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DNA Transposable ElementsTransposasesRetroelementsBase SequenceZea maysMutagenesis, InsertionalShort Interspersed Nucleotide ElementsMolecular Sequence DataTerminal Repeat SequencesRepetitive Sequences, Nucleic AcidDrosophila melanogasterEvolution, MolecularLong Interspersed Nucleotide ElementsGenome, PlantInverted Repeat SequencesGenomeDNA, PlantSequence Analysis, DNAPhylogenyOryza sativaSequence Homology, Nucleic AcidInterspersed Repetitive SequencesGenome, InsectAlu ElementsGenes, PlantEnhancer Elements, GeneticDrosophilaChromosome MappingResponse ElementsModels, GeneticGenes, InsectPromoter Regions, GeneticTranscription, GeneticEuchromatinCloning, MolecularPlasmidsMutationSequence AlignmentRestriction MappingDNAGenetic VariationRecombination, GeneticBlotting, SouthernChromosomes, PlantSpecies SpecificityAmino Acid SequenceChromosomes, Artificial, BacterialIntronsMultigene FamilyCrosses, GeneticGene Transfer, HorizontalCaenorhabditisGene DosageGene Expression RegulationRegulatory Sequences, Nucleic AcidOpen Reading FramesHeterochromatinGonadal DysgenesisConserved SequenceGenomicsNucleic Acid HybridizationDNA Restriction EnzymesGene SilencingDNA, IntergenicArabidopsisChromosome InversionArgonaute ProteinsOryziasTransformation, GeneticDNA-Binding ProteinsAllelesBiological EvolutionDNA PrimersRegulatory Elements, TranscriptionalPolymerase Chain ReactionGene Expression Regulation, PlantDNA MethylationRNA, PlantGenome, HumanGene DuplicationRNA, Small InterferingGenome, FungalTranscription FactorsAnimals, Genetically ModifiedEye ColorGenesDrosophila ProteinsMolecular Sequence AnnotationExonsPlantsTransposon ResolvasesGenome SizeNucleotidyltransferasesChromosomes, InsectAnthocyaninsGerm CellsTrace ElementsChromosomesSorghumPhenotype
GenomesMiniature inverted-repeat transposable elementGenesMethylationSequences that can moveTransposonsMaizeInsertionsTranspositionGenomicRepeatsMutationsRNAsLess abundantEvolutionIsolatesTranscriptionalSpeciesGypsySINEsMarinerRetrotransposonsGeneticsProkaryotesProteinsSuperfamilyCopiesMarkersRepeatIntergenicWidespreadClassPromoterProportionRegulatory elementsMolecularIntegrativeHumanCRISPRPopulationsUpstreamImportantGenetic elementsHighlyReview
Genomes14
  • Methylated CG (mCG) is the most abundant form of mC in plant genomes and predominantly occurs in noncoding regions such as transposable elements and other repetitive DNA regions 14 , 15 . (nature.com)
  • Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. (biomedcentral.com)
  • Transposable elements were initially viewed as "selfish" DNA or "parasitic" elements because of their deleterious effects on host genomes [ 7 ]. (biomedcentral.com)
  • Transposable elements can be considered as a source of raw material for primitive genomes, tools of genetic innovation, and ancestors of modern genes (e.g., ncRNA) [ 15 ]. (biomedcentral.com)
  • However, to explore in deep the variations within different genomes, such as SNPs (single nucleotide polymorphism), INDELs (Insertion-deletion), satellites and transposable elements, we need high-quality genomes. (uni-potsdam.de)
  • In chapter 2, we identified that sea turtle genomes contain a significant proportion of TEs, with differences in TE abundance between species, and the discovery of a recent expansion of Penelope-like elements (PLEs) in the highly conserved sea turtle genome provides new insights into the dynamics of TEs within Testudines. (uni-potsdam.de)
  • Here we confirm that high-quality genomes are fundamental for the study of transposable element evolution and the conservation within the clade. (uni-potsdam.de)
  • The most abundant class of transposable elements in plant genomes are the long terminal repeat (LTR) retrotransposons. (edu.sa)
  • PIWI-interacting RNAs (piRNAs) are responsible for preventing the movement of transposable elements in germ cells and protect the integrity of germline genomes. (biomedcentral.com)
  • Interspersed repetitions called transposable elements (TEs), commonly referred to as mobile elements, make up a significant portion of the genomes of higher animals. (biomedcentral.com)
  • Both LINEs and SINEs elements, despite the differences in structure and transposition mechanisms ( [44] ), are ubiquitous components of eukaryotic genomes, playing a major role in their evolution. (sisef.it)
  • It is therefore clear that retrotransposable elements build large parts of eukaryotic genomes ( [40] ). (sisef.it)
  • The observed differences in genome size in plants are accompanied by variations in the content of LTR retrotransposons, demonstrating that such elements might be important players in the evolution of plant genomes, along with polyploidy ( [11] ). (sisef.it)
