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
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 ...
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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 ...
Epigenetic modifications have an important role to explain part of the intra-and inter-species variation in gene expression. They also have a role in the control of transposable elements (TEs) whose activity may have a significant impact on genome evolution by promoting various mutations, which are expected to be mostly deleterious. A change in the local epigenetic landscape associated with the presence of TEs is expected to affect the expression of neighboring genes since these modifications occurring at TE sequences can spread to neighboring sequences. In this work, we have studied how the epigenetic modifications of genes are conserved and what the role of TEs is in this conservation. For that, we have compared the conservation of the epigenome associated with human duplicated genes and the differential presence of TEs near these genes. Our results show higher epigenome conservation of duplicated genes from the same family when they share similar TE environment, suggesting a role for the differential
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 ...
Horizontal transfer (HT) of genetic material is central to the architecture and evolution of prokaryote genomes. Within eukaryotes, the majority of HTs reported so far are transfers of transposable elements (TEs). These reports essentially come from studies focusing on specific lineages or types of TEs. Because of the lack of large-scale survey, the amount and impact of HT of TEs (HTT) in eukaryote evolution, as well as the trends and factors shaping these transfers, are poorly known. Here, we report a comprehensive analysis of HTT in 195 insect genomes, representing 123 genera and 13 of the 28 insect orders. We found that these insects were involved in at least 2,248 HTT events that essentially occurred during the last 10 My. We show that DNA transposons transfer horizontally more often than retrotransposons, and unveil phylogenetic relatedness and geographical proximity as major factors facilitating HTT in insects. Even though our study is restricted to a small fraction of insect biodiversity ...
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 ...
A transposable element (TE, transposon, or jumping gene) is a nucleic acid sequence in DNA that can change its position within ... Repbase - a database of transposable element sequences Dfam - a database of transposable element families, multiple sequence ... Zhou W, Liang G, Molloy PL, Jones PA (August 2020). "DNA methylation enables transposable element-driven genome expansion". ... Zhou W, Liang G, Molloy PL, Jones PA (August 2020). "DNA methylation enables transposable element-driven genome expansion". ...
"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 ... Cytosine deamination can alter the genome's many regulatory functions; previously silenced transposable elements (TEs) may ... product of cytosine deamination and not part of DNA) by uracil-DNA glycosylase, generating an abasic (AP) site. The resulting ...
... 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 ...
Transposable elements (transposons, TEs, 'jumping genes') are short strands of repetitive DNA that can self-replicate and ... Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis." Genome ... While transposable elements may affect any number of different cell-types in an animal, be a skin cell, a liver cell, a brain ... Though transposable elements were discovered due in large part to their deleterious effects, epigenetic research has shown that ...
Since DNA methylation occurs mostly in transposable elements (TE), DDM1 is thought to be a crucial function in silencing TEs. ... DDM1 is required for DNA methylation in highly heterochromatin transposable elements. DDM1, therefore, often silences ... DDM1, Decreased DNA Methylation I, is a plant gene that encodes a nucleosome remodeler which facilitates DNA methylation. The ... transposable elements but the mutation in Arabidopsis thaliana is not embryo lethal. DDM1 mutants have also been described to ...
... (MITEs) are a group of non-autonomous Class II transposable elements (DNA ... "Miniature inverted-repeat transposable elements (MITEs) and their relationship with established DNA transposons". In Craig N, ... Lu C, Chen J, Zhang Y, Hu Q, Su W, Kuang H (March 2012). "Miniature inverted-repeat transposable elements (MITEs) have been ... They can form stable DNA secondary structures which can be very useful in identifying them. A few Stowaway elements also ...
... 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 ...
It is even suggested that DNA methylation evolved precisely for this purpose. DNA methylation of transposable elements has been ... suggesting that the DNA methylation of transposable elements led to a noticeable increase in the mass of DNA. A function that ... Ancient DNA methylation reconstruction, a method to reconstruct high-resolution DNA methylation from ancient DNA samples. The ... "DNA methylation enables transposable element-driven genome expansion". Proceedings of the National Academy of Sciences of the ...
... 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: ...
Kidwell, M. G. and D. R. Lisch (2001) Perspective: Transposable elements, parasitic DNA and genome evolution. Evolution 55:1-24 ... Transposable elements as sources of variation in animals and plants. Proc. Natl. Acad. Sci. 94: 7704-7711. ... lead to collaborative studies resulting in the discovery of hybrid dysgenesis and the isolation of transposable P elements. ... at the University of Arizona has increasingly focused on the evolutionary significance of transposable genetic elements. In ...
... 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. Examples ... 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 ...
... including highly repetitive DNA sequences for their size. Transposable elements accumulate nucleotide substitutions over ... high genome wide repetitive DNA density; and recent transposable element expansions. Genetic diversity in leafy seadragons and ... Transposable element density is enriched near expanded gene families, and low near contracted gene families. For example, BovB ... Often, transposable elements have significant mutational effects on their hosts, some even contributing to organismic evolution ...
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 ...
"Nomenclature of transposable elements in prokaryotes". DNA insertion elements, plasmids, and episomes. [Cold Spring Harbor, N.Y ... "Nomenclature of transposable elements in prokaryotes" (PDF). Plasmid. 2 (3): 466-473. doi:10.1016/0147-619X(79)90030-1. PMID ... "Nomenclature of transposable elements in prokaryotes". Gene. 5 (3): 197-206. doi:10.1016/0378-1119(79)90078-7. PMID 467979. ... His most prominent discovery was the proposal of the "Campbell model" of virus insertion, where viral DNA is inserted into the ...
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 ...
... with a specific focus on transposable elements in DNA. It was established in 2010 and is published by BioMed Central. The ... "Mobile DNA". 2017 Journal Citation Reports. Web of Science (Science ed.). Clarivate Analytics. 2018. Official website v t e ( ... Mobile DNA is a peer-reviewed online-only open access scientific journal covering genomics, ...
Since nearly all RT genes function in retrovirus replication and/or the movement of transposable elements, it is reasonable to ... Multicopy single-stranded DNA (msDNA) is a type of extrachromosomal satellite DNA that consists of a single-stranded DNA ... or even between DNA polymerases using DNA as a template, versus DNA polymerases using RNA as a template. The catalytic region ... The priming of msDNA synthesis offers a fascinating challenge to our understanding of DNA synthesis. DNA polymerases (which ...
... 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 ...
... is an enzyme that in humans is encoded by the PGBD5 gene. PGBD5 is a DNA transposase ... "PGBD5 piggyBac transposable element derived 5 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 8 April ... Shao, Benjamin (2018-05-01). "Effects of PiggyBac Transposable Element Derived 5 (PGBD5) in Cortical Tissue". Honors Scholar ... Research, American Association for Cancer (2018-01-01). "The DNA Transposase PGBD5 Sensitizes Tumors to Inhibition of DNA ...
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 ...
Simsek, M.; DasSarma, S.; RajBhandary, U. L.; Khorana, H. G. (1982-12-01). "A transposable element from Halobacterium halobium ... and DNA repair systems. DasSarma's recent research (2010's) on an Antarctic halophilic microorganism, Halorubrum lacusprofundi ... "High-frequency spontaneous mutation in the bacterio-opsin gene in Halobacterium halobium is mediated by transposable elements ... In early work (1980's), he discovered mobile genetic elements in halophilic Archaea, while a graduate student with H. Gobind ...
Anderson SN, Zhou P, Higgins K, Brandvain Y, Springer NM (April 2021). "Widespread imprinting of transposable elements and ... Magee DA, Sikora KM, Berkowicz EW, Berry DP, Howard DJ, Mullen MP, Evans RD, Spillane C, MacHugh DE (October 2010). "DNA ... Sikora KM, Magee DA, Berkowicz EW, Berry DP, Howard DJ, Mullen MP, Evans RD, Machugh DE, Spillane C (January 2011). "DNA ... for the origin of this genetic variation states that the host-defense system responsible for silencing foreign DNA elements, ...
