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.
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.
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).
Enzymes that recombine DNA segments by a process which involves the formation of a synapse between two DNA helices, the cleavage of single strands from each DNA helix and the ligation of a DNA strand from one DNA helix to the other. The resulting DNA structure is called a Holliday junction which can be resolved by DNA REPLICATION or by HOLLIDAY JUNCTION RESOLVASES.
Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.
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).
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.
A plant species of the family POACEAE. It is a tall grass grown for its EDIBLE GRAIN, corn, used as food and animal FODDER.
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.
Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).
Nucleotide sequences repeated on both the 5' and 3' ends of a sequence under consideration. For example, the hallmarks of a transposon are that it is flanked by inverted repeats on each end and the inverted repeats are flanked by direct repeats. The Delta element of Ty retrotransposons and LTRs (long terminal repeats) are examples of this concept.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. They also have an open reading frame that is related to the reverse transcriptase of retroviruses but they do not contain LTRs (long terminal repeats). Copies of the LINE 1 (L1) family form about 15% of the human genome. The jockey elements of Drosophila are LINEs.
The genetic complement of a plant (PLANTS) as represented in its DNA.
Nucleic acid sequences involved in regulating the expression of genes.
Copies of nucleic acid sequence that are arranged in opposing orientation. They may lie adjacent to each other (tandem) or be separated by some sequence that is not part of the repeat (hyphenated). They may be true palindromic repeats, i.e. read the same backwards as forward, or complementary which reads as the base complement in the opposite orientation. Complementary inverted repeats have the potential to form hairpin loop or stem-loop structures which results in cruciform structures (such as CRUCIFORM DNA) when the complementary inverted repeats occur in double stranded regions.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
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.
Deoxyribonucleic acid that makes up the genetic material of plants.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
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.
The relationships of groups of organisms as reflected by their genetic makeup.
Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.
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.
Copies of transposable elements interspersed throughout the genome, some of which are still active and often referred to as "jumping genes". There are two classes of interspersed repetitive elements. Class I elements (or RETROELEMENTS - such as retrotransposons, retroviruses, LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS) transpose via reverse transcription of an RNA intermediate. Class II elements (or DNA TRANSPOSABLE ELEMENTS - such as transposons, Tn elements, insertion sequence elements and mobile gene cassettes of bacterial integrons) transpose directly from one site in the DNA to another.
The genetic complement of an insect (INSECTS) as represented in its DNA.
The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). It is derived from the 7SL RNA component of the SIGNAL RECOGNITION PARTICLE and contains an RNA polymerase III promoter. Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
The functional hereditary units of PLANTS.
Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.
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.
Any method used for determining the location of and relative distances between genes on a chromosome.
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.
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 INSECTS.
Chromosome regions that are loosely packaged and more accessible to RNA polymerases than HETEROCHROMATIN. These regions also stain differentially in CHROMOSOME BANDING preparations.
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.
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.
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.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
Genotypic differences observed among individuals in a population.
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
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.
Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.
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.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
DNA 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.
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.
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)
Deliberate breeding of two different individuals that results in offspring that carry part of the genetic material of each parent. The parent organisms must be genetically compatible and may be from different varieties or closely related species.
The naturally occurring transmission of genetic information between organisms, related or unrelated, circumventing parent-to-offspring transmission. Horizontal gene transfer may occur via a variety of naturally occurring processes such as GENETIC CONJUGATION; GENETIC TRANSDUCTION; and TRANSFECTION. It may result in a change of the recipient organism's genetic composition (TRANSFORMATION, GENETIC).
A genus of small free-living nematodes. Two species, CAENORHABDITIS ELEGANS and C. briggsae are much used in studies of genetics, development, aging, muscle chemistry, and neuroanatomy.
The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.
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).
The portion of chromosome material that remains condensed and is transcriptionally inactive during INTERPHASE.
A number of syndromes with defective gonadal developments such as streak GONADS and dysgenetic testes or ovaries. The spectrum of gonadal and sexual abnormalities is reflected in their varied sex chromosome (SEX CHROMOSOMES) constitution as shown by the karyotypes of 45,X monosomy (TURNER SYNDROME); 46,XX (GONADAL DYSGENESIS, 46XX); 46,XY (GONADAL DYSGENESIS, 46,XY); and sex chromosome MOSAICISM; (GONADAL DYSGENESIS, MIXED). Their phenotypes range from female, through ambiguous, to male. This concept includes gonadal agenesis.
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 systematic study of the complete DNA sequences (GENOME) of organisms.
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)
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.
Interruption or suppression of the expression of a gene at transcriptional or translational levels.
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.
A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.
An aberration in which a chromosomal segment is deleted and reinserted in the same place but turned 180 degrees from its original orientation, so that the gene sequence for the segment is reversed with respect to that of the rest of the chromosome.
A family of RNA-binding proteins that has specificity for MICRORNAS and SMALL INTERFERING RNA molecules. The proteins take part in RNA processing events as core components of RNA-induced silencing complex.
The only genus in the family Oryziinae, order BELONIFORMES. Oryzias are egg-layers; other fish of the same order are livebearers. Oryzias are used extensively in testing carcinogens.
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.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
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.
Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.
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.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.
Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.
Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.
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.
Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.
Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.
The complete gene complement contained in a set of chromosomes in a fungus.
ANIMALS whose GENOME has been altered by GENETIC ENGINEERING, or their offspring.
Color of the iris.
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.
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.
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
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.
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
Recombinases that involved in the propagation of DNA TRANSPOSONS. They bind to transposon sequences found at two different sites along the same stretch of DNA and bring them into close proximity. The enzymes then catalyze the double strand cleavage, exchange of double strands and rejoining of DNA helices so that the DNA transposon is formed into a circular PLASMID.
The amount of DNA (or RNA) in one copy of a genome.
A class of enzymes that transfers nucleotidyl residues. EC 2.7.7.
Structures within the CELL NUCLEUS of insect cells containing DNA.
A group of FLAVONOIDS derived from FLAVONOLS, which lack the ketone oxygen at the 4-position. They are glycosylated versions of cyanidin, pelargonidin or delphinidin. The conjugated bonds result in blue, red, and purple colors in flowers of plants.
The reproductive cells in multicellular organisms at various stages during GAMETOGENESIS.
A group of chemical elements that are needed in minute quantities for the proper growth, development, and physiology of an organism. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
A plant genus of the family POACEAE. The grain is used for FOOD and for ANIMAL FEED. This should not be confused with KAFFIR LIME or with KEFIR milk product.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
A computer based method of simulating or analyzing the behavior of structures or components.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.
Retroviruses that have integrated into the germline (PROVIRUSES) that have lost infectious capability but retained the capability to transpose.
Substances that comprise all matter. Each element is made up of atoms that are identical in number of electrons and protons and in nuclear charge, but may differ in mass or number of neutrons.
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.
The functional hereditary units of BACTERIA.
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 presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.
Databases devoted to knowledge about specific genes and gene products.
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.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.
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.
The female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in human and other male-heterogametic species.
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.
Deoxyribonucleic acid that makes up the genetic material of fungi.
Deletion of sequences of nucleic acids from the genetic material of an individual.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
Mutation process that restores the wild-type PHENOTYPE in an organism possessing a mutationally altered GENOTYPE. The second "suppressor" mutation may be on a different gene, on the same gene but located at a distance from the site of the primary mutation, or in extrachromosomal genes (EXTRACHROMOSOMAL INHERITANCE).
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
The deletion and reinsertion of a segment of a nucleic acid sequence in the same place, but flipped in an opposite orientation.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
A pyrimidine base that is a fundamental unit of nucleic acids.
A subfamily in the family ATELIDAE, comprising three genera: woolly monkeys (Lagothrix), spider monkeys (Ateles), and woolly spider monkeys (Brachyteles).
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 genus of silkworm MOTHS in the family Bombycidae of the order LEPIDOPTERA. The family contains a single species, Bombyx mori from the Greek for silkworm + mulberry tree (on which it feeds). A native of Asia, it is sometimes reared in this country. It has long been raised for its SILK and after centuries of domestication it probably does not exist in nature. It is used extensively in experimental GENETICS. (From Borror et al., An Introduction to the Study of Insects, 4th ed, p519)
Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)
A small order of primarily marine fish containing 340 species. Most have a rotund or box-like shape. TETRODOTOXIN is found in their liver and ovaries.
A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.
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.
The occurrence in an individual of two or more cell populations of different chromosomal constitutions, derived from a single ZYGOTE, as opposed to CHIMERISM in which the different cell populations are derived from more than one zygote.
A family of flowering plants in the order Caryophyllales, with about 60 genera and more than 800 species of plants, with a few shrubs, trees, and vines. The leaves usually have nonindented edges.
A plant genus of the family POLYGONACEAE that contains patientosides and other naphthalene glycosides.
Copies of DNA sequences which lie adjacent to each other in the same orientation (direct tandem repeats) or in the opposite direction to each other (INVERTED TANDEM REPEATS).
The male sex chromosome, being the differential sex chromosome carried by half the male gametes and none of the female gametes in humans and in some other male-heterogametic species in which the homologue of the X chromosome has been retained.
Genes that are introduced into an organism using GENE TRANSFER TECHNIQUES.
Plants or plant parts which are harmful to man or other animals.
A large family of narrow-leaved herbaceous grasses of the order Cyperales, subclass Commelinidae, class Liliopsida (monocotyledons). Food grains (EDIBLE GRAIN) come from members of this family. RHINITIS, ALLERGIC, SEASONAL can be induced by POLLEN of many of the grasses.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
The genetic complement of a BACTERIA as represented in its DNA.
The discipline studying genetic composition of populations and effects of factors such as GENETIC SELECTION, population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES.
Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
A subclass of histone deacetylases that are NAD-dependent. Several members of the SIRTUINS family are included in this subclass.
The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.
Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
A zinc-containing enzyme which oxidizes primary and secondary alcohols or hemiacetals in the presence of NAD. In alcoholic fermentation, it catalyzes the final step of reducing an aldehyde to an alcohol in the presence of NADH and hydrogen.
Established cell cultures that have the potential to propagate indefinitely.
The clear constricted portion of the chromosome at which the chromatids are joined and by which the chromosome is attached to the spindle during cell division.
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)
Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.
The fluctuation of the ALLELE FREQUENCY from one generation to the next.
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.
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.
Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.
A plant genus of the family CARYOPHYLLACEAE. The common name of campion is also used with LYCHNIS. The common name of 'pink' can be confused with other plants.
A nucleic acid sequence that contains an above average number of GUANINE and CYTOSINE bases.
A genus of short-tailed OPOSSUMS in the family Didelphidae found in South American, chiefly Brazil. They are opossums least well-adapted to arboreal life.
The asymmetrical segregation of genes during replication which leads to the production of non-reciprocal recombinant strands and the apparent conversion of one allele into another. Thus, e.g., the meiotic products of an Aa individual may be AAAa or aaaA instead of AAaa, i.e., the A allele has been converted into the a allele or vice versa.
Highly repetitive DNA sequences found in HETEROCHROMATIN, mainly near centromeres. They are composed of simple sequences (very short) (see MINISATELLITE REPEATS) repeated in tandem many times to form large blocks of sequence. Additionally, following the accumulation of mutations, these blocks of repeats have been repeated in tandem themselves. The degree of repetition is on the order of 1000 to 10 million at each locus. Loci are few, usually one or two per chromosome. They were called satellites since in density gradients, they often sediment as distinct, satellite bands separate from the bulk of genomic DNA owing to a distinct BASE COMPOSITION.
Sequential operating programs and data which instruct the functioning of a digital computer.
An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.
Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.
An enzyme that synthesizes DNA on an RNA template. It is encoded by the pol gene of retroviruses and by certain retrovirus-like elements. EC 2.7.7.49.
A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.
Enzymes that catalyze the incorporation of deoxyribonucleotides into a chain of DNA. EC 2.7.7.-.
A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.
The functional hereditary units of FUNGI.
PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.
Actual loss of portion of a chromosome.
Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young.
A plant genus of the family SOLANACEAE. Members contain NICOTINE and other biologically active chemicals; its dried leaves are used for SMOKING.
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)
The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.
A species of mosquito in the genus Anopheles and the principle vector of MALARIA in Africa.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
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 ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.
