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.
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.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
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).
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.
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.
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).
A species of fruit fly much used in genetics because of the large size of its chromosomes.
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.
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.
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.
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.
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.
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.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
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.
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).
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.
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.
Nucleic acid sequences involved in regulating the expression of genes.
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.
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.
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.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
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.
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 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)
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
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.

Nonmethylated transposable elements and methylated genes in a chordate genome. (1/9797)

The genome of the invertebrate chordate Ciona intestinalis was found to be a stable mosaic of methylated and nonmethylated domains. Multiple copies of an apparently active long terminal repeat retrotransposon and a long interspersed element are nonmethylated and a large fraction of abundant short interspersed elements are also methylation free. Genes, by contrast, are predominantly methylated. These data are incompatible with the genome defense model, which proposes that DNA methylation in animals is primarily targeted to endogenous transposable elements. Cytosine methylation in this urochordate may be preferentially directed to genes.  (+info)

A cis-acting A-U sequence element induces kinetoplastid U-insertions. (2/9797)

A 34-nucleotide A-U sequence located immediately upstream of the editing sites of the Leishmania tarentolae cytochrome b mRNA induces a mitochondrial extract to insert U nucleotides independent of guide RNA. Insertions are localized to positions immediately 5' and 3' of the A-U sequence. When placed within an unedited mammalian transcript, the A-U sequence is sufficient to induce U-insertions. The sequence has a high degree of similarity with the templating nucleotides of a cytochrome b guide RNA and with a sequence adjacent to the editing sites in ND7 mRNA, the other characterized kinetoplastid mRNA supporting guide RNA-independent U-insertions. At least one protein specifically interacts with the A-U sequence. The reaction is consistent with a mechanism proposed for guide RNA-directed editing.  (+info)

Efflux-mediated aminoglycoside and macrolide resistance in Burkholderia pseudomallei. (3/9797)

Burkholderia pseudomallei, the causative agent of melioidosis, is intrinsically resistant to a wide range of antimicrobial agents including beta-lactams, aminoglycosides, macrolides, and polymyxins. We used Tn5-OT182 to mutagenize B. pseudomallei to identify the genes involved in aminoglycoside resistance. We report here on the identification of AmrAB-OprA, a multidrug efflux system in B. pseudomallei which is specific for both aminoglycoside and macrolide antibiotics. We isolated two transposon mutants, RM101 and RM102, which had 8- to 128-fold increases in their susceptibilities to the aminoglycosides streptomycin, gentamicin, neomycin, tobramycin, kanamycin, and spectinomycin. In addition, both mutants, in contrast to the parent, were susceptible to the macrolides erythromycin and clarithromycin but not to the lincosamide clindamycin. Sequencing of the DNA flanking the transposon insertions revealed a putative operon consisting of a resistance, nodulation, division-type transporter, a membrane fusion protein, an outer membrane protein, and a divergently transcribed regulatorprotein. Consistent with the presence of an efflux system, both mutants accumulated [3H] dihydro streptomycin, whereas the parent strain did not. We constructed an amr deletion strain, B. pseudomallei DD503, which was hypersusceptible to aminoglycosides and macrolides and which was used successfully in allelic exchange experiments. These results suggest that an efflux system is a major contributor to the inherent high-level aminoglycoside and macrolide resistance found in B. pseudomallei.  (+info)

Molecular diversity and evolutionary relationships of Tn1546-like elements in enterococci from humans and animals. (4/9797)

We report on a detailed study on the molecular diversity and evolutionary relationships of Tn1546-like elements in vancomycin-resistant enterococci (VRE) from humans and animals. Restriction fragment length polymorphism (RFLP) analysis of the VanA transposon of 97 VRE revealed seven different Tn1546 types. Subsequent sequencing of the complete VanA transposons of 13 VRE isolates representing the seven RFLP types followed by sequencing of the identified polymorphic regions in 84 other VanA transposons resulted in the identification of 22 different Tn1546 derivatives. Differences between the Tn1546 types included point mutations in orf1, vanS, vanA, vanX, and vanY. Moreover, insertions of an IS1216V-IS3-like element in orf1, of IS1251 in the vanS-vanH intergenic region, and of IS1216V in the vanX-vanY intergenic region were found. The presence of insertion sequence elements was often associated with deletions in Tn1546. Identical Tn1546 types were found among isolates from humans and farm animals in The Netherlands, suggesting the sharing of a common vancomycin resistance gene pool. Application of the genetic analysis of Tn1546 to VRE isolates causing infections in Hospitals in Oxford, United Kingdom, and Chicago, Ill., suggested the possibility of the horizontal transmission of the vancomycin resistance transposon. The genetic diversity in Tn1546 combined with epidemiological data suggest that the DNA polymorphism among Tn1546 variants can successfully be exploited for the tracing of the routes of transmission of vancomycin resistance genes.  (+info)

Many class I integrons comprise distinct stable structures occurring in different species of Enterobacteriaceae isolated from widespread geographic regions in Europe. (5/9797)

Three sizes of inserted regions of DNA (800, 1,000, and 1,500 bp) were shown to be common among class I integrons in unrelated clinical isolates of Enterobacteriaceae from different European hospitals. Sequencing showed that 800-bp inserted regions comprised identical sequences including aacA4, that 1,000-bp inserted regions included aadA, and that 1,500-bp inserted regions included dfrI and aadA1, irrespective of host species and geographic origin. In addition promoter sequences were mostly identical for each size class. These data suggest that inserted gene cassettes and promoter regions of integrons are conserved and stable, with resistance genes transferred more often as part of the entire integron structure than as individual gene cassettes.  (+info)

Molecular characterization of the nitrite-reducing system of Staphylococcus carnosus. (6/9797)

Characterization of a nitrite reductase-negative Staphylococcus carnosus Tn917 mutant led to the identification of the nir operon, which encodes NirBD, the dissimilatory NADH-dependent nitrite reductase; SirA, the putative oxidase and chelatase, and SirB, the uroporphyrinogen III methylase, both of which are necessary for biosynthesis of the siroheme prosthetic group; and NirR, which revealed no convincing similarity to proteins with known functions. We suggest that NirR is essential for nir promoter activity. In the absence of NirR, a weak promoter upstream of sirA seems to drive transcription of sirA, nirB, nirD, and sirB in the stationary-growth phase. In primer extension experiments one predominant and several weaker transcription start sites were identified in the nir promoter region. Northern blot analyses indicated that anaerobiosis and nitrite are induction factors of the nir operon: cells grown aerobically with nitrite revealed small amounts of full-length transcript whereas cells grown anaerobically with or without nitrite showed large amounts of full-length transcript. Although a transcript is detectable, no nitrite reduction occurs in cells grown aerobically with nitrite, indicating an additional oxygen-controlled step at the level of translation, enzyme folding, assembly, or insertion of prosthetic groups. The nitrite-reducing activity expressed during anaerobiosis is switched off reversibly when the oxygen tension increases, most likely due to competition for electrons with the aerobic respiratory chain. Another gene, nirC, is located upstream of the nir operon. nirC encodes a putative integral membrane-spanning protein of unknown function. A nirC mutant showed no distinct phenotype.  (+info)

Protein ProQ influences osmotic activation of compatible solute transporter ProP in Escherichia coli K-12. (7/9797)

ProP is an osmoregulatory compatible solute transporter in Escherichia coli K-12. Mutation proQ220::Tn5 decreased the rate constant for and the extent of ProP activation by an osmotic upshift but did not alter proP transcription or the ProP protein level. Allele proQ220::Tn5 was isolated, and the proQ sequence was determined. Locus proQ is upstream from prc (tsp) at 41.2 centisomes on the genetic map. The proQ220::Tn5 and prc phenotypes were different, however. Gene proQ is predicted to encode a 232-amino-acid, basic, hydrophilic protein (molecular mass, 25,876 Da; calculated isoelectric point, 9.66; 32% D, E, R, or K; 54.5% polar amino acids). The insertion of PCR-amplified proQ into vector pBAD24 produced a plasmid containing the wild-type proQ open reading frame, the expression of which yielded a soluble protein with an apparent molecular mass of 30 kDa. Antibodies raised against the overexpressed ProQ protein detected cross-reactive material in proQ+ bacteria but not in proQ220::Tn5 bacteria. ProQ may be a structural element that influences the osmotic activation of ProP at a posttranslational level.  (+info)

Characterization of an insertion sequence element associated with genetically diverse plant pathogenic Streptomyces spp. (8/9797)

Streptomycetes are common soil inhabitants, yet few described species are plant pathogens. While the pathogenicity mechanisms remain unclear, previous work identified a gene, nec1, which encodes a putative pathogenicity or virulence factor. nec1 and a neighboring transposase pseudogene, ORFtnp, are conserved among unrelated plant pathogens and absent from nonpathogens. The atypical GC content of nec1 suggests that it was acquired through horizontal transfer events. Our investigation of the genetic organization of regions adjacent to the 3' end of nec1 in Streptomyces scabies 84.34 identified a new insertion sequence (IS) element, IS1629, with homology to other IS elements from prokaryotic animal pathogens. IS1629 is 1,462 bp with 26-bp terminal inverted repeats and encodes a putative 431-amino-acid (aa) transposase. Transposition of IS1629 generates a 10-bp target site duplication. A 77-nucleotide (nt) sequence encompassing the start codon and upstream region of the transposase was identified which could function in the posttranscritpional regulation of transposase synthesis. A functional copy of IS1629 from S. turgidiscabies 94.09 (Hi-C-13) was selected in the transposon trap pCZA126, through its insertion into the lambda cI857 repressor. IS1629 is present in multiple copies in some S. scabies strains and is present in all S. acidiscabies and S. turgidiscabies strains examined. A second copy of IS1629 was identified between ORFtnp and nec1 in S. acidiscabies strains. The diversity of IS1629 hybridization profiles was greatest within S. scabies. IS1629 was absent from the 27 nonpathogenic Streptomyces strains tested. The genetic organization and nucleotide sequence of the nec1-IS1629 region was conserved and identical among representatives of S. acidiscabies and S. turgidiscabies. These findings support our current model for the unidirectional transfer of the ORFtnp-nec1-IS1629 locus from IS1629-containing S. scabies (type II) to S. acidiscabies and S. turgidiscabies.  (+info)