Junk DNA List of sequenced eukaryotic genomes Non-coding DNA Plant DNA C-values Database Selfish DNA Transposable elements ... Some single-celled organisms have much more DNA than humans, for reasons that remain unclear (see non-coding DNA and C-value ... therefore the spread of the transposable elements will positively affect the rate of deletion. The loss of those genes in the ... Genome size is the total amount of DNA contained within one copy of a single complete genome. It is typically measured in terms ...
Short interspersed nuclear elements (SINEs) are non-autonomous, non-coding transposable elements (TEs) that are about 100 to ... CS1 Russian-language sources (ru), Molecular biology, Repetitive DNA sequences, Mobile genetic elements, Non-coding DNA, ... However, there are studies which suggest that retro-transposable elements such as short-interspersed nuclear elements are not ... SINEs nonetheless depend on enzymes coded by other DNA elements and are thus known as non-autonomous retrotransposons as they ...
DNA - DNA fragmentation - DNA replication - DNA sequence - DNA topology - DNA transposable element - DNA virus - DNA-binding ... RNA-directed DNA polymerase - rod outer segment - rough ER sarcoplasmic reticulum - satellite DNA - scientific notation - SDS- ... element - element symbol - ELISA - ELISPOT - embryo - embryonal development - emulsion - endergonic reaction - endodermis - ... cyclic AMP-responsive DNA-binding protein - cyclic electron flow - cyclic nucleotide - cyclic peptide - cyclin - cyclin A - ...
For example, transposable elements containing a marker are mobilized into the genome at random. These transposons are often ... When DNA absorbs short wave UV light, dimerizing and oxidative mutations can occur which can cause severe damage to the DNA ... transposable elements). Subsequent breeding takes place, mutant individuals are isolated, and then the gene is mapped. Forward ... Since a known fragment of DNA was inserted this can make mapping and cloning the gene much easier. Once mutagenized and ...
The transposable P elements, also known as transposons, are segments of bacterial DNA that are translocated into the genome, ... P elements are administered in pairs of two, which flank the DNA insertion region of interest. Additionally, P elements often ... which shows improved transgene insertion of large DNA fragments that are unable to be transposed by P elements alone. This ... biolistics which is the procedure of shooting DNA bullets into cells, and also delivering DNA into the egg that has just been ...
... transposable elements, cell type (deconvolution) and the presence of neoantigens. Prior to RNA-Seq, gene expression studies ... cDNA synthesis: RNA is reverse transcribed to cDNA because DNA is more stable and to allow for amplification (which uses DNA ... next-gen sequencing of complementary DNA (cDNA), notably RNA-Seq. The general steps to prepare a complementary DNA (cDNA) ... Variant calling in RNA-Seq is similar to DNA variant calling and often employs the same tools (including SAMtools mpileup and ...
Kazazian's book Mobile DNA: Finding Treasure in Junk (2011) gives an overview of research on transposable elements. It does a " ... Lab member Hagop Youssoufian found a long interspersed nuclear element (LINE) insertion, a mobile DNA element or transposon ... The Kazazian lab was the first to discover a jumping gene in humans, and to demonstrate that a transposable element caused ... Feschotte, Cédric (3 October 2012). "Review of Mobile DNA - finding treasure in junk by Haig H Kazazian". Mobile DNA. 3 (1): 16 ...
This includes the discovery of transposable elements and illumination of their evolutionary history. Bartolomé et al 2009 find ... A majority of the genome is under selection of some sort, and a supermajority of this is occurring in non-coding DNA. Effective ... Gilbert, Clément; Peccoud, Jean; Cordaux, Richard (2021-01-07). "Transposable Elements and the Evolution of Insects" (PDF). ... Melanin's ability to protect DNA against ionizing radiation has been most extensively demonstrated in Drosophila, including in ...
His graduate work focused on studying transposable elements in plants. Dan then worked as a postdoctoral fellow at Johns ... Plant Physiol 161: 1-8 Baller J.A., Gao J. and Voytas D.F. (2011) Access to DNA establishes a secondary target site bias for ... 32(9):886-7. Baltes N.J., Gil-Humanes J., Cermak T., Atkins P.A. and Voytas D.F. (2014) DNA Replicons for Plant Genome ... Dan is best known for his pioneering work to develop methods for precisely altering DNA sequences in living cells, enabling ...
"Inhibition of RNA Interference and Modulation of Transposable Element Expression by Cell Death in Drosophila". This paper ... The DNA-damaged larvae (or the adults into which they develop) are then screened for mutations. When a phenotype of interest is ... "Inhibition of RNA Interference and Modulation of Transposable Element Expression by Cell Death in Drosophila". Genetics. 188 (4 ... Bushy, Daniel; John Locke (November 1, 2004). "Mutations in Su(var)205 and Su(var)3-7 Suppress P-Element-Dependent Silencing in ...
June 2010). "Comparative analysis of transposable element vector systems in human cells". Molecular Therapy. 18 (6): 1200-9. ... Several different mobile host DNA insertions have been identified within the few-polyhedra (FP) locus of the baculoviruses ... Both of these elements are part of a larger family of TTAA-target site specific insertion elements that includes the T. ni ... These elements were originally defined in the Cabbage Looper, but appear to be common among other animals as well. They might ...
Matthews et al., 2018 finds A. aegypti to carry a large and diverse number of transposable elements. Their analysis suggests ... The effort in sequencing its DNA was intended to provide new avenues for research into insecticides and possible genetic ... AC with 0 elements, Aedes, Insects described in 1762, Dengue fever, Insect vectors of human pathogens, Yellow fever, ... based on mitochondrial DNA variations". Genetics Research. 86 (1): 1-11. doi:10.1017/S0016672305007627. PMID 16181519. Eisen, L ...
However, analysis of transposable element insertions supports a three-way top-level split between Xenarthra, Afrotheria and ... 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 ... If a particular piece of mitochondrial DNA mutates randomly every few million years, it will have changed several times in the ...
Further development in integration site preferences of transposable elements is expected to advance the technologies of human ... Transposase acts like DNA scissors; it is an enzyme that cuts through double-stranded DNA to remove the transposon, then ... The formation of the transposition complex In this step the DNA bends and folds into a pre-excision synaptic complex so the two ... Both the excision and insertion of the transposon leaves single or double stranded gaps in the DNA, which are repaired by host ...
Examples of such elements include plasmids, transposable genetic elements, and genomic islands, which can be transferred ... The DNA sequences bound by mecI and blaI are identical; therefore, blaI can also bind the mecA operator to repress ... Owing to the size of the SCCmec element and the constraints of horizontal gene transfer, a minimum of five clones are thought ... The arginine catabolic mobile element (ACME) is a virulence factor present in many MRSA strains but not prevalent in MSSA. SpeG ...
The repeated DNA sequence includes short repetitive sequences, transposable elements (including insertion sequence elements, ... miniature inverted-repeat transposable elements, a Group II intron), and a greatly amplified integrative and conjugative ... DNA analyses have shown that the GroES and GroEL genes are indeed present in O. tsutsugamushi with slight variation in ... With a genome of only 2.0-2.7 Mb, it has the most repeated DNA sequences among bacterial genomes sequenced so far. The disease ...
... begins by transducing[clarification needed] bacterial populations with transposable elements[ ... fragmented DNA including the left and right transposon and 16 base pair of surrounding genomic DNA is produced. The 16 base ... use a DNA shearing[clarification needed] technique that produce a range of PCR product sizes that could cause shorter DNA ... After transduction, the DNA is cleaved[clarification needed] and the inserted sequence amplified through PCR. The recognition ...