A plant genus of the family POACEAE that is the source of EDIBLE GRAIN. A hybrid with rye (SECALE CEREALE) is called TRITICALE. The seed is ground into FLOUR and used to make BREAD, and is the source of WHEAT GERM AGGLUTININS.
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)
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.
Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.
Short RNA, about 200 base pairs in length or shorter, that does not code for protein.
The common chimpanzee, a species of the genus Pan, family HOMINIDAE. It lives in Africa, primarily in the tropical rainforests. There are a number of recognized subspecies.
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 determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.
A parasexual process in BACTERIA; ALGAE; FUNGI; and ciliate EUKARYOTA for achieving exchange of chromosome material during fusion of two cells. In bacteria, this is a uni-directional transfer of genetic material; in protozoa it is a bi-directional exchange. In algae and fungi, it is a form of sexual reproduction, with the union of male and female gametes.
BEETLES in the family Curculionidae and the largest family in the order COLEOPTERA. They have a markedly convex shape and many are considered pests.
A genus of mosquitoes (CULICIDAE) frequently found in tropical and subtropical regions. YELLOW FEVER and DENGUE are two of the diseases that can be transmitted by species of this genus.
The reproductive organs of plants.
... transposable elements that are mobile fragments of DNA, most of which are nonfunctional in humans; and pseudogenes, ... Susumu Ohno coined the phrase "junk DNA" to describe these nonfunctional swaths of DNA. They include introns, genetic sequences ... variation in rates of turnover across functional element classes in the human lineage". PLOS Genetics. 10 (7): e1004525. doi: ... While the C-value paradox unraveled with the discovery of massive sequences of noncoding DNA, resolution of the G-value paradox ...
A transposable element (TE or transposon) is a DNA sequence that can change its position within a genome, sometimes creating or ... Transposable elements make up a large fraction of the genome and are responsible for much of the mass of DNA in a eukaryotic ... The most common transposable element in humans is the Alu sequence. It is approximately 300 bases long and can be found between ... When the transposable elements lack additional genes, they are known as insertion sequences. ...
Transposable elements Barbara McClintock discovered transposable elements (also known as transposons and jumping genes), DNA ... sequences which change their position within the genome. Transposons make up a large fraction of the DNA in eukaryotic cells ( ... The existence of this element was predicted by Dmitri Mendeleev. Ida Noddack was nominated three times for the Nobel Prize in ... Mills, R.E., Bennett, E.A., Iskow, R.C. and Devine, S.E. (2007). "Which transposable elements are active in the human genome ...
... s are a superfamily of DNA transposons, or Class II transposable elements, that are common in the genomes of ... "A resurrected mammalian hAT transposable element and a closely related insect element are highly active in human cell culture ... Superfamilies are identified by shared DNA sequence and ability to respond to the same transposase. Common features of hAT ... Although no extant active example is known, laboratory-generated consensus sequences of active SPIN elements are able to ...
... : a retrotransposon of Drosophila combining structural features of DNA viruses, retroviruses and non-viral transposable ... Retrotransposon-like sequences are expressed in Y chromosomal lampbrush loops of Drosophila hydei. J Mol Biol 203:689-97. ... The name micropia is an artificial word, i.e. a concoction of "microcloning" and "copia-like element". Huijser, P., C. ... elements. J Mol Biol 204:233-46. Lankenau, S., V. G. Corces, and D. H. Lankenau. 1994. The Drosophila micropia retrotransposon ...
DNA methylation frequently occurs in repeated sequences, and helps to suppress the expression and mobility of 'transposable ... Slotkin RK, Martienssen R (April 2007). "Transposable elements and the epigenetic regulation of the genome". Nature Reviews ... An epigenetically inherited element such as the PSI+ system can act as a "stop-gap", good enough for short-term adaptation that ... Leonhardt H, Page AW, Weier HU, Bestor TH (November 1992). "A targeting sequence directs DNA methyltransferase to sites of DNA ...
Transposable elements (TEs) include a wide variety of DNA sequences that all have the ability to move to new locations in the ... Transposable elements[edit]. Transposable elements self-replicate through two main mechanisms: via an RNA intermediate ("copy- ... Transposable elements[edit]. To model the dynamics of transposable elements (TEs) within a genome, one has to realize that the ... While many transposable elements seem to do no good for the host, some transposable elements have been "tamed" by molecular ...
Transposable elements-repetitious sequences of DNA that can insert themselves into any part of the genome-can encourage ectopic ... and have mutation rates high enough to disrupt the homology between transposable element sequences sufficiently to prevent ... The frequency of ectopic recombination of transposable elements has been linked to both higher copy numbers of transposable ... A test for the role of natural selection in the stabilization of transposable element copy number in a population of Drosophila ...
The repeated DNA sequence includes short repetitive sequences, transposable elements (including insertion sequence elements, ... and a greatly amplified integrative and conjugative element (ICE) called the rickettsial amplified genetic element (RAGE). RAGE ... With a genome of only 2.0-2.7 Mb, it has the most repeated DNA sequences among bacterial genomes sequenced so far. The disease ... With about 42-47% of repetitive sequences, O. tsutsugamushi has the most highly repeated bacterial genome sequenced as of 2013 ...
... interspersed repetitive sequences MeSH G06.184.603.080.708.330.200 - dna transposable elements MeSH G06.184.603.080.708.330. ... vitamin d response element MeSH G06.184.603.080.689.675.850 - TATA box MeSH G06.184.603.080.689.687 - regulatory sequences, ... alu elements MeSH G06.184.603.080.708.800 - tandem repeat sequences MeSH G06.184.603.080.708.800.140 - dna repeat expansion ... base sequence MeSH G06.184.603.080.040 - at rich sequence MeSH G06.184.603.080.380 - gc rich sequence MeSH G06.184.603.080. ...
They are class II transposable elements (TEs) that move through a DNA intermediate, as opposed to class I TEs, retrotransposons ... Dfam, a database of repeating DNA sequences Repbase, a database and classification system for repeating DNA sequences DNA ... The transposase enzyme then disconnects the element from the flanking DNA of the original donor site and mediates the joining ... DNA transposons can move in the DNA of an organism via a single-or double-stranded DNA intermediate. DNA transposons have been ...
Repression of transposable elements[edit]. DNA methylation is a powerful transcriptional repressor, at least in CpG dense ... or DNA sequencing (MeDIP-seq).. *Pyrosequencing of bisulfite treated DNA. This is sequencing of an amplicon made by a normal ... DNA methylation is a process by which methyl groups are added to the DNA molecule. Methylation can change the activity of a DNA ... Abbreviations: S-Adenosyl-L-homocysteine (SAH), S-adenosyl-L-methionine (SAM), DNA methyltransferase (DNA MTase), Uracil-DNA ...
Alu sequences, classified as a short interspersed nuclear element, are the most abundant mobile elements in the human genome. ... that the majority of non-coding DNA in large genomes finds its origin in the selfish amplification of transposable elements, of ... Non-coding DNA sequences are components of an organism's DNA that do not encode protein sequences. Some non-coding DNA is ... protein-coding DNA sequences account for only about 20% of conserved DNA, with the remaining 80% of conserved DNA represented ...
Transposable elements (TEs) include a wide variety of DNA sequences that all have the ability to move to new locations in the ... introns as mobile genetic elements Junk DNA Mobile genetic elements Mutation Noncoding DNA Retrotransposon Transposable element ... While many transposable elements seem to do no good for the host, some transposable elements have been "tamed" by molecular ... B chromosomes and transposable elements. The contribution of transposable elements to the genome is especially well studied in ...
DNA methylation frequently occurs in repeated sequences, and helps to suppress the expression and mobility of 'transposable ... Slotkin RK, Martienssen R (April 2007). "Transposable elements and the epigenetic regulation of the genome". Nature Reviews ... An epigenetically inherited element such as the PSI+ system can act as a "stop-gap", good enough for short-term adaptation that ... DNA damageEdit. DNA damage can also cause epigenetic changes.[25][26][27] DNA damage is very frequent, occurring on average ...
Transposable elements (TEs) are sequences of DNA with a defined structure that are able to change their location in the genome ... Retrotransposon is a transposable element that transpose through an RNA intermediate. Retrotransposons are composed of DNA, but ... Noncoding sequences include introns, sequences for non-coding RNAs, regulatory regions, and repetitive DNA. Noncoding sequences ... genomecenter.howard.edu Build a DNA Molecule Some comparative genome sizes DNA Interactive: The History of DNA Science DNA From ...
Repetitive DNA is not easily analysed by next generation DNA sequencing methods, which struggle with homopolymeric tracts. ... Almost 50% of the human genome is contained in various types of transposable elements (also called transposons, or 'jumping ... Junk DNA. *Long interspersed repetitive element. *Microsatellite instability. *Mobile element. *Short interspersed repetitive ... Repetitive DNA is not easily analysed by next generation DNA sequencing methods, which struggle with homopolymeric tracts. ...
Deniz Ö, Frost JM, Branco MR (July 2019). "Regulation of transposable elements by DNA modifications". Nature Reviews. Genetics ... In the second part of the pathway, the RdDM DNA methylation machinery is guided to DNA sequences complementary to the sRNAs ... "ARGONAUTE 6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation". The EMBO Journal. 34 (1 ... RdDM plays a key role in silencing these mobile DNA elements in plants by adding DNA methylation over new TE insertions and ...
... is a transposable element, which is a sequence of DNA that is capable of mediating its own movement from one position in ... Tn10 has a composite structure and it is composed of a pair of insertion sequence elements (IS10) flanking five genes. Only one ... The transposase protein recognizes the ends of the element and cuts it from the original locus. The protein-DNA complex then ... Two comprehensive reviews of Tn10 biology are available as chapters in the book Mobile DNA and Mobile DNA II. Bender J, ...
Insertions can be reversed by excision of the transposable element. Deletions remove one or more nucleotides from the DNA. Like ... Molecular sequence analysis: With rapid development of DNA sequencing technology, an enormous amount of DNA sequence data is ... They are usually caused by transposable elements, or errors during replication of repeating elements. Insertions in the coding ... Various methods have been developed to infer the DFE from DNA sequence data. By examining DNA sequence differences within and ...
Families of transposable elements-derived lincRNAs have been implicated in the regulation of pluripotency. Human pluripotency- ... "Intergenic" refers to long non-coding RNAs that are transcribed from non-coding DNA sequences between protein-coding genes, ... Sonic hedgehog induces transcription of Evf-2 from an ultra-conserved element located between the Dlx5 and Dlx6 genes during ... Large-scale sequencing of cDNA libraries and more recently transcriptomic sequencing by next generation sequencing indicate ...
A transposable element (TE, transposon, or jumping gene) is a DNA sequence that can change its position within a genome, ... Transposable elements make up a large fraction of the genome and are responsible for much of the mass of DNA in a eukaryotic ... When the transposable elements lack additional genes, they are known as insertion sequences. In humans, the most common TE is ... Decrease in DNA Methylation I (DDM1) Evolution of sexual reproduction Insertion sequence Intragenomic conflict P element ...
The transposable P elements, also known as transposons, are segments of bacterial DNA that are translocated into the genome, ... Additionally, P elements often consist of two plasmid components, one known as the P element transposase and the other, the P ... Transgene describes a segment of DNA containing a gene sequence that has been isolated from one organism and is introduced into ... P elements are administered in pairs of two, which flank the DNA insertion region of interest. ...
... an insertion sequence element, or an IS element) is a short DNA sequence that acts as a simple transposable element. Insertion ... certain eukaryotic DNA sequences belonging to the family of Tc1/mariner transposable elements may be considered to be, ... DNA composition). Mobile genetic elements Mahillon, Jacques; Chandler, Michael (1998-09-01). "Insertion Sequences". ... sequences have two major characteristics: they are small relative to other transposable elements (generally around 700 to 2500 ...
... are a group of non-autonomous Class II transposable elements (DNA sequences). Being non-autonomous, MITEs cannot code for their ... One type of autonomous element can give rise to one or more MITE families. Based on their relations in sequences of TIRs with ... "Miniature inverted-repeat transposable elements (MITEs) and their relationship with established DNA transposons". In Craig N, ... Lu C, Chen J, Zhang Y, Hu Q, Su W, Kuang H (March 2012). "Miniature inverted-repeat transposable elements (MITEs) have been ...