Author Summary Transposable elements are mobile DNA elements that are a prevalent component of many eukaryotic genomes. While transposable elements can often have deleterious effects through insertions into protein-coding genes they may also contribute to regulatory variation of gene expression. There are a handful of examples in which specific transposon insertions contribute to regulatory variation of nearby genes, particularly in response to environmental stress. We sought to understand the genome-wide influence of transposable elements on gene expression responses to abiotic stress in maize, a plant with many families of transposable elements located in between genes. Our analysis suggests that a small number of maize transposable element families may contribute to the response of nearby genes to abiotic stress by providing stress-responsive enhancer-like functions. The specific insertions of transposable elements are often polymorphic within a species. Our data demonstrate that allelic variation
This chapter provides a general description of the types of genetic variation caused by transposable elements in animals and plants, and examines this variation within an evolutionary framework. It focuses on the variation induced by transposable elements in their host organisms. The host variation associated with transposable elements can result from several interconnected aspects of transposable element activity. Estimates of the frequencies of new transposable element-induced mutations have been made under laboratory conditions and varied over an enormous range. The partial or complete sterility associated with several systems of hybrid dysgenesis in Drosophila provides an interesting aspect of variation associated with transposable element activity. Heterochromatin proteins can recognize and silence transposable elements, some of which target heterochromatin for insertion. Thus, the evolution of heterochromatin could have led to a self-perpetuating expansion of domains rich in transposable elements.
Transposable elements are endogenous DNA sequences able to integrate into and multiply within genomes. They constitute a major source of genetic innovations, as they can not only rearrange genomes but also spread ready-to-use regulatory sequences able to modify host gene expression, and even can give birth to new host genes. As their evolutionary success depends on their vertical transmission, transposable elements are intrinsically linked to reproduction. In organisms with sexual reproduction, this implies that transposable elements have to manifest their transpositional activity in germ cells or their progenitors. The control of sexual development and function can be very versatile, and several studies have demonstrated the implication of transposable elements in the evolution of sex. In this review, we report the functional and evolutionary relationships between transposable elements and sexual reproduction in animals. In particular, we highlight how transposable elements can influence expression of
The beta-glucuronidase reporter gene has been used to develop a sensitive assay for the excision of transposable elements introduced into transgenic plants. The reporter gene, inactivated by the insertion of the maize transposable element Activator (Ac) into the 5-untranslated leader, was introduced into the genome of tobacco by Agrobacterium-mediated transformation. Reactivation of the beta-glucuronidase gene was detected in transgenic plants using a fluorometric or histochemical assay. Reactivation of the reporter gene was dependent on the presence of the transposase of Ac, and resulted from the excision of the Ac element. This assay, together with the improved methods for visualization, will provide a valuable and rapid method for studying the basic mechanism of transposition in plants and for developing modified transposable element systems suitable for gene tagging in transgenic plants.. ...
TY - THES. T1 - An En/Spm based transposable element system for gene isolation in Arabidopsis thaliana. AU - Aarts, M.G.M.. N1 - WU thesis 2194 90-5485-622-X Proefschrift Wageningen. PY - 1996. Y1 - 1996. N2 - At the start of the research described in this thesis, the main aim was to develop, study and apply an efficient En/Spm-I/dSpm based transposon tagging system in Arabidopsis thaliana to generate tagged mutants and to provide insights in the possibilities for future applications of such a transposon tagging system in studying plant gene functions. The first step was the introduction of an active En/Spm-I/dSpm system into Arabidopsis. Initially a very simple T-DNA construct was transformed, containing a nearly full En-1 element, without left and right border sequences, and with its promoter replaced by the stronger CaMV 35S promoter. As the same construct harboured a non-autonomous I/dSpm element, only one T-DNA transformation was needed. Transformation of this in cis two- element ...
Transposable elements are mobile genetic elements that are prevalent in plant genomes and are silenced by epigenetic modification. Different epigenetic modification pathways play distinct roles in the control of transposable element transcription, replication and recombination. The Arabidopsis genome contains families of all of the major transposable element classes, which are differentially enriched in particular genomic regions. Whole genome sequencing and DNA methylation profiling of hundreds of natural Arabidopsis accessions has revealed that transposable elements exhibit significant intraspecific genetic and epigenetic variation, and that genetic variation often underlies epigenetic variation. Together, epigenetic modification and the forces of selection define the scope within which transposable elements can contribute to, and control, genome evolution.. ...
Transposons are mobile DNA segments that can disrupt gene function by inserting in or near genes. Here, we show that insertional mutagenesis by the PiggyBac transposon can be used for cancer gene discovery in mice. PiggyBac transposition in genetically engineered transposon-transposase mice induced cancers whose type (hematopoietic versus solid) and latency were dependent on the regulatory elements introduced into transposons. Analysis of 63 hematopoietic tumors revealed that PiggyBac is capable of genome-wide mutagenesis. The Piggybac screen uncovered many cancer genes not identified in previous retroviral or Sleeping Beauty transposon screens, including Spic, which encodes a PU.1-related transcription factor, and Hdac7, a histone deacetylase gene. PiggyBac and Sleeping Beauty have different integration preferences. To maximize the utility of the tool, we engineered 20 mouse lines to be compatible with both transposases in constitutive, tissue-, or temporal-specific mutagenesis. Mice with ...
A chimeric white gene (wpch) and other constructs containing the transposable element mariner from Drosophila mauritiana were introduced into the germline of Drosophila melanogaster using transformation mediated by the P element. In the absence of other mariner elements, the wpch allele is genetically stable in both germ cells and somatic cells, indicating that the peach element (i.e., the particular copy of mariner inserted in the wpch allele) is inactive. However, in the presence of the active element Mos1, the wpch allele reverts, owing to excision of the peach element, yielding eye-color mosaics and a high rate of germline reversion. In strains containing Mos1 virtually every fly is an eye-color mosaic, and the rate of wpch germline reversion ranges from 10 to 25%, depending on temperature. The overall rates of mariner excision and transposition are approximately sixfold greater than the rates in comparable strains of Drosophila simulans. The activity of the Mos1 element is markedly affected ...
TY - JOUR. T1 - Regulation of Tcl transposable elements in Caenorhabditis elegans.. AU - Emmons, S. W.. AU - Ruan, K. S.. AU - Levitt, A.. AU - Yesner, L.. PY - 1985. Y1 - 1985. N2 - C. elegans strains contain variable numbers of a 1.6-kb transposable genetic element. Activity of this element, which is denoted Tcl, shows regulation at at least two levels. At one level, excision of Tcl elements occurs in somatic cells at a frequency several orders of magnitude higher than in germ cells. Evidence is presented suggesting that this results from regulation at the level of trans-acting functions that are required for excision or that repress excision. At the second level, germ line transposition of Tcl occurs at greater frequency in some strains than in others. The hypothesis is proposed that this is because Tcl is one component of a two-element system, the second element of which differs between strains. Evidence for a second putative transposable element family in C. elegans is presented. This ...
Transposon insertion site profiling chip (TIP-chip) was invented by Researchers at the Johns Hopkins High Throughput Biology Center. Tip-chip can be used to help identify otherwise elusive disease-causing mutations in the 97 percent of the genome long believed to be
With regard to the origin of the human species, when the chimp genome was sequenced, it was found to contain nearly all of the transposable elements that the human genome had. The transposable elements were arranged in the same places on chromosomes that were >95% identical in their sequences. I summarized these findings in a paper for OPBSG in 2006. The presence of many transposable elements in the human genome implied that they originated by transposition, and the presence of the same transposable elements in the chimp genome implied that humans and chimps shared a common ancestor. Why? Because of the staggering similarity ...
This chapter discusses the different classes of mobile elements seen in some of the best-characterized animal genome and plant genome. It talks about the some of the general concepts behind the colonization of genomes by mobile elements. There are basically three classes of autonomous mobile elements, all three of which can be found to various extents in different genomes of all animals and plants. These are the DNA transposons, the long terminal repeat (LTR) retrotransposons, and the non-LTR retrotransposons. DNA transposons are very common in the Caenorhabditis elegans genome, as well as several relatively high-copy-number families of their nonautonomous relatives, miniature inverted-repeat transposable elements (MITEs). Other site-specific mobile elements are the HetA and TART elements that make up the telomeres in Drosophila. Only sporadic data are available on mobile elements in reptiles, amphibians, and fish. Almost all the classes of mobile elements are present to some degree in almost all animal
Schöffl, F., Arnold, W., Pühler, A., Altenbuchner, J., & Schmitt, R. (1981). The tetracycline resistance transposons Tn1721 and Tn1771 have three 38-base-pair repeats and generate five-base-pair direct repeats. Mol Gen Genet, 181(1), 87-94. doi:10.1007/ ...
Though transposable elements make up around half of the human genome, the repetitive nature of their sequences makes it difficult to accurately align conventional sequencing reads. However, in light of new advances in sequencing technology, such as increased read length and paired-end libraries, these repetitive regions are now becoming easier to align to. This study investigates the mappability of transposable elements with 50 bp, 76 bp and 100 bp paired-end read libraries. With respect to those read lengths and allowing for 3 mismatches during alignment, over 68, 85, and 88% of all transposable elements in the RepeatMasker database are uniquely mappable, suggesting that accurate locus-specific mapping of older transposable elements is well within reach.
DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
Transposable elements (TEs) have been highly influential in shaping the structure and evolution of mammalian genomes, as exemplified by TE-derived sequence contributing between 38 and 69% of genomic sequence [1-8]. TE insertions also can influence the transcription, translation or function of genes [1-7]. Functional effects of TE insertions include their regulation of transcription by acting as alternative promoters or as enhancer elements and via the generation of antisense transcripts, or of transcriptional silencers. TEs can alter splice sites or RNA editing, provide alternative poly-adenylation signals or exons, modify chromatin structure or alter translation. Furthermore, TE insertion has been suggested to be a mechanism by which new co-regulatory networks arise [1-7].. TEs are classified on the basis of their transposition mechanism [9]. A class I retrotransposon propagates in the host genome through an intermediate RNA step, requiring a reverse transcriptase to revert it to DNA before ...
Fingerprint Dive into the research topics of Color reversion of the albino medaka fish associated with spontaneous somatic excision of the Tol-1 transposable element from the tyrosinase gene. Together they form a unique fingerprint. ...
The mariner family of transposable elements is one of the most widespread in the Metazoa. It is subdivided into several subfamilies that do not mirror the phylogeny of these species, suggesting an ancient diversification. Previous hybridization and PCR studies allowed a partial survey of mariner diversity in the Metazoa. In this work, we used a comparative genomics approach to access the genus-wide diversity and evolution of mariner transposable elements in twenty Drosophila sequenced genomes. We identified 36 different mariner lineages belonging to six distinct subfamilies, including a subfamily not described previously. Wide variation in lineage abundance and copy number were observed among species and among mariner lineages, suggesting continuous turn-over. Most mariner lineages are inactive and contain a high proportion of damaged copies. We showed that, in addition to substitutions that rapidly inactivate copies, internal deletion is a major mechanism contributing to element decay and the
P element excision generates a DNA double-strand break at the transposon donor site. Genetic studies have demonstrated a strong bias toward repair of P element-induced DNA breaks by homologous recombination with the sister chromatid, suggesting that P element excision occurs after DNA replication, i …
THE Activator/Dissociation (Ac/Ds) transposon family has been extensively characterized since its discovery in maize ,60 years ago (McClintock 1946; Kunze and Weil 2002). Ac/Ds are class II DNA transposons that belong to the hAT superfamily of plant transposable elements (Kunze and Weil 2002). Ac is a 4565-bp autonomous element capable of catalyzing the transposition of itself and nonautonomous Ds elements (McClintock 1949, 1951). Ac encodes a 3.5-kb open reading frame (ORFa) that directs the synthesis of an 807-amino-acid transposase (TPase) essential for both Ac and Ds transposition (Fedoroff et al. 1983; Kunze et al. 1987). The 11 bp imperfect terminal inverted repeats (TIR) and ∼240 bp of subterminal sequences are critical for TPase binding and transposition of both Ac and Ds (Coupland et al. 1988, 1989).. In contrast to the highly conserved structure of Ac elements (Fedoroff et al. 1983; Behrens et al. 1984; Muller-Neumann et al. 1984; Pohlman et al. 1984), Ds elements are structurally ...
Mutator-like transposable elements (MULEs) are widespread across fungi, plants and animals. Most of the research of MULEs has focused on plant where they are discovered and have significant impact on genome structure. Despite being widespread, only a few active MULEs have been identified, meanwhile, the transposition mechanism of the MULEs is previously unknown. Pack-MULEs are able to capture and amplify genes or gene fragments on a large scale, and a subset of plant Pack-MULEs have been shown to be likely playing functional roles in regulating gene expression and providing novel coding capacities. However, the presence of Pack-MULEs in non-plant species has not been reported.. In this study we report that Muta1 identified from the mosquito Aedes aegypti is capable of excision and reinsertion in a yeast transposition assay, element reinsertion generated either 8 bp or 9 bp target site duplications (TSDs) with no apparent sequence preference. Mutagenesis analysis revealed the importance of ...
PiggyBac Transposable Element Derived 5 is an enzyme that in humans is encoded by the PGBD5 gene.[1] PGBD5 is a DNA transposase related to the ancient PiggyBac transposase first identified in the cabbage looper moth, Trichoplusia ni.[2] The gene is believed to have been domesticated over 500 million years ago in the common ancestor of cephalochordates and vertebrates.[3] The putative catalytic triad of the protein composed of three aspartic acid residues is conserved among PGBD5-like genes through evolution,[4], and is distinct from other PiggyBac-like genes.[3] PGBD5 has been shown to be able to transpose DNA in a sequence-specific, cut-and-paste fashion.[4] PGBD5 has also been proposed to mediate site-specific DNA rearrangements in human tumors.[5] ...
The PiggyBac (PB) transposon has emerged as a novel mutagenesis tool for understanding gene function and for phenotypic screening in eukaryotes
misc{7861784, abstract = {DNA transposons are a class of mobile genetic elements that can autonomously move from one genomic location to another. They are powerful drivers of genetic change and have played a significant role in the evolution of many genomes. One such transposable element, IS608 from Helicobacter pylori employs a unique mechanism of transposition as it transposes in a single-stranded DNA form and inserts specifically 3 of a specific tetranucleotide sequence (Kersulyte et al., 2002; Guynet et al., 2008). Previous structural (Ronning et al., 2005; Barabas et al, 2008) and biochemical studies (Ton-Hoang et al., 2005) of IS608, revealed that the element chooses its integration site specifically via base-pairing between the transposon and the target DNA. This unique feature allowed re-directing transposon integration to various four-nucleotide sequences by simply modifying the transposon DNA sequence. A key feature of the retargeting strategy was that, unlike the previous attempts to ...
Described is a mechanism for dependably synchronizing data element activities on web pages among a group of browsers. The web browsers retrieve web pages from an HTTP server. Each of the web pages contains at least one data element and embeds a Master Applet and at least one DTS Applet (DTS stands for data tracking and synchronization). In response the data element activities (such as entering data into a data field) performed at a browser, the DTS Applet passes the activities to the Master Applet, which in turn reports the activities (together with the URL of the web page on which the data element activities have occurred) to a tracking server. The tracking server sends the activity report (together with the URL of the web page on which the data element activities have occurred) to the Master Applets at all participant browsers. The participant Master Applets then instruct their respective DTS Applets to display the data element activities on the web page identified by the URL.
1) a small deletion occurs in the transposase gene of an IS element and plasmid is integrated , 2) a small deletion occurs in the transposase gene of an IS element , 3) two IS elements integrate into a chromosome with only a small distance separating them , 4) an IS element integrates with another IS element with the help of a plasmid
Both classes of transposable elements (DNA and RNA) are tightly regulated at the transcriptional level leading to the inactivation of transposition via epigenetic mechanisms. Due to the high copies number of these elements, the hypothesis has emerged that their regulation can coordinate a regulatory network of genes. Herein, we investigated whether transposition regulation of HsMar1, a human DNA transposon, differs in presence or absence of endogenous HsMar1 copies. In the case where HsMar1 transposition is regulated, the number of repetitive DNA sequences issued by HsMar1 and distributed in the human genome makes HsMar1 a good candidate to regulate neighboring gene expression by epigenetic mechanisms. A recombinant active HsMar1 copy was inserted in HeLa (human) and CHO (hamster) cells and its genomic excision monitored. We show that HsMar1 excision is blocked in HeLa cells, whereas CHO cells are competent to promote HsMar1 excision. We demonstrate that de novo HsMar1 insertions in HeLa cells (human)
Not so conserved after all - Multiple independent losses of the piRNAs in nematodes revealed. A new study carried out by Peter Sarkies (Transgenerational Epigenetic Inheritance & Evolution) in collaboration with Eric Miska (Gurdon Institute, Cambridge) reveals astonishing insights into the evolution of transposon-silencing mechanisms in nematode worms.. Transposons are selfish DNA pieces that insert themselves into the genome. Like a computer virus, they copy themselves and proliferate, which can disrupt essential gene functions.. Because transposons are so disruptive, there is huge selective pressure on organisms to silence them and stop them spreading. Organisms have evolved ingenious ways to suppress transposon activity, especially in the reproductive cells, where a transposition event affects subsequent generations.. The front line of defence against transposons in most animals, from nematode worms to humans, are tiny sequences of RNA, known as Piwi interacting small RNAs (piRNAs). These ...
Sequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and provide an opportunity for comprehensive annotation of TEs. Numerous methods exist for annotation of each class of TEs, but their relative performances have not been systematically compared. Moreover, a comprehensive pipeline is needed to produce a non-redundant library of TEs for species lacking this resource to generate whole-genome TE annotations. We benchmark existing programs based on a carefully curated library of rice TEs. We evaluate the performance of methods annotating long terminal repeat (LTR) retrotransposons, terminal inverted repeat (TIR) transposons, short TIR transposons known as miniature inverted transposable elements (MITEs), and Helitrons. Performance metrics include sensitivity, specificity, accuracy, precision, FDR, and F1. Using the most robust programs, we create a
During her studies on maize development and chromosomal breakages in maize, McClintock discovered that maize plants which develop patched kernels do not inherit this phenotype in a Mendelian fashion ...
Transposable elements may acquire unrelated gene fragments into their sequences in a process called transduplication. Transduplication of protein-coding genes is common in plants, but is unknown of in animals. Here, we report that the Turmoil-1 transposable element in C. elegans has incorporated two protein-coding sequences into its inverted terminal repeat (ITR) sequences. The ITRs of Turmoil-1 contain a conserved RNA recognition motif (RRM) that originated from the rsp-2 gene and a fragment from the protein-coding region of the cpg-3 gene. We further report that an open reading frame specific to C. elegans may have been created as a result of a Turmoil-1 insertion. Mutations at the 5 splice site of this open reading frame may have reactivated the transduplicated RRM motif. This article was reviewed by Dan Graur and William Martin. For the full reviews, please go to the Reviewers Reports section.