This research prompted the first discovery of a transposable element, and from there transposon mutagenesis have been exploited ... After introducing 9-base pair 5' ends in target DNA, the transposon and its incorporated genes are inserted into the target DNA ... Transposons as a genetic tool Transposable element Transposase Barbara McClintock "Feeding hungry mouths". Biotechnology ... The same enzymatic catalytic site which cleaved the DNA is responsible for integrating the DNA into the genome, duplicating the ...
Hypomethylation of DNA can lower genomic stability, induce the reactivation of transposable elements, and cause the loss of ... DNA methylation uses the structure of dna at different stages of life to determine an age. DNA methylation is the methylation ... In other words, the more "tightly" held the DNA region then the more stable and "younger" the species. Looking at DNA ... Horvath S (2013). "DNA methylation age of human tissues and cell types". Genome Biology. 14 (10): R115. doi:10.1186/gb-2013-14- ...
... the movement of transposable elements (or retrotransposons) or deletions, among other genetic changes. Genomics offers insight ... Studying the noncoding DNA of domesticated species is made possible by genomics, which provides the genetic sequence of the ... However, looking solely at genes, or coding DNA, can be ineffective when examining certain traits or studying the evolution of ... Since core genes are conserved between and among species, examining DNA sequences for these genes in multiple individuals of a ...
Transposable Elements & Genome Stability Peter Baumann: Chromosome Dynamics, Telomeres & Ageing Petra Beli: Chromatin Biology ... Current joint Research Initiatives: The SFB 1361 on "Regulation of DNA Repair and Genome Stability" funded by the DFG The " ... "IMB starts international PhD program on "Dynamics of Gene Regulation, Epigenetics and DNA Damage Response"". www.uni-mainz.de. ... "IMB starts international PhD program on "Dynamics of Gene Regulation, Epigenetics and DNA Damage Response"". www.uni-mainz.de. ...
Cohen, Stanley N.; Shapiro, James A. (1980). "Transposable Genetic Elements" (PDF). Scientific American. 242 (2): 40-49. ... Next, the frog DNA fragments were combined with the plasmid, which had also been cleaved with EcoRI. The sticky ends of the DNA ... He was vocal in the recombinant DNA controversy as the United States government attempted to develop policies for DNA research ... Government efforts resulted in the creation of the Recombinant DNA Advisory Committee and the publication of Recombinant DNA ...
... is a transposable element, which is a sequence of DNA that is capable of mediating its own movement from one position in ... Mobile DNA II. Washington, D.C.: American Society for Microbiology. pp. 457 - 483. (DNA mobile genetic elements). ... The transposase protein recognizes the ends of the element and cuts it from the original locus. The protein-DNA complex then ... Two comprehensive reviews of Tn10 biology are available as chapters in the book Mobile DNA and Mobile DNA II. Bender J, ...
We conclude that the targets of both DNA methylation and histone H3K9 methylation pathways are transposable elements genome- ... Our findings also suggest that RNA-directed DNA methylation is required to silence isolated elements that may be too small to ... CMT3 and KYP targets show similar proximal distributions that correspond to the overall distribution of transposable elements ... Thus, parallel pathways would be needed to maintain silencing of transposable elements. ...
Pilot sequencing of onion genomic DNA reveals fragments of transposable elements, low gene densities, and significant gene ...
... we studied the overlap of its active developmental enhancers with transposable element … ... DNA Transposable Elements / genetics* * Databases, Genetic * E1A-Associated p300 Protein / metabolism * Embryo, Mammalian ... A family of transposable elements co-opted into developmental enhancers in the mouse neocortex Nat Commun. 2015 Mar 25;6:6644. ... we studied the overlap of its active developmental enhancers with transposable element (TE) families and compared this overlap ...
DNA Transposable Elements1. *DNA, Recombinant1. *Guidelines as Topic1. *Long Interspersed Nucleotide Elements1 ... Nucleic Acids, the Genetic Code, and Transposable Genetic Elements: A Life in Research1 ... Nucleic Acids, the Genetic Code, and Transposable Genetic Elements: A Life in Research ... 2. A Summary of the National Institutes of Health (USA) Guidelines for Recombinant DNA Research Format: Text ...
Transposable elements (TEs) are mobile DNA and constitute approximately half of the human genome. LINE-1 (L1) is the only ... We observed significantly (p,0.05) lower L1 mRNA expression, higher L1 DNA methylation, and less L1 DNA in accessible chromatin ... T3 was two doses of DNA vector followed by two doses of NYVAC vector and gp120 Env protein; and T4 was two doses of DNA vector ... We aimed to assess the safety and immunogenicity of a multivalent HIV vaccine including either DNA or NYVAC vectors alone or in ...
Transposable elements. all mobile DNA segments in the genome.. Transposase. enzyme encoded by transposon that catalyzes their ... These genetic elements were thought to be largely deleterious. However, when coupled with alternative splicing, there appears ... movement of a genetic element from one location of the genome to another. ...
epigenomics (sRNA/DNA methylation) - Population genomics of transposable elements Bio. - 2018 to present / Doctoral researcher ... mainly transposable elements, and their regulatory epigenetic mechanisms. These elements are drivers of genome size in ... Transposable Elements - Long-read sequencing Bio. - 2021 to present / PhD student / Max Planck Institute for Biology Tübingen ... DNA methylation and histone modification patterns lead to chromatin alteration. These marks are involved in transposable ...
Instead, nearly every element of transposon biology has been integrated into host biology. Here we review how host genome ... DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat. ... Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat. Genet. 42, 631-634 (2010). ... Specific subfamilies of transposable elements contribute to different domains of T lymphocyte enhancers. Proc. Natl Acad. Sci. ...
Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends Ecol Evol. ... bats and poxviruses may also serve as facilitators in the horizontal transfer of transposable elements to other species (4-6). ... Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods. Proc Natl Acad Sci U S A. 2008;105:17023-8 . ... Chordopoxviridae is a subfamily of Poxviridae that contains large double-stranded DNA viruses that replicate in the cellular ...
Transposable elements (TEs) are mobile DNA and constitute approximately half of the human genome. LINE-1 (L1) is the only ... Terms: DNA or Deoxyribonucleic acid OR DNA or Deoxyribonucleic acid 43 - 43 of 582 Bibliographic entries ... We observed significantly (P < 0.05) lower L1 mRNA expression, higher L1 DNA methylation, and less L1 DNA in accessible ... Thereafter, mixed gastrocnemius tissue was harvested and analyzed for L1 mRNA expression and DNA content along with other L1 ...
Harbinger; DNA transposon; Transposable Element; Interspersed repeat; Harbinger2; Harbinger2-2_TMe Source: Tuber melanosporum ... Harbinger2-2_TMe belongs to a novel clade, Harbinger2, of Harbinger DNA transposons. This clade includes transposons present in ...
About half of the mammalian genome comprises transposable elements. Given their repetitive nature, reads associated with these ... This enables the identification of transposable element interaction profiles for individual ERV families and integration events ... providing a powerful tool for uncovering the individual transposable element insertions that interact with and potentially ... elements are generally discarded or randomly distributed among elements of the same type in genome-wide analyses. Thus, it is ...
... explains what these mobile genetic elements are, how they are more harmful than benign and where their weaknesses may lie. ... The flowers showy color patterns are due to transposable elements, or DNA sequences that can move locations within a genome. ... Q. Transposons are mobile genetic elements. How and why do they move?. There are two main groups: DNA transposons move using ... You can think of transposons as viruses -there are some viruses that are, in fact, transposable elements. HIV (human ...