However, using transposable element can bring more advantages. Transposable elements were first discovered by Barbara ... "DNA sequencing How to determine the sequence of bases in a DNA molecule". Archived from the original on 2013-10-21. Retrieved ... The size of transposable element is between 750 and 40000bp. Transposable element can be mainly classified as two classes: One ... Genome survey sequencing is a new way to map the genome sequences since it is not dependent on mRNA. Current genome sequencing ...
There are three major classes of transposable elements, distinguished by the mechanisms by which they proliferate. DNA ... Integrase, an enzyme encoded by the LTR retrotransposon, then reincorporates the element at a new target site. These elements ... A conserved non-coding sequence (CNS) is a DNA sequence of noncoding DNA that is evolutionarily conserved. These sequences are ... The elements produced by this process are called SINEs. When conserved regulatory transposable elements are active in a genome ...
Insertions add one or more extra nucleotides into the DNA. They are usually caused by transposable elements, or errors during ... Molecular sequence analysis: With rapid development of DNA sequencing technology, an enormous amount of DNA sequence data is ... Insertions can be reversed by excision of the transposable element.. *Deletions remove one or more nucleotides from the DNA. ... Various methods have been developed to infer the DFE from DNA sequence data.[81][82][83][84] By examining DNA sequence ...
Tn3 and related transposable elements: site-specific recombination and transposition. In Berg, D. E., Howe, M. (eds) Mobile DNA ... Akopian A, He J, Boocock MR, Stark WM (July 2003). "Chimeric recombinases with designed DNA sequence recognition". Proc. Natl. ... The Tn3 transposon is a 4957 base pair mobile genetic element, found in prokaryotes. It encodes three proteins: β-lactamase, an ... 163-184 4.Grindley, N.D.F. (2002). The movement of Tn3-like elements: transposition and cointegrate resolution. In Mobile DNA ...
The presence of transposable elements is another influential element of non-homologous crossover. Repetitive regions of code ... Most DNA is composed of base pair sequences repeated very large numbers of times.[24] These repetitious segments, often ... This is done by comparing the occurrence of a specific DNA sequence with the appearance of a disease. When a high correlation ... DNA repair theory[edit]. Crossing over and DNA repair are very similar processes, which utilize many of the same protein ...
The terminal inverted repeats are 80% AT-rich, are 96.6% identical, and define a larger family of repetitive elements. Southern ... A dispersed family of repetitive DNA sequences exhibits characteristics of a transposable element in the genus Lycopersicon.. R ... A dispersed family of repetitive DNA sequences exhibits characteristics of a transposable element in the genus Lycopersicon.. R ... A dispersed family of repetitive DNA sequences exhibits characteristics of a transposable element in the genus Lycopersicon.. R ...
1988 Molecular study of the retrovirus-like transposable element 412, a 20-OH ecdysone responsive repetitive sequence in ... 1985 Extrachromosomal DNA forms of copia-like transposable elements, F elements and middle repetitive DNA sequences in ... 1982; Engel 1988). P elements were later shown to be DNA transposons (TEs that transpose via a DNA intermediary) and I elements ... sequences derived from TEs, but no longer recognizable as TEs and that appear as "unique" DNA sequences), non-TE sequences ...
One class of sequence elements that is enriched in lncRNA is represented by transposable elements (TEs), repetitive mobile ... Keywords: evolution; functional domain; genome; lncRNA; long noncoding RNA; repeat element; transposable element; transposon. ... DNA-, and protein-binding domains. We propose that these reflect a more general phenomenon of exaptation during lncRNA ... The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs RNA. 2014 Jul;20(7):959-76. doi: ...
These events create ragged transitions between unique and repetitive sequences in the zone between euchromatic and beta … ... restructuring of the genomic landscape by transposition and duplication has recently added hundreds of kilobases of TE sequence ... Base Sequence * Centromere / genetics * Chromosomes / genetics * DNA Transposable Elements / genetics* * Drosophila ... Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome ...
... was sequenced. Totally, 92- and 84.3-Gb sequence data were obtained and assembled to 137,772 and 149,997 contigs with a N50 ... Distribution pattern of DNA transposons in the genomes of dromedary, Bactrian, and cattle was similar in contrast with LINE, ... were sequenced. Totally, 92 and 84.3 Gb sequence data were obtained and assembled to 137772 and 149997 contigs with a N50 ... along with simple sequence repeats (SSRs) are prevalent in eukaryotic genome, especially in mammals. Repetitive sequences form ...
Transposable elements (TEs) are genomic parasites with major impacts on host genome architecture and host adaptation. A proper ... From: Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes ...
Transposable elements (TEs) are DNA sequences that colonize every genome and have a great impact on the genome evolution and ... the P element (37), the hobo element (38), and the I element (39). It has also been shown experimentally that D. melanogasters ... Transposable elements (TEs) are repeated DNA sequences that can constitute a substantial part of genomes. Studying TEs ... 1997) Testing transposable elements as genetic drive mechanisms using Drosophila P elements constructs as a model system. ...
... sequences predominated. At the chromosomal level, different TE clones demonstrated sequence-specific patterning, emphasizing ... Individual genotypes were analyzed cytogenetically using the cloned TE fragments as the DNA probes for fluorescence in situ ... Altogether, the obtained data highlight the current species-specific organization and patterning of the mobile element fraction ... transposable elements (TEs)-is a prevailing genomic fraction in cereals that underlies extensive genome reshuffling and ...
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 ... Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been ... DNA; Insertion Sequence Element; Sequence Element, Insertion; Tn Element; Transposable Element, DNA; Transposable Elements, DNA ...
Plant Transposable Elements von - Englische E-Books aus der Kategorie Biologie günstig bei exlibris.ch kaufen & sofort ... junk DNA.. Klappentext. Transposable elements are DNA sequences with the capacity to move within a genome. Although their ... How to classify transposable elements.- Transposable element annotation in completely sequenced eukaryote genomes.- Using ... Transposable elements are short lengths of DNA with the capacity to move between different points within a genome. This process ...
... in all sequence contexts [8]. Considering that DNA demethylation or hypermethylation of transposable element sequences is ... The prevalence of transposable elements and their inherent sequence similarity makes them a prime target for illegitimate and ... The bias of methylation toward repetitive DNA suggests that silencing of transposable elements is one of the primary roles of ... F. Sabot, R. Guyot, T. Wicker et al., "Updating of transposable element annotations from large wheat genomic sequences reveals ...
Publications] S. Takahashi: Capturing of a genomic HMG domain sequence by an En/Spm related transposable element Tpnl in the ... The major DNA-based controlling transposable elements in higher plants can be classified into three groups : the Ac/Ds (or hAT ... Publications] S.Takahashi: Capturing of a genomic HMG domain sequence by an En/Spm related transposable element Tpnl in the ... Transposition and gene regulation of DNA transposable elements in plants. Research Project ...
Amino acid sequence of a putative transposase protein of the medaka fish transposable element Tol2 deduced from mRNA nucleotide ... DNA-based transposable elements. Four major classes of transposable elements are known: viral family retrotransposons, long ... DNA-based transposable elements appear to have been nearly or completely inactivated in vertebrates. Therefore the elements of ... interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs) and DNA-based transposable elements. The ...
This ability can be harmful for hosts if transposable elements destroy functioning genes, but it can also bring advantages. ... From an evolutionary point of view, transposable elements diversify the genome and open up chances for adaptation. ... Transposable elements are DNA sequences that are capable of changing their genome position by cut and paste or copy and paste ... Transposable elements are DNA sequences that are capable of changing their genome position by cut and paste or copy and paste ...
Satellite DNA Sequences Have No Known Function *The Evolution of Genomes Has Been Accelerated by Transposable Elements ... Transpositional Recombination Can Insert a Mobile Genetic Element into Any DNA Sequence ... Some Transposable Elements Are Close Relatives of Retroviruses *Other Transposable Elements Transfer Themselves Directly from ... Tandemly Repeated DNA Sequences Tend to Remain the Same *The Evolution of the Globin Gene Family Shows How Random DNA ...
A transposable element (TE or transposon) is a DNA sequence that can change its position within a genome, sometimes creating or ... Transposable elements make up a large fraction of the genome and are responsible for much of the mass of DNA in a eukaryotic ... The most common transposable element in humans is the Alu sequence. It is approximately 300 bases long and can be found between ... When the transposable elements lack additional genes, they are known as insertion sequences. ...
Sequence Analysis.. DNA sequence data was compiled by using gcg software. Short sequence repeats were identified by the ... The Cs1 element is bordered by a 20-bp perfect TIR sequence that contains conserved 5′-CACTA-3′ ends. Most other CACTA elements ... Sequence analysis of Candystripe1 reveals several features that are conserved among transposable elements of the En/Spm family ... 2A). However, because no landmarks of a transposable element were identified in this sequence, we further isolated the 3′ end ...
Base Sequence. Color. Cryptochromes. DNA Transposable Elements / physiology. DNA-Binding Proteins / physiology*. Flavoproteins ... 1989;The ocs-element is a component of the promoters of several T-DNA and plant viral genes.Embo J 8:4197-4204. [pmid: 2591372] ... 0/Arabidopsis Proteins; 0/CRY1 protein, Arabidopsis; 0/Cryptochromes; 0/DNA Transposable Elements; 0/DNA-Binding Proteins; 0/ ... Genomic regions flanking the T-DNA insertions in the hfr1-23 mutants were isolated by PCR [42]. All primer sequences are shown ...
Chromothripsis is a mutational event driven by tens to hundreds of double-stranded DNA breaks which occur in a single event ... Ewing AD (2015) Transposable element detection from whole genome sequence data. BMC Mobile DNA 6:24. https://doi.org/10.1186/ ... Burns KH (2017) Transposable elements in cancer. Nat Rev Cancer 17:415-424. https://doi.org/10.1038/nrc.2017.35 CrossRefPubMed ... Mathias SL, Scott AF, Kazazian HH et al (1991) Reverse transcriptase encoded by a human transposable element. Science 254:1808- ...
DNA Transposable Elements (Structure) -2 key features. -inverted repeat sequences at terminal ends of element. -gene that ... structurally similar to DNA transposons: the ends of the element contain repeated DNA sequences and the body of the element ... transposable elements insert themselves randomly in the genome. -if an element drops into and disrupts a coding sequence (exon ... determined sequence of P-element -molecular methods could be employed to determine the location of the P-element in the genome ...
A genome of 534 Mb was assembled from long read PacBio DNA sequencing of DNA from a highly inbred strain. Analysis of molecular ... The C. hominivorax genome was searched for repetitive DNA sequences including transposable elements. Repetitive sequences were ... RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl Acad. Sci. USA https://doi.org/ ... Of the transposable elements, the most abundant were DNA elements (6.9% of the genome) and LINEs (2.3% genome; Supplementary ...
We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the ... assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of ... Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional ... transposable elements; Class I LTR-retrotransposons; Class II DNA transposons; transcriptome; expressed sequence tags; ...
DNA sequences) can actually change position in the chromosomes. These mobile DNA sequences are calle ... Ty elements transpose by making RNA copies of the integrated DNA sequence and then creating a new Ty element by reserve ... DNA sequences) can actually change position in the chromosomes. These mobile DNA sequences are called transposable elements or ... DNA sequences) can actually change position in the chromosomes. These mobile DNA sequences are called transposable elements or ...
One form of hemophilia is due to the insertion of a transposable genetic element. (DNA sequence that can be copied and moved in ... see also Blotting; Disease, Genetics of; Genetic Counseling; Inheritance Patterns; Mutation; Transposable Genetic Elements; X ... Using DNA testing (direct analysis of the genes), it is possible to determine whether a woman is a "carrier" of the hemophilia ... Linkage analysis using DNA polymorphisms to track defective FVIII or FIX genes is possible in large families. Use of intragenic ...
A large variety of DNA molecules, derived as restriction fragments from both prokaryotic (Ross et al., 1982; Stellwagen, 1983; ... Garrett, J.E. and Carroll, D. (1986). Txl: a transposable element from Xenopus laevis with some unusual properties. Mol. Cell. ... Clustered and interspersed repetitive DNA sequence family of Chironomus: the nucleotide sequence of the Cla-elements and of ... Hagerman P.J. (1988) Sequence-Dependent Curvature of DNA. In: Wells R.D., Harvey S.C. (eds) Unusual DNA Structures. Springer, ...