Embryonic stem cells modified to lack DNA methylation allowing transposons to become active. DNA shown in blue. Cells containing active transposons shown in red.
Transposons or Transposable elements (TEs) are mobile genes capable of mobilization from one genomic location to another through non-homologous recombination. As this movement is mediated by its own proteins and does not contribute to the survival of the host that it inhabits, they are known as selfish genomic parasites. Despite their capacity for transposition inside genomes, they can frequently transpose the species boundaries and consequently migrate from one species to another. Such phenomenon is called Horizontal Transposons Transfer. HTT was first discovered by Daniels et al. (1984) when analysing a P element that was transferred from Drosophila willistoni to D. melanogaster. Since then, many more cases have been documented in the literature. Moreover, in the last years, such discoveries have been boosted by the unprecedented amount of new genomes available. Despite the recognition of HTT as a common phenomenon in recent years, it is still difficult to draw major conclusions about HTT ...
The availability of several whole genome sequences makes comparative analyses possible. In primate genomes, the priority of transposable elements (TEs) is significantly increased because they account for ~45% of the primate genomes, they can regulate the gene expression level, and they are associated with genomic fluidity in their host genomes. Here, we developed the BLAST-like alignment tool (BLAT) based comparative analysis for transposable elements (BLATCAT) program. The BLATCAT program can compare specific regions of six representative primate genome sequences (human, chimpanzee, gorilla, orangutan, gibbon, and rhesus macaque) on the basis of BLAT and simultaneously carry out RepeatMasker and/or Censor functions, which are widely used Windows-based web-server functions to detect TEs. All results can be stored as a HTML file for manual inspection of a specific locus. BLATCAT will be very convenient and efficient for comparative analyses of TEs in various primate genomes ...
A family of novel mobile DNA elements is described, examples of which are found at several independent locations and encode a variety of antibiotic resistance genes. The complete elements consist of two conserved segments separated by a segment of variable length and sequence which includes inserted antibiotic resistance genes. The conserved segment located 3′ to the inserted resistance genes was sequenced from Tn21 and R46, and the sequences are identical over a region of 2026 bases, which includes the sulphonamide resistance gene sull, and two further open reading frames of unknown function. The complete sequences of both the 3′ and 5′ conserved regions of the DNA element have been determined. A 59-base sequence element, found at the junctions of inserted DNA sequences and the conserved 3′ segment, is also present at this location in the R46 sequence. A copy of one half of this 59-base element is found at the end of the sull gene, suggesting that sull, though part of the conserved ...
Transposable Elements 2016, Meeting on Transposable Elements is a Genetics Meeting, organized in Cold Spring Harbor, New York. Learn More About Event
Dysregulation of transposable elements in Gasz testes.(A-B) Quantitative RT-PCR analysis of transposable elements in testes from embryonic, newborn, 7- and 1
A Genetic Screen Using the PiggyBac Transposon in Haploid Cells Identifies Parp1 as a Mediator of Olaparib Toxicity. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Background The revolutionary concept of jumping genes was conceived by McClintock in the late 1940s while studying the Activator/Dissociation (Ac/Ds) system in maize. Transposable elements (TEs) represent the most abundant component of many eukaryotic genomes. Mobile elements are a driving force of eukaryotic genome evolution. McClintocks Ac, the autonomous element of the Ac/Ds system, together with hobo from Drosophila and Tam3 from snapdragon define an ancient and diverse DNA transposon superfamily named hAT. Other members of the hAT superfamily include the insect element Hermes and Tol2 from medaka. In recent years, genetic tools derived from the cut and paste Tol2 DNA transposon have been widely used for genomic manipulation in zebrafish, mammals and in cells in vitro ...
Multiple methods have been introduced over the past 30 years to identify the genomic insertion sites of transposable elements and other DNA elements that integrate into genomes. However, each of these methods suffer from limitations that can frustrate attempts to map multiple insertions in a single genome and to map insertions in genomes of high complexity that contain extensive repetitive DNA. I introduce a new method for transposon mapping that is simple to perform, can accurately map multiple insertions per genome, and generates long sequence reads that facilitate mapping to complex genomes. The method, called TagMap, for Tagmentation-based Mapping, relies on a modified Tn5 tagmentation protocol with a single tagmentation adaptor followed by PCR using primers specific to the tranposable element and the adaptor sequence. Several minor modifications to normal tagmentation reagents and protocols allow easy and rapid preparation of TagMap libraries. Short read sequencing starting from the adaptor ...
Transposable elements (TEs) are mobile genetic elements. They are a significant component of many eukaryotic genomes. They are involved in chromosomal rearrangement by serving as substrates for homologous recombination, in creating new genes through a process of TE domestication, and in modifying and shuffling existing genes by transducing neighboring sequences (Lander et al., 2001). Therefore, both active and inactive TEs are potentially potent agents for genomic change (Kidwell and Lisch, 2001, 2002; Rizzon et al., 2002; Petrov et al., 2003). In the meantime, active TEs are being explored as useful tools for genetic transformation and possible gene drive mechanisms to deliver genes in natural populations (Ashburner et al.,1998; Alphey et al.,2002; Handler and OBrochta, 2004). My thesis project focuses on AGH1, a novel DNA-mediated TE in Anopheles gambiae and related mosquitoes. I have studied its genomic structure, insertion polymorphism, evolution, and transposition activity. As part of ...
Genomes of higher plants vary significantly in their size and complexity. Repetitive DNA sequences have been shown to be the major determinant of genome sizes in higher plants [13]. The prevalence of transposable elements and retroelements can promote unequal crossing-over leading to transposon-mediated rearrangements and gene duplications [40]. It has been hypothesized that transposable elements play a major role in the expansion and diversification of transmembrane receptor kinase-type disease resistance Xa21 gene family [9]. The abundance of retroelements has been observed in several genomic regions containing R genes or RGA loci, such as barley powdery mildew resistance gene, Mla, and Citrus virus resistance gene, Ctv [7, 8]. The variability among 14 rice Xa21 gene members has been considered to be generated mainly from the rearrangements mediated by transposon-like elements [9]. Rps1-k genes are arranged closely. About 38 copies of Rps1-k-like sequences were predicted to exist in the ...
DUGi: Viewing Item from repository DUGiDocs: Transposable elements (TEs) are mobile DNA sequences that have the ability to jump from one location of the genome to another and create copies of them during the process. Although their activity can create mostly harmful mutation, it also represent an important source of genetic variation that have been shown to rewire and fine-tune regulatory networks. Stress response mechanisms are highly conserved across organisms and a major target of natural selection. Despite the latest advances in evolutionary biology, adaptation process remains poorly understood. Therefore, studying stress pathways provide a great opportunity to study how adaptive processes occur. In this study we aim to identify genome-wide putatively adaptive TEs that are candidates to modulate stress response by the addition of stress response elements (SREs) in the promoter of Drosophila melanogaster genes. We combine bioinformatics and population genetics approaches to discard SREs found by
Vitamin B12 has been broadly associated to methionine metabolism, which is an integral part for organic methylation reactions, together with DNA methylation. However, the connection between vitamin B12 and DNA methylation continues to be controversial. In addition, theres rising proof for the affiliation between vitamin B12 and the danger of colorectal most cancers (CRC), though … Read more. ...
Transfer RNA (tRNA)-derived small RNAs (tsRNAs) have been discovered to play vital roles in the incidence and improvement of cancers. However, the tsRNA profile in gastric cancer is unknown. In this examine, we aimed to determine the worldwide tsRNA profile in plasma from gastric cancer sufferers and elucidate the function of tRF-33-P4R8YP9LON4VDP in gastric cancer. … Read more. ...
Read The rice R gene family: two distinct subfamilies containing several miniature inverted-repeat transposable elements, Plant Molecular Biology on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Bacterial insertion sequences are the simplest form of autonomous mobile DNA. It is unknown whether they need to have beneficial effects to infect and persist in bacterial populations, or whether horizontal gene transfer suffices for their persistence. We address this question by using branching process models to investigate the critical, early phase of an insertion sequence infection. We find that the probability of a successful infection is low and depends linearly on the difference between the rate of horizontal gene transfer and the fitness cost of the insertion sequences. Our models show that the median time to extinction of an insertion sequence that dies out is very short, while the median time for a successful infection to reach a modest population size is very long. We conclude that horizontal gene transfer is strong enough to allow the persistence of insertion sequences, although infection is an erratic and slow process. ...
DNA transposons are ubiquitous components of eukaryotic genomes. Academ superfamily of DNA transposons is one of the least characterized DNA transposon superfamilies in eukaryotes. DNA transposons belonging to the Academ superfamily have been reported from various animals, one red algal species Chondrus crispus, and one fungal species Puccinia graminis. Six Academ families from P. graminis encode a helicase in addition to putative transposase, while some other families encode a single protein which contains a putative transposase and an XPG nuclease. Systematic searches on Repbase and BLAST searches against publicly available genome sequences revealed that several species of fungi and animals contain multiple Academ transposon families encoding a helicase. These AcademH families generate 9 or 10-bp target site duplications (TSDs) while Academ families lacking helicase generate 3 or 4-bp TSDs. Phylogenetic analysis clearly shows two lineages inside of Academ, designated here as AcademH and AcademX for
The gammaherpesviruses include the human pathogens Epstein-Barr virus and Kaposis sarcoma-associated herpesvirus. These viruses establish life-long infections of the host and are associated with a number of malignancies. To better understand gammaherpesvirus pathogenesis, we and others have begun to utilize infection of mice with murine gammaherpesvirus 68 (γHV68). γHV68 is a member of the gamma-2-herpesvirus subfamily based on genome sequence (13, 51). Sequence analysis of γHV68 identified 80 ATG-initiated open reading frames (ORFs) predicted to encode proteins of at least 100 amino acids in length (51). The majority of these ORFs were homologous to known genes present in other gammaherpesviruses (51). The requirement for most of the predicted ORFs during viral replication in vitro is unknown.. Traditional methods of generating mutations in gammaherpesviruses are time-consuming and labor intensive. Homologous recombination in mammalian cells relies on the use of a genetic marker (e.g., ...
al., 1994), it was observed that a 3.8-kb HindIII fragment was present in multiple copies in X. campestris pv. juglandis genome when the fragment was used as a probe in the Southern hybridization with HindIII-digested genomic DNA of X. campestris pv. juglandis. To further localize the repetitive sequence, several subclones from the fragment were used as probes to hybridize with HindIII-digested genomic DNA. The Southern hybridization using 2.0-kb PstI-ClaI fragment as a probe showed the same repetitive pattern as 3.8-kb HindIII fragment; in contrast, the probes outside the 2.0-kb fragment hybridized only to a single genomic restriction fragment, indicating that the repetitive sequence was within the 2.0-kb PstI-ClaI fragment. The 2.0-kb fragment was ligated into pBluescript SK(+), resulting in plasmid pISJ12. The insertion sequence-like element in the fragment was named IS1403 afterward.. To isolate a homologous IS from X. campestris pv. campestris XCC1-1, a 0.5-kb AvaII internal fragment of ...
ISfinder (www-is.biotoul.fr) is a dedicated database for bacterial insertion sequences (ISs). It has superseded the Stanford reference center. One of its functions is to assign IS names and to provide a focal point for a coherent nomenclature. It is also the repository for ISs. Each new IS is indexe …
In this study, first we showed that the Tol2 transposon system is a useful technique in generating stable transfected primary culture cells and, second, we demonstrated that the Tol2 transposon system is applicable to the study of circadian clock oscillations.. The Tol2 transposon was originally discovered from Medaka fish (Orzyias latipes) [12]. An active autonomous member of Tol2 was first identified by the analysis using zebrafish embryos [13]. Since then, the Tol2 transposon system has been mainly used for random insertion mutagenesis and transgene in zebrafish [14]. Although recent reports have indicated that the transposon systems such as piggyBac and SleepingBeauty in addition to Tol2 are also active in mammalian cells [15, 16], few studies have been reported that utilized the Tol2 system for transfection to mammalian primary culture cells. In the present study, we showed that the Tol2 transposon system is a useful tool in generating stable transfected primary culture cells such as MEF ...
We present data on the relationship between the rate of transposition and copy number in the genome for the copia and Doc retrotransposons of Drosophila melanogaster. copia and Doc transposition rates were directly measured in sublines of the isogenic 2b line using individual males or females, respectively, with a range of copia copy numbers from 49 to 103 and Doc copy numbers from 112 to 235 per genome. Transposition rates varied from 3 x 10(-4) to 2 x 10(-2) for copia and from 2 x 10(-4) to 2 x 10(-3) for Doc. A positive relationship between transposition rate and copy number was found both for copia and for Doc when the data were analysed across all the 2b individuals; no significant correlation was found when the data were analysed across the subline means for both retrotransposons tested. Overall, correlation between copia and Doc transposition rate and their copy number in the genome, if any, was not negative, which would be expected if transposable elements (TEs) self-regulate their copy number.
Miniature inverted repeat transposable elements (MITEs) are abundant non-autonomous elements, playing important roles in shaping gene and genome evolution. Their characteristic structural features are suitable for automated identification by computational approaches, however, de novo MITE discovery at genomic levels is still resource expensive. Efficient and accurate computational tools are desirable. Existing algorithms process every member of a MITE family, therefore a major portion of the computing task is redundant. In this study, redundant computing steps were analyzed and a novel algorithm emphasizing on the reduction of such redundant computing was implemented in MITE Digger. It completed processing the whole rice genome sequence database in ~15 hours and produced 332 MITE candidates with low false positive (1.8%) and false negative (0.9%) rates. MITE Digger was also tested for genome wide MITE discovery with four other genomes. MITE Digger is efficient and accurate for genome wide retrieval of
TY - JOUR. T1 - Germline transgenesis of the chordate Ciona intestinalis with hyperactive variants of sleeping beauty transposable element. AU - Hozumi, Akiko. AU - Mita, Kaoru. AU - Miskey, Csaba. AU - Mates, Lajos. AU - Izsvak, Zsuzsanna. AU - Ivics, Zoltan. AU - Satake, Honoo. AU - Sasakura, Yasunori. PY - 2013/1/1. Y1 - 2013/1/1. N2 - Background: Transposon-mediated transgenesis is an excellent method for creating stable transgenic lines and insertional mutants. In the chordate Ciona intestinalis, Minos is the only transposon that has been used as the tool for germline transformation. Adding another transposon system in this organism enables us to conduct genetic techniques which can only be realized with the use of two transposons. Results: In the present study, we found that another Tc1/mariner superfamily transposon, sleeping beauty (SB), retains sufficient activity for germline transformation of C. intestinalis. SB shows efficiencies of germline transformation, insertion into gene coding ...
Large-scale sequencing of human cancer genomes and mouse transposon-induced tumors has identified a vast number of genes mutated in different cancers. One of the outstanding challenges in this field is to determine which genes, when mutated, contribute to cellular transformation and tumor progression. To identify new and conserved genes that drive tumorigenesis we have developed a novel cancer model in a distantly related vertebrate species, the zebrafish, Danio rerio. The Sleeping Beauty (SB) T2/Onc transposon system was adapted for somatic mutagenesis in zebrafish. The carp ß-actin promoter was cloned into T2/Onc to create T2/OncZ. Two transgenic zebrafish lines that contain large concatemers of T2/ OncZ were isolated by injection of linear DNA into the zebrafish embryo. The T2/OncZ transposons were mobilized throughout the zebrafish genome from the transgene array by injecting SB11 transposase RNA at the 1-cell stage. Alternatively, the T2/OncZ zebrafish were crossed to a transgenic line that
TY - JOUR. T1 - Characterization of Gandalf, a new inverted-repeat transposable element of Drosophila koepferae. AU - Marín, Ignacio. AU - Fontdevila, Antonio. PY - 1995/8/1. Y1 - 1995/8/1. N2 - The cloning and characterization of Gandalf, a new DNA-transposing mobile element obtained from the Drosophila koepferae (repleta group) genome is described. A fragment of Gandalf was found in a middle repetitive clone that shows variable chromosomal localization. Restriction, Southern blot, PCR and sequencing analyses have shown that most Gandalf copies are about 1 kb long, are flanked by 12 by inverted terminal repeats and contain subterminal repetitive regions on both sides of the element. As with other elements of the DNA-transposing type (known as the Ac family), the Gandalf element generates 8 by direct duplications at the insertion point. Coding region analysis has shown that the longer open reading frame found in Gandalf copies could encode part of a protein. However, whether or not the 1 kb ...
Transposable elements (TEs) are ubiquitous DNA sequences that can change their positions within a genome or transfer horizontally among genomes (Gilbert et al. 2010). TE movements may cause mutations, affect gene expression, and change genome sizes and structures; therefore, they are considered an important force in gene and genome evolution (Kazazian 2004). TEs are grouped into two major classes according to their transposition mechanism and sequence features. Class I elements, retrotransposons, mobilize via a copy-and-paste model and have the potential to dramatically increase copy number; whereas, class II elements, DNA transposons, transpose via a cut-and-paste model or rolling-circle replication (Kapitonov and Jurka 2001; Wicker et al. 2007). Class II elements have been further divided into 12 superfamilies (Feschotte and Pritham 2007; Wicker et al. 2007). Except for the Helitron and Crypton superfamilies, all class II elements have terminal inverted repeats (TIRs). To date, only six ...
Cell culture and transposition assay HEK 293 cells had been maintained in MEMa medium supplemented with 10% FBS, 100 units ml penicillin, and a hundred ug mL streptomycin. The specifics for your transposition assays had been described pre viously. Inhibitors,Modulators,Libraries Exercise assay in the piggyBac transposase A equivalent procedure as thorough previously was employed to co transfect a hundred ng of piggyBac donor, with various quantity of the piggyBac helper, pCMV Myc piggyBac, ranging from 0 300 ng into 1. 2 105 of HEK 293 cells. pcNDA3. 1NEO, an empty vector used in our prior examine, was employed to best the total level of DNA transfected to 400 ng. Each and every trans fection condition was completed in triplicate. Twenty 4 hours just after transfection, one fifth of transfected cells were subjected to transposition assay.. The remaining transfected cells in triplicate had been pooled and grew in the 35 mm plate for a further twenty four hours prior to staying subjected to ...
TY - JOUR. T1 - Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome. AU - Greally, John M.. PY - 2002/1/8. Y1 - 2002/1/8. N2 - To test whether regions undergoing genomic imprinting have unique genomic characteristics, imprinted and nonimprinted human loci were compared for nucleotide and retroelement composition. Maternally and paternally expressed subgroups of imprinted genes were found to differ in terms of guanine and cytosine, CpG, and retroelement content, indicating a segregation into distinct genomic compartments. Imprinted regions have been normally permissive to L1 long interspersed transposable element retroposition during mammalian evolution but universally and significantly lack short interspersed transposable elements (SINEs). The primate-specific Alu SINEs, as well as the more ancient mammalian-wide interspersed repeat SINEs, are found at significantly low densities in imprinted regions. The latter paleogenomic signature ...
Transposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Class I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on the expression ...