DNA Transposable Elements Medicine & Life Sciences 77% * Diptera Medicine & Life Sciences 65% ... Carr, M. (2008). Multiple subfamilies of mariner transposable elements are present in stalk-eyed flies (Diptera: Diopsidae). ... Carr, M 2008, Multiple subfamilies of mariner transposable elements are present in stalk-eyed flies (Diptera: Diopsidae), ... Multiple subfamilies of mariner transposable elements are present in stalk-eyed flies (Diptera: Diopsidae). Genetica. 2008 Feb ...
Chromosome structure and transposable elements. Mutation and DNA repair. Genomics and proteomics. Organelle genomes. ... Chemical nature of DNA. Replication transcription, RNA processing and translation. Control of gene expression in prokaryotes ... The chemistry of the important plant nutrient elements P, K and N is explained. ...
Transposable elements were once considered junk DNA with little or no function. Now it appears that they may be one of the ... These genetic gaps have primarily been caused by the activity of retroviral-like transposable element sequences, said McDonald ... 1) actually there is no proof that DNA is the unique cause of the formation of a certain species. It is likely that many other ... of regulatory elements in DNA segments that are regarded as promoter regions.. The researchers presentation is titled, Genome- ...
AT-low complexity regions and mobile DNA elements. The genomic k-mers distribution and CpG rate of C. cardunculus, compared ... RAD tags were sequenced from the genomic DNA of three C. cardunculus mapping population parents, generating 9.7 million reads, ... approach with the Illumina DNA sequencing platform to effect the rapid and mass discovery of SNP markers for C. cardunculus. ... We have combined the recently developed restriction-site associated DNA (RAD) ...
... is characterized by a bi-directional genome size evolution resulting in a 25-fold difference in nuclear DNA content. This is ... is characterized by a bi-directional genome size evolution resulting in a 25-fold difference in nuclear DNA content. This is ... Repetitive DNA, such as tandem repeats and transposable elements, constitutes a considerable part of plant genomes (Lopez- ... TABLE 1. Primer combinations used to amplify unique and repeated DNA elements of Genlisea nigrocaulis (Gn) and G. hispidula (Gh ...
DNA hypomethylation promotes transposable element expression and activation of immune signaling in renal cell cancer Authors: ...
The P-element, a DNA-based transposable element, recently invaded two Drosophila species: D. melanogaster in the 20th century, ... Transposable elements (TEs) are genomic parasites that proliferate within host genomes, and can also invade new species. ... a syndrome of abnormal phenotypes that are due to P-element inflicted DNA damage. In D. melanogaster, lines collected after the ... element damage and expression of maternal P-element piRNAs, or other known factors influencing hybrid dysgenesis, suggesting ...
... and the recently discovered high rates of remobilization of endogenous transposable elements. These findings are discussed in ... and the recently discovered high rates of remobilization of endogenous transposable elements. These findings are discussed in ... and the recently discovered high rates of remobilization of endogenous transposable elements. These findings are discussed in ... and the recently discovered high rates of remobilization of endogenous transposable elements. These findings are discussed in ...
DNA hypomethylation promotes transposable element expression and activation of immune signaling in renal cell cancer. JCI ... DNA Repair (Amst). 2020 Feb;86:102754. PMID:31794893.. Chen L, Vasoya RP, Toke NH, Parthasarathy A, Luo S, Chiles E, Flores J, ... DNA polymerase η mutational signatures are found in a variety of different types of cancer. Cell Cycle. 2018;17(3):348-355. ... Mahdi AH, Huo Y, Tan Y, Simhadri S, Vincelli G, Gao J, Ganesan S, Xia B. Evidence of Intertissue Differences in the DNA Damage ...
She examined the role of transposable elements (TE)-DNA sequences that move from one location on the genome to another-in the ...
DNA Transposable Elements; Cloning, Molecular; Transformation, Bacterial; Amino Acid Sequence; Oxidation-Reduction; Phenotype; ...
This research led to innovative methods of DNA sequencing that revealed integration behavior of transposable elements. With ... The biological impact of transposable elements. Transposable elements were highly active throughout evolution resulting in ... Transposable element insertions in fission yeast drive adaptation to environmental stress. Genome Res. 2019;29(1):85-95. ... Recent work relies on the vast databases of human genetics to understand the role of transposable elements in human disease. ...
In C. fontanae, up to 40 chromosomes were identified to bear a part of the major ribosomal DNA, while in C. albula only 8-10 ... These experiments showed a clear co-localization of the ribosomal DNA and the retrotransposon Rex1 in a pericentromeric region ... We provide indirect evidence that ribosomal DNA probably utilized the spreading mechanism of retrotransposons subsequently ... experiments consistently revealed a distinct variation in the copy number of loci of the major ribosomal DNA (the 45S unit) ...
... ranging from rDNA and microsatellites to transposable elements. Of particular interest to us is how these repeats contribute to ... In addition to repetitive DNA, we also study the evolution of introns and novel genes (orphans). ... The laboratory has a long-standing interest in the evolution of repetitive DNA, ...
... and post insertion changes like inter or intra element recombination, disruption etc. Although such changes have been studied ... of multiple whole genome sequences has facilitated in silico identification of fixed and polymorphic transposable elements (TE ... Mobile or transposable elements (TEs) are DNA sequences that have the ability to hop (transpose) in the genome, within their ... Recurrent recruitment of the THAP DNA-binding domain and molecular domestication of the P-transposable element. Mol Biol Evol ...
A study suggests that the direct transfer of DNA methylation marks from one generation to the next is much less common than ... All of the mutant mice have a gene, Agouti, that influences coat color, and an adjacent transposable element-a DNA sequence ... The screen did identify one transposable element that, like the element abutting the Agouti gene, displayed a bit of memory, ... The screen identified dozens of these transposable elements but revealed that only rarely do they work as promoters to control ...
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. ... Errors introduced during DNA repair[edit]. See also: DNA damage (naturally occurring) and DNA repair ... or extrachromosomal DNA.[1] Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral ...