Dna array explanation free. What is Dna array? Meaning of Dna array medical term. What does Dna array mean? ... Looking for online definition of Dna array in the Medical Dictionary? ... See also retrotransposon and transposable genetic elements.. open DNA complex. a local opening of about 10 base pairs formed at ... repeat DNA, repetitive DNA. includes (a) satellite DNA and so-called (b) interspersed repeated DNA sequences. The latter are ...
... transposable elements that are mobile fragments of DNA, most of which are nonfunctional in humans; and pseudogenes, ... Susumu Ohno coined the phrase "junk DNA" to describe these nonfunctional swaths of DNA. They include introns, genetic sequences ... variation in rates of turnover across functional element classes in the human lineage". PLOS Genetics. 10 (7): e1004525. doi: ... While the C-value paradox unraveled with the discovery of massive sequences of noncoding DNA, resolution of the G-value paradox ...
... are a group of non-autonomous Class II transposable elements (DNA sequences). Being non-autonomous, MITEs cannot code for their ... One type of autonomous element can give rise to one or more MITE families. Based on their relations in sequences of TIRs with ... "Miniature inverted-repeat transposable elements (MITEs) and their relationship with established DNA transposons". In Craig N, ... Lu C, Chen J, Zhang Y, Hu Q, Su W, Kuang H (March 2012). "Miniature inverted-repeat transposable elements (MITEs) have been ...
Simsek, M.; DasSarma, S.; RajBhandary, U. L.; Khorana, H. G. (1982-12-01). "A transposable element from Halobacterium halobium ... Berquist, Brian R.; DasSarma, Shiladitya (2003-10-15). "An Archaeal Chromosomal Autonomously Replicating Sequence Element from ... "High-frequency spontaneous mutation in the bacterio-opsin gene in Halobacterium halobium is mediated by transposable elements ... and DNA repair systems. DasSarmas recent research (2010s) on an Antarctic halophilic microorganism, Halorubrum lacusprofundi ...
  • The idea that some genetic factors are able to move around chromosomes emerged more than 60 years ago when Barbara McClintock first suggested that such elements existed and had a major role in controlling gene expression and that they also have had a major influence in reshaping genomes in evolution. (genetics.org)
  • Today, we recognize that the findings about genomic changes affected by transposable elements have considerably altered our view of the ways in which genomes evolve and work. (genetics.org)
  • The recent availability of genome sequences has provided unparalleled insights into the broad-scale patterns of transposable element (TE) sequences in eukaryotic genomes. (nih.gov)
  • Nevertheless, the difficulties that TEs pose for genome assembly and annotation have prevented detailed, quantitative inferences about the contribution of TEs to genomes sequences. (nih.gov)
  • Repetitive sequences form approximately one-third of the camelid genomes, so study on this part of genome can be helpful in providing deeper information from the genome and its evolutionary path. (frontiersin.org)
  • Contrary to the observed results in the genomes of cattle, sheep, horse, and pig, no endogenous retrovirus-K (ERVK) elements were found in the camel genome. (frontiersin.org)
  • Distribution pattern of DNA transposons in the genomes of dromedary, Bactrian, and cattle was similar in contrast with LINE, SINE, and long terminal repeat (LTR) families. (frontiersin.org)
  • Elements like RTE-BovB belonging to LINEs family in cattle and sheep genomes are dramatically higher than genome of dromedary. (frontiersin.org)
  • Transposable elements (TEs) are repeated DNA sequences that can constitute a substantial part of genomes. (pnas.org)
  • TEs are mobile DNA sequences able to invade populations and to duplicate within genomes by various molecular mechanisms ( 2 ) and can be found in multiple copies in virtually all living species. (pnas.org)
  • Although most prokaryotes harbor only a few insertion sequences, large eukaryotic genomes (including plants, amoeba, or animals) may contain up to 80% of TE-derived sequences. (pnas.org)
  • In plants, TEs comprise up to 80% of the genomes, with prevailing long terminal repeat (LTR) families of Ty1- copia and Ty3- gypsy retrotransposons [ 2 , 3 ], which vary extensively in their sequence motifs and abundances, even between closely related species [ 4 , 5 ]. (hindawi.com)
  • The present book gives an overview of the impact of transposable elements on plant genomes and explains how to recognize and study transposable elements, e.g. by using state-of-the-art strategies like 'new generation sequencing. (exlibris.ch)
  • Transposable element annotation in completely sequenced eukaryote genomes. (exlibris.ch)
  • Transposable elements are present in multicopies in host genomes and, in many cases, albeit not all, autonomous copies exist including a gene for their own transposase. (bioone.org)
  • Before and after the exposure, they sequence the flies' genomes. (phys.org)
  • Transposable elements have contributed to the evolution of the genomes through induction of chromosomal rearrangements. (ukessays.com)
  • Eukaryotic genomes are usually littered with transposable elements (TEs) and repeats, which pose threats to genome stability due to their tendency to move or recombine. (prolekare.cz)
  • The nucleosome is a fundamental structural and functional chromatin unit that affects nearly all DNA-templated events in eukaryotic genomes. (plantphysiol.org)
  • Eukaryotic genomes consist of DNA that is packaged together with histone proteins into chromatin. (plantphysiol.org)
  • A substantial portion of animal genomes is composed of repetitive sequences, including gene duplicates, satellite DNA, and transposable elements. (elifesciences.org)
  • However, data concerning the organization and location of the repetitive DNA sequences in the genomes of these karyomorphs are still lacking. (scielo.br)
  • The data also showed that the histone sites are organized in a differentiated manner in the genomes of S. marmoratus, while the transposable elements Rex1 and Rex3 do not seem to be compartmentalized in this group. (scielo.br)
  • The genomes of eukaryotic organisms are characterlittle information regarding other types of sequences, such as ized by a large number of repetitive DNA segments. (scielo.br)
  • Depending upon the similarity of their terminal inverted repeats and target site duplications, most of the MITEs in plant genomes are divided into two major groups: Tourist-like MITEs (derived from PIF) and Stowaway-like MITEs (derived from Tc1/mariner).Stowaway and Tourist elements differ remarkably in their sequences but they have been found to have significant structural similarities. (wikipedia.org)
  • We isolated and measured the fitness of thousands of independent adaptive clones and sequenced the genomes of hundreds of clones. (stanford.edu)
  • However, when their genomes were later sequenced, researchers were surprised to learn that the DNA sequences of human and chimpanzee genes are nearly identical. (futurity.org)
  • The research shows that these genomic "gaps" between the two species are predominantly due to the insertion or deletion (INDEL) of viral-like sequences called retrotransposons that are known to comprise about half of the genomes of both species. (futurity.org)
  • Transposable elements were formerly thought to be found only in a few species, but now they are recognized as components of the genomes of virtually all species. (psu.edu)
  • In fact, transposable elements (both active and inactive) occupy approximately half the human genome and a substantially greater fraction of some plant genomes! (psu.edu)
  • Since viruses move between individuals, at least some transposable elements can move between genomes (between individuals) as well as within an individual s genome. (psu.edu)
  • Given their prevalence in genomes, the function (if any) of transposable elements has been much discussed but is little understood. (psu.edu)
  • Transposable elements are major forces in the evolution and rearrangement of genomes (Fig. 9.1). (psu.edu)
  • But a large part of genomes are made up of DNA sequences that do not code for any traits. (brighthub.com)
  • Insertion sequence (IS) elements are a diverse group of specialized DNA segments that move to new sites in prokaryotic and eukaryotic genomes by mechanisms that do not require extensive DNA sequence homology (for reviews see references 5 , 7 , and 19 ). (asm.org)
  • One of the basic assumptions of genetics is that the genomes of individuals belonging to a single species are colinear at the sequence level and contain the same gene complement. (plantcell.org)
  • They claimed that the differences between the sequences of the human and chimpanzee genomes could not be explained by evolution. (blogspot.com)
  • The second one shows that the mutation rate from direct sequencing of the genomes of parents and children agrees pretty much with the biochemical estimate. (blogspot.com)
  • Transposable elements (TEs) are mobile DNA sequences found in the genomes of almost all species. (ebscohost.com)
  • By measuring the normalized coverage of TE sequences within genes, we identified sets of genes with conserved extremes of high/low TE density in the genomes of human, mouse and cow and denoted them. (ebscohost.com)
  • Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. (biomedcentral.com)
  • The way the copy number of TEs is contained in genomes depends thus on the element considered, and on various forces acting simultaneously, indicating that models of TE dynamics should include details of each element. (cambridge.org)
  • This was realized by sequencing and comparing the entire genomes of a total of 5 species of cichlid fish that live in the 3 great lakes and their surrounding rivers. (titech.ac.jp)
  • Specifically, compared to ancestor species living in the rivers, the genomes of the cichlid fish that live in the 3 great lakes had remarkable gene duplication (3) , coding sequence diversification in the gene coding region (4) , and genetic expression divergence associated with transposable element (5) insertions. (titech.ac.jp)
  • Transposable elements (TEs) are mobile sequences found in nearly all eukaryotic genomes. (biomedcentral.com)
  • The number of sequenced genomes is rapidly rising, and the need to identify TEs within them is also growing. (biomedcentral.com)
  • In this work, we describe a homology-based approach for the automatic identification of high-quality consensus TEs, aimed for use in the analysis of newly sequenced genomes. (biomedcentral.com)
  • We apply our approach to newly sequenced genomes and successfully identify consensus TEs that are up to 99% identical to manually annotated TEs. (biomedcentral.com)
  • Transposable elements (TEs) are a type of repetitive sequence that have been found in nearly all eukaryotic genomes. (biomedcentral.com)
  • SINCE the radical suggestion by Barbara McClintock in the 1950s, based on her extensive genetic analyses in maize, that some genes might move along chromosomes, our knowledge of transposable elements (TEs) has vastly increased. (genetics.org)
  • The mutable flecked, speckled, r-1, and purple alleles in I. nil were caused by insertions of Tpn1 and its relatives in the En/Spm superfamily, Tpn2, Tpn3, and Tpn4, into the genes for anthocyanin coloration in wers, i.e. (nii.ac.jp)
  • Similarly, the flaked and pink mutants of I. purpurea have distantly related elements, Tip1OO and Tip201, in the Ac/Ds superfamily inserted into the CHS-D and F3'H genes, respectively. (nii.ac.jp)
  • This ability can be harmful for hosts if transposable elements destroy functioning genes, but it can also bring advantages. (phys.org)
  • Three well characterized maize transposons- Ac/Ds , En/Spm , and Mu ( 4 - 6 )-have been used in gene-tagging approaches to isolate a large number of plant genes ( 3 , 7 ). (pnas.org)
  • Thus, the identification of an active transposable element for gene tagging in sorghum could provide a new route to the isolation of the corresponding maize genes. (pnas.org)
  • High overrepresentation of W-boxes and OCS elements were found in these genes, indicating that this strong cry1 and HFR1 co-regulation on gene expression is possibly through these two cis-elements. (biomedsearch.com)
  • In summary, HFR1, which is fine-tuned by cry1, is crucial for regulating global gene expression in cry1-mediated early blue light signaling, especially for the function of genes containing W-boxes and OCS elements. (biomedsearch.com)
  • Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. (mdpi.com)
  • However, researchers have found that some genes (DNA sequences) can actually change position in the chromosomes. (ukessays.com)
  • IS elements were first identified in E. coli , from the observations that some mutations affecting the expression of genes, that control the metabolism of the sugar glucose, did not have properties typical of a point mutations or deletions. (ukessays.com)
  • Promoters present within the IS elements may also effect by altering the expression of nearby genes. (ukessays.com)
  • An orderly arrangement of DNA sequences on a small solid support, usually a membrane or glass slide, used to quickly survey the simultaneous expression of many genes. (thefreedictionary.com)
  • A collection of tens of thousands of DNA single-strand molecular probes capable of detecting specific genes or measuring gene expression in a sample of tissue. (thefreedictionary.com)
  • and pseudogenes, nonfunctional DNA sequences that originated from functional genes. (wikipedia.org)
  • Unfortunately, the G-value paradox simply picked up where the C-value paradox left off, because the discrepancy persisted when comparisons were narrowed to just protein-coding genes Estimates of the number of coding genes in the human genome reached upwards of 100,000 prior to the human genome project, but since have dwindled to as low as 19,000 following completion of that massive sequencing effort and subsequent refinements. (wikipedia.org)
