been demonstrated to bind ... Nucleosome position is not random, and determine the accessibility of DNA to regulatory proteins. This determines differences ... "Nucleic Acids Research. 40 (22): 11450-62. PMC 3526280 . PMID 23034806. doi:10.1093/nar/gks891.. ...
... nucleic acid extraction and amplification, sequencing library preparation, sequencing and bioinformatic data analysis. It is ... "Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress". PLOS ... Single cell sequencing examines the sequence information from individual cells with optimized next-generation sequencing (NGS) ... specific sequences may be transcribed inefficiently, thus causing sequence drop-out or generating incomplete sequences.[1][40] ...
Nucleic Acids Res. 38 (20): 6895-905. doi:10.1093/nar/gkq604. PMC 2978373 . PMID 20624818. Almeida MI, Reis RM, Calin GA (2010 ... The mature ~21nt miRNAs are processed from hairpin precursor sequences by the Dicer enzyme. The dominant mature miRNA sequence ... Zhao C, Sun G, Li S, Shi Y (2009). "A feedback regulatory loop involving microRNA-9 and nuclear receptor TLX in neural stem ... Lau NC, Lim LP, Weinstein EG, Bartel DP (2001). "An abundant class of tiny RNAs with probable regulatory roles in ...
Nucleic Acids Res., 34 (8): 2428-37, doi:10.1093/nar/gkl287, PMC 1458515, PMID 16682450. ... and their coding sequence is grouped and regulated together in a regulatory region, containing a promoter and an operator. Most ... where they specify the amino acid sequence of the protein products of gene expression. RNA polymerase transcribes primary ... portions of coding regions may serve as regulatory sequences in the pre-mRNA as exonic splicing enhancers or exonic splicing ...
transcription factor activity, sequence-specific DNA binding. • transcription regulatory region DNA binding. • sequence- ... "Nucleic Acids Res. 23 (7): 1184-91. doi:10.1093/nar/23.7.1184. PMC 306829 . PMID 7739897.. ... "HMGB1 interacts with many apparently unrelated proteins by recognizing short amino acid sequences". J. Biol. Chem. 277 (9): ... RNA polymerase II transcription factor activity, sequence-specific DNA binding. Cellular component. • nucleoplasm. • actin ...
"Nucleic Acids Research. 38 (Database issue): D190-D195. doi:10.1093/nar/gkp951. PMC 2808932. PMID 19900971.. ... Targeted amplicon sequencingEdit. Targeted amplicon sequencing relies on having some expectations about the composition of the ... that promoted accumulation of colonic regulatory T cells, and strains that modulated mouse adiposity and cecal metabolite ... "Nucleic Acids Research. 38 (Database issue): D355-D360. doi:10.1093/nar/gkp896. PMC 2808910. PMID 19880382.. ...
Hasler J, Strub K, (2006). "Alu elements as regulators of gene expression". Nucleic Acids Research 34 (19): 5491-5497 ... Bora, NS; Gobleman, CL; Atkinson, JP; Pepose, JS; Kaplan, HJ (1993). "Differential expression of the complement regulatory ... "Sequence organization of the human genome". Cell 6: 345-358, 1975 *↑ ... A common haplotype in the complement regulatory gene factor H (HF1/CFH) predisposes individuals to age-related macular ...
"Evolution of an Enzyme from a Noncatalytic Nucleic Acid Sequence". Scientific Reports. 5: 11405. doi:10.1038/srep11405. PMC ... while proteins are built from up to twenty different amino acids with various functional groups, nucleic acids are built from ... "Nucleic Acids Research. 33 (19): 6151-63. doi:10.1093/nar/gki930. PMC 1283523. PMID 16286368.. ... "Nucleic Acids Research. 31 (20): 5982-92. doi:10.1093/nar/gkg791. PMC 219472. PMID 14530446.. ...
"Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid" (PDF). Nature. 171 (4356): 737-8. Bibcode: ... The nucleotide sequence of a messenger RNA is used to create an amino acid sequence in protein; this translation between ... Transcription factors are regulatory proteins that bind to DNA, either promoting or inhibiting the transcription of a gene.[72] ... Next-generation sequencing (or high-throughput sequencing) came about due to the ever-increasing demand for low-cost sequencing ...
"siVirus: web-based antiviral siRNA design software for highly divergent viral sequences". Nucleic Acids Research. 34 (Web ... MREs are sequences to which miRNAs bind. These are prevalent motifs within 3'-UTRs. Among all regulatory motifs within the 3'- ... "Nucleic Acids Research. 33 (Web Server issue): W589-91. doi:10.1093/nar/gki419. PMC 1160180. PMID 15980542.. ... "Nucleic Acids Research. 32 (Web Server issue): W113-20. doi:10.1093/nar/gkh408. PMC 441546. PMID 15215362.. ...
nucleic acid binding. • Rho GTPase binding. • double-stranded DNA binding. • RNA binding. • GO:0001200, GO:0001133, GO:0001201 ... RNA polymerase II regulatory region sequence-specific DNA binding. • GO:0001106 transcription corepressor activity. • GO: ...
"Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs". Nucleic Acids Res. 31 (13 ... Specifically, they discovered that the catalytic subunit p110 dimerizes with the regulatory subunit p85,[11] and that the SH2 ... March 1993). "SH2 domains recognize specific phosphopeptide sequences". Cell. 72 (5): 767-78. doi:10.1016/0092-8674(93)90404-E ... In 1994, the Cantley lab published a novel strategy to determine the sequence specificity of phosphopeptide binding domains ( ...