  • For example, in Neurospora , DNA methylation occurs at repeated sequences that are targeted for point mutation [ 5 ]. (biomedcentral.com)
  • 2) also if #1 is ok, 98.6% genomic identity between chimp and human (= 22.4 million DNA bases) is highly debatable, because genomic comparison can be done in many different ways and depends on many presuppositions. (blogspot.com)
  • RAD tags were sequenced from the genomic DNA of three C. cardunculus mapping population parents, generating 9.7 million reads, corresponding to ~1 Gbp of sequence. (biomedcentral.com)
  • Transposable elements (TEs) are genomic parasites that proliferate within host genomes, and can also invade new species. (bl.uk)
  • To determine mechanisms how such extensive genome alternation might have arisen, a PCR screening for retrotransposons from genomic DNA of both species was performed. (biomedcentral.com)
  • Does your genomic DNA contains a transposable element that does not contain any recombinant and/or synthetic nucleic acids? (stanford.edu)
  • Tagmentation-based mapping (tagmap) of mobile DNA genomic insertion sites. (janelia.org)
  • 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. (janelia.org)
  • Sequences were identified corresponding to the tRNA (pro) primer binding site in genomic RNA and the reverse-transcribed minus strong stop DNA. (princeton.edu)
  • In particular, we focus on the recent studies implicating DNA transposases RAG1/2 and PGBD5 as oncogenic mutators that promote genomic rearrangements in childhood leukemias and solid tumors. (mdc-berlin.de)
  • Most 24-nt siRNAs are dependent on RNA Pol IV and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and establish DNA methylation at thousands of genomic loci in a process called RNA-directed DNA methylation (RdDM). (nsf.gov)
  • 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)
  • Feschotte, C. & Pritham, E. J. DNA transposons and the evolution of eukaryotic genomes. (nature.com)
  • Harbinger2-2_TMe belongs to a novel clade, Harbinger2, of Harbinger DNA transposons. (girinst.org)
  • 4Tran provides new insight into the manner in which transposons contribute to chromosome architecture and identifies target genes that transposable elements can potentially control. (springer.com)
  • These mobile elements, which have been propagated in the genomes of all eukaryotic species, can be classified as either DNA transposons or retrotransposons, depending on their mode of transposition. (springer.com)
  • DNA transposons propagate via a cut and paste mechanism while retrotransposons use a copy and paste mode of action that relies on an RNA intermediate [ 21 ]. (springer.com)
  • Brown researcher John Sedivy, lead author of a sweeping review article about transposons, explains what these mobile genetic elements are, how they are more harmful than benign and where their weaknesses may lie. (brown.edu)
  • As researchers learn more about these so-called mobile genetic elements, they've found increasing evidence that transposons influence and even promote aging and age-related diseases like cancer as well as neurogenerative and autoimmune disorders, says John Sedivy, a professor of biology and director of the Center on the Biology of Aging at Brown . (brown.edu)
  • Since the dawn of life, the researchers noted, transposons have coevolved with their host genomes, but it's been more of a competitive existence than a peaceful one, earning them the nicknames of "junk DNA" and "molecular parasites. (brown.edu)
  • Q. Transposons are mobile genetic elements. (brown.edu)
  • There are two main groups: 'DNA transposons' move using a DNA intermediate in a 'cut and paste' mechanism, and retrotransposons move using a 'copy and paste' mechanism that involves an RNA intermediate. (brown.edu)
  • You can think of transposons as viruses -there are some viruses that are, in fact, transposable elements. (brown.edu)
  • Q. Scientists have known about these rogue genetic elements for awhile, but transposons are an increasingly important area of study. (brown.edu)
  • Hackett, PB , Starr, TK & Cooper, LJN 2015, Risks of Insertional Mutagenesis by DNA Transposons in Cancer Gene Therapy . (umn.edu)
  • Cooper, Laurence J.N. / Risks of Insertional Mutagenesis by DNA Transposons in Cancer Gene Therapy . (umn.edu)
  • Based on the mechanism of transposition [reviewed in [ 5 ]], TEs are broadly divided into two classes - Class I or Retrotransposons and Class II or DNA transposons. (biomedcentral.com)
  • Sequences of DNA that can move about the genome, such as transposons , make up a major fraction of the genetic material of plants and animals, and may have been important in the evolution of genomes. (wikipedia.org)
  • Transposable elements (TEs), also known as "jumping genes" or transposons, are sequences of DNA that move (or jump) from one location in the genome to another. (thecreationclub.com)
  • Maize geneticist Barbara McClintock discovered TEs in the 1940s, and for decades thereafter, most scientists dismissed transposons as useless or "junk" DNA. (thecreationclub.com)
  • Capy, P. Taming, domestication and exaptation: trajectories of transposable elements in genomes. (nature.com)
  • Although poxviruses are known to have incorporated host genes into their genomes to subvert the host immune system ( 3 ), bats and poxviruses may also serve as facilitators in the horizontal transfer of transposable elements to other species ( 4 - 6 ). (cdc.gov)
  • This enables the identification of transposable element interaction profiles for individual ERV families and integration events specific to particular genomes. (springer.com)
  • When these elements move from one chromosome or part of a chromosome to another, they amplify and increase their presence in genomes, sometimes to dramatic levels. (brown.edu)
  • Fluorescence in situ hybridization (FISH) experiments consistently revealed a distinct variation in the copy number of loci of the major ribosomal DNA (the 45S unit) between C . albula and C . fontanae genomes. (biomedcentral.com)
  • We provide indirect evidence that ribosomal DNA probably utilized the spreading mechanism of retrotransposons subsequently affecting recombination rates in both genomes, thus, leading to a rapid genome divergence. (biomedcentral.com)
  • TEs represent miniature genomes with a versatile repertoire of cis regulatory elements and/or trans acting factors. (biomedcentral.com)
  • In a series of experiments examining the T cells and B cells of multiple generations of Agouti Viable Yellow mice, the researchers screened the animals' genomes searching for transposable elements that were methylated similarly to the one that sits next to the Agouti gene. (the-scientist.com)
  • [1] Viral genomes contain either DNA or RNA . (wikipedia.org)
  • 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. (janelia.org)
  • Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. (ttu.edu)
  • Repetitive DNA, especially the remnants of transposable elements , makes up a large fraction of many genomes, especially eukaryotic . (wordpress.com)
  • Transposable elements (TEs) are mobile DNA fragments that amplify within genomes, sometimes inserting within or near genes. (southcoastbiosciencesdtp.ac.uk)
  • By the mid-1990s, the extraordinary advances in DNA cloning, amplification and sequencing had made feasible the mapping and sequencing of whole genomes. (taylorfrancis.com)
  • Different classes of transposable element and retroviral-derived sequences were characterized in plant and animal genomes and shown to be major drivers of phenotypic innovation. (taylorfrancis.com)
  • The experts analyzed the genomes of five asexual Timema species and of closely related sexual species, and compared their transposable element contents (DNA sequences that can change their position within a genome), genes evolving under positive selection and heterozygosity. (sib.swiss)
  • But the real thrust of the book is to get up to date with contemporary achievements in sequencing genomes and creating transgenic entities i.e. organisms which have had the DNA of completely separate organisms stitched into them. (wordpress.com)
  • van de Lagemaat, L. N., Landry, J.-R., Mager, D. L. & Medstrand, P. Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. (nature.com)
  • In contrast to 4Tran-PCR, Capture-4Tran can uniquely identify both ends of an interaction that involve retroviral repeat sequences, providing a powerful tool for uncovering the individual transposable element insertions that interact with and potentially regulate target genes. (springer.com)
  • In C . fontanae , up to 40 chromosomes were identified to bear a part of the major ribosomal DNA, while in C . albula only 8-10 chromosomes possessed these genes. (biomedcentral.com)
  • In addition to repetitive DNA, we also study the evolution of introns and novel genes (orphans). (vetmeduni.ac.at)
  • The screen identified dozens of these transposable elements but revealed that only rarely do they work as promoters to control the expression of adjacent genes. (the-scientist.com)
  • [8] Due to the damaging effects that mutations can have on genes, organisms have mechanisms such as DNA repair to prevent or correct mutations by reverting the mutated sequence back to its original state. (wikipedia.org)