  • Examples of mechanisms that produce such changes are DNA methylation and histone modification , each of which alters how genes are expressed without altering the underlying DNA sequence. (wikipedia.org)
  • Genes are sections of DNA that contain the instructions for making proteins or other molecules, and so determine the physical characteristics of each organism. (elifesciences.org)
  • Transposable elements are sequences of DNA that are also called 'jumping genes' because they can make copies of themselves and these copies of the transposable element can move to other locations in the genome. (elifesciences.org)
  • Some transposable elements contain sequences that switch on nearby genes. (elifesciences.org)
  • If different copies of a transposable element that contains such a regulatory sequence insert themselves in more than one place, it can result in a network of genes that can all be controlled in the same way. (elifesciences.org)
  • This process is called dosage compensation and in 2013 the 77 ISX regulatory sequences on the fruit fly's X chromosome were shown to help recruit the molecular machinery that carries out dosage compensation to nearby genes, albeit inefficiently. (elifesciences.org)
  • These histone genes and transposable elements (TEs). (scielo.br)
  • 2003). However, the vast majority of mapping studies carried out on Neotropical fishes were focused on the location of ribosomal sites, and there is still very little information regarding other types of sequences, such as histone genes and transposable elements (TEs). (scielo.br)
  • Even though studies on physical mapping of histone genes and TEs are few, interesting features about those sequences have been revealed, such as association with other repetitive families (Cioffi et al. (scielo.br)
  • How could random mutations produce three new catalytic/degradative genes without at least some changes being made to the transposable elements? (talkorigins.org)
  • It is very likely that the genes arose on different plasmids and were stitched together by the transposable elements at a later stage. (talkorigins.org)
  • As TEs carry 'ready-to-use' cis -elements, their insertions can impact gene regulation on a genome-wide scale by providing assorted regulatory elements to the adjacent genes. (g3journal.org)
  • Moreover, quadruplexes found in solo LTRs, as well as in 3 ends of 5-truncated copies of LINE-1 elements, can affect expression of neighboring genes. (muni.cz)
  • GEORGIA TECH (US) - While the DNA sequence of genes between humans and chimpanzees is nearly identical, a new study finds the insertion and deletion of large pieces of DNA near genes are highly variable. (futurity.org)
  • Our findings are generally consistent with the notion that the morphological and behavioral differences between humans and chimpanzees are predominately due to differences in the regulation of genes rather than to differences in the sequence of the genes themselves," says McDonald. (futurity.org)
  • Sequences similar to the consensus Ste12p binding site in the upstream regions of the FIG1, FIG2, KAR5/FIG3, and FIG4 genes. (nih.gov)
  • An upstream regulatory element termed the PRE has been identified as mediating the pheromone-induced transcription of a number of genes involved in the mating response (e.g. (nih.gov)
  • We searched the regions immediately upstream of the four novel FIG genes characterized in this study and found sequences matching the PRE consensus (Fig. 2). (nih.gov)
  • 1992), failed to identify sequences in the upstream regions of the FIG1-4 genes closely matching the consensus binding site. (nih.gov)
  • Some transposition events inactivate genes, since the coding potential or expression of a gene is disrupted by insertion of the transposable element. (psu.edu)
  • In other cases, transposition can activate nearby genes by bringing an enhancer of transcription (within the transposable element) close enough to a gene to stimulate its expression. (psu.edu)
  • A particular type of transposable element can activate, inactivate or have no effect on nearby genes, depending on exactly where it inserts, it s orientation and other factors. (psu.edu)
  • Sequence comparison of 10 representative IS Hp609 elements revealed higher levels of DNA sequence matches (99%) than those seen in normal chromosomal genes (88 to 98%) or in other IS elements (95 to 97% for IS 605 , IS 606 , and IS 607 ) from the same H. pylori populations. (asm.org)
  • Each of the four known species of IS elements in H. pylori (IS 605 , IS 606 , IS 607 , and IS Hp608 ) belongs to the distinctive IS 605 mobile element family, and each seems to be chimeric, containing two transposition-related genes, orfA and orfB , that may have different phylogenetic origins ( 12 , 14 , 16 ). (asm.org)
  • Our results indicate that no significant effects of elevated p CO 2 and associated carbonate chemistry changes on the physiological performance of the cells were observed after 15 generations whereas the expression of genes encoding histones and other genes involved in chromatin structure were significantly down-regulated, while the expression of transposable elements (TEs) and genes encoding histone acetylation enzymes were significantly up-regulated. (frontiersin.org)
  • Maize ESTs and/or maize massively parallel signature sequencing tags were identified for the majority of the nonshared genes or homologs of them. (plantcell.org)
  • Frequently, retroelement insertions create a different sequence environment adjacent to conserved genes. (plantcell.org)
  • Surprisingly, much of the intergenic sequence was different, and four of the genes also differed between the two maize inbred lines. (plantcell.org)
  • Gene Properties and Chromatin State Influence the Accumulation of Transposable Elements in Genes. (ebscohost.com)
  • Moreover, spacing between syntenic genes is also conserved, even though syntenic TEs have been replaced by new insertions over time, suggesting that distances between genes, but not sequences, are under evolutionary constraints. (biomedcentral.com)
  • DNA and RNA data are utilized to annotate many genes and protein functions in the draft genome. (biomedcentral.com)
  • Most of the short DNA elements cluster near genes that play a decisive role during an organism's first weeks after conception. (creation.com)
  • Kuff, Intracisternal A-particle genes as movable elements in the mouse genome. (xenbase.org)
  • Martens, Polymorphism and absence of Leu-enkephalin sequences in proenkephalin genes in Xenopus laevis. (xenbase.org)
  • Young mammalian cells are characterized by DNA hypermethylation over the genome, with the exception of CpG islands within the promoters of expressed genes. (sciencemag.org)
  • However, DNA methylation also increases in a nonstochastic manner over the CpG islands of certain genes, correlating with their heterochromatinization and silencing. (sciencemag.org)
  • Post-genomic research in his laboratory established the core and signature proteins in halophilic Archaea, and the function of many genes and genetic elements, including multiple replication origins, general transcription factors, and DNA repair systems. (wikipedia.org)
  • The putative element (Lyt1) is 1340 bp long, has terminal inverted repeats of approximately 235 bp and is flanked by 9-bp direct repeats. (genetics.org)
  • The terminal inverted repeats are 80% AT-rich, are 96.6% identical, and define a larger family of repetitive elements. (genetics.org)
  • All IS elements end with identical or near identical inverted repeats (IR's) of 9 to 41 bp, but in opposite orientations. (ukessays.com)
  • For example, the inverted repeats of IS1 consist of 23 bp, but the sequences are not completely identical. (ukessays.com)
  • Presences of inverted repeats (IR's) are essential as transposase recognizes these sequences to initiate transpositions. (ukessays.com)
  • Gel mobility shift assays demonstrate that MURA is a DNA-binding protein that specifically binds to sequences within the highly conserved Mu element terminal inverted repeats (TIRs). (asm.org)
  • This cutting and pasting requires short DNA segments at either end that are inverted repeats of each other called insertion sequences. (encyclopedia.com)
  • The central region of some more complex transposable elements is sometimes flanked by short, direct repeats, which are then flanked by the inverted repeats. (brighthub.com)
  • Many, but not all, species of elements terminate in short inverted repeats (size range, 9 to 40 bp) and generate short direct repeats of target sequences (typically 2 to 9 bp) when they transpose. (asm.org)
  • Transposons are typically bounded by terminal inverted repeats (TIRs), which flank and serve as the recognition sequence for the transposase. (biomedcentral.com)
  • Inverted repeats of 5 bp and apparent target site duplications of 5 bp surround the sequenced solo LTR. (xenbase.org)
  • Using a high-resolution annotation of TEs in Release 4 genome sequence, we revise estimates of TE abundance in Drosophila melanogaster. (nih.gov)
  • Here, we describe the transposition dynamics of cut-and-paste mariner elements during experimental (short- and longer-term) evolution in Drosophila melanogaster . (pnas.org)
  • 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. (curehunter.com)
  • Kofler found a transposable element in the fly species Drosophila simulans, the so-called P-element. (phys.org)
  • The discovery of the P-element in Drosophila simulans offers the unique possibility to investigate the way transposable elements are regulated and how they survive. (phys.org)
  • To this end we are using two transposable elements from Drosophila, the I factor, an element related to the LINE 1 elements that make up nearly 20% of the human genome, and mariner, an element related to those being developed as vectors for transgenesis and gene therapy. (ed.ac.uk)
  • Transposable elements (TEs) allow rewiring of regulatory networks, and the recent amplification of the ISX element dispersed 77 functional but suboptimal binding sites for the dosage compensation complex to a newly formed X chromosome in Drosophila. (elifesciences.org)
  • A fruit fly called Drosophila miranda has a transposable element called ISX that has, over time, placed up to 77 regulatory sequences around one of this species' sex chromosomes. (elifesciences.org)
  • In addition to the Alu sequences in humans, about 3 percent of the fruit fly Drosophila melanogaster genome is made up of transposable element DNA. (encyclopedia.com)
  • What transposable elements tell us about genome organization and evolution: the case of Drosophila. (semanticscholar.org)
  • Molecular paleontology of transposable elements in the Drosophila melanogaster genome. (semanticscholar.org)
  • On the abundance and distribution of transposable elements in the genome of Drosophila melanogaster. (semanticscholar.org)
  • In this study, we showed that a previously identified putatively adaptive mutation, the insertion of the transposable element FBti0019627, mediates resistance to both natural and synthetic xenobiotics in Drosophila melanogaster. (prolekare.cz)
  • Marlor, The Drosophila melanogaster gypsy transposable element encodes putative gene products homologous to retroviral proteins. (xenbase.org)
  • Mount, Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins. (xenbase.org)
  • Mobile elements move to new sites in the genome either through an RNA intermediate via a copy-and-paste mechanism (retrotransposons of Class I) or directly through a cut-and-paste mechanism (transposons of Class II) [ 1 , 2 , 6 ], generating the basis for genetic variability in somatic and generative tissues and resulting in intraspecific variations [ 7 , 8 ]. (hindawi.com)
  • and (2) DNA elements (class 2 transposons) have DNA as their intermediate molecule [ 2 ]. (hindawi.com)
  • [3] Transposons are also very useful to researchers as a means to alter DNA inside a living organism. (wikipedia.org)
  • There are at least two classes of TEs: Class I TEs or retrotransposons generally function via reverse transcription , while Class II TEs or DNA transposons encode the protein transposase , which they require for insertion and excision, and some of these TEs also encode other proteins. (wikipedia.org)
  • The insertion element, named Candystripe1 ( Cs1 ), is present in the second intron of the Y gene and shares features of the CACTA superfamily of transposons. (pnas.org)
  • These mobile DNA sequences are called transposable elements or simply transposons . (ukessays.com)
  • Structure and function of an AT-rich, interspersed repetitive sequence from Chironomus thum mi: solenoidal DNA, 142 bp palindrome-frame and homologies with the sequence for site-specific recombination of bacterial transposons. (springer.com)
  • No particular DNA sequence serves as the target site for transposons. (encyclopedia.com)
  • Prokaryote transposons may replicate DNA as well as cut and paste it. (encyclopedia.com)
  • Transposons in eukaryotes do not replicate DNA. (encyclopedia.com)
  • A closer look reveals the presence of some interesting elements, like the mobile transposons. (brighthub.com)
  • We will look at two main types of transposable elements: DNA transposons and retrotransposons. (brighthub.com)
  • Finally, some DNA transposons actually will replicate themselves, with the copy then being inserted into the target site. (brighthub.com)
  • Class I retrotransposons travel through an RNA intermediate by copy and paste, while class II DNA transposons have a DNA intermediate and generally move by cut and paste. (biomedcentral.com)
  • Class II TEs, or transposons, are DNA-mediated and transpose through the use of a transposase enzyme. (biomedcentral.com)
  • One type encodes proteins which induces the transposable element to move directly to a new position or replicate the transposable element to produce a new element that integrates elsewhere in the genome. (ukessays.com)
  • Eventually, researchers recognized that not all DNA contributes directly to the production of proteins and other biological functions. (wikipedia.org)