"siVirus: web-based antiviral siRNA design software for highly divergent viral sequences". Nucleic Acids Res 34 (Web Server ... Jones-Rhoades M, Bartel D, Bartel B (2006). "MicroRNAS and their regulatory roles in plants". Annu Rev Plant Biol 57: 19-53. ... "Nucleic Acids Res 33 (Web Server issue): W589-91. PMC 1160180. PMID 15980542. doi:10.1093/nar/gki419.. ... "Nucleic Acids Res 32 (Web Server issue): W113-20. PMC 441546. PMID 15215362. doi:10.1093/nar/gkh408.. ...
Jeang, K. T. (1996) In: Human Retroviruses and AIDS: "A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences". Los ... In molecular biology, Tat is a protein that is encoded for by the tat gene in HIV-1.[1][2] Tat is a regulatory protein that ... The minimum Tat sequence that can mediate specific TAR binding in vitro has been mapped to a basic domain of 10 amino acids, ... The amino acid sequence of the protein transduction domain is YGRKKRRQRRR.[13] The nuclear localisation signal found within the ...
"Nucleic Acids Res. 39: D663-669. doi:10.1093/nar/gkq1022. PMC 3013650 . PMID 21051350.. CS1 maint: Explicit use of et al. (link ... Non-regulatory allostery[edit]. A non-regulatory allosteric site is any non-regulatory component of an enzyme (or any protein ... This is particularly useful for GPCRs where selective orthosteric therapy has been difficult because of sequence conservation ... but also has benzodiazepine and general anaesthetic agent regulatory binding sites. These regulatory sites can each produce ...
... proteins or nucleic acids in most cases) led scientists to the conclusion that individual chemicals are required for the ... After sequencing of the human genome allowed rapid cloning and synthesis of large quantities of purified proteins, it has ... regulatory exclusivity, marketing and the need to balance secrecy with communication.[9] Meanwhile, for disorders whose rarity ... They have salicylic acid binding proteins (SABPs) that have shown to affect multiple animal tissues.[70] The first discovered ...
"Nucleic Acids Research. 15 (16): 6733. doi:10.1093/nar/15.16.6733. PMC 306135 . PMID 2888085.. ... 150 amino acids make up a regulatory domain, thought to control access of substrates to the active site.[17] In humans there ... Lüdecke B, Bartholomé K (Jun 1995). "Frequent sequence variant in the human tyrosine hydroxylase gene". Human Genetics. 95 (6 ... amino acid binding. • monooxygenase activity. • protein domain specific binding. Cellular component. • cytoplasm. • cytosol. • ...
The deduced amino acid sequence can be saved in various formats and searched against the sequence database using the BLAST ... "Nucleic Acids Research. 42 (D1): D60-D67. doi:10.1093/nar/gkt952. ISSN 0305-1048. PMC 3964959. PMID 24163100.. ... "Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1859 (10): 1259-1268. doi:10.1016/j.bbagrm.2016.07.004. PMID ... The tool efficiently finds the ORFs for corresponding amino acid sequences and converts them into their single letter amino ...
cis-Regulatory Remodeling of the SCL Locus during Vertebrate Evolution Berthold Göttgens, Rita Ferreira, Maria-José Sanchez, ... Functional Analysis of a Novel cis-Acting Regulatory Region within the Human Ankyrin Gene (ANK-1) Promoter Karina Laflamme, ... 14-3-3 (Bmh) Proteins Inhibit Transcription Activation by Adr1 through Direct Binding to Its Regulatory Domain P. K. Parua, S. ... Two G-Rich Regulatory Elements Located Adjacent to and 440 Nucleotides Downstream of the Core Poly(A) Site of the Intronless ...
Genome Biology Papers on Regulatory Element, Single-Cell Integration, Sequence Simulation Tools. ... Home » Tools & Technology » Sample Prep » Zymo Research, Tecan Partner to Automate Viral Nucleic Acid Extraction ... Zymo Research, Tecan Partner to Automate Viral Nucleic Acid Extraction. Apr 01, 2020 ... In Genome Biology this week: algorithm to assess regulatory features, approach to integrate multiple single-cell RNA-seq ...
Regulatory Sequences, Nucleic Acid * Repressor Proteins / metabolism Substances * CCCTC-Binding Factor * CTCF protein, human ...
Here, we present a comparative analysis of the yeast Saccharomyces cerevisiae based on high-quality draft sequences of three r ... Molecular Sequence Data * Open Reading Frames / genetics * Regulatory Sequences, Nucleic Acid / genetics* ... Sequencing and comparison of yeast species to identify genes and regulatory elements Nature. 2003 May 15;423(6937):241-54. doi ... Here, we present a comparative analysis of the yeast Saccharomyces cerevisiae based on high-quality draft sequences of three ...
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 ...
Analysis of ARG-surrounding sequences identify genes encoding putative mobilisation elements such as transposases and ... Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 29, 2607-2618 (2001). ... Predicted dissemination confirmed in sequence read archive. Sequence read archive (SRA) is a public repository of sequence data ... The obtained sequences clustered at 98% identity and coverage using cd-hit31. Noisy sequences were filtered out using RESFAM32 ...
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 ...