  • [16] [17] Other types of mutation occasionally create new genes from previously noncoding DNA . (wikipedia.org)
  • [23] Another effect of these mobile DNA sequences is that when they move within a genome, they can mutate or delete existing genes and thereby produce genetic diversity. (wikipedia.org)
  • TOM BUREAU SPECIALIZES IN DETECTIVESTYLE PLANT GENOMICS: he examines the little-understood elements in between genes called non-coding DNA and also meticulously documents plant growth to find defects caused by the suppression of a single gene. (mcgill.ca)
  • the rest is stuff in between the genes that we refer to as non-coding DNA heavily populated by transposable elements. (mcgill.ca)
  • Recently, though, there has been a lot of interest in these elements because a subset of them does appear to have a function, especially in the regulation of genes. (mcgill.ca)
  • Plant breeders are starting to realize that non-coding DNA could be quite important agriculturally, and our counterparts in the human genomics world are in the same place: there are many known diseases where the genes are not defective but their regulation is being changed. (mcgill.ca)
  • McClintock, however, was among the first researchers to suggest that these mysterious mobile elements of the genome might play some kind of regulatory role, determining which genes are turned on and when this activation takes place. (thecreationclub.com)
  • Age and sex effects on DNA methylation sites linked to genes implicated in severe COVID-19 and SARS-CoV-2 host cell entry. (uu.se)
  • Homologs of the myc and max genes were cloned from the fruit fly Drosophila melanogaster and their protein products (dMyc and dMax) were shown to heterodimerize, recognize the same DNA sequence as their vertebrate homologs, and activate transcription. (fhcrc.org)
  • Accordingly, gene bodies of protein-coding genes had intermediate H3K23me1 levels, which coexisted with CG DNA methylation. (diagenode.com)
  • Researchers established that genes shown in native cells lap over genes shown in the blastocyst, all the same the cells transposable-element profile coincide with one another being blastocyst, and prior developmental stage. (studydriver.com)
  • In other words, up to 90% of the DNA-bound RNA polymerase is not transcribing protein-coding genes. (science20.com)
  • We have determined the DNA sequence of two fragments which complement mutations in the SIR2 and SIR3 genes and show that these contain the structural genes by mapping the cloned sequences onto the yeast chromosome. (ox.ac.uk)
  • DNA methylation occurs at preferred sites in eukaryotes. (biomedcentral.com)
  • In Arabidopsis , DNA cytosine methylation is maintained by three subfamilies of methyltransferases with distinct substrate specificities and different modes of action. (biomedcentral.com)
  • We find an inverse relationship between element size and loss of methylation in ago4 and drm mutants. (biomedcentral.com)
  • We conclude that the targets of both DNA methylation and histone H3K9 methylation pathways are transposable elements genome-wide, irrespective of element type and position. (biomedcentral.com)
  • Our findings also suggest that RNA-directed DNA methylation is required to silence isolated elements that may be too small to be maintained in a silent state by a chromatin-based mechanism alone. (biomedcentral.com)
  • DNA cytosine methylation is an ancient process, found in both prokaryotes and eukaryotes, and catalyzed by a single family of methyltransferases [ 1 ]. (biomedcentral.com)
  • In prokaryotes, cytosine-5 methyltransferases protect target sites from cleavage by partner restriction endonucleases, but in eukaryotes, the function of DNA methylation is less clear. (biomedcentral.com)
  • In fungi and plants, however, the localized nature of DNA methylation makes it possible to identify sequences that are targeted for DNA methylation. (biomedcentral.com)
  • An additional form of DNA methylation is found in the model plant Arabidopsis , where short dense CG methylation clusters are occasionally found in genic regions that are otherwise devoid of methylation [ 8 ]. (biomedcentral.com)
  • Although many DNA methylation targets are known, it has been unclear how these sites are recognized by DNA methyltransferases. (biomedcentral.com)
  • however, the mechanism by which siRNA production leads to de novo DNA methylation is not known. (biomedcentral.com)
  • Another open question is how some forms of DNA methylation are maintained during rounds of cell division. (biomedcentral.com)
  • In the case of CG sites, a member of the Dnmt1 subfamily of DNA methyltransferases maintains methylation by specifically methylating hemi-methylated sites behind the replication fork [ 15 ], but in cases of non-CG methylation, there does not appear to be a comparable reaction. (biomedcentral.com)
  • Non-CG methylation in Neurospora is maintained by the action of a histone H3 lysine-9 (H3K9) methyltransferase [ 5 ], so the successive action of a histone methyltransferase and a DNA methyltransferase suffices to maintain methylation indefinitely. (biomedcentral.com)
  • We observed significantly (P DNA methylation, and less L1 DNA in accessible chromatin regions in EX versus SED rats. (cdc.gov)
  • However, this effect was not facilitated through increased L1 DNA methylation. (cdc.gov)
  • The RAD sequence has also been informative for characterizing the repetitive DNA component of the C. cardunculus genome, in particular allowing some inferences to be made regarding the contribution of DNA methylation in inhibiting its expansion. (biomedcentral.com)
  • A study suggests that the direct transfer of DNA methylation marks from one generation to the next is much less common than scientists previously thought. (the-scientist.com)
  • ABOVE: Agouti Viable Yellow mice share the same DNA sequence, but have different methylation patterns. (the-scientist.com)
  • To dig into the problem experimentally, Ferguson-Smith and her colleagues decided to rigorously test the idea that transposable elements act generally as gene promoters and that the methylation marks on these elements could be passed from one generation to the next. (the-scientist.com)
  • Researchers have postulated that transposable elements may have methylation marks resistant to reprogramming-so, in theory, these marks should be most likely to be inherited. (the-scientist.com)
  • The methylation marks on these transposable elements are also wiped clean and reprogrammed after fertilization, the team found, meaning they can't be directly passed from generation to generation ( Cell , 175:1259-71.e13, 2018). (the-scientist.com)
  • In the past, researchers suggested that the epigenetically regulated Agouti trait was the tip of the iceberg for DNA methylation-based epigenetic inheritance, he says. (the-scientist.com)
  • The screen did identify one transposable element that, like the element abutting the Agouti gene, displayed a bit of memory, Ferguson-Smith says, "but our data suggested that memory is not being conferred by DNA methylation. (the-scientist.com)
  • The researchers could see that methylation marks on this transposable element were erased between generations, and reestablished again in a form reminiscent of what was found in the parental generation. (the-scientist.com)
  • Methylmercury-induced DNA methylation-From epidemiological observations to experimental evidence. (uu.se)
  • In transposable elements it co-localized with CG, CHG and CHH DNA methylation as well as with the heterochromatic histone mark H3K9me2. (diagenode.com)
  • The histone methyltransferase KRYPTONITE and normal DNA methylation were required for normal levels of H3K23me1 on transposable elements. (diagenode.com)
  • We also identified new substrates for the other three RDRs (RDR1, RDR2, and RDR6) as well as the RDR2 cofactor RNA-directed DNA methylation 12 (RDM12) and the RDR6 cofactor suppressor of gene silencing 3 (SGS3). (nsf.gov)
  • With a new focus on the regulation of gene expression, Theunissen turned to chemical modification to the DNA called methylation. (studydriver.com)
  • Early embryos, saw a genome-wide DNA methylation levels decreasing dramatically compared to those in the egg and sperm, extending smidgen about the blastocyst. (studydriver.com)
  • Treat ment in the parental UROtsa cells with five AZC, a com monly employed agent to find out DNA methylation standing, was proven to possess no impact on MT 3 mRNA expres sion. (hifpathway.com)
  • A transposable element (TE, transposon, or jumping gene) is a nucleic acid sequence in DNA 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)
  • Instead, nearly every element of transposon biology has been integrated into host biology. (nature.com)
  • Fig. 2: Transposon-derived gene regulatory elements diversify host gene isoforms and enrich expression regulation modality. (nature.com)
  • These include duplication of target site, 3' and 5' flank transduction, deletion of the target locus, 5' truncation or partial deletion and inversion of the transposon, and post insertion changes like inter or intra element recombination, disruption etc. (biomedcentral.com)