  • Two years ago, Zhang lab members discovered a class of RNA-programmable systems in prokaryotes called OMEGAs, which are often linked with transposable elements, or "jumping genes," in bacterial genomes and likely gave rise to CRISPR-Cas systems. (mit.edu)
Miniature inverted-repeat transposable element1
  • In maize, a miniature inverted-repeat transposable element (MITE) inserted into the promoter of the NAC gene ( ZmNAC111 ) has been found to enhance drought tolerance at the seedling stage [ 20 ]. (biomedcentral.com)
Genes11
  • By extension of these and related findings, we propose that restriction of mobile element insertions in a mammalian genome is mediated in part by the presence of KZNFs evolved to recognize sequences within active TE families, and that the arms race created by this process has lead to the exceptional proliferation of lineage-specific ZNF genes in different mammalian lineages. (escholarship.org)
  • Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases. (lookformedical.com)
  • Here we report a detailed analysis of repetitive elements in the papaya genome, including transposable elements (TEs), tandemly-arrayed sequences, and high copy number genes. (ugr.es)
  • The strand-biased circularizing integrative elements (SEs) are putatively non-mobilizable integrative elements for transmitting antimicrobial resistance genes. (biomedcentral.com)
  • Transposable elements have the unique ability to move within our DNA, causing or reversing mutations, altering genes, and even affecting the size of our genome. (lu.se)
  • These elements appear to influence the expression of both protein-coding genes and non-coding transcripts in the human brain through various mechanisms," says Raquel Garza. (lu.se)
  • Jumping genes" (more formally known as transposable elements or transposons) are DNA sequences that can move from one location of the genome to another. (bigthink.com)
  • For example, retrovirus-type jumping genes are more abundant in postmortem human brain tissue obtained from Alzheimer's disease patients than in tissue from healthy controls, and these same jumping genes promote nerve cell death in fruit flies. (bigthink.com)
  • Unlike CRISPR proteins, Fanzor enzymes are encoded in the eukaryotic genome within transposable elements, and the team's phylogenetic analysis suggests that the Fanzor genes have migrated from bacteria to eukaryotes through so-called horizontal gene transfer. (mit.edu)
  • General characteristics, phylogenomic relationships, transposable elements, sex-related genes, protein family evolution, genes related to protein degradation (MEROPS), carbohydrate-active enzymes (CAZymes), melanin synthesis and secondary metabolism were investigated and compared between species. (nau.edu)
  • Transposable elements (TEs) are an important source of genetic diversity and can be co-opted for the regulation of host genes. (sciencegate.app)
Methylation3
Sequences that can move1
Transposons4
  • Like other elements from the IS200 / IS605 and IS607 families, these TnpB-only transposons lack TIRs and TSDs. (biomedcentral.com)
  • One possibility is that these elements represent non-autonomous derivatives of IS607 or IS200 / IS605 -like transposons, where TnpA is deleted. (biomedcentral.com)
  • Heterochromatin is an inert region in the genome and composed of mainly remnants of transposons and repetitive elements. (omicsdi.org)
  • We found a low content of mobile elements, with DNA transposons from Tc1/Mariner superfamily being the most abundant across analysed species. (nau.edu)
Maize3
Insertions3
  • Transposable elements (TEs) are an important source of gene regulatory elements and are abundant and active in our genome, but new insertions can be deleterious to the host. (escholarship.org)
  • Many computational methods have been developed to detect non-reference transposable element (TE) insertions using short-read whole genome sequencing data. (biomedcentral.com)
  • Transposable elements (TEs) are ancient (retro)-virus insertions inside a host genome and are peculiar mobile genetic elements accounting for a large proportion of repetitive DNA regions ( [29] ). (sisef.it)
Transposition2
  • Non-LTR retrotransposons need both RT and endonuclease (EN) in their transposition process termed target site-primed reverse transcription (TPRT) [ 12 ]. (biomedcentral.com)
  • Interestingly, numerous IS elements (for example, IS1341 , IS809 and IS1136 ) encode TnpB as the only protein (putative transposase), but the supporting evidence for TnpB-mediated transposition is still missing. (biomedcentral.com)
Genomic3