The morphological stasis of coelacanths has long suggested a slow evolutionary rate. General genomic stasis might also imply a decrease of transposable elements activity. To evaluate the potential activity of transposable elements (TEs) in living fossil species, transcriptomic data of Latimeria chalumnae and its Indonesian congener Latimeria menadoensis were compared through the RNA-sequencing mapping procedures in three different organs (liver, testis, and muscle). The analysis of coelacanth transcriptomes highlights a significant percentage of transcribed TEs in both species. Major contributors are LINE retrotransposons, especially from the CR1 family. Furthermore, some particular elements such as a LF-SINE and a LINE2 sequences seem to be more expressed than other elements. The amount of TEs expressed in testis suggests possible transposition burst in incoming generations. Moreover, significant amount of TEs in liver and muscle transcriptomes were also observed. Analyses of elements ...
The nivea locus of Antirrhinum majus encodes the enzyme chalcone synthase required for the synthesis of red anthocyanin pigment. The stable allele niv-44 contains an insertion in the nivea gene (Tam2) which has all the structural features of a transposable element. We have shown that this insertion can excise from the nivea locus when niv-44 is combined with another allele (niv-99) in a heterozygote. Activation of Tam2 excision is caused by a factor tightly linked to the niv-99 allele and may be due to complementation between Tam2 and a related element, Tam1. Factors which repress the excision of Tam2 and Tam1 are also described. Repression is not inherited in a simple mendelian way. Many stable mutations may be due to the insertion of transposable elements. Our data suggest that their stability may be due to the absence in the genome of activating factors and to the presence of repressors.
Recent analysis of the human and mouse genomes has shown that a substantial proportion of protein coding genes and cis-regulatory elements contain transposable element (TE) sequences, implicating TE domestication as a mechanism for the origin of genetic novelty. To understand the general role of TE domestication in eukaryotic genome evolution, it is important to assess the acquisition of functional TE sequences by host genomes in a variety of different species, and to understand in greater depth the population dynamics of these mutational events. Using an in silico screen for host genes that contain TE sequences, we identified a set of 63 mature chimeric transcripts supported by expressed sequence tag (EST) evidence in the Drosophila melanogaster genome. We found a paucity of chimeric TEs relative to expectations derived from non-chimeric TEs, indicating that the majority (~80%) of TEs that generate chimeric transcripts are deleterious and are not observed in the genome sequence. Using a pooled-PCR
The expression of chromosomal AmpC β-lactamase in Pseudomonas aeruginosa is negatively regulated by the activity of an amidase, AmpD. In the present study we examined resistant clinical P. aeruginosa strains and several resistant variants isolated from in vivo and in vitro biofilms for mutations in ampD to find evidence for the genetic changes leading to high-level expression of chromosomal β-lactamase. A new insertion sequence, IS1669, was found located in the ampD genes of two clinical P. aeruginosa isolates and several biofilm-isolated variants. The presence of IS1669 in ampD resulted in the expression of high levels of AmpC β-lactamase. Complementation of these isolates with ampD from the reference P. aeruginosa strain PAO1 caused a dramatic decrease in the expression of AmpC β-lactamase and a parallel decrease of the MIC of ceftazidime to a level comparable to that of PAO1. One highly resistant, constitutive β-lactamase-producing variant contained no mutations in ampD, but a point ...
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TY - JOUR. T1 - Insertional mutagenesis by the Tol2 transposon-mediated enhancer trap approach generated mutations in two developmental genes. T2 - tcf7 and synembryn-like. AU - Nagayoshi, Saori. AU - Hayashi, Eriko. AU - Abe, Gembu. AU - Osato, Naoki. AU - Asakawa, Kazuhide. AU - Urasaki, Akihiro. AU - Horikawa, Kazuki. AU - Ikeo, Kazuho. AU - Takeda, Hiroyuki. AU - Kawakami, Koichi. PY - 2008/1. Y1 - 2008/1. N2 - Gene trap and enhancer trap methods using transposon or retrovirus have been recently described in zebrafish. However, insertional mutants using these methods have not been reported. We report here development of an enhancer trap method by using the Tol2 transposable element and identification and characterization of insertional mutants. We created 73 fish lines that carried single copy insertions of an enhancer trap construct, which contained the zebrafish hsp70 promoter and the GFP gene, in their genome and expressed GFP in specific cells, tissues and organs, indicating that the ...
High-throughput analysis of genome-wide transposon mutant libraries is a powerful tool for (conditional) essential gene discovery. Recently, several next generation sequencing approaches, e.g. Tn-seq, INseq and TraDIS, have been developed that accurately map the site of transposon insertions by mutant-specific amplification and sequence readout of DNA flanking the transposon insertions site, assigning a measure of essentiality based on the number of reads per gene or per mutant. However, analysis of these large and complex datasets is hampered by the lack of an easy to use and automated tool for transposon insertion sequencing data ...
Many new Drosophila genomes have been sequenced in recent years using new-generation sequencing platforms and assembly methods. Transposable elements (TEs), being repetitive sequences, are often misassembled, especially in the genomes sequenced with short reads. Consequently, the mobile fraction of many of the new genomes has not been analyzed in detail or compared with that of other genomes sequenced with different methods, which could shed light into the understanding of genome and TE evolution. Here we compare the TE content of three genomes: D. buzzatii st-1, j-19, and D. mojavensis. We have sequenced a new D. buzzatii genome (j-19) that complements the D. buzzatii reference genome (st-1) already published, and compared their TE contents with that of D. mojavensis. We found an underestimation of TE sequences in Drosophila genus NGS-genomes when compared to Sanger-genomes. To be able to compare genomes sequenced with different technologies, we developed a coverage-based method and applied it to the D
The Tn3 transposon is a 4957 base pair mobile genetic element, found in prokaryotes. It encodes three proteins: β-lactamase, an enzyme that confers resistance to β-lactam antibiotics (and is encoded by the gene Bla). Tn3 transposase (encoded by gene tnpA) Tn3 resolvase (encoded by gene tnpR) Initially discovered as a repressor of transposase, resolvase also plays a role in facilitating Tn3 replication (Sherratt 1989). The transposon is flanked by a pair of 38bp inverted repeats. This first stage is catalysed by transposase. The plasmid containing the transposon (the donor plasmid) fuses with a host plasmid (the target plasmid). In the process, the transposon and a short section of host DNA are replicated. The end product is a cointegrate plasmid containing two copies of the transposon. Shapiro (1978) proposed the following mechanism for this process: Four single-strand cleavages occur - one on each strand of the donor plasmid and one on each strand of the target plasmid. The donor and target ...
Research in the Arkhipova lab is focused on transposable elements (TEs) in chromosomal DNA. As part of the A. vaga genome sequencing consortium, we have analyzed repetitive DNA content in the genome of the bdelloid rotifer, Adineta vaga (pictured), a microscopic freshwater invertebrate that reproduces asexually. This is the first representative of the Phylum Rotifera for which a complete genome sequence has been determined. We found that TEs and TE-related sequences occupy an unusually small proportion of the A. vaga genome assembly (ca. 3% of genomic DNA). This is in contrast with other aquatic metazoans such as Hydra or Nematostella, where TEs make up 57% and 26% of the genome, respectively. Another surprising feature is the high diversity of TE families and the extremely low number of copies for each family, which indicates that the incoming TEs do not proliferate efficiently in A. vaga. Out of 254 families, the overwhelming majority (208) is represented by only one or two full-length copies ...
Tn-Seq is an experimental method for probing the functions of genes through construction of complex random transposon insertion libraries and quantification of each mutants abundance using next-generation sequencing. An important emerging application of Tn-Seq is for identifying genetic interactions, which involves comparing Tn mutant libraries generated in different genetic backgrounds (e.g. wild-type strain versus knockout strain). Several analytical methods have been proposed for analyzing Tn-Seq data to identify genetic interactions, including estimating relative fitness ratios and fitting a generalized linear model. However, these have limitations which necessitate an improved approach. We present a hierarchical Bayesian method for identifying genetic interactions through quantifying the statistical significance of changes in enrichment. The analysis involves a four-way comparison of insertion counts across datasets to identify transposon mutants that differentially affect bacterial fitness
Interestingly there is no rule such as the higher evolved an organism the more transposable elements. Although we find more transposable elements in higher evolved organisms this rule can not be maintained if compared single species as frogs and humans.. Transposons most often code for transposase the enzyme responsible for the transposon dislocation. As Transposons are so common in a genome it is not surprising that transposases are the most common genes in a genome [2].. ...
antibody-antibodies.com is the marketplace for research antibodies. Find the right antibody for your research needs. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective.
The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing errors in the prediction of protein-coding genes and preventing the analysis of repetitive sequences and genome architecture. Here, we re-sequenced the genome using single-molecule real-time (SMRT) sequencing technology and, in combination with optical map data, this provided a gapless assembly of all twelve chromosomes except for the ribosomal DNA repeat cluster on chromosome 7. The more accurate gene annotation made possible by this new assembly revealed a large repertoire of secondary metabolism (SM) key genes (89) and putative biosynthetic pathways (77 SM gene clusters). The two mini-chromosomes differed from the ten core chromosomes in being repeat- and AT-rich and gene-poor but were significantly enriched with genes encoding putative secreted effector proteins. Transposable elements (TEs)
At the beginning of this week we spoke to Dr. Michael Hynes, who was able to give us E. coli SM10 and SM17-1 cells containing the plasmid pOT182. This plasmid contains an E. coli origin of replication, allowing it to act as a suicide vector when transferred to a different bacterial species. pOT182 contains a Tn5 transposon element containing a promotorless lacZ gene, genes for tetracycline resistance as well as a beta-lactamase, transposase and an E. coli origin of replication. These elements are bordered by insertion element sequences which are recognised by the transposase. When transferred to a different host through conjugation, the plasmid itself can no longer replicate. The transposase however can recognise and transfer the sequence between the insertion elements in a cut-and-paste fashion randomly into the genome. In this fashion, the tetracycline and beta-lactam resistant traits would only persist in cells in which the transposon has jumped into the genome, allowing these antibiotics to ...
Pyrenophora teres, P. teres f. teres (PTT) and P. teres f. maculata (PTM) cause significant diseases in barley, but little is known about the large-scale genomic differences that may distinguish the two forms. Comprehensive genome assemblies were constructed from long DNA reads, optical and genetic maps. As repeat masking in fungal genomes influences the final gene annotations, an accurate and reproducible pipeline was developed to ensure comparability between isolates. The genomes of the two forms are highly collinear, each composed of 12 chromosomes. Genome evolution in P. teres is characterized by genome fissuring through the insertion and expansion of transposable elements (TEs), a process that isolates blocks of genic sequence. The phenomenon is particularly pronounced in PTT, which has a larger, more repetitive genome than PTM and more recent transposon activity measured by the frequency and size of genome fissures. PTT has a longer cultivated host association and, notably, a greater range ...
Plant Epigenetics Unit Assistant Professor Hidetoshi Saze​ Abstract Epigenetic Regulation of Genes and Transposable Elements in Plants We are trying to understand epigenetic mechanisms for regulation of gene and transposon activities in the genomes of model plant systems such as Arabidopsis thaliana and rice, using genetic, biochemical and genomic approaches. In addition, we
Adaptation requires genetic variation, but founder populations are generally genetically depleted. Here we sequence two populations of an inbred ant that diverge in phenotype to determine how variability is generated. Cardiocondyla obscurior has the smallest of the sequenced ant genomes and its structure suggests a fundamental role of transposable elements (TEs) in adaptive evolution. Accumulations of TEs (TE islands) comprising 7.18% of the genome evolve faster than other regions with regard to single-nucleotide variants, gene/exon duplications and deletions and gene homology. A non-random distribution of gene families, larvae/adult specific gene expression and signs of differential methylation in TE islands indicate intragenomic differences in regulation, evolutionary rates and coalescent effective population size. Our study reveals a tripartite interplay between TEs, life history and adaptation in an invasive species. ...
Knockout Sudoku allows construction of whole-genome knockout collections for a wide range of microorganisms at a lower cost and increased speed, using combinatorial pooling, next-generation sequencing, and a Bayesian inference algorithm to process and annotate extremely large progenitor transposon insertion mutant collections. Knockout Sudoku is a method for the construction of whole-genome knockout collections for a wide range of microorganisms with as little as 3 weeks of dedicated labor and at a cost of ∼$10,000 for a collection for a single organism. The method uses manual 4D combinatorial pooling, next-generation sequencing, and a Bayesian inference algorithm to rapidly process and then accurately annotate the extremely large progenitor transposon insertion mutant collections needed to achieve saturating coverage of complex microbial genomes. This method is ∼100× faster and 30× lower in cost than the next comparable method (In-seq) for annotating transposon mutant collections by combinatorial
Processes and new genetic materials are provided for cloning specific DNA fragments by using a unique conjugative transposon designated Tn916. The transposon is used to first target specific genes by insertional inactivation. A restriction fragment containing the inserted transposon is then inserted into a plasmid vector and transformed into Escherichia coli or other suitable host by selection for the transposon encoded tetracycline (Tc) resistance. The transformants so produced are then grown in the absence of tetracycline conditions under which Tn916 excises from the chimeric plasmid thus restoring the integrity of the DNA into which the transposon was originally inserted. This process provides a new and useful way of producing new life forms that are useful for making desired products having established utility.
Uncontrolled transposable element (TE) insertions and excisions can cause chromosome breaks and mutations with dramatic deleterious effects. The PIWI interacting RNA (piRNA) pathway functions as an adaptive TE silencing system during germline development. Several essential piRNA pathway proteins appear to be rapidly evolving, suggesting that TEs and the silencing machinery may be engaged in a classical evolutionary arms race. Using a variety of molecular evolutionary and population genetic approaches, we find that the piRNA pathway genes rhino, krimper, and aubergine show patterns suggestive of extensive recurrent positive selection across Drosophila species. We speculate that selection on these proteins reflects crucial roles in silencing unfamiliar elements during vertical and horizontal transmission of TEs into naive populations and species, respectively.
The discovery of transposable elements (TEs) by Barbara McClintock in the 1940s, triggered a new dawning in the development of evolutionary theory. However, similar to Gregor Mendels development of the laws of heredity in the nineteenth century, it was a long time before the full significance of this discovery was appreciated. Nevertheless, by the beginning of the 21st century, the study and recognition of TEs as significant factors in evolution was well underway. However, many evolutionary biologists still choose to ignore them, to highlight the loss of fitness in some individuals caused by TEs, or concentrate on the supposed parasitic nature of TEs, and the diseases they cause.. The major concept and theme of this thesis is that the ubiquitous and extremely ancient transposable elements are not merely junk DNA or selfish parasites but are instead powerful facilitators of evolution. They can create genomic dynamism, and cause genetic changes of great magnitude and variety in the ...
Transposed elements (TEs) are known to affect transcriptomes, because either new exons are generated from intronic transposed elements (this is called exonization), or the element inserts into the exon, leading to a new transcript. Several examples in the literature show that isoforms generated by an exonization are specific to a certain tissue (for example the heart muscle) or inflict a disease. Thus, exonizations can have negative effects for the transcriptome of an organism. As we aimed at detecting other tissue- or tumor-specific isoforms in human and mouse genomes which were generated through exonization of a transposed element, we designed the automated analysis pipeline SERpredict (SER = S pecific E xonized R etroelement) making use of Bayesian Statistics. With this pipeline, we found several genes in which a transposed element formed a tissue- or tumor-specific isoform. Our results show that SERpredict produces relevant results, demonstrating the importance of transposed elements in shaping both
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The transposable element (TE), Tn5, is a conservative transposon that is able to insert a segment of genes bordered by specific 19bp insertion sequences (IS) from one part of the genome (e.g. plasmid vector) randomly to another location, such as the chromosome (Reznikoff, 2008). The transposition event is catalyzed by a transposase enzyme encoded by Tnp gene included in the TE. By inserting a vector construct containing the TE with selectable markers (such as tetracyclin resistance and lacZ) into an organism with a desirable phenotype, we can find out what genetic elements (e.g. genes and promoters) are responsible for that particular function. This can happen via a random insertion of a TE containing a promoterless reporter gene downstream of promoter elements that creates a transcriptional fusion, providing activity in response to specific environmental stimuli. Another advantage of using a transposon approach is that it creates a saturating library of mutants where all possible genetic ...
Stable transgenesis is an undeniable key to understanding any genetic system. Retrovirus-based insertional strategies, which feature several technical challenges when they are used, are often limited to one particular species, and even sometimes to a particular cell type as the infection depends on certain cellular receptors. A universal-like system, which would allow both stable transgene expression independent of the cell type and an efficient sorting of transfected cells, is required when handling cellular models that are incompatible with retroviral strategies. We report here on the combination of a stable insertional transgenesis technique, based on the Tol2 transposon system together with the magnetic cell sorting (MACS) technique, which allows specific selection of cells carrying the transgene in an efficient, reliable and rapid way. This new Tol2/MACS system leads to stable expression in a culture of primary chicken erythroid cells highly enriched in cells expressing the transgene of interest.
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 ... Transposable elements represent one of several types of mobile genetic elements. TEs are assigned to one of two classes ... The DNA-transposase complex then inserts its DNA cargo at specific DNA motifs elsewhere in the genome, creating short TSDs upon ...
"DNA methylation enables transposable element-driven genome expansion". Proceedings of the National Academy of Sciences of the ... In DNA, this reaction, if detected prior to passage of the replication fork, can be corrected by the enzyme thymine-DNA ... many regulatory functions are related to the loss in CPG sites due to the presence of transposable elements. TEs have been ... product of cytosine deamination and not part of DNA) by uracil-DNA glycosylase, generating an abasic (AP) site. The resulting ...
... transposable elements that are mobile fragments of DNA, most of which are nonfunctional in humans; and pseudogenes, ... ENCODE Project Consortium) (September 2012). "An integrated encyclopedia of DNA elements in the human genome". Nature. 489 ( ... The sheer amount of DNA in an organism, measured by the mass of DNA present in the nucleus or the number of constituent ... Susumu Ohno coined the phrase "junk DNA" to describe these nonfunctional swaths of DNA. They include introns, genetic sequences ...
... a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses". Gene. 390 (April): 3-17. doi ... Jurka is best known for his work on eukaryotic transposable elements (TEs), including the discovery of the major families of ... In 2006 they reported a study of a new, self-synthesizing transposable element called Polinton or Maverick, which is present ... Jurka J, Bao W, Kojima K (June 2011). "Families of transposable elements, population structure and the origin of species". ...
"Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates". Genome ... The analysis of SINEs - Short INterspersed Elements - LINEs - Long INterspersed Elements - or truncated LTRs - Long Terminal ... October 2003). "Alu elements and hominid phylogenetics". Proc. Natl. Acad. Sci. U.S.A. 100 (22): 12787-91. doi:10.1073/pnas. ... The target sites are relatively unspecific so that the chance of an independent integration of exactly the same element into ...