  • Gene expression can be controlled through the action of repressor proteins that attach to silencer regions of the DNA. (wikipedia.org)
  • The autonomous MuDR element of the Mutator (Mu) transposable element family of maize encodes at least two proteins, MURA and MURB. (asm.org)
  • Frameshifts in non-repetitive sequences usually end up with a high probability of producing a premature stop codon, resulting in production of short non-functional proteins. (talkorigins.org)
  • However, repetitive sequences are very likely to not produce premature stop codons, and it is likely that long, functional proteins can be produced by frameshifts in these proteins. (talkorigins.org)
  • the main difference between the two elements is that retroviruses also encode a variety of other viral proteins, some which allow the virus to survive outside the host. (brighthub.com)
  • Many IS elements specify just a single transposase protein that acts in concert with host proteins at each end of the element to mediate insertion. (asm.org)
  • Other, more complex elements, such as Tn 7 , specify two or more proteins that act together as the transposase, plus additional proteins that help select insertion sites or affect the efficiency of transposition. (asm.org)
  • Host proteins can also affect the frequency or specificity of transposition of certain elements. (asm.org)
  • In gonadal tissues, the Piwi-interacting (piRNA) pathway preserves genomic integrity by employing 23 29 nucleotide (nt) small RNAs complexed with argonaute proteins to suppress parasitic mobile sequences of DNA called transposable elements (TEs). (visembryo.com)
  • Fanning, The LINE-1 DNA sequences in four mammalian orders predict proteins that conserve homologies to retrovirus proteins. (xenbase.org)
  • The schematic at the top depicts the reduction in the level of bulk histone proteins during aging (for example, as seen in budding yeast), leading to a more open chromatin structure and subsequent transcriptional activation of the normally silenced Ty elements. (sciencemag.org)
  • Subsequent sequence analysis indicated that only one copy of the 9-bp direct repeat (target site) was present, suggesting that transposition of the element into the ARPI gene occurred after the divergence of the red-fruited and green-fruited Lycopersicon species. (genetics.org)
  • Rapid restructuring of the genomic landscape by transposition and duplication has recently added hundreds of kilobases of TE sequence to pericentromeric regions in D. melanogaster. (nih.gov)
  • Therefore the elements of the medaka fish Oryzias latipes that still have transposition activity provide precious materials for studying transposition mechanisms, as well as the evolution, of transposable elements in vertebrates. (bioone.org)
  • Copies that do not carry the transposase gene or carry an imperfect gene are called non-autonomous copies, these being thought to be produced from autonomous copies by errors during transposition or subsequent mutational sequence changes. (bioone.org)
  • Usually the frequency of transposition varies with different elements, but it is very low, as higher frequency may lead to lethality. (ukessays.com)
  • An enzyme called transposase , encoded by the IS element, is responsible for transposition of the IS elements. (ukessays.com)
  • We have studied several aspects of the molecular biology of transposable elements and are particularly interested in how they transpose and how transposition is regulated. (ed.ac.uk)
  • Steady-state nucleosome distribution affects DNA-binding interactions required for nuclear processes such as transcription, replication, recombination, repair, and transposition ( Jiang and Pugh, 2009 ). (plantphysiol.org)
  • The final method of changing the DNA in a genome that we will consider is transposition , which is the movement of DNA from one location to another. (psu.edu)
  • Much of the mechanism of transposition is distinctive for these two classes, but all transposable elements effectively insert at staggered breaks in chromosomes. (psu.edu)
  • When transposition generates two copies of the same sequence in the same orientation, recombination can delete the DNA between them. (psu.edu)
  • As part of the mechanism of transposition, additional DNA sequences can be mobilized. (psu.edu)
  • In this manner, transposition can move DNA sequences that are not normally part of a transposable element to new locations. (psu.edu)
  • Although transposition occurs at a low frequency, evolution has provided ample time in which to transpose elements. (encyclopedia.com)
  • Just as occurs with retrotransposons, there have been cases observed in which DNA transposable elements have lost the enzymes necessary for transposition. (brighthub.com)
  • The replication of sequences to be inserted into new locations, as well as the filling in of gaps created by transposition, often increase the amount of genetic information in a genome. (brighthub.com)
  • TEs are classified according to their transposition mechanism into Class I and Class II elements. (biomedcentral.com)
  • The normally heterochromatinized retrotransposable elements become euchromatinized, leading to their transcription and transposition elsewhere into the genome. (sciencemag.org)
  • Some researchers did not even believe that these unconventional DNA insertions actually moved or moved with significant frequency and so thought that they could not possibly contribute to genetic diversity. (genetics.org)
  • this means that initially none of the 77 insertions carried the two mutations, but now 30% of the 77 elements have the mutations in all flies, and 41% have them in only some flies. (elifesciences.org)
  • This implies that regulatory sequences derived from transposable elements evolve in a way that is fundamentally different from those that arise by other means, as the direct conversion between these insertions allows fine-tuning mutations to spread more rapidly. (elifesciences.org)
  • The process of moving from one place to another involves a type of recombination, insertions of transposable elements can cause mutations, and some transpositions are replicative, generating a new copy while leaving the old copy intact. (psu.edu)
  • The copia, mdg1 and gypsy elements show evidence for a deficiency of insertions on the X chromosomes, a result consistent with selection against the mutational effects of insertions. (cambridge.org)
  • We have developed an algorithm, called Mobster, to detect non-reference mobile element insertions in next generation sequencing data from both whole genome and whole exome studies. (biomedcentral.com)
  • While SNPs certainly contribute to ecologically relevant phenotypes, these efforts ignore other types of mutations, such as those caused by transposable element (TE) insertions. (prolekare.cz)
  • Chromothripsis is a mutational event driven by tens to hundreds of double-stranded DNA breaks which occur in a single event between a limited number of chromosomes. (springer.com)
  • Recently, retrotransposons-a type of "jumping gene"-have been implicated as one means to generate double-stranded DNA breaks during chromothripsis and as sequences which can contribute to the final configuration of the derived chromosomes. (springer.com)
  • Insertion sequences (IS) or IS elements is the simplest transposable element found in bacterial chromosomes and plasmids. (ukessays.com)
  • To anchor polished contigs onto chromosomes with high accuracy, two complementary technologies: OM (Supplementary Table 2 ) and Hi-C sequencing (Supplementary Table 1 ) were employed. (nature.com)
  • The results indicated that both histone sequences seem to be linked with one another and are scattered all over the chromosomes of the complement, with a little compartmentalization in one acrocentric pair, which is different from observations in other fish groups. (scielo.br)
  • Retroposons are also thought to have created the repetitive Alu sequences that make up a very large fraction of human chromosomes. (encyclopedia.com)
  • Allelic chromosomal regions totaling more than 2.8 Mb and located on maize ( Zea mays ) chromosomes 1L, 2S, 7L, and 9S have been sequenced and compared over distances of 100 to 350 kb between the two maize inbred lines Mo17 and B73. (plantcell.org)
  • There is no strong evidence of a systematic accumulation of elements in the distal and proximal regions of the chromosomes where crossing over and ectopic exchanges are reduced. (cambridge.org)
  • Southern analysis and genomic dot-blot reconstructions detected at least 41 copies of Lyt1-hybridizing sequences in red-fruited Lycopersicon spp. (genetics.org)
  • In this article, I summarize the main events that influenced my thinking about transposable elements as a young scientist and the influence and role of these specific genomic elements in evolution over subsequent years. (genetics.org)
  • The history of these genomic elements provides one of the best examples of how scientific concepts in biology emerge and then evolve into new concepts. (genetics.org)
  • Repetitive DNA-specifically, transposable elements (TEs)-is a prevailing genomic fraction in cereals that underlies extensive genome reshuffling and intraspecific diversification in the wild. (hindawi.com)
  • Following chromosomal shattering, DNA fragments are stitched together in a seemingly random manner resulting in complex genomic rearrangements including sequence shuffling, deletions, and inversions of varying size. (springer.com)
  • The mechanisms catalyzing DNA breakage and coordinating the "random" assembly of genomic fragments are actively being investigated. (springer.com)
  • Experimentally validated NOL plots provide a novel genomic annotation that highlights gene structures, repetitive elements, and chromosome-scale domains likely to reflect regional gene density. (plantphysiol.org)
  • This annotation provides sequence-based comprehensive coverage across the entire genome, including repetitive genomic regions typically excluded from experimental genomics data. (plantphysiol.org)
  • Our study advances plant chromatin research by defining the potential contribution of the DNA sequence to observed nucleosome positioning and provides an invariant baseline annotation against which other genomic data can be compared. (plantphysiol.org)
  • The present work aimed to investigate the location of the Rex3 and Rex6 transposable elements in the hybrid and in the species, in addition to checking the genomic organization of the 18S and 5S rDNA in tambacu. (science.gov)
  • While cancer genome sequencing has been instrumental in identifying the genomic alterations that occur in human tumors, the consequences of these alterations on tumor growth remain largely unexplored. (stanford.edu)
  • Sequence analysis suggested that IS Hp609 can insert at many genomic sites with its left end preferentially next to TAT, with no target specificity for its right end, and without duplicating or deleting target sequences. (asm.org)
  • 2) also if #1 is ok, 98.6% genomic identity between chimp and human (= 22.4 million DNA bases) is highly debatable, because genomic comparison can be done in many different ways and depends on many presuppositions. (blogspot.com)
  • Mobile elements are major drivers in changing genomic architecture and can cause disease. (biomedcentral.com)
  • These ME families continue to change the genomic architecture by inserting into new regions in the DNA, transducing DNA, shuffling exons, and creating processed pseudogenes. (biomedcentral.com)
  • Church, Genomic sequencing. (xenbase.org)
  • The abnormal chromatin state in old cells also leads to new transposable elements being inserted into the genome and genomic instability, including DNA mutations. (sciencemag.org)
  • Knockdown of the Alu element transcripts in human adult stem cells leads to escape from senescence and reduced genomic instability. (sciencemag.org)
  • Repetitive DNA-specifically, transposable elements (TEs)-constitutes at least 45% of the human genome, wherein the fraction of long interspersed nucleotide element (LINE) retrotransposons is 17% [ 1 ]. (hindawi.com)
  • Four major classes of transposable elements are known: viral family retrotransposons, long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs) and DNA-based transposable elements. (bioone.org)
  • Recently, we reported that many plant long-terminal repeat (LTR) retrotransposons contain DNA quadruplex-forming sequences at precise positions inside their LTRs and that quadruplexes are better preserved in evolutionary younger elements. (muni.cz)
  • Here, we propose that this way retrotransposons can serve as vehicles for spread of DNA quadruplexes. (muni.cz)
  • Within the category of retrotransposons, researchers have found some elements that are similar to retroviruses, called viral retrotransposons, which possess long terminal repeats, or LTRs, as well as elements called LINES, which do not have LTRs. (brighthub.com)
  • it is thought that these elements take advantage of the enzyme encoded by other retrotransposons. (brighthub.com)
  • On average, more than 50% of the compared sequence is noncolinear, mainly because of the insertion of large numbers of long terminal repeat (LTR)-retrotransposons. (plantcell.org)
  • Retrotransposons transcribe themselves to RNA and are reverse transcribed back into DNA by the reverse transcriptase enzyme, the "copy-and-paste" mechanism. (biomedcentral.com)
  • The presence or absence of long terminal repeats (LTRs) further classifies retrotransposons into non-LTR and LTR elements. (biomedcentral.com)
  • Flügel, Nucleotide sequence analysis of a cloned DNA fragment from human cells reveals homology to retrotransposons. (xenbase.org)
  • A transposable element ( TE or transposon ) is a DNA sequence that can change its position within a genome , sometimes creating or reversing mutations and altering the cell's genetic identity and genome size . (wikipedia.org)
  • The transposon is named Candystripe1 ( Cs1 ) and is a member of the CACTA family of plant transposable elements. (pnas.org)
  • Previous studies have reported a correlation between Mu transposon inactivation and methylation of the Mu element TIRs. (asm.org)