Genome sequence analysis of strain WPAGA1 revealed that the assembled fine genome contains 6,610,326 bp with 32.89% G+C content ... a schematic of various polysaccharide-degrading metabolic pathways were deduced from the genome sequence. This study showed ... a schematic of various polysaccharide-degrading metabolic pathways were deduced from the genome sequence. This study showed ... Genome sequence analysis of strain WPAGA1 revealed that the assembled fine genome contains 6,610,326 bp with 32.89% G+C content ...
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 ...
Nucleic Acids Research. 44 (8): 3750-3762.. * Gemayel, R., M. D. Vinces, M. Legendre, and K. J. Verstrepen. 2010. Variable ... tandem repeats accelerate evolution of coding and regulatory sequences. Annual Review Genetics. 44: 445-477. ... One class of repetitious human genome sequences recently highlighted in the news is called tandem repeats (TRs). These are ... Epigenetic modification is the addition of molecular tags to the DNA molecule without changing the actual DNA sequence. The ...
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. ...
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]. *Locus Control Region [G05.360.080.689.450] ... A regulatory region first identified in the human beta-globin locus but subsequently found in other loci. The region is ... Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element. ... Base Sequence [G02.111.570.080]. *Regulatory Sequences, Nucleic Acid [G02.111.570.080.689]. *Locus Control Region [G02.111. ...
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 ...
Recombinant and/or synthetic nucleic acids that encode for the functional form(s) of select toxins if the nucleic acids: ... This Guidance also provides a list of the nucleic acids that are regulated as well as those nucleic acids that are not ... Subject: Regulatory Interpretation regarding synthetically created DNA sequence. This response addresses your January 3, 2017 ... Nucleic acids that can produce infectious forms of any of the select agent viruses. ...
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. ...
  • We then developed methods for direct identification of genes and regulatory motifs. (
  • Analysis of ARG-surrounding sequences identify genes encoding putative mobilisation elements such as transposases and integrases that may be involved in gene transfer between genomes. (
  • Down-regulation of DNA replication genes and up-regulation of abscisic acid pathway genes were observed. (
  • Sequence analysis identified 10 putative open reading frames (ORFs) flanking the previously characterized CTB1 and CTB3 genes that encode, respectively, the polyketide synthase and a dual methyltransferase/monooxygenase required for cercosporin production. (
  • Their idea that a single regulatory sequence, the operon, controlled and co-ordinated the expression of several structural genes opened up the way for our present day understanding of gene expression in prokaryotes. (
  • Consequently, now that many eukaryotic genes have been cloned and partially or completely sequenced the DNA base sequences have been rigorously searched for structures equivalent to the prokaryotic operator, terminator or replicator signals. (
  • A regulatory sequence near the 3′ end of sea urchin histone genes. (
  • All identified CNS s were integrated in the PLAZA 3.0 Dicots comparative genomics platform ( ) together with new functionalities facilitating the exploration of conserved cis-regulatory elements and their associated genes. (
  • A regulatory sequence is a segment of a nucleic acid molecule which is capable of increasing or decreasing the expression of specific genes within an organism. (
  • Cis-regulatory DNA sequences that are located in DNA regions distant from the promoters of genes can have very large effects on gene expression, with some genes undergoing up to 100-fold increased expression due to such a cis-regulatory sequence. (
  • In addition to variants found in splice sites and protein coding genes regulatory variants and those found in DNA methylated regions, explained considerable variation in milk production and fertility traits. (
  • Several plant stress genes have previously been shown to be calcium-regulated, and in one case, a specific promoter motif Abscisic Acid Responsive-Element (ABRE) has been found to be regulated by calcium. (
  • Instead of using predicted genes or CDSs to query public databases, entries from public DNA or protein databases are used as queries to search a local database of the unannotated genome sequence to predict CDSs. (
  • Genes associated with the cis-regulatory functions of intragenic LINE-1 elements. (
  • Thousands of intragenic long interspersed element 1 sequences (LINE-1 elements or L1s) reside within genes. (
  • These intragenic L1 sequences are conserved and regulate the expression of their host genes. (
  • After a permutation based statistical analysis and a multiple hypothesis testing, 73 genes were found to induce significant regulatory changes (upregulation and/or downregulation) in genes with L1s. (
  • The draft sequences of the OS27 genome contained 3766 coding sequences, which included intact genes for 28 glycoside hydrolases and many hypothetical proteins unusual among G. thermodenitrificans . (
  • The learning of global genetic regulatory networks from expression data is a severely under-constrained problem that is aided by reducing the dimensionality of the search space by means of clustering genes into putatively co-regulated groups, as opposed to those that are simply co-expressed . (
  • The genes in such clusters are often assumed to be co-regulated, i.e . to share the same regulatory controls, thereby implying biological relevance for such a pre-clustering step. (
  • Cis -regulatory sequences control when, where and with what intensity genes are expressed. (
  • Computational methods are often used to predict gene regulatory elements from a set of promoter sequences of similarly behaving genes, e.g. a set of co-expressed genes. (
  • Citation Query Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. (
  • Since this regional-based approach proved effective for protein coding genes, it is natural to assess its application to noncoding exome sequence. (
  • To assess whether noncoding sequence can predict genes that cause human disease through gene dosage aberration, we derive two measures: a phylogenetic conservation based score and a score reflecting intolerance to standing variation in a human population. (