... a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses". Gene. 390 (1-2): 3-17. doi: ... Polintons encode up to 10 proteins, the key elements being the protein-primed type B DNA polymerase and the retroviral-like ... Meanwhile, an overlapping class of transposable element was described under the name polintons, derived from the key proteins ... Feschotte, C; Pritham, E (October 2005). "Non-mammalian c-integrases are encoded by giant transposable elements". Trends in ...
In addition, spermatogenesis fails due to sperm DNA damage caused by the derepression of transposable elements. MAEL has also ... Short RNAs are well-known to silence TEs (transposable elements) through the RNAi (RNA interference) pathway, and Piwi- ... Identification of a novel human cancer/testis gene MAEL that is regulated by DNA methylation. Molecular Biology Reports. 37: ...
... a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses". Gene. 390 (1-2): 3-17. doi: ... Putative proteins with homology to the KilA-N domain have also been identified in Maverick transposable elements of the ... It is a novel conserved DNA-binding domain is found at the N-terminus of the poxvirus D6R/NIR proteins. It is also found in a ... The KilA-N domain has been suggested to be homologous to the fungal DNA-binding APSES domain. In all proteins shown to contain ...
Martienssen's work explains the effect on plants of 'jumping genes', or DNA transposable elements, reported in 1951 by Barbara ... "Somatically heritable switches in the DNA modification of Mu transposable elements monitored with a suppressible mutant in ... subscription or UK public library membership required) Slotkin, R. Keith; Martienssen, Robert (2007). "Transposable elements ... Working with maize, yeast and the weed Arabidopsis, he focuses on the chemical modifications to DNA that determine which genes ...
... including long terminal repeat transposable elements. Despite recent advances in massively parallel DNA sequencing, the ... A large proportion of the spruce genome consists of repetitive DNA sequences, ...
... : a retrotransposon of Drosophila combining structural features of DNA viruses, retroviruses and non-viral transposable ... 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 ...
The sugar pine contains extended regions of non-coding DNA, most of which is derived from transposable elements. The genome of ... The transposable elements that make up the megagenome are linked to the evolutionary change of the sugar pine. ... with a stable diploid genome that is expanded by the proliferation of transposable elements, in contrast to the frequent ...
Tol2 is the only natural DNA transposable element in vertebrates from which an autonomous member has been identified. In 2008, ... Tol2 element which encodes a gene for a fully functional transposase capable of catalyzing transposition in the zebrafish germ ... These genes have the DNA base pairs AC and TG as repeated sequences at the ends of each intron. On the 3'ss (3' splicing site ... They start mineralising bone elements as early as 4 days post fertilisation. Recently, adult zebrafish are being used to study ...
A transposable element (TE) (also called a transposon or jumping gene) is a mobile segment of DNA that can sometimes pick up a ... Successful transfer of a transposable element requires delivery of DNA from donor to host cell (and to the germ line for multi- ... HTT can occur with any type of transposable elements, but DNA transposons and LTR retroelements are more likely to be capable ... Schaack S, Gilbert C, Feschotte C (September 2010). "Promiscuous DNA: horizontal transfer of transposable elements and why it ...
Transposable elements are regions of DNA that can be inserted into the genetic code through one of two mechanisms. These ... The most common transposable element in the human genome is the Alu sequence, which is present in the genome over one million ... "A unified classification system for eukaryotic transposable elements". Nature Reviews Genetics. 8 (12): 973-82. doi:10.1038/ ... Gene duplication is the process by which a region of DNA coding for a gene is duplicated. This can occur as the result of an ...
Spontaneous mutations arise from sources including errors in DNA replication, spontaneous lesions, and transposable genetic ... "Shaping bacterial genomes with integrative and conjugative elements". Research in Microbiology. 155 (5): 376-86. doi:10.1016/j. ... It can occur during meiosis or replication of DNA, as well as due to ionizing or UV radiation, transposons, mutagenic chemicals ... Carroll, Sean B.; Grenier, Jennifer; Weatherbee, Scott (2005). From DNA to Diversity: Molecular Genetics and the Evolution of ...
Her research focuses on the molecular mechanisms of transposable elements, or mobile sequences of DNA found in the genomes of ... Throughout her career, Craig has focused her research interests on transposable elements, or sequences of DNA that can change ... where she studied the chemistry of DNA repair and the mechanisms of the cellular SOS response to DNA damage. She was ... position in a genome; such elements are found in the genomes of nearly all known organisms and gave rise to a large fraction of ...
... 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 ... "Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates". Genome Biology and ... the Activator or Ac element from Zea mays, and the Tam3 element from Antirrhinum majus. The superfamily has been divided based ...
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 ... Bacteria also use DNA adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA adenine ... DNA damage can also cause epigenetic changes.[27][28][29] DNA damage is very frequent, occurring on average about 60,000 times ...
The transposable P elements, also known as transposons, are segments of bacterial DNA that are transferred into the fly genome ... It is caused by mutations in the gene WRN that encodes a protein with essential roles in repair of DNA damage. Mutations in the ... The under-replication of rDNA occurs resulting in only 20% of DNA compared to the brain. Compare to the 47%, less rDNA in ... More than 60% of the genome appears to be functional non-protein-coding DNA[72] involved in gene expression control. ...
Transposable elements-repetitious sequences of DNA that can insert themselves into any part of the genome-can encourage ectopic ... The frequency of ectopic recombination of transposable elements has been linked to both higher copy numbers of transposable ... It follows that transposable elements that are shorter, transpose themselves less often, and have mutation rates high enough to ... A test for the role of natural selection in the stabilization of transposable element copy number in a population of Drosophila ...
... are homologous to other subtelomeres that are located at different chromosomes and are a type of transposable element, DNA ... Most vertebrate telomeric DNA consists of long (TTAGGG)n repeats of variable length, often around 3-20kb. Subtelomeres are ... Subtelomeres are considered to be the most distal (farthest from the centromere) region of unique DNA on a chromosome, and they ... Sgo2 remains in subtelomeres, whose cells lack telomere DNA. Sgo2 represses the expression of subtelomeric genes that is in a ...
... and provided the definitive link between transposable elements (active elements) and interspersed repetitive DNA (mutated ... Alu elements are retrotransposons and look like DNA copies made from RNA polymerase III-encoded RNAs. Alu elements do not ... Kidwell, Margaret G; Lisch, Damon R (2001). "Perspective: Transposable Elements, Parasitic Dna, and Genome Evolution". ... Alu elements are the most abundant transposable elements, containing over one million copies dispersed throughout the human ...
... are class I transposable elements in the DNA of some organisms and belong to the group of long interspersed nuclear elements ( ... Erwin JA, Marchetto MC, Gage FH (August 2014). "Mobile DNA elements in the generation of diversity and complexity in the brain ... A typical L1 element is approximately 6,000 base pairs (bp) long and consists of two non-overlapping open reading frames (ORF) ... The 5' UTR of the L1 element contains a strong, internal RNA Polymerase II transcription promoter in sense The 5' UTR of mouse ...
Repetitive DNA is primarily derived from transposable elements (TEs), which include DNA transposons belonging to around 20 ... GIRI has hosted three international conferences devoted to the genomic impact of eukaryotic transposable elements. "Home Page ... An ancient element from the Transib superfamily was identified as the evolutionary precursor of the Recombination activating ... GIRI develops and maintains Repbase Update, a database of prototypic sequences representing repetitive DNA from different ...
Tn3 and related transposable elements: site-specific recombination and transposition. In Berg, D. E., Howe, M. (eds) Mobile DNA ... 163-184 4.Grindley, N.D.F. (2002). The movement of Tn3-like elements: transposition and cointegrate resolution. In Mobile DNA ... Reed RR, Grindley ND (September 1981). "Transposon-mediated site-specific recombination in vitro: DNA cleavage and protein-DNA ... "Molecular model for the transposition and replication of bacteriophage Mu and other transposable elements" (PDF). PNAS. 76 (4 ...
Insertions add one or more extra nucleotides into the DNA. They are usually caused by transposable elements, or errors during ... Insertions can be reversed by excision of the transposable element.. *Deletions remove one or more nucleotides from the DNA. ... Bernstein C, Prasad AR, Nfonsam V, Bernstein H. (2013). DNA Damage, DNA Repair and Cancer, New Research Directions in DNA ... Errors introduced during DNA repairEdit. See also: DNA damage (naturally occurring) and DNA repair ...
Transposable elements (TEs) are sequences of DNA with a defined structure that are able to change their location in the genome ... genomecenter.howard.edu Build a DNA Molecule Some comparative genome sizes DNA Interactive: The History of DNA Science DNA From ... Retrotransposon is a transposable element that transpose through an RNA intermediate. Retrotransposons are composed of DNA, but ... However, this special characteristic is caused by the presence of repetitive DNA, and transposable elements (TEs). A typical ...
... 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, ... they are small relative to other transposable elements (generally around 700 to 2500 bp in length) and only code for proteins ... DNA composition). Mobile genetic elements Mahillon, Jacques; Chandler, Michael (1998-09-01). "Insertion Sequences". ...
... physical properties of DNA affecting target site selection of sleeping beauty and other Tc1/mariner transposable elements. J ... Plasterk, R.H., Z. Izsvak, and Z. Ivics, Resident aliens: the Tc1/mariner superfamily of transposable elements. Trends Genet, ... are engineered DNA-binding proteins that facilitate targeted editing of the genome by creating double-strand breaks in DNA at ... SB, like other DNA transposons, mobilizes itself via a cut-and-paste mechanism whereby a transposase enzyme, encoded by the ...
... at Stanford University School of Medicine with an interest in molecular genetics and particular focus on transposable elements. ... They constructed segments of recombinant Drosophila DNA, amplified them in bacteria, and injected them in per mutant animals. A ... 2] He worked in Dave Hogness' lab and became familiar with the methods of recombinant DNA.[6] Two years later, he joined ...
Eukaryotic transposable elements and genome evolution. Trends in Genetics. 1989, 5: 103-107. ISSN 0168-9525. doi:10.1016/0168- ... 微衛星序列在DNA複製時容易發生滑動而造成其長度改變。圖中的每個方格代表相同的一段重複序列,黑色是舊的DNA,在DNA複製時作
Medstrand P, van de Lagemaat L, Dunn C, Landry J, Svenback D, Mager D (2005). "Impact of transposable elements on the evolution ... This DNA can be incorporated into host genome as a provirus that can be passed on to progeny cells. The retrovirus DNA is ... It has been speculated that the RNA to DNA transcription processes used by retroviruses may have first caused DNA to be used as ... All members of Group VI use virally encoded reverse transcriptase, an RNA-dependent DNA polymerase, to produce DNA from the ...
Other endogenous factors can also lead to mosaicism including mobile elements, DNA polymerase slippage, and unbalanced ... Somatic mosaics are common in embryogenesis due to retrotransposition of L1 and Alu transposable elements.[11] In early ... DNA from undifferentiated cell types may be more susceptible to mobile element invasion due to long, un-methylated regions in ... "Every Cell in Your Body Has the Same DNA. Except It Doesn't". The New York Times. 21 May 2018. Archived from the original on 23 ...
Transposable element *Class I or retrotransposon. *Class II or DNA transposon. *Plasmid *Fertility ... Main articles: RNA and DNA. The major difference between RNA and DNA is the presence of a hydroxyl group at the 2'-position of ... This forces an RNA double helix to change from a B-DNA structure to one more closely resembling A-DNA. ... DNA and proteins seemed the dominant macromolecules in the living cell, with RNA only aiding in creating proteins from the DNA ...
... fully half of our DNA is made up of "transposable elements," or "transposons," virus-like genetic material that has the special ... Når transposonerne hopper ud og ind af generne kan de efterlade dele af deres DNA-sekvens eller tage et stykke af DNA-strengen ... Der findes fire typer transposoner, opdelt i to overordnede grupper: DNA-transposoner og retrotransposoner. DNA-transposoner ... åbne DNA-strengen det pågældende sted hvor transposonet vil placere sig i genomet. DNA-transposoner kaldes derfor også for cut- ...
... is widespread along the genome and plays an important role in regulating gene expression by repressing transposable elements.[ ... as well as the limited amount of DNA extracted from a single cell. Due to scant amounts of DNA, accurate analysis of DNA poses ... Single-cell genome (DNA) sequencing[edit]. Single-cell DNA genome sequencing involves isolating a single cell, amplifying the ... Single-cell DNA methylome sequencing quantifies DNA methylation. There are several known types of methylation that occur in ...
However, analysis of transposable element insertions supports a three-way top-level split between Xenarthra, Afrotheria and ... Mitochondrial DNA's mutation rate in mammals varies from region to region - some parts hardly ever change and some change ... Mammalian mitochondrial DNA mutates so fast that it causes a problem called "saturation", where random noise drowns out any ... Since this group has living members, DNA analysis can be applied in an attempt to explain the evolution of features that do not ...
"The evolution of RNAi as a defence against viruses and transposable elements", Philosophical Transactions of the Royal Society ... Transcription is when RNA is made from DNA. During transcription, RNA polymerase makes a copy of a gene from the DNA to mRNA as ... AU-rich element decayEdit. The presence of AU-rich elements in some mammalian mRNAs tends to destabilize those transcripts ... These structural mRNA elements are involved in regulating the mRNA. Some, such as the SECIS element, are targets for proteins ...
... are a type of DNA that can move around within the genome. They include: *Transposons (also called transposable elements) * ... Mobile genetic elements. DNA sequence whose position in the genome is variable ... Mobile genetic elements : protocols and genomic applications. Humana Press. ISBN 1-58829-007-7 ... Barbara McClintock was awarded the 1983 Nobel Prize in Physiology or Medicine "for her discovery of mobile genetic elements".[1 ...
... a defensive RNA-silencing against viruses and transposable elements". Heredity. 96 (2): 195-202. doi:10.1038/sj.hdy.6800789. ... From the Dolan DNA Learning Center of Cold Spring Harbor Laboratory.. *RNAi screens in C. elegans in a 96-well liquid format ... The 3'-UTR often contains microRNA response elements (MREs). MREs are sequences to which miRNAs bind. These are prevalent ... The ancestral function of the RNAi system is generally agreed to have been immune defense against exogenous genetic elements ...
Buchon N, Vaury C (2006). "RNAi: a defensive RNA-silencing against viruses and transposable elements". Heredity 96 (2): 195-202 ... Do Dolan DNA Learning Center do Cold Spring Harbor Laboratory.. *Cribado de RNAi en C. elegans en formato líquido de 96 pozos e ... "Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing". Nucleic Acids Res 34 (21): 6233-46. PMC ...
... can be particularly prone to mutation (suggesting it has active transposable elements), and thanks to its long ... The general DNA profiles of both pinot gris and blanc are identical to pinot noir;[12] and other pinots, pinot moure and pinot ... Gouget noir is sometimes confused as being a clone of Pinot noir but DNA analysis has confirmed that it is a distinct variety.[ ...
SpcDNAs are derived from repetitive sequences such as satellite DNA, retrovirus-like DNA elements, and transposable elements in ... Extrachromosomal DNA was found to be structurally different from nuclear DNA. Cytoplasmic DNA is less methylated than DNA found ... It is also referred to as extranuclear DNA or cytoplasmic DNA. Most DNA in an individual genome is found in chromosomes but DNA ... Mitochondrial DNA is a main source of this extrachromosomal DNA in eukaryotes. Extrachromosomal DNA is often used in research ...
Hickey, Donal A. (1992). "Evolutionary dynamics of transposable elements in prokaryotes and eukaryotes". Genetica (Dordrecht, ... Carroll, Sean B.; Grenier, Jennifer K.; Weatherbee, Scott D. (2005) From DNA to Diversity: Molecular Genetics and the Evolution ... Petrov, Dmitri A. (May 2002). "DNA loss and evolution of genome size in Drosophila". Genetica (Dordrecht, the Netherlands: ... June 2006). "A Unique Recent Origin of the Allotetraploid Species Arabidopsis suecica: Evidence from Nuclear DNA Markers". ...
The presence of transposable elements is another influential element of non-homologous crossover. Repetitive regions of code ... DNA repair theoryEdit. Crossing over and DNA repair are very similar processes, which utilize many of the same protein ... She used modified patterns of gene expression on different sectors of leaves of her corn plants show that transposable elements ... Meiotic recombination may be initiated by double-stranded breaks that are introduced into the DNA by exposure to DNA damaging ...
... and for her identification and description of transposable genetic (mobile) elements. ... for his part in the demonstration that the transforming factor in bacteria is due to deoxyribonucleic acid (DNA) and the ...
Almost 50% of the human genome is contained in various types of transposable elements (also called transposons, or 'jumping ... DNA. The name "satellite" DNA refers to the early observation that centrifugation of genomic DNA in a test tube separates a ... DNA refers to the early observation that centrifugation of genomic DNA in a test tube separates a prominent layer of bulk DNA ... A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from 1-6 or more base pairs) are ...
Families of transposable elements-derived lincRNAs have been implicated in the regulation of pluripotency. Human pluripotency- ... DNA and Cell Biology. 25 (3): 135-41. doi:10.1089/dna.2006.25.135. PMID 16569192. Lin R, Maeda S, Liu C, Karin M, Edgington TS ... Alu elements in humans and analogous B1 and B2 elements in mice have succeeded in becoming the most abundant mobile elements ... The abundance and distribution of Alu elements and similar repetitive elements throughout the mammalian genome may be partly ...
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 ... Transposable elements represent one of several types of mobile genetic elements. TEs are assigned to one of two classes ... The DNA-transposase complex then inserts its DNA cargo at specific DNA motifs elsewhere in the genome, creating short TSDs upon ...
"Eukaryotic Transposable Elements and Genome Evolution Special Feature: Transposable elements and the evolution of eukaryotic ... Sanger, F.; Coulson, A.R.; Hong, G.F.; Hill, D.F.; Petersen, G.B. (1982). "Nucleotide sequence of bacteriophage lambda DNA". ... Kidwell MG, Lisch DR (2000 Mar). "Transposable elements and host genome evolution". Trends in ecology & evolution 15 (3): 95-99 ... Kazazian, H. H. (12 March 2004). "Mobile Elements: Drivers of Genome Evolution". Science 303 (5664): 1626-1632. Bibcode:2004Sci ...
Hickey DA (1992). "Evolutionary dynamics of transposable elements in prokaryotes and eukaryotes". Genetica 86 (1-3): 269-74. ... Pagsisekwensiya ng DNA[baguhin , baguhin ang batayan]. Ang komparison ng sekwensiyang DNA ay nagbibigay ng kakayahan upang ang ... Ang mga basurang DNA ay bumubuo ng 98% ng genome ng tao samantalang ang may silbing DNA ay bumubuo lamang ng 2% ng genome ng ... Ang ilang pangunahing uri ng mga mutasyon sa DNA ay: Henetikong pagbura kung saan ang isa o maraming mga base ng DNA ay nabura ...
June 2016). "The industrial melanism mutation in British peppered moths is a transposable element". Nature. 534 (7605): 102-105 ... Carroll, Sean B.; Grenier, Jennifer K.; Weatherbee, Scott D. (2005). From DNA to Diversity: Molecular Genetics and the ... Carroll, Sean B.; Grenier, Jennifer K.; Weatherbee, Scott D. (2005). From DNA to Diversity: Molecular Genetics and the ... However, many mutations in non-coding DNA have deleterious effects.[91][92] Although both mutation rates and average fitness ...
Pathogenic tau can also cause neuronal death through transposable element dysregulation.[105] ... Wozniak MA, Mee AP, Itzhaki RF (January 2009). "Herpes simplex virus type 1 DNA is located within Alzheimer's disease amyloid ... "Pathogenic tau-induced piRNA depletion promotes neuronal death through transposable element dysregulation in neurodegenerative ... and economic elements.[14] Exercise programs may be beneficial with respect to activities of daily living and can potentially ...
Hickey, Donal A. (1992). "Evolutionary dynamics of transposable elements in prokaryotes and eukaryotes". Genetica. Dordrecht, ... Arvelige træk er gået fra den ene generation til den næste via DNA, et molekyle, der er kode for genetisk information.[45] DNA ... hvis DNA-sekvensen variere på et sted imellem individer, er de forskellige former af denne sekvens kaldet alleler. DNA- ... Før en celle deler sig, kopieres DNA'et, således at hver af de resulterende to celler vil arve DNA-sekvensen. Dele af et 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 ...
For example, in Saccharomyces cerevisiae TEC-1 regulates the transposable element TY1 and is involved in pseudohyphale growth ( ... The binding of MEF2 on the DNA induces and potentiates TEAD2 recruitment at MCAT sequences that are adjacent to MEF2 binding ... SRF (Serum response factor) and TEAD2 interact through their DNA binding domain, respectively the MADS domain and the TEA ... Bürglin TR (July 1991). "The TEA domain: a novel, highly conserved DNA-binding motif". Cell. 66 (1): 11-2. doi:10.1016/0092- ...
Kidwell, M.G. (2005). "Transposable elements". in ed. T.R. Gregory. The Evolution of the Genome. San Diego: Elsevier. பக். 165- ... Craig NL, Craigie R, Gellert M, and Lambowitz AM (ed.) (2002). Mobile DNA II. Washington, DC: ASM Press. பன்னாட்டுத் தரப்புத்தக ... Rubin GM, Spradling AC (October 1982). "Genetic transformation of Drosophila with transposable element vectors". Science 218 ( ... "Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete ...