  • The transposon encodes enzymes that cut the transposon from the DNA sequence and reinsert it elsewhere. (encyclopedia.com)
  • These insertion sequences are duplicated by the transposon enzymes at the insertion site, also called the target site. (encyclopedia.com)
  • transposon ( transposable genetic element ) A mobile genetic element, known informally as a 'jumping gene', that can become integrated at many different sites in the genome, either by moving from place to place or by producing copies of itself that insert elsewhere in the genome. (encyclopedia.com)
  • This filling in of the gaps leads to duplication of short DNA sequences flanking the transposon and this has been hypothesized as a mechanism behind gene duplication. (brighthub.com)
  • Paulson, A transposon-like element in human DNA. (xenbase.org)
  • Transposable elements are DNA sequences that are capable of changing their genome position by cut and paste or copy and paste through the enzyme transposase. (phys.org)
  • Characterization of the maize Mutator transposable element MURA transposase as a DNA-binding protein. (asm.org)
  • Based on amino acid sequence similarity, previous studies have reported that MURA is likely to be a transposase. (asm.org)
  • The transposase adheres to a "cut-and-paste" mechanism, as it cuts out the TE from the host DNA and allows it to insert at a new site in the host DNA. (biomedcentral.com)
  • The second type of transposable element is related to retrovirus. (ukessays.com)
  • The evolutionary factors explaining the distribution of transposable elements (TEs) across organisms are still poorly understood ( 1 ). (pnas.org)
  • From an evolutionary point of view, transposable elements diversify the genome and open up chances for adaptation. (phys.org)
  • These results describe a novel route by which fully functional regulatory elements can arise rapidly from TEs and implicate non-allelic gene conversion as having an important role in accelerating the evolutionary fine-tuning of regulatory networks. (elifesciences.org)
  • Last month I explained how the difference in DNA sequence between chimps and humans corresponds to what we would predict from evolutionary theory. (blogspot.com)
  • Our results reveal the complexity of the evolutionary dynamics of the ancient element Copia25 in angiosperm, involving several processes including sequence conservation, rapid turnover, stochastic losses and horizontal transfer. (deepdyve.com)
  • Miniature transposable sequences are frequently mobilized in the bacterial plant pathogen Pseudomonas syringae pv. (wikipedia.org)
  • The abundance and sequence homogeneity of IS Hp609 and of this nonmobile remnant suggested a recent bottleneck and then rapid spread in H. pylori populations, possibly selected by the contributions of the elements to bacterial fitness. (asm.org)
  • 5000 bp) and unique nucleotide sequence. (ukessays.com)
  • The SV40 nucleotide sequence (appendix A): in DNA Tumor Viruses, J. Tooze, ed. (springer.com)
  • Complete nucleotide sequence of SV40 DNA. (springer.com)
  • The term also refers to the changes themselves: functionally relevant changes to the genome that do not involve a change in the nucleotide sequence . (wikipedia.org)
  • Nucleotide sequence of a gene encoding an organophosphorus nerve agent degrading enzyme from Alteromonas haloplanktis. (ebscohost.com)
  • Transposable elements are ubiquitous specific DNA sequences of the genome found in both prokaryotes and eukaryotes. (ukessays.com)
  • N2 - Transposable elements (TEs) are ubiquitous genome inhabitants in eukaryotes. (muni.cz)
  • These movable elements are ubiquitous in the biosphere, and are highly successful in propagating themselves. (psu.edu)
  • Intensive investigations of various polyploid systems revealed that allopolyploidization event is associated with widespread changes in genome structure, methylation, and expression involving low- and high-copy, coding and noncoding sequences. (hindawi.com)
  • The bias of methylation toward repetitive DNA suggests that silencing of transposable elements is one of the primary roles of DNA methylation [ 8 ]. (hindawi.com)
  • Mechanisms are in place to silence these elements, such as RNA-directed DNA methylation (RdDM) and histone H3 lysine 9 dimethylation (H3K9me2) in plants. (prolekare.cz)
  • These RNAs then recruit protein factors to deposit DNA methylation or H3K9me2 to silence the loci. (prolekare.cz)
  • In this study, we found that treatment of plants with camptothecin, a TOP1α inhibitor, or loss of function in TOP1α, led to the de-repression of RdDM target loci, which was accompanied by loss of H3K9me2 or DNA methylation. (prolekare.cz)
  • DNA methylation and histone H3 lysine 9 (H3K9) methylation are two chromatin modifications widely employed by eukaryotes to maintain genome stability [1] , [2] . (prolekare.cz)
  • H3K9 methylation and DNA methylation are targeted via small interfering RNAs (siRNAs) to repeats and transposable elements (TEs) and are required for their transcriptional silencing [1] , [2] . (prolekare.cz)
  • In plants, cytosine methylation is established through a process known as RNA-directed DNA methylation (RdDM), which involves small and long noncoding RNAs produced by plant-specific RNA polymerases, Pol IV and Pol V, respectively [2] . (prolekare.cz)
  • Through the concerted action of these two polymerases, siRNA-AGO4 becomes localized to target loci, and this ultimately recruits the methyltransferase DRM2, which effects de novo DNA methylation. (prolekare.cz)
  • In contrast to CG and CHG methylation, which can be maintained through the DNA methyltransferases MET1 and CMT3, respectively, CHH methylation is propagated by constant de novo methylation through RdDM [2] , [10] . (prolekare.cz)
  • H3K9me2 and CHG methylation act in a self-reinforcing loop to promote the maintenance of these marks by histone methyltransferases KRYPTONITE (KYP or SUVH4), SUVH5 and SUVH6 and the DNA methyltransferase CMT3 [14] . (prolekare.cz)
  • In fact, a recent study revealed a strong genome-wide inter-dependence between non-CG (CHG and CHH) DNA methylation and H3K9 dimethylation [16] . (prolekare.cz)
  • The resulting abnormal chromatin state is characterized by different histone variants being incorporated, altered DNA methylation patterns, and altered histone modification patterns, resulting in the recruitment of different chromatin modifiers. (sciencemag.org)
  • Fig. 3 Summary of DNA methylation changes during aging. (sciencemag.org)
  • Loss of DNA methylation leads to activation of normally silenced DNA sequences like the transposable elements. (sciencemag.org)
  • We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. (mdpi.com)
  • The basic subunit of chromatin, the nucleosome, is composed of approximately 150 bp of DNA wrapped 1.65 times around a histone octamer. (plantphysiol.org)
  • In this study we made a physical mapping of the H3 and H4 histone multigene family and the transposable elements Rex1 and Rex3 in the genome of three known S. marmoratus karyomorphs. (scielo.br)
  • Taken together, our integrative analyses reveal that epigenetic elements such as TEs, histone modifications and lncRNAs may have important roles in the acclimation of diatoms to elevated p CO 2 over short time scales and thus may influence longer term adaptive processes in response to progressive ocean acidification. (frontiersin.org)
  • Transposable elements are also called selfish DNA parasites because they spread through their hosts, such as humans, animals, plants as well as bacteria and, thus, provide for their own survival.Robert Kofler from the Institute of Population Genetics at the Vetmeduni Vienna analysed flies from all over the world. (phys.org)
  • DNA topoisomerase is an enzyme that releases the torsional stress in DNA generated during DNA replication or transcription. (prolekare.cz)
  • As quadruplexes can modulate molecular processes, quadruplexes found at specific distances upstream and downstream from the endogenous TE promoter can affect transcription of the element. (muni.cz)
  • 1987). These sequences represent potential binding sites for Ste12p, the transcription factor that mediates pheromone-induced transcription, and are generally found upstream of pheromone-induced protein coding sequences (Kronstad et al. (nih.gov)
  • Liao, The upstream activation site of a Ty2 element of yeast is necessary but not sufficient to promote maximal transcription of the element. (xenbase.org)
  • Such elements encode a reverse transcriptase for making copies of DNA from their RNA transcripts, which subsequently integrate at new sites in the genome. (ukessays.com)
  • If the two copies are in the opposite orientations, recombination will invert the DNA between them. (psu.edu)
  • DNA located between two copies of a transposable element can be moved together with them when they move. (psu.edu)
  • Multiple copies of 1A11 -related sequences were found in the Xenopus genome, constituting solo LTRs (long terminal repeats) of 1267 bp, and unique region copies (i.e., sequences internal to the repeats in the cDNA). (xenbase.org)
  • At the chromosomal level, different TE clones demonstrated sequence-specific patterning, emphasizing the effect of the TE fraction on the Ae . (hindawi.com)
  • In the wild, ongoing chromosomal rearrangements lead to considerable changes in the numbers, sizes, and positions of highly repetitive DNA clusters and underlie the divergence of natural populations [ 21 ]. (hindawi.com)
  • The chromosomal location of the mobile elements Rex3 and Rex6 in C. macropomum , P. mesopotamicus , and in the hybrid between these species enabled knowledge expansion and the generation of data on such mobile elements. (science.gov)
  • The gene (opa) encoding an OPAA was cloned from the chromosomal DNA of Alteromonas. (ebscohost.com)
  • The advantages of this host species and their elements, together with results so far obtained, are here described. (bioone.org)
  • The P-element was discovered twice in a new species within one hundred years. (phys.org)
  • Therefore we can assume that transposable elements are transferred across the species faster than we thought. (phys.org)
  • Although variegation mutants have been described in at least 35 plant species ( 3 ), active transposable elements have been isolated from only a minority of these plants. (pnas.org)
  • It is not even clear whether transposable elements should be considered an integral part of a species genome, or if they are successful parasites. (psu.edu)
  • Bennetzen and Ma, 2003 ), this fundamental assumption remained unchallenged until recently, as few extensive comparisons of DNA sequences outside of transcribed regions have been performed among individuals of the same species. (plantcell.org)
  • 1) actually there is no proof that DNA is the unique cause of the formation of a certain species. (blogspot.com)
  • The genome of bread wheat ( Triticum aestivum L.), one of the most important crop species, has also undergone massive TE amplification with more than 85% of it being derived from such repeat elements. (biomedcentral.com)
  • Similarity sequence searches and PCR analyses show that this retrotransposon with LTRs (Long Terminal Repeats) is widely distributed among the Rubiaceae family and that it is also present in other distantly related species belonging to Asterids, Rosids and monocots. (deepdyve.com)
  • A particular situation is the high sequence identity found between the Copia25 sequences of Musa, a monocot, and Ixora, a dicot species (Rubiaceae). (deepdyve.com)
  • Transposable elements as causative agents of variegation and genetic variation were first discovered in maize by Barbara McClintock in the 1940s ( 1 ) and since have been found in many organisms. (pnas.org)
  • Transposable elements were discovered by Barbara McClintock in maize in 1950. (ukessays.com)
  • In the 1940s, Barbara McClintock first discovered mobile genetic elements in corn that caused differences in gene expression , resulting in kernels containing dots of different colors against a background predominant color. (encyclopedia.com)
  • Barbara McClintock, who discovered the first mobile genetic elements in maize, was also the first to recognize the true nature of such jumping genetic elements. (creation.com)
  • Using probes from the maize p1 gene that cross-hybridize with the sorghum Y gene, we isolated the y-cs allele containing a large insertion element. (pnas.org)
  • Our analysis suggests that Cs1 -homologous sequences are present in low copy number in sorghum and other grasses, including sudangrass, maize, rice, teosinte, and sugarcane. (pnas.org)
  • Of several members of this family, the En/Spm element of maize has been best understood at the genetic and molecular levels. (pnas.org)
  • The significance of MURA's interaction with the TIRs of Mu elements is discussed in the context of what is known about the regulation and mechanisms of Mutator activities in maize. (asm.org)
  • showed that HBr markers could be used along with other molecular markers to study genotype of related maize inbred lines Software like FINDMITE use sequence entries of some average sized bp to identify MITE families. (wikipedia.org)
  • Fu and Dooner (2002) compared maize ( Zea mays ) sequences at the bz1 locus in the B73 and McC inbred lines. (plantcell.org)
  • Insertion of IS element takes place at a target site with which the IS element has no sequence homology ( Fig.6.20 ). (ukessays.com)
  • These types of elements are found in both prokaryotes and eukaryotes. (ukessays.com)
  • Such elements are found only in eukaryotes. (ukessays.com)
  • In eukaryotes, transposable elements can move to a new position within the same chromosome or to a different chromosome. (ukessays.com)
  • The sheer amount of DNA in an organism, measured by the mass of DNA present in the nucleus or the number of constituent nucleotide pairs, varies by several orders of magnitude among eukaryotes and often is unrelated to an organism's size or developmental complexity. (wikipedia.org)