  • Discrete and heterogeneous high molecular weight RNAs complementary to a long dispersed repeat family (a possible transposon) of human DNA. (wikidata.org)
  • TnCentral: a Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis. (cdc.gov)
  • Recent work relies on the vast databases of human genetics to understand the role of transposable elements in human disease. (nih.gov)
  • Garcia-Perez, J. R., Widmann, T. J. & Adams, I. R. The impact of transposable elements on mammalian development. (nature.com)
  • 3 Thus some evolutionists have often "blindly and rigidly" accepted the idea that transposable elements are selfish junk. (amos37.com)
  • 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)
  • These genetic elements were thought to be largely deleterious. (cell.com)
  • Gifford, W. D., Pfaff, S. L. & Macfarlan, T. S. Transposable elements as genetic regulatory substrates in early development. (nature.com)
  • They live in the genome, including the germline so that eggs and sperm carry these genetic elements and pass them along to future generations. (brown.edu)
  • In addition, Dr. Levin develops novel technologies that rely on transposable elements to characterize genetic function genome-wide. (nih.gov)
  • Mutations may also result from insertion or deletion of segments of DNA due to mobile genetic elements . (wikipedia.org)
  • Mutations can involve the duplication of large sections of DNA, usually through genetic recombination . (wikipedia.org)
  • Here, we review the physiologic functions and oncogenic activities of transposable genetic elements. (mdc-berlin.de)
  • 8 Others have argued that Alu elements serve as "molecular fossils," providing clues to genetic ancestry based on identical insertion points. (amos37.com)
  • About half of the mammalian genome comprises transposable elements. (springer.com)
  • A large portion of a typical mammalian genome is comprised of transposable elements (TEs) however they are typically ignored in high-throughput sequencing-based studies due to their repetitive nature [ 17 , 18 ]. (springer.com)
  • L1 elements are highly repeated mammalian DNA sequences whose structure suggests dispersal by retrotransposition. (nyu.edu)
  • Last month I explained how the difference in DNA sequence between chimps and humans corresponds to what we would predict from evolutionary theory. (blogspot.com)
  • The repetitive fraction of the genome had a high representation of retrotransposon sequence, followed by simple repeats, AT-low complexity regions and mobile DNA elements. (biomedcentral.com)
  • Current high throughput sequencing technology, which produces DNA sequence at a rate several orders of magnitude faster than conventional methods, is effective as a platform for SNP (single nucleotide polymorphism) discovery. (biomedcentral.com)
  • Transposable elements were highly active throughout evolution resulting in genome landscapes dominated by sequence repeats. (nih.gov)
  • All of the mutant mice have a gene, Agouti , that influences coat color, and an adjacent transposable element-a DNA sequence that can move about the genome, creating or reversing mutations-that promotes the gene's expression. (the-scientist.com)
  • In biology , a mutation is an alteration in the nucleic acid sequence of the genome of an organism , virus , or extrachromosomal DNA . (wikipedia.org)
  • 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. (janelia.org)
  • Short read sequencing starting from the adaptor sequence generates oriented reads that flank and are oriented toward the transposable element insertion site. (janelia.org)
  • If the cell reproduces, each of its progeny also has that DNA sequence. (thecreationclub.com)
  • A consensus L1 element encodes a protein with sequence similarity to known reverse transcriptases. (nyu.edu)
  • We determined the nucleotide sequence of both 588-base-pair TRS elements and the adjacent host and viral junctions of an integrated MSV cloned in bacteriophage λ. (princeton.edu)
  • Some similarities of TRS and prokaryotic insertion sequence elements are discussed. (princeton.edu)
  • For the first time the full complement of DNA sequence information in bacteria, simple eukaryotes, fungi, plants and animals began to be revealed, enabling comparative genomics to interrogate evolutionary relationships and functional indices at increasingly high resolution. (taylorfrancis.com)
  • Unusual domains of human alphoid satellite DNA with contiguous non-satellite sequences: sequence analysis of a junction region. (wikidata.org)
  • 5 An Alu element is a short sequence of DNA able to migrate throughout the genome. (amos37.com)
  • 18 Worse, Alu elements diverge up to twenty percent from the supposed human consensus sequence, making it questionable as to whether the similarities are truly shared anyway. (amos37.com)
  • Interestingly, this specificity factor is comparable to that observed for typical sequence-specific DNA-binding proteins binding a high-affinity site, as compared with a nonspecific site. (science20.com)
  • Enhancing rice grain production by manipulating the naturally evolved cis-regulatory element-containing inverted repeat sequence of OsREM20 . (cas.cn)
  • It is to the ribosome that transfer RNA (tRNA) brings along amino acids, which are then intricately assembled according to the sequence of bases found on the original DNA. (wordpress.com)
  • Professor Faulkner is a computational and molecular biologist with expertise in genomics and transposable elements and his team studies DNA changes to determine how they impact human biology. (alarabiya.net)
  • To gain insight into its evolution and the gene regulatory codes that pattern it, we studied the overlap of its active developmental enhancers with transposable element (TE) families and compared this overlap to uniformly shuffled enhancers. (nih.gov)
  • The monophyletic carnivorous genus Genlisea (Lentibulariaceae) is characterized by a bi-directional genome size evolution resulting in a 25-fold difference in nuclear DNA content. (frontiersin.org)
  • Surprisingly, however, these lines show no correlation between tolerance to P- element damage and expression of maternal P-element piRNAs, or other known factors influencing hybrid dysgenesis, suggesting mechanisms contribute to P-element suppression prior to the evolution of piRNA suppression. (bl.uk)
  • The laboratory has a long-standing interest in the evolution of repetitive DNA, ranging from rDNA and microsatellites to transposable elements. (vetmeduni.ac.at)
  • Satellitome comparison of two oedipodine grasshoppers highlights the contingent nature of satellite DNA evolution. (uu.se)
  • In-Depth Satellitome Analyses of 37 Drosophila Species Illuminate Repetitive DNA Evolution in the Drosophila Genus. (uu.se)
  • Since their discovery in maize in the 1950's, the roles and characteristics of transposable elements (TEs) have continued to be focal areas of research for their roles in genome evolution. (furman.edu)
  • Transposable elements become entrenched in the genome throughout evolution. (studydriver.com)
  • The analysis revealed insertional elements flanked by IS 481 , which has been previously regarded as the important component for bacterial evolution. (jgenomics.com)
  • A new study in Evolution Letters suggests that transposable elements are important for both developmental processes and evolutionary diversification in snakes and lizards. (extendedevolutionarysynthesis.com)
  • CMT3 and KYP targets show similar proximal distributions that correspond to the overall distribution of transposable elements of all types, whereas DRM targets are distributed more distally along the chromosome. (biomedcentral.com)
  • Changes in chromosome number may involve even larger mutations, where segments of the DNA within chromosomes break and then rearrange. (wikipedia.org)
  • Within each territory, the DNA of the chromosome is not spread out evenly. (thecreationclub.com)
  • The P-element, a DNA-based transposable element, recently invaded two Drosophila species: D. melanogaster in the 20th century, and D. simulans, in the 21st. (bl.uk)
  • Transposition of elements of the 412, copia and 297 dispersed repeated gene families in Drosophila. (wikidata.org)
  • Ribosomal insertion-like elements in Drosophila melanogaster are interspersed with mobile sequences. (wikidata.org)
  • Abstract Transposable elements (TEs) constitute over 90% of the wheat genome. (deepdyve.com)
  • Our current studies focus on the integration of transposable elements and how de novo insertion modifies host biology. (nih.gov)
  • 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)
  • Our focal region flanked the element in an area known as the terminal inverted repeats (TIRs). (furman.edu)
  • The Dnmt3 subfamily of DNA methyltransferases, which includes Arabidopsis DRM1 and DRM2, can methylate de novo [ 9 ], but there are no known sequences in common among target sites. (biomedcentral.com)
  • Chordopoxviridae is a subfamily of Poxviridae that contains large double-stranded DNA viruses that replicate in the cellular cytoplasm and are known to infect a wide range of vertebrates. (cdc.gov)
  • However, a recent study demonstrated that one set of transposable elements (the HERV-H subfamily) has a particularly interesting function, which indicates that a creation scientist's prediction I wrote about nine years ago has been confirmed. (thecreationclub.com)