With the Sleeping Beauty (SB) DNA transposon, a reconstructed Tc1/mariner element, as the driving force, DNA transposable ... Mobilization of DNA transposable elements from lentiviral vectors.. Bak RO1, Mikkelsen JG. ... or be directly imported into the nucleus where it may interact with both linear DNA and circular DNA intermediates (1- and 2- ... It is not known whether linear viral DNA serves as a substrate for SB transposition. Single-stranded RNA (ssRNA) is shown in ...
... Research in the Arkhipova lab is focused on transposable ... elements (TEs) in chromosomal DNA. As part of the A. vaga genome sequencing consortium, we have analyzed repetitive DNA content ... 3% of genomic DNA). This is in contrast with other aquatic metazoans such as Hydra or Nematostella, where TEs make up 57% and ... On balance, bdelloid genomes, despite being relatively open to assimilation of foreign DNA, are apparently able to control ...
However, researchers have found that some genes (DNA sequences) can actually change position in the chromosomes. These mobile ... www.ukessays.com/essays/health/transposable-dna-elements-8312.php?vref=1 ,title=Transposable DNA Elements ,publisher=UKEssays. ... Transposable DNA Elements. [online]. Available from: https://www.ukessays.com/essays/health/transposable-dna-elements-8312.php? ... November 2018). Transposable DNA Elements. Retrieved from https://www.ukessays.com/essays/health/transposable-dna-elements-8312 ...
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 ... Element, IS; Elements, IS; Transposable Elements; IS Element; Transposable Element; DNA Transposable Element; Elements, ...
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 ... A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution. Christian Biémont ... A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution. Christian Biémont ...
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 ... A dispersed family of repetitive DNA sequences exhibits characteristics of a transposable element in the genus Lycopersicon. ...
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 ... Kofler found a transposable element in the fly species Drosophila simulans, the so-called P-element. This transposable element ...
Transposable elements are pieces of DNA that are actively replicating and moving around your genome, jumping from place to ... Mobile genetic elements include pieces of DNA inserted into your genome by lurking retroviruses such as HIV. As Halloween ... DNA Interest Group Event: Transposable Elements- The Ghosts in Our DNA. Library EventDNA Interest Group Event: Transposable ... DNA Interest Group Event: Transposable Elements- The "Ghosts" in Our DNA. Traditionally, the human genome has been thought of ...
... to validate and quantify somatic mosaic events contributed by transposable-element insertions, copy-number... ... Analysis of Mosaic Transposable-Element Insertions, Copy-Number Variants, and Single-Nucleotide Variants. In: Karlin-Neumann G ... In the ddPCR assay, sample or template DNA is partitioned into tens of thousands of individual droplets such that when DNA ... Analysis of Mosaic Transposable-Element Insertions, Copy-Number Variants, and Single-Nucleotide Variants. ...
Examination of genome-wide DNA methylation status within 928 TE subfamilies in human embryonic and adult tissues identified ... derived sequences comprise half of the human genome and DNA methylome and are presumed to be densely methylated and inactive. ... You are here: Home / Platforms / Scientific Publications / DNA hypomethylation within specific transposable element families ... Home › Platforms › Scientific Publications › DNA hypomethylation within specific transposable element families associates with ...
Characterization of the maize Mutator transposable element MURA transposase as a DNA-binding protein.. M I Benito, V Walbot ... The autonomous MuDR element of the Mutator (Mu) transposable element family of maize encodes at least two proteins, MURA and ... Characterization of the maize Mutator transposable element MURA transposase as a DNA-binding protein. ... Characterization of the maize Mutator transposable element MURA transposase as a DNA-binding protein. ...
... a class of structurally and functionally related genetic elements that includes linear DNA plasmids, transposable elements, and ... a class of structurally and functionally related genetic elements that includes linear DNA plasmids, transposable elements, and ... a class of structurally and functionally related genetic elements that includes linear DNA plasmids, transposable elements, and ... a class of structurally and functionally related genetic elements that includes linear DNA plasmids, transposable elements, and ...
The major DNA-based controlling transposable elements in higher plants can be classified into three groups : the Ac/Ds (or hAT ... Transposition and gene regulation of DNA transposable elements in plants. Research Project ... Publications] S. Takahashi: Capturing of a genomic HMG domain sequence by an En/Spm related transposable element Tpnl in the ... Publications] S.Takahashi: Capturing of a genomic HMG domain sequence by an En/Spm related transposable element Tpnl in the ...
DNA Topoisomerase 1α Promotes Transcriptional Silencing of Transposable Elements through DNA Methylation and Histone Lysine 9 ... DNA Topoisomerase 1α Promotes Transcriptional Silencing of Transposable Elements through DNA Methylation and Histone Lysine 9 ... DNA Topoisomerase 1α Promotes Transcriptional Silencing of Transposable Elements through DNA Methylation and Histone Lysine 9 ... H3K9 methylation and DNA methylation are targeted via small interfering RNAs (siRNAs) to repeats and transposable elements (TEs ...
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 ... 1). This element belongs to the hAT transposable element family (Calvi et al., 1991; Atkinson et al., 1993) that includes hobo ...
Transposable DNA elements - Part 1: basics and importance. Transposable DNA elements - Part 3 TEs and and other key mechanisms ... Transposable DNA elements - Part 1: basics and importance. Transposable DNA elements - Part 3 TEs and and other key mechanisms ... SIRT6 has a unique role in silencing transposable elements. Specifically, it silences transposable elements, telomeric DNA, and ... of genomic DNA consists of transposable elements, yet more than 50% of de novo mutations arise from these transposable elements ...
Germline transposition of these elements can lead to polymorphic TE (polyTE) loci that differ between individuals with respect ... The human genome contains several active families of transposable elements (TE): Alu, L1 and SVA. ...
... heterogeneous elements. The complete DNA sequences of the 2.9 kb element and four small elements (previously isolated from ... Each small element appears to have arisen from the 2.9 kb element by a different internal deletion. P elements have 31 bp ... Structures of P transposable elements and their sites of insertion and excision in the Drosophila melanogaster genome.. OHare ... The basis of this specificity has been investigated by DNA sequence analysis of the sites where 18 P elements are found. A ...
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Transposable elements Discrete sequences in the genome that have the ability to translocate or copy itself across to other ... 5 Classes of transposable elements. Classes of mobile elements. DNA transposons, e.g., Tc-1/mariner, have inverted terminal ... Transposable Elements (Transposons) DNA elements capable of moving ("transposing") about the genome Discovered by Barbara ... Download ppt "mobile DNA: transposable elements" * Ppt on palliative care pain management end of life care Ppt on power ...
A test for the role of natural selection in the stabilization of transposable element copy number in a population of Drosophila ... DNA Transposable Elements* * Drosophila melanogaster / genetics* * Models, Genetic * Nucleic Acid Hybridization * Selection, ... A test for the role of natural selection in the stabilization of transposable element copy number in a population of Drosophila ...
DNA-, and protein-binding domains. We propose that these reflect a more general phenomenon of exaptation during lncRNA ... 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. ... The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs RNA. 2014 Jul;20(7):959-76. doi: ...
DNA transposable elements, class 2 elements, have become a source of material for coordination of eukaryotic gene regulatory ... The Impact of DNA Transposable Elements on Allelic Diversity in Maize. Han, Jong-Jin ... The Impact of DNA Transposable Elements on Allelic Diversity in Maize. Login ... Transposable elements (TE) are indispensible to understand the evolution of genes and genomes in almost all organisms. ...
... canonical RdDM functions through RNA polymerase IV to reinforce pre-existing transposable element silencing. Recent ... Chromatin modifications such as DNA methylation are targeted to transposable elements by small RNAs in a process termed RNA- ... ARGONAUTE 6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation. EMBO J. 2014;34:20-35. ... Transposable elements (TEs) are mobile fragments of DNA that can generate mutations and genome instability. To repress TE ...
Class II DNA transposons, predominant TEs in fish genomes, are significantly GC-poorer than Class I retrotransposons. The AT/GC ... Long-term accumulation of GC-poor(er) Class II DNA transposons might indeed have influenced AT/GC homogenization of fish ... Teleost fish genome size has been repeatedly demonstrated to positively correlate with the proportion of transposable elements ... Genome size, transposable elements, and nucleotide composition. a Abundance of transposable elements in 29 teleosts, one non- ...
Alu Elements , Coat Protein Complex I , DNA , DNA Transposable Elements , Endogenous Retroviruses , Genetic Variation , Genome ... DNA / DNA Transposable Elements / Pan troglodytes / Genome / Endogenous Retroviruses Language: English Journal: Genomics & ... DNA / DNA Transposable Elements / Pan troglodytes / Genome / Endogenous Retroviruses Language: English Journal: Genomics & ... Since the advent of whole-genome sequencing, transposable elements (TEs), just thought to be junk DNA, have been noticed ...
Repression of transposable elements[edit]. DNA methylation is a powerful transcriptional repressor, at least in CpG dense ... 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 ... Ancient DNA methylation reconstruction, a method to reconstruct high-resolution DNA methylation from ancient DNA samples. The ...
Transposable Elements DNA are discrete segments of DNA which as mobile genetic elements can excise and reintegrate to another ... DNA Transposable Elements. "DNA Transposable Elements (DNA Transposons)" Transposable Elements. In genetic science, DNA ... Transposable Elements DNA ⌊Cytogenetics. ⌊Genetic Structures. ⌊Mobilomes. ⌊Mobile Genetic Elements. ⌊Transposable element ... Transposable Elements are discrete segments of DNA which as mobile genetic elements can excise and reintegrate to another site ...
Alu Elements , Coat Protein Complex I , DNA , DNA Transposable Elements , Endogenous Retroviruses , Genetic Variation , Genome ... DNA / DNA Transposable Elements / Pan troglodytes / Genome / Endogenous Retroviruses Language: English Journal: Genomics & ... Since the advent of whole-genome sequencing, transposable elements (TEs), just thought to be junk DNA, have been noticed ... In this review, we focus on Alu, L1, human endogenous retrovirus, and short interspersed element/variable number of tandem ...
DNA methylation and histone H1 jointly repress transposable elements a… * 20191108 Special Lecture for Life Sciences IBB_Prof. ... DNA methylation and histone H1 mediate transcriptional silencing of genes and transposable elements, but how they interact is ... DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts > 세미나. ... but only weakly de-represses transposable elements. However, H1 loss strongly activates transposable elements hypomethylated ...
  • Hence, SB transposons are efficiently mobilized from HIV-based integrase-defective lentiviral vectors by the hyperactive SB100X transposase, leading to the genomic insertion of lentivirally delivered DNA in a reaction controlled by a nonviral integration machinery. (nih.gov)
  • These mobile DNA sequences are called transposable elements or simply transposons . (ukessays.com)
  • They differ from retroviruses and related retro-type transposons which have direct repeats on both their genomic ends and exploit RNA intermediates for replication of their DNA. (asm.org)
  • TEs in Maize Figure 13.25Figure 2 : Colour variations in maize caused by DNA transposons. (slideplayer.com)
  • DNA transposons, e.g. (slideplayer.com)
  • Other LTR retrotransposons that are responsible for most mobile-element insertions in mice are the intracisternal A-particles (IAPs), early transposons (Etns), and mammalian LTR-retrotransposons (MaLRs). (slideplayer.com)
  • Transposons encode transposases that catalyse transposition events Regulation of transposase expression essential Regulation of transposition activity is essential to balance the adaptive advantages provided by transposable elements to their host genome, at the same time limiting the damage they might cause by potentially lethal DNA rearrangements. (slideplayer.com)
  • In particular, mobility of DNA transposons has been used for insertional mutagenesis to generate new alleles in plants and animals. (stonybrook.edu)
  • Sequencing of the duplication break point suggested that CACTA and MITE transposons, which are another classes of DNA transposons in maize, may be involved in this regional duplication, which results in dosage-dependent upregulation of both genes. (stonybrook.edu)
  • Class II DNA transposons, predominant TEs in fish genomes, are significantly GC-poorer than Class I retrotransposons. (biomedcentral.com)
  • Long-term accumulation of GC-poor(er) Class II DNA transposons might indeed have influenced AT/GC homogenization of fish genomes and requires further investigation. (biomedcentral.com)
  • 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)
  • Background: Mutator-like transposable elements, a class of DNA transposons, exist pervasively in both prokaryotic and eukaryotic genomes, with more than 10,000 copies identified in the rice genome. (edu.sa)
  • 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)
  • 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)
  • Transposable elements, or transposons, are, by far, the most dynamic part of the eukaryotic genome, and the majority, often the vast majority, of plant genomes are composed of these genomic parasites. (purdue.edu)
  • variety of transposable elements and DNA transposons in general. (github.com)
  • DNA transposons from barrel medic. (girinst.org)
  • DNA transposons from the Drosophila ficusphila genome. (girinst.org)
  • DNA transposons from the potato genome. (girinst.org)
  • The transposable element Uhu from Hawaiian Drosophila--member of the widely dispersed class of Tc1-like transposons. (semanticscholar.org)
  • All known transposable elements in eukaryotes belong to two types: retrotransposons and DNA transposons. (pnas.org)
  • Despite an enormous diversity of eukaryotic TEs, they belong to only two types, called retrotransposons and DNA transposons. (pnas.org)
  • The endonuclease domain in LTR retrotransposons is usually called integrase (INT) and is distantly related to the DDE transposases (TPase) encoded by Mariner DNA transposons ( 6 ). (pnas.org)
  • DNA transposons identified so far in eukaryotes belong to two classes characterized by the so-called "cut-and-paste" ( 7 ) and "rolling-circle" ( 8 ) mechanisms of transposition. (pnas.org)
  • Unlike retrotransposons, which synthesize their DNA copies by using their own RNA-dependent DNA polymerase (reverse transcriptase), DNA transposons cannot synthesize DNA. (pnas.org)
  • The two major subdivisions are class I (retrotransposons) and class II (DNA transposons), which differ according to their mechanism of transposition. (biomedcentral.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)
  • On balance, bdelloid genomes, despite being relatively open to assimilation of foreign DNA, are apparently able to control proliferation of incoming TEs through a multi-layered system of genome defense, including RNA-mediated silencing, mutation, and deletion via homologous recombination and non-homologous end-joining. (mbl.edu)
  • Transposable elements have contributed to the evolution of the genomes through induction of chromosomal rearrangements. (ukessays.com)
  • 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)
  • Invertrons, a class of structurally and functionally related genetic elements that includes linear DNA plasmids, transposable elements, and genomes of adeno-type viruses. (asm.org)
  • 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)
  • 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)
  • Transposable elements (TE) are indispensible to understand the evolution of genes and genomes in almost all organisms. (stonybrook.edu)
  • Since the advent of whole- genome sequencing, transposable elements (TEs), just thought to be 'junk' DNA , have been noticed because of their numerous copies in various eukaryotic genomes . (bvsalud.org)
  • In this review , we focus on Alu, L1, human endogenous retrovirus , and short interspersed element / variable number of tandem repeats /Alu (SVA) elements and discuss how they have affected primate genomes , especially the human and chimpanzee genomes , since their divergence. (bvsalud.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)
  • Elements like RTE-BovB belonging to LINEs family in cattle and sheep genomes are dramatically higher than genome of dromedary. (frontiersin.org)
  • 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)
  • 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)
  • Conclusions: Our results suggest that DNA methylation may be a primary mechanism to facilitate the origination, survival, and regulation of genes derived from Mutator-like transposable elements, thus contributing to the evolution of gene innovation and novelty in plant genomes. (edu.sa)
  • 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)
  • 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)
  • What's in the DNA is not so important-it's the fact that they introduce themselves into other genomes and cause disruption of genes and how they are regulated. (phys.org)
  • Genomes are dynamic entities: new functional elements appear and old ones become extinct. (scientificamerican.com)
  • It has long been recognized that bats and birds contain less DNA in their genomes than their non-flying relatives. (royalsocietypublishing.org)
  • Evolutionists once thought that transposable DNA elements, also called jumping genes, were merely the ancestral vestiges of viruses that maliciously infested and bloated the genomes of plants and animals. (icr.org)
  • Genomes of most eukaryotes are populated by DNA copies of parasitic elements known as transposable elements (TEs) capable of reproducing themselves in the host genome in a non-Mendelian fashion ( 1 , 2 ). (pnas.org)
  • The most highly conserved noncoding elements (HCNEs) in mammalian genomes cluster within regions enriched for genes encoding developmentally important transcription factors (TFs). (psu.edu)
  • Transposable Elements (TEs) are key components that shape the organization and evolution of genomes. (biomedcentral.com)
  • Transposable elements (TEs) are mobile genetic element able to transpose and multiply in genomes. (biomedcentral.com)
  • 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)
  • But a large part of genomes are made up of DNA sequences that do not code for any traits. (brighthub.com)
  • 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)
  • Much of the human genome, and as we are now finding out much of primate genomes, have a lot of transposable elements in them. (anthropology.net)
  • Genomic comparisons suggest that most properties of genomes tend to increase with genome size, but the fraction of the genome that comprises transposable elements (TEs) and other repetitive elements tends to increase disproportionately. (els.net)
  • Larger genomes tend to have larger amounts of most genome components, but the proportional representation of different types of DNA changes dramatically. (els.net)
  • With the Sleeping Beauty (SB) DNA transposon, a reconstructed Tc1/mariner element, as the driving force, DNA transposable elements have emerged as new gene delivery vectors with therapeutic potential. (nih.gov)
  • Previous studies have reported a correlation between Mu transposon inactivation and methylation of the Mu element TIRs. (asm.org)
  • A transposable element (TE, transposon, or jumping gene) 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 transposase makes a staggered cut at the target site producing sticky ends, cuts out the DNA transposon and ligates it into the target site. (wikipedia.org)
  • Identification of a regulatory transposon that controls the Mutator system of transposable elements. (purdue.edu)
  • Transib-type DNA transposon from the Drosophila ficusphila genome: consensus. (girinst.org)
  • DNA transposon from the potato genome, consensus. (girinst.org)
  • Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus. (semanticscholar.org)
  • Whereas a retrotransposon is transposed (retroposed) via reverse transcription of its mRNAs, a DNA transposon is transposed via transfer of its genomic copy from one site to another. (pnas.org)
  • A typical autonomous mariner ( 9 ), hAT ( 10 ), piggyBac ( 11 ), P ( 12 ), Merlin ( 13 ), or Transib ( 14 ) DNA transposon encodes only a single protein called transposase, which acts as an endonuclease and catalyses transfer of transposon DNA strands from one genomic site to another. (pnas.org)
  • In the En / Spm ( 10 ), MuDR ( 15 ), Harbinger ( 16 ), and Helitron ( 8 ) superfamilies, an autonomous transposon usually encodes a TPase and one DNA-binding protein. (pnas.org)
  • Journal Article] Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing in Arabidopsis thaliana F1 epihybrids. (nii.ac.jp)
  • 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)
  • Alu elements are classified as a type of transposon where copy is made of RNA, not DNA. (anthropology.net)
  • We found that TEs and TE-related sequences occupy an unusually small proportion of the A. vaga genome assembly ( ca . 3% of genomic DNA). (mbl.edu)
  • 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)
  • DNA methylation is essential for normal development and is associated with a number of key processes including genomic imprinting , X-chromosome inactivation , repression of transposable elements , aging , and carcinogenesis . (wikipedia.org)
  • [12] [16] By contrast, the genome of most plants, invertebrates, fungi, or protists show "mosaic" methylation patterns, where only specific genomic elements are targeted, and they are characterized by the alternation of methylated and unmethylated domains. (wikipedia.org)