  • In addition, thousands of non-coding RNAs that are transcribed from DNA but not translated into protein have emerged as important regulators of gene expression and development in humans and other eukaryotes. (wikipedia.org)
  • A growing number of RIDLs have been experimentally defined, where TE-derived fragments of lncRNA act as RNA-, DNA-, and protein-binding domains. (nih.gov)
  • We propose that these reflect a more general phenomenon of exaptation during lncRNA evolution, where inserted TE sequences are repurposed as recognition sites for both protein and nucleic acids. (nih.gov)
  • The example is also noteworthy in that the sequences giving rise to the anomalous behavior lie entirely within the coding sequences for the major capsid protein (VP1) gene. (springer.com)
  • The key point is that the mutation must be some sort of "regulatory" change as the sequence of the protein product is unaffected. (columbia.edu)
  • The area in a living organism's genome DNA sequence that forms the template for mRNA translated into protein. (titech.ac.jp)
  • In the laboratory of Edward Rubin at the University of California, Berkeley, postdoctoral fellow Nadav Ahituv combined the human version of the LF-SINE sequence with a "reporter" gene that would produce an easily recognizable protein if the LF-SINE were serving as its on-off switch. (creation.com)
  • An IS elements can integrate at random locations along the chromosome often inducing mutations, by disrupting either the coding or regulatory sequence of a gene. (ukessays.com)
  • The distribution of nucleosomes is controlled by a combination of factors including chromatin regulatory complexes and features intrinsic to the DNA sequence. (plantphysiol.org)
  • The regulatory sequences contained within transposable elements are not always optimal, but they can be fine-tuned through evolution. (elifesciences.org)
  • A few Stowaway elements also contain cis-acting regulatory domains. (wikipedia.org)
  • A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks. (ebscohost.com)
  • A team of investigators lead by Haussler recently provided direct evidence that even when a short interspersed nucleotide element (SINE) lands at some distance from a gene, it can take on a regulatory role with powerful regulatory functions. (creation.com)
  • Many of those sequences were located in gene deserts, which are in fact so clogged with regulatory DNA elements that they have recently been renamed regulatory jungles . (creation.com)
  • It was many years, however, before the accumulation of data and theories showed that this latter revolutionary idea was correct although, understandably, it fell far short of our present view of the significant influence of what are now known as "transposable elements" in evolution. (genetics.org)
  • One class of sequence elements that is enriched in lncRNA is represented by transposable elements (TEs), repetitive mobile genetic sequences that have contributed widely to genome evolution through a process termed exaptation. (nih.gov)
  • Transposable elements (TEs) are DNA sequences that colonize every genome and have a great impact on the genome evolution and structure. (pnas.org)
  • MITEs, miniature elements with a major role in plant genome evolution. (exlibris.ch)
  • In 1970, Ohno proposed that evolution moves forward via whole genome duplication [ 14 ], an idea which is gaining momentum due to more sensitive sequence analysis used to investigate polyploidy [ 13 ]. (hindawi.com)
  • The availability of complete genome sequences has revealed the significant role that these elements play in genome evolution, organization and stability. (ed.ac.uk)
  • Transposable elements are well known as possible agents of evolution. (talkorigins.org)
  • Both polyploidization and transposable element (TE) activity are known to be major drivers of plant genome evolution. (g3journal.org)
  • I challenged the Intelligent Design Creationists to explain not only that the sequences are similar but that the degree of similarity is evidence of evolution. (blogspot.com)
  • IS elements can also induce deletions and inversions in the adjacent DNA thereby causing mutations. (ukessays.com)
  • Sharing of this haplotype indicates that high levels of gene conversion among ISX elements allow them to 'crowd-source' refining mutations, and a refining mutation that occurs at any single ISX element can spread in two dimensions: horizontally across insertion sites by non-allelic gene conversion, and vertically through the population by natural selection. (elifesciences.org)
  • Ellison and Bachtrog uncovered two mutations that make the ISX transposable element better at recruiting the dosage compensation molecular machinery. (elifesciences.org)
  • The same mutations have spread between the different ISX elements because transposable elements with the mutations have been used to directly convert other ISX elements without them. (elifesciences.org)
  • Furthermore, the transposable elements (IS6100) are present in many different bacteria and are very strongly conserved, suggesting they do not tolerate mutations very well. (talkorigins.org)
  • So given that the transposable elements are conserved in sequence between different bacteria, and that you don't need many mutations to make a functional nylonase, this objection is void. (talkorigins.org)
  • Here, we used a DNA barcoding approach to generate the genotype-to-fitness map for adaptation-driving mutations from a Saccharomyces cerevisiae population experimentally evolved by serial transfer under limiting glucose. (stanford.edu)
  • Morrish TA, Gilbert N, Myers JS et al (2002) DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. (springer.com)
  • Don Batten suggests the presence of transposable elements means the plasmid is "designed" to be adaptive. (talkorigins.org)
  • Here, in order to improve our understanding regarding the camel genome architecture, the whole genome of the two dromedaries (Yazdi and Trodi camels) was sequenced. (frontiersin.org)
  • We have previously reported whole-genome sequencing data for wild and cultivated soybeans, and demonstrated the high genome diversity in wild soybean populations compared with cultivated soybean 9 . (nature.com)
  • State-of-the-art whole-genome sequencing technologies were used to assemble a high-quality reference genome for wild soybean accession W05 with long contigs and high sequence fidelity. (nature.com)
  • Publications] N.Ishikawa: 'The transposable element Tip 100 found at the mutable flaked allele for flower variegation of the common morning glory. (nii.ac.jp)
  • The P1-vv allele specifies variegated kernel pericarp pigmentation, and this allele contains an Ac transposable element insertion in the P1-rr gene. (pnas.org)
  • A classic example is the r allele ( rugosus ) of the gene encoding a starch branching enzyme in peas is nonfunctional due to the insertion of a transposable element. (psu.edu)
  • This particular segment of DNA is called insertion sequence 1, or IS1 ( Fig.6.19 ). (ukessays.com)
  • Investigation of the btuB gene revealed that it was disrupted by the IS 2 insertion sequence element in most of the resistant E. coli isolates. (asm.org)
  • A dispersed family of repetitive DNA sequences exhibits characteristics of a transposable element in the genus Lycopersicon. (genetics.org)
  • The DNA and RNA sequence data were obtained using Illumina HiSeq 2000 sequencing technology, from which we performed de novo genome assembly and gene annotation. (biomedcentral.com)
  • Responses of transposable elements to polyploidy. (exlibris.ch)
  • The last class, also called terminal-inverted-repeat elements, is different from the others in that elements move directly from DNA to DNA, that is, without forming RNA intermediates. (bioone.org)
  • Cs1 is 23,018 bp in size and is bordered by 20-bp terminal inverted repeat sequences. (pnas.org)
  • Stowaway elements possess target site specificity, have small size and conserved terminal inverted repeat. (wikipedia.org)
  • Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. (mdpi.com)
  • Sequence specificity of curved DNA. (springer.com)
  • Publications] A.Hoshino: 'Gene duplication and mobile genetic elements in the morning glories. (nii.ac.jp)
  • How does a mobile DNA sequence find its target? (phys.org)
  • Transposable elements represent one of several types of mobile genetic elements . (wikipedia.org)
  • Kazazian HH Jr, Moran JV (2017) Mobile DNA in health and disease. (springer.com)
  • The findings are reported in the most recent issue of the online, open-access journal Mobile DNA . (futurity.org)
  • They continue to be able to move thanks to the presence of enzymes encoded by other mobile elements. (brighthub.com)
  • The detection of mobile elements is hindered due to the low mappability of their highly repetitive sequences. (biomedcentral.com)
  • Mobster uses discordant read pairs and clipped reads in combination with consensus sequences of known active mobile elements. (biomedcentral.com)
  • Mobile elements (MEs) or transposable elements are DNA sequences that can be autonomously copied or moved through the genome, yet their highly repetitive sequence structure makes them difficult to detect. (biomedcentral.com)
  • The idea that mobile genetic elements are involved in creating variation is not new. (creation.com)
  • When it was discovered that more than half of the human genome consists of (remnants of) mobile elements, McClintock's ideas were revived and further developed by Roy Britten and Eric Davidson. (creation.com)
  • In early work (1980's), he discovered mobile genetic elements in halophilic Archaea, while a graduate student with H. Gobind Khorana (Nobel laureate) and Uttam L. RajBhandary at MIT. (wikipedia.org)
  • The entire sequence of transposable elements is usually methylated in Arabidopsis , in all sequence contexts [ 8 ]. (hindawi.com)
  • Flavell, A Ty1-copia group retrotransposon sequence in a vertebrate. (xenbase.org)
  • Transposable elements can cause deletions or inversions of DNA. (psu.edu)
  • Glue for jumping elements: Epigenetic means for controlling transposable elements in plants. (exlibris.ch)
  • [9] A consensus definition of the concept of epigenetic trait as "stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence" was formulated at a Cold Spring Harbor meeting in 2008, [4] although alternate definitions that include non-heritable traits are still being used. (wikipedia.org)
  • Accumulating evidence strongly suggests that the pathogenesis of melanoma is also shaped by the aberrant activity of epigenetic factors that regulate gene expression through the modification of DNA and chromatin. (intechopen.com)
  • A significant number of clones consisted of intercalated fragments of TEs of various types, in which Fatima (Ty3- gypsy ) sequences predominated. (hindawi.com)
  • Transposable elements are relatively short sequences of DNA that can move around the genome by themselves. (talkorigins.org)
  • The article focuses on the study by L. Z. Hong and colleagues on EcoP151-tagged digital gene expression (EDGE), which uses unique tag for expressed transcript to avoid the need for a high-quality reference genome as required for RNA sequencing (RNA-seq). (ebscohost.com)
  • The DNA sequence was not inherited but directly transferred from one organism to another. (phys.org)
  • Sequence dependence of the curvature of DNA: a test of the phasing hypothesis. (springer.com)
  • Our approach is able to generate high-quality consensus TE sequences automatically, requiring the user to only provide a few basic parameters. (biomedcentral.com)
  • The nylB gene does most of the heavy lifting, so to speak, and it is the nylB gene that was formed from a deletion mutation and subsequent frame shift in the RSII repetitive element. (talkorigins.org)
  • The researchers now want to study the spread of the P-element under such conditions. (phys.org)
  • One strain produced by researchers had lost nylA as the transposable elements cut it out. (talkorigins.org)
  • To see if a 'broken' pathway led to unchecked copying of Transposable Elements ( TE s), researchers molecularly altered the cells to glow green when specific TE s moved around in the genome. (visembryo.com)
  • Using other techniques, researchers found piwi -lacking flies had greater DNA damage compared to flies with a working piwi gene. (visembryo.com)
  • Considering that DNA demethylation or hypermethylation of transposable element sequences is associated with their activation or silencing, respectively. (hindawi.com)
  • Moreover, the impact of transposable elements on plant genome structure and function is reviewed in detail, and also illustrated in examples and case studies. (exlibris.ch)
  • Transposable element (TE) activation and accumulation generates significant genetic variation that can confer a range of effects on genome structure and function. (g3journal.org)
  • Mathias SL, Scott AF, Kazazian HH et al (1991) Reverse transcriptase encoded by a human transposable element. (springer.com)
  • The reverse transcriptase is often encoded by the element itself. (brighthub.com)
  • Crasta K, Ganem NJ, Dagher R et al (2012) DNA breaks and chromosome pulverization from errors in mitosis. (springer.com)
  • the replication of euchromatic gene-rich DNA occurs earlier in the S-phase. (hindawi.com)
  • The first one shows that the mutation rate can be estimated from the known properties of the DNA replication complex and repair mechanisms. (blogspot.com)
  • Discrete segments of DNA which can excise and reintegrate to another site in the genome. (curehunter.com)
  • Here, plant genome organization was addressed by means of cloning and sequencing TE fragments of different types, which compose the largest portion of the Aegilops speltoides genome. (hindawi.com)
  • Individual genotypes were analyzed cytogenetically using the cloned TE fragments as the DNA probes for fluorescence in situ hybridization (FISH). (hindawi.com)
  • A large variety of DNA molecules, derived as restriction fragments from both prokaryotic (Ross et al. (springer.com)
  • Temperature and salt dependence of the gel migration anomaly of curved DNA fragments. (springer.com)