  • recognizing that these three regions are only a subset of the relevant regulatory sequence for protein-coding genes. (
  • To explore the phylogenetic limits of conservation of cis-regulatory elements, we used transgenesis to test the functions of enhancers of four genes from several species spanning the phylum Nematoda. (
  • We therefore performed enhancer swap experiments with regulatory elements of genes expressed in two subsets of neurons and in the developing intestine. (
  • We simulate expression of four segmentation genes during early fruit fly development using a hybrid reaction-diffusion and thermodynamic computational model, fit to empirical expression patterns and to wild-type regulatory sequences. (
  • Enhancers are regulatory DNA sequences that control when, and in what tissue, particular genes are turned on and off. (
  • Comparison of these three genes shows homology of 78-81% on the nt level and 83-87% homology on the amino acid level. (
  • In DNA, regulation of gene expression normally happens at the level of RNA biosynthesis (transcription), and is accomplished through the sequence-specific binding of proteins (transcription factors) that activate or inhibit transcription. (
  • Among this constellation of sequences, enhancers and their associated transcription factor proteins have a leading role in the regulation of gene expression. (
  • Mediator (coactivator) (a complex usually consisting of about 26 proteins in an interacting structure) communicates regulatory signals from enhancer DNA-bound transcription factors directly to the RNA polymerase II (RNAP II) enzyme bound to the promoter. (
  • While large centrally curated database have emerged for proteins (UniProt [ 21 ]) or human genetics (OMIM [ 22 ]), funding for large-scale curation of an open-access regulatory sequence collection appears unlikely. (
  • Both of these proteins contain an ETX/MTX2 domain and share common sequence features with the β-pore-forming toxins. (
  • Phase separated condensates are membraneless organelles containing high densities of proteins and nucleic acids. (
  • Here we present, as part of the ENCODE (Encyclopedia of DNA Elements) project, data and analyses from chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experiments using the human HepG2 cell line for 208 chromatin-associated proteins (CAPs). (
  • Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. (
  • This protein contains seven highly conserved zinc finger repeats that exhibit striking sequence similarity to retroviral nucleic acid binding proteins (NBPs). (
  • Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical shape (e.g. the "B-form" DNA double helix). (
  • The motif analysis automatically identified 72 genome-wide elements, including most known regulatory motifs and numerous new motifs. (
  • We mapped macrophage transcription start sites, defining over-represented cis -regulatory motifs within AAMφ-associated promoters. (
  • Evening expression of arabidopsis GIGANTEA is controlled by combinatorial interactions among evolutionarily conserved regulatory motifs. (
  • Bioinformatic analysis for unknown PAX9 regulatory motifs indicated a novel post-transcriptional regulatory mechanism involving a Musashi protein. (
  • Implications for finding sequence motifs in regulatory regions. (
  • One important association is the presence of one or more common cis-regulatory motifs. (
  • We have developed an algorithm, cMonkey, that detects putative co-regulated gene groupings by integrating the biclustering of gene expression data and various functional associations with the de novo detection of sequence motifs. (
  • 4. Boeva, V. (2016) Analysis of genomic sequence motifs for deciphering transcription factor binding and transcriptional regulation in Eukaryotic cells. (
  • 8. Siebert, M. and Söding, J. (2016) Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences. (
  • Sequence motifs representing transcription factor binding sites (TFBS) are commonly encoded as position frequency matrices (PFM) or degenerate consensus sequences (CS). (
  • The computational identification of over-represented motifs in sets of DNA sequences is, in particular, a task where post-processing can dramatically simplify the analysis. (
  • Matlign is a user-friendly tool for post-processing large collections of DNA sequence motifs. (
  • Starting from a large number of potential regulatory motifs, Matlign provides a researcher with a non-redundant set of motifs, which can then be further associated to known regulatory elements. (
  • Of these, CSs could be analysed using conventional sequence alignment methods, such as those in the Emboss-package [ 7 ], but these tools are not designed for analyses of hundreds of motifs and, hence, are inconvenient to use. (
  • NestedMICA is a new, scalable, pattern-discovery system for finding transcription factor binding sites and similar motifs in biological sequences. (
  • It also performs robustly on synthetic sequences containing multiple significant motifs. (
  • When tested on a real set of regulatory sequences, NestedMICA produced motifs which were good predictors for all five abundant classes of annotated binding sites. (
  • Short motifs, similar to known regulatory sequences in C. elegans, can be detected in most of the cis elements. (
  • Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences. (
  • We confirm and expand the current catalogue of DNA sequence motifs for transcription factors, and describe motifs that correspond to other transcription factors that are co-enriched with the primary ChIP target. (
  • In addition to highlighting potentially active regulatory DNA elements by direct measurement, ChIP-seq data can define DNA sequence motifs that can be used, often in conjunction with expression data and chromatin accessibility maps, to infer likely binding events in other cellular contexts without performing direct assays. (
  • Outside of gene exons, there exist regulatory sequence motifs and motifs within the "junk", such as satellite DNA. (
  • Within a sequence or database of sequences, researchers search and find motifs using computer-based techniques of sequence analysis, such as BLAST. (
  • We isolated a cowpox virus from the lesions and sequenced its whole genome. (
  • The large phylogenetic distance between the currently sequenced dicot plant species hampers the use of lift overs, in which detected transcription factor binding sites ( TFBS s) are transferred from one species to another through whole-genome alignments. (
  • There are an exceedingly large number of sequence variants discovered through whole genome sequencing in most populations, including cattle. (