  • These elements can capture ectopic genomic sequences that lead to the formation of new gene structures. (edu.sa)
  • Furthermore, we determine that Mutator-like transposable elements capture parental sequences preferentially from genomic regions with low methylation levels and high recombination rates. (edu.sa)
  • 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)
  • Transposable elements as sources of genomic variation. (purdue.edu)
  • In fact, more and more biologists now regard repetitive elements as genomic treasures. (scientificamerican.com)
  • With the wealth of genomic sequence information at our disposal, we are slowly uncovering the importance of non-protein-coding DNA. (scientificamerican.com)
  • In fact, new genomic elements are being discovered even in the human genome, five years after the deciphering of the full sequence. (scientificamerican.com)
  • Retrotransposons are ubiquitous genetic elements known to generate multiple types of genomic alterations. (asm.org)
  • In addition to this solo repeat, we isolated a genomic clone that contained direct repeats of the α element separated by an intervening region of approximately 5.5 kb. (asm.org)
  • We have used genomic sequencing data extracted from the first assembly of the Xenopus tropicalis genome combined with a degenerated PCR approach to identify multiple lineages of Tc1 related transposable elements. (semanticscholar.org)
  • In this method, genomic DNA is treated with sodium bisulphite (BS) to convert cytosine, but not methylcytosine, to uracil, and subsequent high-throughput sequencing. (psu.edu)
  • They shape the genomic landscape by providing novel DNA sequences at various locations, by contributing to chromosomal rearrangements, gene duplications, gene loss and inactivation and by accelerating evolution. (biomedcentral.com)
  • 2007. Long-term patterns of genomic P element content and P-M characteristics of D. melanogaster in eastern Australia. (bgsu.edu)
  • 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)
  • 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)
  • To elucidate the evolution of this rich repertoire, the mobile elements of the genome were characterized, including four plasmids with varying degrees of conservation and mosaicism and eleven chromosomal genomic islands. (nih.gov)
  • 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)
  • The Drosophila genus is one of the main model organisms in evolutionary studies, including those investigating the role of transposable elements (TE) in genomic evolution both at the nucleotide and chromosome levels. (springer.com)
  • Bensasson D, Petrov DA, Zhang DX, Hartl DL and Hewitt GM (2001) Genomic gigantism: DNA loss is slow in mountain grasshoppers. (els.net)
  • 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)
  • Structures of P transposable elements and their sites of insertion and excision in the Drosophila melanogaster genome. (nih.gov)
  • We have isolated and characterized several members of the P transposable element family from a Drosophila melanogaster P strain. (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)
  • Mobile Minos elements from Drosophila hydei encode a two-exon transposase with similarity to the paired DNA-binding domain. (semanticscholar.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)
  • We are involved in two main areas of genetic research with eukaryotic organisms: The role of mutation in evolution and the genetics of transposable DNA elements of Drosophila. (bgsu.edu)
  • 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)
  • Subunits of SB100X (indicated by purple circles) may be incorporated directly into the PIC (indicated by a stippled arrow and a question mark) or be directly imported into the nucleus where it may interact with both linear DNA and circular DNA intermediates (1- and 2-LTR circles) to facilitate transposition into randomly chosen TA-dinuclotides in the genome. (nih.gov)
  • It is not known whether linear viral DNA serves as a substrate for SB transposition. (nih.gov)
  • 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)
  • 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)
  • A model for replication and integration of invertrons is presented, as well as a model for transposition of transposable elements. (asm.org)
  • 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)
  • We found that RNA polymerase II expression-dependent forms of RdDM function on over 20 % of transcribed transposable elements, including the majority of full-length elements with all of the domains required for autonomous transposition. (biomedcentral.com)
  • 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)
  • 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)
  • Typically these sections of junk DNA come about through transposition, or movement of sections of DNA to different positions in the genome. (scientificamerican.com)
  • Polintons from all these species are characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. (pnas.org)
  • According to the model of Polinton transposition proposed here, a Polinton DNA molecule excised from the genome serves as a template for extrachromosomal synthesis of its double-stranded DNA copy by the Polinton -encoded DNA polymerase and is inserted back into genome by its integrase. (pnas.org)
  • Transposition of a retrotransposon is catalyzed by reverse transcriptase and endonuclease (EN) domains of a polyprotein encoded by itself or by other retrotransposons. (pnas.org)
  • Just as occurs with retrotransposons, there have been cases observed in which DNA transposable elements have lost the enzymes necessary for transposition. (brighthub.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)
  • None of the eleven full copies of IS26, the most frequent IS element in the genome, had the expected 8-bp direct repeat of the integration target sequence, suggesting that each copy underwent homologous recombination subsequent to its last transposition event. (nih.gov)
  • Transposition enables a piece of DNA to move within the same chromosome, or to a different chromosome, to a location with which it has no similarity. (panspermia.org)
  • Transposable element (TE)-derived sequences comprise half of the human genome and DNA methylome and are presumed to be densely methylated and inactive. (bcgsc.ca)
  • The fact that LTR-retrotransposons cannot copy themselves in humans is surprising, since HERVs make up 8-9% of the human genome (in terms of DNA base pairs). (anti-agingfirewalls.com)
  • 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)
  • Transposable elements (TEs) account for at least 50% of the human genome. (semanticscholar.org)
  • I found a paper announcing the creation of a database specific to Alu elements in the human genome, but the link to the database doesn't seem to work. (anthropology.net)
  • Transposable elements can induce various genetic changes. (ukessays.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)
  • 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)
  • Mobile genetic elements include pieces of DNA inserted into your genome by lurking retroviruses such as HIV. (icpl.org)
  • Invertrons are genetic elements composed of DNA with inverted terminal repeats at both ends, covalently bonded to terminal proteins involved in the initiation of DNA replication at both their 5' termini when they exist in the cytoplasm of their host in free form. (asm.org)
  • Publications] A.Hoshino: 'Gene duplication and mobile genetic elements in the morning glories. (nii.ac.jp)
  • 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)
  • Although TEs are selfish genetic elements, many are important in genome function and evolution. (wikipedia.org)
  • Transposable elements represent one of several types of mobile genetic elements. (wikipedia.org)
  • Genetic characterization of the Mutator system in maize: behavior and regulation of Mu elements in a minimal line. (purdue.edu)
  • Elements that use copying mechanisms to move around the genome increase the amount of genetic material. (scientificamerican.com)
  • Although very catchy, the term "junk DNA" repelled mainstream researchers from studying noncoding genetic material for many years. (scientificamerican.com)
  • Genetic manipulation of the elements showed that both loci were heterozygous for Tca1, that both were transcriptionally active, and that deletion of both had no effect on growth rate or germ tube formation. (asm.org)
  • Retrotransposons are known to effect several types of genetic alterations in fungal cells, either directly, by virtue of their mobilization and integration at a locus, or indirectly, via recombination between ectopically located copies of the element ( 2 , 5 ). (asm.org)
  • Meeting report: mobile genetic elements and genome plasticity 2018. (mbl.edu)
  • The fact that this transposable element is essential to proper development in mice illustrates how evolutionary thinking once incorrectly interpreted these genetic features. (icr.org)
  • 3, 4 Far from being useless genetic leftovers, transposable DNAs are central to life. (icr.org)
  • 5, 6 Adding to this amazing discovery is yet another recent report in the journal Nature Genetics showing that a family of transposable elements in mammals contribute hundreds of genetic features called 'enhancers' that modulate gene expression in placental cells. (icr.org)
  • The fact that extensive research is showing that transposable elements are essential to many aspects of gene and genome function illustrates the failure of evolutionary dogma that originally interpreted these as seemingly useless genetic artifacts. (icr.org)
  • Moreover, transposable elements can be used as powerful tools in genetic engineering ( 4 ). (pnas.org)
  • Resistance determinants and mobile genetic elements of an NDM-1-encoding Klebsiella pneumoniae strain. (nih.gov)
  • These strains can accumulate many antibiotic resistance genes though horizontal transfer of genetic elements, those for β-lactamases being of particular concern. (nih.gov)
  • Miller WJ, Capy P. Mobile genetic elements as natural tools for genome evolution . (huffingtonpost.com)
  • Naked nucleic acids are DNA/RNA produced in the laboratory and intended for use in, or as the result of genetic engineering (1). (i-sis.org.uk)
  • All IS elements end with identical or near identical inverted repeats (IR's) of 9 to 41 bp, but in opposite orientations. (ukessays.com)
  • 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)
  • 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)
  • 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)
  • This element was 388 bp in length and bound by a 6-bp inverted repeat similar in sequence to the inverted repeats found in the long terminal repeats (LTRs) of retrotransposons. (asm.org)
  • 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)
  • 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)
  • 1, 2, 3 In fact, a high-profile research paper titled 'Transposable Elements Re-Wire and Fine-Tune the Transcriptome' was just published in the journal PLoS Genetics . (icr.org)
  • Evolutionary genetics, Role of mutation in evolution and aging, Transposable DNA elements, and Molecular evolution. (bgsu.edu)
  • While studying maize genetics more than 60 years ago, Barbara McClintock discovered mobile pieces of DNA, called transposable elements. (nsf.gov)
  • Mu killer causes the heritable inactivation of the Mutator family of transposable elements in Zea mays. (purdue.edu)
  • LEDGF/p75 interacts with viral integrase (IN) proteins, shown as yellow circles attached to the terminal regions of the viral DNA. (nih.gov)
  • 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)
  • The autonomous MuDR element of the Mutator (Mu) transposable element family of maize encodes at least two proteins, MURA and MURB. (asm.org)
  • Indeed, while only 2% of our genome directly codes for the proteins that make up our bodies, over 40% of the remaining 'non-coding' DNA is filled with spam! (slideplayer.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)
  • Interestingly, all animals have a large excess of DNA that does not code for the proteins used to build bodies and catalyze chemical reactions within cells. (scientificamerican.com)
  • In humans, for example, only about 2 percent of DNA actually codes for proteins. (scientificamerican.com)
  • comparison against the transposable element proteins. (github.com)
  • element proteins. (github.com)
  • An LTR retrotransposon may carry three ORFs coding for the gag , env , and pol proteins, the latter is composed of the reverse transcriptase, EN, and aspartyl protease domains ( 5 ). (pnas.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)
  • 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 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)
  • Insertion sequences (IS) or IS elements is the simplest transposable element found in bacterial chromosomes and plasmids. (ukessays.com)
  • 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)
  • In conjugation, bacterial cells actually connect, and the "male" donates a piece of DNA to the "female. (panspermia.org)
  • The piece of DNA in this case was excised earlier from the bacterial chromosome. (panspermia.org)
  • In transduction, a virus takes up a piece of DNA from its bacterial host and incorporates it into its own viral genome. (panspermia.org)
  • Depending on the kind of transduction, some or all of the daughter viruses take copies of parts of the bacterial DNA with them. (panspermia.org)
  • From an evolutionary point of view, transposable elements diversify the genome and open up chances for adaptation. (phys.org)
  • The evolutionary factors explaining the distribution of transposable elements (TEs) across organisms are still poorly understood ( 1 ). (pnas.org)
  • Here, based on whole-genome comparative analyses, we comprehensively investigated processes and mechanisms of the evolution of putative genes derived from Mutator-like transposable elements in ten Oryza species and the outgroup Leersia perieri, bridging 20 million years of evolutionary history. (edu.sa)
  • We explicitly show that methylation levels in the internal and terminated inverted repeat regions of these elements, which might be directed by the 24-nucleotide small RNA-mediated pathway, are different and change dynamically over evolutionary time. (edu.sa)
  • A graphic representation of the BovB element which shows how it has appeared in species that are wide apart on the evolutionary tree -- for example sea urchins and elephants, cows and snakes. (phys.org)
  • It's estimated that well over 50% of non-coding DNA is heavily conserved by evolutionary processes and contributes significantly to fitness. (slashdot.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)
  • However, the past several decades of research have clearly shown that transposable elements play a large diversity of key roles in the genome. (icr.org)
  • Much to the chagrin of evolutionists, the past decade of research has clearly shown that transposable elements play vital and purposeful roles in regulating how genes and the genome function. (icr.org)
  • This particular segment of DNA is called insertion sequence 1, or IS1 ( Fig.6.19 ). (ukessays.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)
  • Insertion of IS element takes place at a target site with which the IS element has no sequence homology ( Fig.6.20 ). (ukessays.com)
  • VFN8 contains a sequence with the structural characteristics of a transposable element. (genetics.org)
  • The DNA sequence was not inherited but directly transferred from one organism to another. (phys.org)
  • How does a mobile DNA sequence find its target? (phys.org)
  • For the HERV sequence to be transcribed, the fossil viral DNA must have an open reading frame (ORF). (anti-agingfirewalls.com)
  • P elements have 31 bp perfect inverse terminal repeats and upon insertion duplicate an 8 bp sequence found only once at the site of insertion. (nih.gov)
  • The basis of this specificity has been investigated by DNA sequence analysis of the sites where 18 P elements are found. (nih.gov)
  • A revertant of one of the white locus mutants has been found to result from precise excision of the P element, restoring the wild-type DNA sequence. (nih.gov)
  • Transposable elements (TEs) along with simple sequence repeats (SSRs) are prevalent in eukaryotic genome, especially in mammals. (frontiersin.org)
  • They are bound to two cytosine nucleotide molecules that make up the DNA sequence. (wikipedia.org)
  • Methylation can change the activity of a DNA segment without changing the sequence. (wikipedia.org)
  • In plants and other organisms, DNA methylation is found in three different sequence contexts: CG (or CpG ), CHG or CHH (where H correspond to A, T or C). In mammals however, DNA methylation is almost exclusively found in CpG dinucleotides, with the cytosines on both strands being usually methylated. (wikipedia.org)
  • 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)
  • The entire sequence of transposable elements is usually methylated in Arabidopsis , in all sequence contexts [ 8 ]. (hindawi.com)
  • This property has allowed researchers to sequence methylated DNA to distinguish non-methylated cytosine (shown up as uracil) and methylated cytosine (unaltered). (wikipedia.org)
  • Structure and chromosomal mapping of a highly polymorphic repetitive DNA sequence from the pseudoautosomal region of the mouse sex chromosomes. (biomedsearch.com)
  • Partial sequence determination demonstrated that the elements from the two loci were nearly identical. (asm.org)
  • More recently, another repetitive element of C. albicans , termed beta, was found to have sequence features suggesting that it was a retrotransposon-derived solo LTR ( 22 ). (asm.org)
  • Interestingly, the characterization of several beta elements demonstrated that each was located adjacent to a tRNA gene analogous to the Ty3 retrotransposon of Saccharomyces cerevisiae ( 11 ), and a limited sequence similarity with the LTRs of Ty3 was also noted ( 22 ). (asm.org)
  • Sequence motifs are only found in DNA―they do not occur in RNA. (brainscape.com)
  • When sequence motifs occur in DNA, they are only found upstream of protein-coding regions. (brainscape.com)
  • Sequence motifs in RNA do not provide any information on possible sequence motifs in DNA. (brainscape.com)
  • In the eukaryotic DNA sequence below, which type of repeat is highlighted? (brainscape.com)
  • This defense mechanism detects DNA sequence duplications and induces irreversible C:G to T:A mutations at a high rate in these sequences. (biomedcentral.com)
  • The enzymes may recognize specific sequences for insertion, though many types of enzyme can actually bind to virtually any sequence, allowing the element to be inserted anywhere. (brighthub.com)
  • 19. Chromosome Structure and DNA Sequence Organization. (textbooks.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)
  • 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)
  • The key here is that the mutation was in an internally repetitive sequence of DNA. (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)
  • 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)
  • Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants. (amedeo.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)
  • 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)
  • 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)
  • The dynamic patterning of DNA and histone methylation throughout oocyte growth presents a doubtlessly vulnerable time for epigenetic disruption due to early life environmental exposure of future moms. (maizetedb.org)
  • DNA methylation and histone H1 mediate transcriptional silencing of genes and transposable elements, but how they interact is unclear. (postech.ac.kr)
  • Here we present the first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome, from both human embryonic stem cells and fetal fibroblasts, along with comparative analysis of messenger RNA and small RNA components of the transcriptome, several histone modifications, and sites of DNA-protein interaction for several key regulatory factors. (psu.edu)
  • Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. (ebi.ac.uk)
  • 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)
  • 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)
  • Accordingly, TEs are subject to tight epigenetic control during the earliest phases of embryonic development via histone and DNA methylation. (semanticscholar.org)
  • 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)
  • It was later found that such changes were induced due to insertion of an approximately 800 base-pair DNA segment in to a gene. (ukessays.com)
  • A segment of DNA 5' to the transcribed region of an auxin-regulated gene, ARPI, from Lycopersicon esculentum Mill. (genetics.org)
  • DNA transposable elements, class 2 elements, have become a source of material for coordination of eukaryotic gene regulatory systems and for chromosomal reconstruction. (stonybrook.edu)
  • When located in a gene promoter , DNA methylation typically acts to repress gene transcription . (wikipedia.org)
  • The complete four-gene element was found in 10 to 40% of strains obtained from Africa, India, Europe, and the Americas but in only 1% of East Asian strains. (asm.org)
  • the replication of euchromatic gene-rich DNA occurs earlier in the S-phase. (hindawi.com)
  • The Maize Regulatory Gene B-Peru contains a DNA rearrangement that specifies tissue-specific expression through both positive and negative promoter elements. (purdue.edu)
  • Transposable elements and host gene evolution. (purdue.edu)
  • Bantysh, O.B. and Buzdin, A.A., Novel Family of Human Transposable Elements Formed Due to Fusion of the First Exon of Gene MAST2 with Retrotransposon SVA, Biochemistry (Moscow) , 2009, vol. 74, no. 12, pp. 1393-1399. (springer.com)
  • The region of DNA sequences before the start of a gene is often called the promoter. (brainscape.com)
  • Only 3% of this aquatic plant's DNA is not part of a known gene , new research shows. (slashdot.org)
  • In contrast, only 2% of human DNA is part of a gene. (slashdot.org)
  • Evidence for localized selection on the U. gibba gene complement, however, does not provide support for the existence of genome-wide selective forces that might favour reduction of nonessential, non-coding DNA. (slashdot.org)
  • 17. Gene Mutation, DNA Repair, and Transposable Elements. (textbooks.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)
  • These two routes have accelerated the fine-tuning of these transposable elements for use in gene regulation. (elifesciences.org)
  • 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)
  • Transformation by the uptake of DNA is recognized to be a significant route of horizontal gene transfer among bacteria, and there is overwhelming evidence that horizontal gene transfer and recombination have been responsible for the recent resurgence of drug and antibiotic resistant infectious diseases. (i-sis.org.uk)
  • If you want to read more about Alus check out this review article but for your sanity's sake I'll wrap up the review of Alu elements… Because Alus are more or less mobile they are important because they affect gene structures, protein sequences, splicing motifs and expression patterns. (anthropology.net)