  • Transposable element insertions in fission yeast drive adaptation to environmental stress. (nih.gov)
  • Further, the evolutionists admit there are thousands of Alu elements in humans that do not share similar locations with primate Alus, and assume they were post-divergence insertions. (amos37.com)
  • 1. Introduction Some DNA sequences possess the unique ability to move from one place in the genome to another, these sequences are usually termed transposable elements (TEs). (deepdyve.com)
  • One argument commonly associated with the parasitic DNA narrative is that humans and chimps share large quantities of similar DNA sequences, usually termed SINE and LINE elements. (amos37.com)
  • We are pleased to introduce Dfam 1.0 , a database of profile HMMs for repetitive DNA elements . (wordpress.com)
  • Short interspersed repetitive DNA elements in eucaryotes: transposable DNA elements generated by reverse transcription of RNA pol III transcripts? (wikidata.org)
  • We used a microarray-based profiling method to explore the involvement of Arabidopsis CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related siRNA silencing component (AGO4) in methylating target loci. (biomedcentral.com)
  • Transposable elements (TEs) are mobile DNA and constitute approximately half of the human genome. (cdc.gov)
  • Thirty five percent of the human genome is comprised of retrotransposon DNA sequences. (brown.edu)
  • Of particular interest are the Alu elements, a type of SINE that is estimated to make up about 11% of the human genome. (amos37.com)
  • It also suggests that certain transposable element bases remained conserved due to their role in transposition. (furman.edu)
  • 1) actually there is no proof that DNA is the unique cause of the formation of a certain species. (blogspot.com)
  • In both species, lines collected before the invasion are susceptible to 'hybrid dysgenesis', a syndrome of abnormal phenotypes that are due to P-element inflicted DNA damage. (bl.uk)
  • In this thesis, I study lines of D. simulans collected early and late in the invasion of the P-element in that species. (bl.uk)
  • These experiments showed a clear co-localization of the ribosomal DNA and the retrotransposon Rex1 in a pericentromeric region of one or two acrocentric chromosomes in both species. (biomedcentral.com)
  • Is your recombinant or synthetic nucleic acid molecule from species that naturally exchange DNA? (stanford.edu)
  • further explanation needed] 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)
  • A unified classification system for eukaryotic transposable elements. (nature.com)
  • Dr. Henry Levin is the head of the Section of Eukaryotic Transposable Elements. (nih.gov)
  • Repetitive sequences in eukaryotic DNA and their expression. (wikidata.org)
  • A single eukaryotic cell is a community, including organelles, such as mitochondria and chloroplast, transposable elements, and the 'host' DNA. (hadanylab.com)
  • We looked into their claims that the human cells and machinery turned COVID-19 RNA into DNA, causing permanent mutations," Professor Faulkner said. (alarabiya.net)
  • We assessed the claims in cells grown in the laboratory, conducted DNA sequencing and found no evidence of COVID-19 in DNA. (alarabiya.net)
  • He explains the central role of the ribosomes, which are the factories where protein synthesis takes place (typical human cells contain about a thousand ribosomes), and the role of messenger RNA in cutting off snippets of DNA and taking them to the ribosome. (wordpress.com)
  • The Cd 2 and As three transformed cell lines showed appreciable MTF one bind ing for the MREc element of your MT 3 promoter inside the absence Inhibitors,Modulators,Libraries of MS 275 when in contrast towards the parental UROtsa cells. (hifpathway.com)
  • There was no binding in the MTF one on the MREe, f, g elements from the MT 3 promoter for parental UROtsa cells unexposed to MS 275. (hifpathway.com)
  • This provides proof the MT 3 gene was not silenced by a mechanism involving DNA methyla tion while in the parental UROtsa cells. (hifpathway.com)
  • If the allele is associated with an insertion of DNA, the insertion symbol is displayed in this field. (flybase.org)
  • Polak, P. & Domany, E. Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes. (nature.com)
  • A yeast transposition assay was performed to identify successful transposition for each mutated base, as colonies only grow if the element transposes. (furman.edu)
  • Approximately half of human DNA comes to pass rom mobile sequences termed transposable elements. (studydriver.com)
  • P-element, a transposable-element based transgenic construct, e.g. (flybase.org)
  • Considering that DNA demethylation or hypermethylation of transposable element sequences is associated with their activation or silencing, respectively. (deepdyve.com)
  • The first one shows that the mutation rate can be estimated from the known properties of the DNA replication complex and repair mechanisms. (blogspot.com)
  • Coronavirus and DNA, virus mutation. (alarabiya.net)
  • Remember, every cell has the same DNA (barring some mutation or chimeric effect). (thecreationclub.com)
  • The element could not transpose when a conserved base was made unreadable through mutation. (furman.edu)
  • Our results show that MER130 elements were recruited, likely through their common regulatory logic, as neocortical enhancers. (nih.gov)
  • The regulatory sequences contained within transposable elements have been broadly dispersed to form gene regulatory networks important for many biological functions. (nih.gov)
  • By contrast, increased developmental complexity correlated with the extent of intronic and intergenic non-protein-coding DNA, indicating that phenotypic radiation and developmental sophistication in multicellular organisms is achieved mainly by regulatory expansion. (taylorfrancis.com)
  • In D. melanogaster, lines collected after the invasion have evolved a maternally acting mechanism that suppresses the effects of the P-element and therefore hybrid dysgenesis. (bl.uk)
  • Retrotransposons transpose via an RNA intermediate which is reverse transcribed and integrated into the genome, thereby duplicating the element (copy paste mechanism). (biomedcentral.com)
  • Is your synthetic nucleic acid designed to: (1) neither replicate nor generate nucleic acids that can replicate in any living cell, and (2) not integrate into DNA, and (3) not produce a toxin that is lethal for vertebrates at an LD50 of less than 100 nanograms per kilogram body weight? (stanford.edu)
  • Transfer of recombinant or synthetic nucleic acid molecules, or DNA or RNA derived from recombinant or synthetic nucleic acid molecules into human research participants. (stanford.edu)
  • Recently, multiple mechanisms of DNA damage and repair have been associated with mutations observed in human cancers. (mdc-berlin.de)
  • This level of fidelity is also similar to the frequency at which incorrect nucleotides or amino acids are incorporated into growing polymers of RNA and protein, although it is far below the 10-8-fold specificity seen for DNA replication, which depends on proofreading mechanisms. (science20.com)
  • P{lacW} , or exogenous DNA inserted via non-transposable element-based means (e.g. homologous recombination), e.g. (flybase.org)
  • Those who have their naturalist blinders on initially thought that they were useless-part of the "junk DNA" that represents all the evolutionary "flotsam and jetsam" that has accumulated over hundreds of millions of years. (thecreationclub.com)
  • Perhaps it won't be long before everyone, critics included, looks at the "junk DNA" concept in the rear-view mirror. (evolutionnews.org)
  • Junk DNA has been getting redress for decades of ignominy. (evolutionnews.org)
  • Most of the genome consists of non-coding sequences, often referred to as "junk DNA. (amos37.com)
  • 17 The assertion of Alu elements as functionless junk is dead. (amos37.com)
  • For example, after the conversion of retroviral RNA into DNA inside a host cell, the newly produced retroviral DNA is integrated into the genome of the host cell. (wikipedia.org)
  • The second open reading frame from the human L1 element L1.2A was expressed as a fusion protein targeted to Tyl virus-like particles in Saccharomyces cerevisiae and shown to have reverse transcriptase activity. (nyu.edu)
  • Stimulation of the Mu A protein-mediated strand cleavage reaction by the Mu B protein, and the requirement of DNA nicking for stable type 1 transpososome formation. (mcmaster.ca)
  • Stimulation of the Mu DNA strand cleavage and intramolecular strand transfer reactions by the Mu B protein is independent of stable binding of the Mu B protein to DNA. (mcmaster.ca)
  • Levin, H. L. & Moran, J. V. Dynamic interactions between transposable elements and their hosts. (nature.com)
  • Parasitic DNA? (amos37.com)
  • Transposable elements are part of the non-coding DNA 1 and are sometimes referred to as "parasitic DNA. (amos37.com)
  • Transposable elements (TEs) 2 are termed parasitic because they can replicate and spread within the genome of an organism. (amos37.com)