  • Our data set consisted of 28.3 million imputed whole genome sequence variants in 16,581 dairy cattle with records for 6 complex trait phenotypes, including production and fertility. (
  • The results demonstrate using functional annotations to filter whole genome sequence variants into more informative subsets could be useful for prioritization of the variants that are more likely to be associated with complex traits. (
  • Whole genome sequencing (WGS) is providing solutions to some of the limitations of GWAS and genomic prediction with SNP genotyping arrays. (
  • The whole genome sequencing method has become the gold standard for understanding the genetic diversity of bacteria [ 8 ]. (
  • Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing," Science , vol. 287, pp. 1816-1820, 2000. (
  • To study the pathogenicity and evolution of the circulating pseudorabies viruses in Fujian Province, mainland China, we isolated and sequenced the whole genome of a wild-type pseudorabies virus strain named "FJ-2012. (
  • 306. It was estimated that there are four copies of pXOCgx01 per cell of Xoc GX01 by PCR assay and the calculation of whole genome shotgun sequencing data. (
  • Genome sequence analysis of strain WPAGA1 revealed that the assembled fine genome contains 6,610,326 bp with 32.89% G+C content, 5036 open reading frames (ORFs) and abundant genomic elements. (
  • We also found sequence variants in target sites for DNA methylation (genomic regions that are found be highly methylated in bovine placentas), captured a significant proportion of the variance. (
  • The available methods often encounter difficulties when dealing with unfinished error-containing genomic sequence. (
  • In this study, we selected representative MRSA strains from patients' systemic surveillance in Yunnan province of China, performed the genomic sequencing and compared their features, together with some food derived strains. (
  • RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. (
  • PipMaker - a web server for aligning two genomic DNA sequences. (
  • A computer program for aligning a cDNA sequence with a genomic DNA sequence. (
  • 1999. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. (
  • The invention relates to the protein and nucleic acids encoding the protein. (
  • 1. An isolated nucleic acid encoding an endothelial estrogen regulated gene-7 protein that has (i) an amino acid sequence which has at least about 95% sequence similarity with SEQ ID NO: 2 and (ii) lysyl oxidase activity. (
  • 2. The isolated nucleic acid of claim 1 , wherein the endothelial estrogen regulated gene-7 protein comprises four scavenger receptor cysteine rich (SRCR) domains having an amino acid sequence at least about 95% identical to the amino acid sequences of SEQ ID NOs: 3, 4, 5, and 6. (
  • 3. The isolated nucleic acid of claim 2 , wherein the endothelial estrogen regulated gene-7 protein comprises four scavenger receptor cysteine rich domains having the amino acid sequences of SEQ ID NOs: 3, 4, 5, and 6. (
  • 5. The isolated nucleic acid of claim 1 , wherein the endothelial estrogen regulated gene-7 protein has the amino acid sequence of SEQ ID NO: 2. (
  • 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. (
  • 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. (
  • Although clinical genome sequence analysis currently focuses on the identification of protein-altering variation, the impact of cis- regulatory mutations can be similarly strong. (
  • Although much emphasis in the age of exome sequencing has been placed on variation within protein-encoding sequences, it is apparent that regulatory sequence disruptions will become a key focus as full genome sequences become widely accessible for medical genetics research. (
  • It binds to AE-1 element present in the proximal promoter of aP2 gene that codes for fatty acid binding protein (FABP4). (
  • Yeast repressor activator protein 1 (RAP1) binds in vitro to specific DNA sequences that are found in diverse genetic elements. (
  • Clustering huge protein sequence sets in linear time. (
  • MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. (
  • Uniclust databases of clustered and deeply annotated protein sequences and alignments. (
  • The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. (
  • MMseqs software suite for fast and deep clustering and searching of large protein sequence sets. (
  • Context similarity scoring improves protein sequence alignments in the midnight zone. (
  • Despite seemingly large phenotypic differences between species across the primate lineage, protein-coding sequences remain highly conserved. (
  • CRISPR-Cas systems can cleave specific target sequences depending on the sequence of a CRISPR-derived guide RNA (gRNA) and the source of the Cas9 protein. (
  • Unit Definition: One unit is defined as the amount of Protein Kinase A regulatory subunit I alpha, required to incorporate 1nmol of phosphate into the specific substrate peptide kemptide (LRRASlG) in one minute at 30°C. (
  • With the use of an oligonucleotide containing the SRE to screen a human hepatoma complementary DNA expression library, a clone for a DNA binding protein was isolated that binds to the conserved SRE octanucleotide in both a sequence-specific and a single-strand--specific manner. (
  • The osmosensor histidine protein kinase EnvZ can phosphorylate the response regulator OmpR, which constitutes a two-component signal transduction and regulatory system. (
  • Consensus methods for DNA and protein sequence alignment. (
  • One class of repetitious human genome sequences recently highlighted in the news is called tandem repeats (TRs). (
  • The study of gene regulation has emerged as a focus of efforts to understand how genome sequences give rise to diverse and complex cells and tissues. (
  • A necessary step for a genome level analysis of the cellular metabolism is the in silico reconstruction of the metabolic network from genome sequences. (
  • The available methods are mainly based on the annotation of genome sequences including two successive steps, the prediction of coding sequences (CDS) and their function assignment. (
  • Single sequencing runs of each genome resulted in draft genome sequences of MY1483/09 and Phil1136/12, which covered 99.85% and 99.92% of the complete genome sequences, respectively. (
  • The B. melitensis genome sequences, and two B. abortus strains used as the outgroup strains, yielded a total of 13,728 SNP sites. (