  • However, researchers have found that some genes (DNA sequences) can actually change position in the chromosomes. (ukessays.com)
  • 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)
  • 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)
  • Transposable elements were discovered by Barbara McClintock in maize in 1950. (ukessays.com)
  • 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)
  • The advantages of this host species and their elements, together with results so far obtained, are here described. (bioone.org)
  • This is the first time anyone has shown that the L1 element , important in humans, has jumped between species. (phys.org)
  • The team also looked at the transfer of BovB elements between species. (phys.org)
  • On the other hand, anonymous sequences that are nonfunctional in one species may, in another organism, become an exon-a section of DNA that is eventually transcribed to messenger RNA. (scientificamerican.com)
  • 2013. Endogenous retroviruses function as species-specific enhancer elements in the placenta. (icr.org)
  • The developmental control of transposable elements and the evolution of higher species. (semanticscholar.org)
  • Even without the extreme examples such as bladderwort we readily observe 10x variability in the amount of DNA between fairly recently separated species. (slashdot.org)
  • 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 extent and causes of between‐species changes in transposable element activity should be characterised, to better understand the drivers of genome expansion. (els.net)
  • DNA topoisomerase is an enzyme that releases the torsional stress in DNA generated during DNA replication or transcription. (prolekare.cz)
  • This misincorporated base will not be corrected during DNA replication as thymine is a DNA base. (wikipedia.org)
  • In DNA, this reaction, if detected prior to passage of the replication fork, can be corrected by the enzyme thymine-DNA glycosylase, which removes the thymine base in a G/T mismatch. (wikipedia.org)
  • a class of transposable elements that replicate and transpose via DNA replication and repair. (brainscape.com)
  • I believe a more prudent falsifiable hypothesis would run along the lines of (and I'm sorry, I'm only a software developer): Due to relaxed external selective pressures the bladderwort's RNA polymerase has become adept at writing coding errors to the 3% noncoded DNA during replication and this actually still serves a vital function -- especially if the bladderwort is to survive in a much larger window than a few generations. (slashdot.org)
  • 12. DNA Replication and Recombination. (textbooks.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)
  • These jumping genes are actually small pieces of DNA that can copy themselves throughout a genome and are known as transposable elements. (phys.org)
  • The second type of transposable element is related to retrovirus. (ukessays.com)
  • A key feature of this activity that has been discovered in the mouse genome involves a specific type of transposable element named MuERV-L. This transposable element is uniquely active in the totipotent cell phase that is critical to forming all of the other cells in the mouse embryo. (icr.org)
  • Chalopin D, Naville M, Plard F, Galiana D and Volff JN (2015) Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. (els.net)
  • many regulatory functions are related to the loss in CPG sites due to the presence of transposable elements. (wikipedia.org)
  • Don Batten suggests the presence of transposable elements means the plasmid is "designed" to be adaptive. (talkorigins.org)
  • Dr. Lisch is interested in the regulation and evolution of plant transposable elements and the role that transposable elements have played in plant evolution. (purdue.edu)
  • Transposable elements are ubiquitous specific DNA sequences of the genome found in both prokaryotes and eukaryotes. (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)
  • Diversity in genome size (DNA content per haploid nucleus) among eukaryotes has been a subject of study since the late 1940s. (royalsocietypublishing.org)
  • Eukaryotes contain numerous transposable or mobile elements capable of parasite-like proliferation in the host genome. (pnas.org)
  • 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)
  • Perspective: Transposable Elements, parasitic DNA, and genome evolution. (purdue.edu)
  • The researchers say that understanding the inheritance of this element is important for understanding the evolution of diseases. (phys.org)
  • Last summer developmental biologist Gill Bejerano, then a postdoctoral fellow at the University of California, Santa Cruz, and now a professor at Stanford University, and his colleagues discovered that during vertebrate evolution, a novel retroposon-a DNA fragment, reverse-transcribed from RNA, that can insert itself anywhere in the genome-was exapted as an enhancer, a signal that increases a gene's transcription. (scientificamerican.com)
  • Neutral Theory, Transposable Elements, and Eukaryotic Genome Evolution. (mbl.edu)
  • One area of research related to the mobilome-that is completely destroying one of the sacred cows of evolution-is the idea that transposable elements are nothing but useless 'junk DNA. (icr.org)
  • The availability of complete genome sequences has revealed the significant role that these elements play in genome evolution, organization and stability. (ed.ac.uk)
  • There would likely be no bladderwort had there been no junk DNA in its ancestral line and other findings point to such noncoded DNA as necessary for evolution [slashdot.org]. (slashdot.org)
  • The regulatory sequences contained within transposable elements are not always optimal, but they can be fine-tuned through evolution. (elifesciences.org)
  • Transposable elements are well known as possible agents of evolution. (talkorigins.org)
  • Schaack S, Gilbert C, Feschotte C. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution . (huffingtonpost.com)
  • Kazazian HH Jr. Mobile elements: drivers of genome evolution . (huffingtonpost.com)
  • Ågren JA and Wright SI (2011) Co‐evolution between transposable elements and their hosts: a major factor in genome size evolution? (els.net)
  • Ågren JA, Huang HR and Wright SI (2016) Transposable element evolution in the allotetraploid Capsella bursa‐pastoris. (els.net)
  • Double insertion of transposable elements provides a substrate for the evolution of satellite DNA. (amedeo.com)
  • Transposable elements make up a large fraction of the genome and are responsible for much of the mass of DNA in a eukaryotic cell. (wikipedia.org)
  • Despite the large amount of accumulated data, the significance of the complex repetitive DNA fraction in the eukaryotic genome restructuring and functioning is still not completely understood. (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)
  • Examples of LTR retrotransposons are human endogenous retroviruses (HERV) (shown) and various Ty elements of S. cerevisiae (not shown). (slideplayer.com)
  • Retrotransposons are commonly grouped into three main orders: Retrotransposons, with long terminal repeats (LTRs), which encode reverse transcriptase, similar to retroviruses Retroposons, long interspersed nuclear elements (LINEs, LINE-1s, or L1s), which encode reverse transcriptase but lack LTRs, and are transcribed by RNA polymerase II Short interspersed nuclear elements (SINEs) do not encode reverse transcriptase and are transcribed by RNA polymerase III (Retroviruses can also be considered TEs. (wikipedia.org)
  • The majority of potential quadruplex-forming sequences (PQS) are located in transposable elements (TEs), especially close to promoters within long terminal repeats of plant LTR retrotransposons. (muni.cz)
  • Conclusions Our results demonstrate that quadruplex DNA located within long terminal repeats of LTR retrotransposons can be formed in vivo and that it plays a regulatory role in the LTR retrotransposon life-cycle, thus also affecting genome dynamics. (muni.cz)
  • However, several groups have reported the presence of retrotransposons or retrotransposon-like elements in this fungus. (asm.org)
  • In addition to the reverse transcriptase/EN polyprotein, most non-LTR retrotransposons code for a second protein characterized by poorly understood activities, including RNA/DNA binding, chaperone, and esterase. (pnas.org)
  • 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)
  • Other studies have also demonstrated the critical involvement of various classes of transposable element DNA during other stages of both embryo development and pregnancy. (icr.org)
  • Here, we describe approaches using droplet digital polymerase chain reaction (ddPCR) to validate and quantify somatic mosaic events contributed by transposable-element insertions, copy-number variants, and single-nucleotide variants. (springer.com)
  • Miotke L, Lau BT, Rumma RT, Ji HP (2014) High sensitivity detection and quantitation of DNA copy number and single nucleotide variants with single color droplet digital PCR. (springer.com)
  • Hence, GC content of a genome (GC G ), i.e., the molar ratio of guanine (G) and cytosine (C) in DNA, is one of the main parameters used to describe nucleotide composition and is frequently related to genome size [ 1 ]. (biomedcentral.com)
  • Relation between amount of DNA (deoxyribonucleic acid) gained/lost due to small indels (calculated as the total size of small insertions minus the total size of small deletions) per single nucleotide mutation and genome size, from direct estimation of insertion and deletion events in mutation studies. (els.net)
  • In a parallel study, I show that a 1.8-Mb chromosomal inversion, mediated by a novel Mu-like element, is responsible for the classical Tunicate1 mutation in maize. (stonybrook.edu)
  • However, H1 loss strongly activates transposable elements hypomethylated through mutation of DNA methyltransferase MET1. (postech.ac.kr)
  • Well, transposable elements can result in rapid adaptation, but the mechanism is pure random mutation and natural selection. (talkorigins.org)
  • The rare exception is the back-mutation, which merely undoes the damage of a previous mutation and restores the affected strand of DNA to its original condition. (panspermia.org)
  • Recombination is a much more powerful mutation way for DNA to change. (panspermia.org)
  • DNA-based transposable elements appear to have been nearly or completely inactivated in vertebrates. (bioone.org)
  • The DNA methylation landscape of vertebrates is very particular compared to other organisms. (wikipedia.org)
  • In vertebrates, around 60-80% of CpG are methylated in somatic cells [15] and DNA methylation appears as a default state that has to be specifically excluded from defined locations. (wikipedia.org)
  • Transposable elements for transgenesis and insertional mutagenesis in vertebrates: a contemporary review of experimental strategies. (semanticscholar.org)
  • They function as viruses, linear DNA plasmids, transposable elements, and sometimes combinations of two of these properties. (asm.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)
  • Such excised pieces of DNA are called plasmids. (panspermia.org)
  • Research in the Arkhipova lab is focused on transposable elements (TEs) in chromosomal DNA. (mbl.edu)
  • 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 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)
  • Transposable elements affect the color of maize kernels and are responsible for the purple-colored sectors and spots shown in this 1949 ear of maize from the McClintock collection. (nsf.gov)
  • Consistent with previous reports, we observe that the putative Mutator-like transposable element-derived genes are generally GC-rich and mainly derive from GC-rich parental sequences. (edu.sa)
  • Lastly, we demonstrate that putative genes derived from Mutator-like transposable elements tend to be expressed in mature pollen, which have undergone de-methylation programming, thereby providing a permissive expression environment for newly formed/transposable element-derived genes. (edu.sa)
  • I found that more than 100 Mu elements per plant transpose mostly into hypomethylated genic regions. (stonybrook.edu)
  • However, those that are working can still copy themselves (LINE-1s) or copy other transposable elements that were never able to copy themselves (i.e. were parasitic transposable elements). (anti-agingfirewalls.com)
  • Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire. (semanticscholar.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)
  • 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)
  • Particularly interesting is the finding that all identified lineage-specific SINE elements show a strong tendency to insert within or in very close proximity to the preexisting MIRs for their efficient integrations, suggesting that the MIR element is a hot spot for successive insertions of other SINEs. (deepdyve.com)
  • Discrete segments of DNA which can excise and reintegrate to another site in the genome. (curehunter.com)
  • In 1972 the late geneticist Susumu Ohno coined the term "junk DNA" to describe all noncoding sections of a genome, most of which consist of repeated segments scattered randomly throughout the genome. (scientificamerican.com)
  • Newly synthesized RNA transcripts (copies of DNA segments) unique to the zygotic genome immediately populate and program the cell nucleus for life's initial stages. (icr.org)
  • The term mobilome refers to a category of transposable DNA segments-sections of DNA that in some cases can excise themselves and move around in the genome (called transposable elements), sometimes taking other pieces of DNA with them. (icr.org)
  • Transposable elements are segments of DNA that jump around, copy, and rearrange themselves. (anthropology.net)
  • DNA sequences that are similar in different organisms are called _______________ sequences. (brainscape.com)
  • Free nucleic acids refer to the laboratory-produced nucleic acids transfected into cells or organisms, whether incorporated as transgenic DNA or not, and subsequently released into the environment by secretion, excretion, waste disposal, death, industrial processing, or carried by liquid streams, or in airborne dust and pollen. (i-sis.org.uk)
  • Its representatives were formed by a rather unusual RNA recombination mechanism, which mediated the formation of fused DNA copies for diverse cellular transcripts. (springer.com)
  • When two strings of similar DNA line up with each other and swap sections, it's called homologous recombination . (panspermia.org)
  • When shorter pieces of similar DNA line up to initiate a swap of longer, dissimilar pieces (of which the shorter pieces can be part), that's called site-specific recombination . (panspermia.org)
  • Teleost fish genome size has been repeatedly demonstrated to positively correlate with the proportion of transposable elements (TEs). (biomedcentral.com)
  • Using nextgen sequencing data to investigate genome size variation and transposable element content. (exlibris.ch)
  • In particular, the spread and loss of transposable elements-sequences that (at least initially) behave as parasites of the host genome-are increasingly understood to be a dominant mode of genome size change in animals and plants (e.g. (royalsocietypublishing.org)
  • Transposable elements and other repetitive DNA represent a major determinant of genome size variation. (els.net)
  • Bennett MD, Price HJ and Johnston JS (2008) Anthocyanin inhibits propidium iodide DNA fluorescence in Euphorbia pulcherrima: implications for genome size variation and flow cytometry. (els.net)
  • When transposable elements cannot copy themselves, they are referred to as being "non-autonomous", which HERVs are in humans (but not rodents). (anti-agingfirewalls.com)
  • Tissue-specific accumulation of MURB, a protein encoded by MuDR, the autonomous regulator of the Mutator transposable element family. (purdue.edu)
  • Analogously to known transposable elements, Polintons exist as autonomous and nonautonomous elements. (pnas.org)
  • Each type includes different classes and families of TEs composed of autonomous and nonautonomous elements. (pnas.org)
  • Whereas an autonomous element encodes a complete set of enzymes characteristic of its family, a nonautonomous element encodes none, or only some of them, and depends on enzymes encoded by its autonomous relative. (pnas.org)
  • A total of 277 elements were identified, corresponding to approximately 14% of the genome, and 164 of these elements are new, of which 32.62% are putatively autonomous and 8.9% are transcriptionally active in adult flies. (springer.com)
  • Here we show that H1 is enriched in methylated sequences, including genes, of Arabidopsis thaliana, yet this enrichment is independent of DNA methylation. (postech.ac.kr)
  • Arabidopsis homologue SUVH4 is directly required for the maintenance of the DNA CpNpG and asymmetric methylation. (ebi.ac.uk)
  • Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. (ebi.ac.uk)
  • Charlesworth B and Charlesworth D (1983) The population dynamics of transposable elements. (els.net)
  • Each cell in our bodies contains thousands of copies of "biological junk mail", except this kind is made of DNA instead of words and data packets. (slideplayer.com)
  • With large-scale sequencing becoming increasingly available, more and more people will come across transposable element sequences in their data, and this volume will hopefully help to convince them that they are not just 'junk DNA. (exlibris.ch)
  • With large-scale sequencing becoming increasingly available, more and more people will come across transposable element sequences in their data, and this volume will hopefully help to convince them that transposable elements are not just "junk" DNA, and may actually be the most interesting and fun part of their data! (exlibris.ch)
  • What is junk DNA, and what is it worth? (scientificamerican.com)
  • And it is because of them that in the early 1990s, the view of junk DNA, especially repetitive elements, began to change. (scientificamerican.com)
  • And so, junk DNA can evolve into functional DNA. (scientificamerican.com)
  • The finding overturns the notion that this repetitive, non-coding DNA, popularly called 'junk' DNA, is necessary for life. (slashdot.org)
  • Too bad you passed up the "my junk ejecting DNA" opportunity for a cheap insightful comment. (slashdot.org)
  • Most of junk DNA is. (slashdot.org)
  • There is a small amount of regulatory elements mixed with all this junk, but the junk itself is not necessary for anything. (slashdot.org)
  • 2011. Mobile DNA: Finding Treasure in Junk (FT Press Science). (huffingtonpost.com)
  • 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)
  • Large 2.9 kb elements are present as multiple highly conserved copies together with smaller (0.5-1.6 kb), heterogeneous elements. (nih.gov)
  • 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)
  • 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)
  • Small RNAs (sRNAs) are the triggers of epigenetic transcriptional silencing targeted to transposable elements (TEs) and transgenes. (biomedcentral.com)
  • Our results demonstrate that H1 and DNA methylation jointly maintain transcriptional homeostasis by silencing transposable elements and aberrant intragenic transcripts. (postech.ac.kr)
  • Horizontal Transfer of a Plant Transposable element. (purdue.edu)
  • Single-stranded RNA (ssRNA) is shown in red, double-stranded DNA (dsDNA) in blue. (nih.gov)
  • Understanding the biology of transposable elements is of great importance because of their increasingly well documented impact on the host genome ( 2 , 3 ). (pnas.org)
  • Loss of H1 disperses heterochromatin, globally alters nucleosome organization, and activates H1-bound genes, but only weakly de-represses transposable elements. (postech.ac.kr)
  • Citation Query Role of transposable elements in heterochromatin and epigenetic control. (psu.edu)
  • Role of transposable elements in heterochromatin and epigenetic control. (psu.edu)
  • The silencing mechanism via DNA CpNpG methylation requires the targeting of chromomethylase CMT3 to methylated histones, probably through an interaction with an heterochromatin protein 1-like adapter. (ebi.ac.uk)
  • An Alu element is an example of a nonautonomous retrotransposon. (slideplayer.com)
  • This element was flanked by α elements, or long terminal repeats (LTRs), and contained an intervening region of 5,614 bp. (asm.org)
  • Classes of mobile elements. (slideplayer.com)
  • Transposable elements (TEs) are mobile fragments of DNA that can generate mutations and genome instability. (biomedcentral.com)
  • Mobile DNA" redirects here. (wikipedia.org)
  • For the academic journal, see Mobile DNA (journal) . (wikipedia.org)
  • This isolated α element was flanked by a 5-bp direct repeat, suggestive of the target site duplication that occurs with integration of mobile elements. (asm.org)
  • They continue to be able to move thanks to the presence of enzymes encoded by other mobile elements. (brighthub.com)
  • Competition with other types of mobile elements [ 22 , 23 ] is a possible explanation. (springer.com)
  • 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)
  • The near-universal replacement of uracil by thymine in DNA, but not RNA, may have evolved as an error-control mechanism, to facilitate the removal of uracils generated by the spontaneous deamination of cytosine. (wikipedia.org)
  • In DNA, this spontaneous deamination is corrected for by the removal of uracil (product of cytosine deamination and not part of DNA) by uracil-DNA glycosylase, generating an abasic (AP) site. (wikipedia.org)
  • The resulting abasic site is then recognised by enzymes (AP endonucleases) that break a phosphodiester bond in the DNA, permitting the repair of the resulting lesion by replacement with another cytosine. (wikipedia.org)
  • DNA ligase then forms a phosphodiester bond to seal the resulting nicked duplex product, which now includes a new, correct cytosine (Base excision repair). (wikipedia.org)
  • DNA cytosine methylation is a central epigenetic modification that has essential roles in cellular processes including genome regulation, development and disease. (psu.edu)
  • Both mechanisms require specific cytosine DNA Methyltransferases (RID1/Masc1) of the Dnmt1 superfamily. (biomedcentral.com)
  • We term such elements Repeat Insertion Domains of LncRNAs (RIDLs). (nih.gov)
  • Zhang, Ya-ping 2005-10-14 00:00:00 An analysis of the nuclear β-fibrinogen intron 7 locus from 30 taxa representing 12 placental orders of mammals reveals the enriched occurrences of short interspersed element (SINE) insertion events. (deepdyve.com)
  • This expression-dependent RdDM mechanism functions through RNAi degradation of transposable element mRNAs into small RNAs guided by the RNA-dependent RNA polymerase 6 (RDR6) protein and is therefore referred to as RDR6-RdDM. (biomedcentral.com)
  • Lastly, we find that RDR6-RdDM preferentially targets long transposable elements due to the specificity of primary small RNAs to cleave full-length mRNAs. (biomedcentral.com)