  • DNA sequences that are not actively transcribed and that are conserved across a large number of related species are called conserved noncoding sequences ( CNS s). (
  • Various software tools also have been developed to identify regulatory regions without using sequence alignments but based on experimental features, such as coregulation, or using advanced computational methods ( MacIsaac and Fraenkel, 2006 ). (
  • Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. (
  • Electronic access to sequence alignments, experimental results and human mutations as an aid to studying globin gene regulation. (
  • Estimating statistical significance of sequence alignments. (
  • The present invention provides methods and probe nucleic acids for detecting mutant forms of target nucleic acids that comprise repetitive nucleotide sequences. (
  • The present invention relates to the detection of target nucleic acids that include repetitive nucleotide sequences. (
  • Repetitive nucleotide sequences, such as direct or inverted repeats, are observed in many organisms. (
  • Epigenetic modification is the addition of molecular tags to the DNA molecule without changing the actual DNA sequence. (
  • Deciphering the molecular mechanisms underlying the binding of the TWIST1/E12 complex to regulatory E-box sequences. (
  • Annotated sets of regulatory sequences, with well understood and independently confirmed function, are necessary to serve as gold standards to support the validation of new molecular techniques and computational algorithms. (
  • 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. (
  • The successful PhD candidate will join our newly established, multidisciplinary research group as the part of the Sheffield Institute for Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology at the University of Sheffield. (
  • Molecular and analytical tools for analyzing metatranscriptomes using high-throughput sequencing have advanced rapidly in recent years and continue to evolve and expand. (
  • Confirmatory sequencing under Good Laboratory Practice (GLP) guidelines provides confirmation of your biologic using Sanger sequencing to support FDA- and EPA- submissions. (
  • Standalone Sanger sequencing services are also available at the GLP-compliant level for integration into client analysis programs. (
  • The cloned and subcloned DNA fragments in pUC19 were sequenced by Sanger sequencing. (
  • The evolution of these sequences, that include enhancers, silencers, insulators and promoters, has progressed in multicellular organisms to the extent that cis-regulatory sequences make up as much as 10% of the human genome. (
  • Ultimately genetics researchers seeking regulatory mutations are best served by high-quality annotations of the human genome, with clearly designated functional elements. (
  • These cis-regulatory sequences include enhancers, silencers, insulators and tethering elements. (
  • Enhancers are sequences of the genome that are major gene-regulatory elements. (
  • Key to this control is the recruitment of transcription factors (TFs) that bind to regulatory sequences, such as promoters, enhancers, repressors and insulators. (
  • After locating orthologs in 11 primates spanning around 40 million years, we synthesized all orthologs as well as computational reconstructions of 9 ancestral sequences for 348 active tiles of 233 putative enhancers. (
  • This finding led to the characterization of a new class of regulatory elements, enhancers. (
  • Therefore, mutations within enhancers generally exhibit lower penetrance than mutations in coding sequences, facilitating the accumulation of variation. (
  • Non-coding cis-regulatory sequences act as the 'eyes' of the genome and their role is to perceive, organise and relay cellular communication information to RNA polymerase II at gene promoters. (
  • Multiple forms of deoxyribonucleic acid-dependent ribonucleic acid polymerase in Xenopus laevis. (
  • A nucleic acid molecule to be sequenced is exposed to a polymerase in the presence of nucleotides which are to be incorporated into a complementary nucleic acid strand. (
  • As the polymerase incorporates individual nucleic acid molecules into a complementary strand, a laser continuously irradiates the donor fluorophore, at a wavelength that causes it to emit an emission signal (but the laser wavelength does not stimulate the acceptor fluorophore). (
  • Binds to the DNA consensus sequence 5-GGTC[TC]CTAA-3. (
  • 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 . (
  • Accuracy assessment of diploid consensus sequences. (
  • Consensus methods for folding single-stranded nucleic acids. (
  • See also consensus sequence. (
  • Usually, however, the first letter is I, and both [RK] choices resolve to R. Since the last choice is so wide, the pattern IQxxxRGxxxR is sometimes equated with the IQ motif itself, but a more accurate description would be a consensus sequence for the IQ motif. (
  • Regulatory sequences are frequently associated with messenger RNA (mRNA) molecules, where they are used to control mRNA biogenesis or translation. (
  • A core set of metatranscriptomic practices can now be identified, with key steps including RNA extraction, messenger RNA (mRNA) enrichment, synthesis of complementary DNA (cDNA), shotgun sequencing of cDNA, and bioinformatic analysis of sequence data. (
  • DAS Tool for Genome Reconstruction from Metagenomes Through the JGI's Emerging Technologies Opportunity Program (ETOP), researchers have developed and improved upon a tool that combines existing DNA sequence binning algorithms, allowing them to reconstruct more near-complete genomes from soil metagenomes compared to other methods. (
  • Here, we show that large-scale chromatin opening and changes in intranuclear positioning of chromosome regions can be induced by normal levels of endogenous transcription factors acting on mammalian regulatory sequences. (
  • Our results indicate that both large-scale chromatin decondensation and changes in nuclear positioning as observed for large, complex gene-rich chromosome regions can be reproduced by endogenous regulatory sequences acting within simple repetitive transgene arrays. (
  • We found that sequence variants in splice site regions and synonymous classes captured the greatest proportion of the variance, explaining up to 50% of the variance across all traits. (
  • Some of the key data resources reporting regulatory regions and delineating specific elements are introduced below. (
  • We investigate the performance of NestedMICA in a range scenario, on synthetic data and a well-characterized set of muscle regulatory regions, and compare it with the popular MEME program. (
  • We find that both scores aid in interpreting loss-of-function mutations and in defining regions of noncoding sequence that are more likely to harbor mutations that influence risk of disease. (
  • Despite strong evidence that regulatory regions can be affected by pathogenic mutations, such as in fragile-X syndrome, β-thalassemia, Charcot-Marie-Tooth neuropathy, breast cancer and others [ 1 - 5 ], little has been done to quantify stretches of regulatory sequence in the context of both phylogenetic conservation and human-specific intolerance to variation, and then correlate it back to disease causing potential. (
  • Validating computer programs for functional genomics in gene regulatory regions. (
  • In this release, we complement HOCOMOCO by MoLoTool (Motif Location Toolbox, that applies HOCOMOCO models for visualization of binding sites in short DNA sequences. (
  • 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. (
  • We show that the new method is significantly more sensitive than MEME: in one case, it successfully extracted a target motif from background sequence four times longer than could be handled by the existing program. (
  • The BaMM web server for de-novo motif discovery and regulatory sequence analysis. (
  • In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. (
  • For example, several groups have modified promoters ( 12 , 13 ) and ribosome binding sites (RBSs) ( 14 ⇓ - 16 ) to see how small sequence changes affect transcription or translation. (
  • We identified a set of promoters where regulatory mechanisms are likely to be shared between the model organism Arabidopsis and other dicots, providing areas of focus for further research. (
  • You will learn cutting edge approaches including next-generation sequencing, non-coding RNA biology, single molecule FRET and biochemical approaches to study chromatin modifications. (
  • In fact, sequence similarity between C. elegans and the distantly related nematodes was no greater than would be expected by chance. (
  • 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. (
  • An alternative is that expression similarity is mediated by divergent regulatory processes [ 7 , 8 ], a phenomenon known as "developmental system drift" [ 9 ]. (
  • 4. The isolated nucleic acid of claim 1 , which is a cDNA. (
  • 6. The isolated nucleic acid of claim 5 , which is a cDNA. (
  • 8. The isolated nucleic acid of claim 7 , which is a cDNA. (
  • Despite knowing about these TR sequences and using them as reliable genetic markers, scientists have known very little about their actual function. (
  • We sequenced the full genome and characterised the genetic diversity of two Brucella melitensis isolates from Malaysia and the Philippines. (
  • 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 . (
  • Functional contributions of cis- regulatory sequence variations to human genetic disease are numerous. (
  • 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. (
  • To capture regulatory function that might be human-specific we formulate a novel human population genetic approach (ncRVIS). (
  • 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 ]. (
  • 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. (
  • 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. (
  • Cis-regulatory sequences also act as major functional targets of epigenetic modification thus representing an important conduit through which changes in DNA-methylation affects disease susceptibility. (
  • This suggests that the presence of σ sequences at the locus is required for the methylation changes that are observed following paramutation. (
  • 2004. CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting. (
  • Powerful comparative genomics methods, such as phylogenetic footprinting, can be used for the detection of conserved noncoding sequences ( CNS s), which are functionally constrained and can greatly help in reducing the number of false-positive elements. (
  • The second approach is based on the phylogenetic conservation of a gene's noncoding exome sequence using GERP++. (
  • While methods to assess phylogenetic conservation at a single site are established, such as GERP++ [ 6 , 7 ], purely phylogenetic approaches are at a risk of ignoring human specific regulatory sequence [ 8 , 9 ]. (
  • In Genome Biology this week: algorithm to assess regulatory features, approach to integrate multiple single-cell RNA-seq datasets, and more. (
  • 1998. Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. (
  • A greedy algorithm for aligning DNA sequences. (
  • oryzicola , and the first completely sequenced plasmid from Xanthomonas oryzae species. (
  • In an electrophoretic mobility shift assay CBP60g and SARD1 were shown to bind specifically to a 10mer oligonucleotide with the sequence GAAATTTTGG. (
  • Nucleic Acids Research, Vol. 45, Issue. (
  • Nucleic Acids Research, Vol. 46, Issue. (
  • Talks focused on regulatory issues and emerging topics in research. (
  • A comprehensive understanding of the metabolic network at the system level is particularly important for both biotechnological and biomedical research and is now made possible by rapid advances in genome sequencing and functional genomics. (
  • Nucleic Acids Research 46 (W1), pp. (
  • Nucleic Acids Research 45 (D1), pp. (
  • DOE JGI Database of DNA viruses and retroviruses debuts on IMG platform In a series of four articles published in the Database issue of the Nucleic Acids Research journal, DOE JGI researchers report on the latest updates to several publicly accessible databases and computational tools that benefit the global community of microbial researchers. (
  • Meet a JGI User: Tobias Erb "The JGI has been crucial for our research because it has provided the scientific community with a tremendous amount of gene sequences over the last couple of years. (
  • 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. (
  • 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. (
  • Here, we present a comparative analysis of the yeast Saccharomyces cerevisiae based on high-quality draft sequences of three related species (S. paradoxus, S. mikatae and S. bayanus). (
  • Regulatory sequence analysis tools. (
  • Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element. (
  • Sequence analysis revealed the presence of cepI , a luxI homolog, located 727 bp upstream and divergently transcribed from cepR . (
  • This chapter explores key questions that researchers should consider before beginning a metatranscriptomic study and then describes in detail the major steps of a sequencing-based metatranscriptomic analysis, from RNA isolation to functional and taxonomic analysis of sequence data. (
  • A typical workflow for metatranscriptome sequence analysis. (
  • This process may require months of manual exploration and validation of the sequence data, often using task-specific scripts beyond the scope of the standard analysis pipeline. (
  • Complete sequence and detailed analysis of the first indigenous plasmid from Xanthomonas oryzae pv. (
  • Comparative sequence analysis of the mouse and human Lgn1/SMA interval. (
  • Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6. (
  • Analysis of the quality and utility of random shotgun sequencing at low redundancies. (
  • A bioconductor package for analysis of high-throughput sequencing data processed by restriction enzyme digestion. (
  • Computer analysis of nucleic acid sequences. (
  • 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. (
  • 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. (
  • Evolution of Regulatory Systems in Bacteria. (
  • 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. (
  • We simulate the evolution of regulatory sequences involved in Drosophila melanogaster embryo segmentation during early development. (
  • Together, this database and its associated tools provide computational and experimental biologists with resources to predict interactions between Drosophila TFs and target cis -regulatory sequences. (
  • 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. (
  • En el 2000 logra el reconocimiento de su laboratorio como el Nodo Nacional de Bioinformática dentro de la agrupación internacional EMBNET. (
  • In three species, the identified CNS s were evaluated using TF chromatin immunoprecipitation sequencing data, resulting in significant overlap for the majority of data sets. (
  • Large-scale chromatin immunoprecipitation (ChIP) experiments provide the vast majority of data, eclipsing the compiled information of the past 25 years derived from targeted studies of specific regulatory elements. (
  • Consistent with this view, we study the evolutionary dynamics of biological regulatory sequences employing a systems level approach. (
  • To elucidate the biological functions of the plasmid, we have sequenced and comprehensively annotated the plasmid. (
  • 1998. DIALIGN: Finding local similarities by multiple sequence alignment. (
  • 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. (
  • In nature complementarity is the base principle of DNA replication and transcription as it is a property shared between two DNA or RNA sequences , such that when they are aligned antiparallel to each other, the nucleotide bases at each position in the sequences will be complementary , much like looking in the mirror and seeing the reverse of things. (
  • This complementary base pairing allows cells to copy information from one generation to another and even find and repair damage to the information stored in the sequences. (
  • Nucleic acids strands may also form hybrids in which single stranded DNA may readily anneal with complementary DNA or RNA. (
  • Two strands of complementary sequence are referred to as sense and anti-sense . (
  • While the anti-sense strand is the strand that is complementary to the sense sequence. (
  • Compared to other gene finding methods such as CRITICA our method is more suitable for exploiting sequences of low genome coverage. (
  • Here we explore the existing methods and software for prediction of functional variation situated in the cis- regulatory sequences governing gene transcription and RNA processing. (
  • Like several previous methods, NestedMICA tackles this problem by optimizing a probabilistic mixture model to fit a set of sequences. (
  • To assess the levels of contribution from information beyond conservation, we adapted CADD and GWAVA into regionalized scores in a way analogous to ncGERP by taking the average CADD and subsequently the average GWAVA score across a gene's noncoding proximal regulatory sequence as its ncCADD and ncGWAVA score, respectively (Methods). (
  • The questions and methods described here provide an introductory framework for environmental microbiologists interested in using metatranscriptome sequencing to explore microbial community gene expression. (
  • One possibility is that ancestral gene regulatory programs are strictly retained. (
  • 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. (
  • 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. (
  • Despite different sources, all isolates were identical regarding 16S rRNA gene sequences and were categorized as Geobacillus thermodenitrificans . (
  • By examining the function of cis regulatory sequences from four different nematode species in transgenic C . elegans , we sought to determine the extent of cis -regulatory conservation within this phylum. (
  • 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. (
  • Gene Ontology (GO) annotations related to this gene include nucleic acid binding and DNA-binding transcription factor activity . (
  • 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. (
  • 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 . (
  • Determining the evolutionary and functional importance of regulatory sequence composition is impeded without a detailed knowledge of the genotype-phenotype map. (
  • 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. (
  • 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. (
  • A workshop series on how to efficiently manage and analyze sequencing data. (
  • PAZAR is an open-access and open-source database of transcription factor and regulatory sequence annotation with associated web interface and programming tools for data submission and extraction. (
  • Existing regulatory sequence data collections are generated primarily in a need-driven manner. (
  • Patterns of PAX9 open-reading frame evolution.Although under tight purifying selection, PAX9 exhibits patterns of saturation and recurrent substitution contingent on the level of comparison (amino acid versus nucleotide) as well as the amount of evolutionary time considered in the data. (
  • Despite availability of vast amount of sequencing data, to date, a comprehensive map of the polyadenylation events in maize is not available. (
  • We use these data to quantify the relationship between sequence and functional divergence, and to identify CpG deamination as a potentially important force in driving changes in enhancer activity during primate evolution. (

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