  • Transposable elements (TEs) are DNA segments that are duplicated and inserted into genomic DNA by a variety of mechanisms. (biomedcentral.com)
  • Transposable elements are one of the major sources of genomic instability through various mechanisms, including de novo insertion, insertion-mediated genomic deletion, and recombination-associated genomic deletion. (genominfo.org)
  • All three putative protein and exon sequences were conserved, but the corresponding genomic sequences were extremely variable mainly due to the invasion of miniature inverted-repeat transposable elements (MITEs) into introns. (biomedcentral.com)
Repeats2
  • Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. (lookformedical.com)
  • Among the tandem repeats, microsatellites are the most abundant in number, but represent only 0.19% of the genome. (ugr.es)
Mutations2
  • To finish this recipe, let's add some somatic mutations and abundant transposable elements. (plantae.org)
  • As the human genome evolved, many transposable sequences collected mutations repressing their ability to move to avoid harmful interruptions. (georgeonin.com)
RNAs3
  • This project is based on the hypothesis that LINE-1 elements constitute critical entities in glioma initiation and progression, by acting as a source of regulatory elements and coopted functional RNAs in tumor cells. (lu.se)
  • However, the most abundant class of small RNAs in flowering plants is poorly understood. (arizona.edu)
  • Known as Pol IV-dependent (p4-)siRNAs, these small RNAs are associated with transcriptional gene silencing, transposable elements and heterochromatin formation. (arizona.edu)
Less abundant1
  • Minisatellites and satellites are less abundant, but represent 0.68% and 0.43% of the genome, respectively, due to greater repeat length. (ugr.es)
Evolution6
  • 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. (edu.au)
  • In Lund, researchers are investigating these repetitive regions of our DNA to understand the role transposable elements play in human brain development and evolution. (lu.se)
  • Neutral Theory, Transposable Elements, and Eukaryotic Genome Evolution. (mbl.edu)
  • The analysis demonstrated the presence of multiple copies of retrotransposable elements inside the genome of beech, in accordance with the viral quasi-species theory of retrotransposon evolution. (sisef.it)
  • The identification of retrotransposable elements in forest trees represents an important step toward the understanding of mechanisms of genome evolution. (sisef.it)
  • Despite this and despite abundant evidence of dispersal evolution during expansions, the impact of density-dependent dispersal and its evolution on expansion dynamics remains understudied. (sciencegate.app)
Isolates1
  • Furthermore, 36 (28.6%) out of 126 isolates had a transposable element (TE) insertion in AVR-Pib , which resulted in altered virulence. (researchsquare.com)
Transcriptional3
  • KRAB domain Zinc Finger Proteins (KZNFs) are candidate transcription factors for recognizing viral or mobile element DNA and recruiting transcriptional repression complexes in primates. (escholarship.org)
  • Humans have ~150 primate-specific KZNFs that could recruit KAP1-corepressor complex through their KRAB domain to target active or recently active mobile elements for transcriptional repression. (escholarship.org)
  • Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements. (fudan.edu.cn)
Species3
  • Transposable elements are able to affect conserved and divergent chromatin looping and contribute to cell- and species-specific gene regulation [ 11 ]. (biomedcentral.com)
  • As testudine have a slow mutation rate lower only to crocodilians, with more than 300 species, adapted to different environments all across the globe, the testudine clade can help us to Transposable elements (TEs) are loci that can replicate and multiply within the genome of their host. (uni-potsdam.de)
  • Retrotransposable elements are well characterized in model or crop species like Arabidopsis thaliana and Oryza sativa , but are poorly known in forest tree species. (sisef.it)
Gypsy1
  • The top two most abundant Gypsy families in S. alba preferentially insert in gene-poor regions. (sciencegate.app)
SINEs2
  • The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. (lookformedical.com)
  • There are 250000 copies of LINE elements in Lilium ( [21] ) and SINEs are represented, for example, by 50000 copies in tobacco ( [46] ). (sisef.it)
Mariner1
  • The two forms possess similar complements of TE families with Tc1/Mariner and LINE-like Tad-1 elements more abundant in PTT. (edu.au)
Retrotransposons4
  • Their latest investigations have led them to a specific family of transposable elements known as LINE-1 retrotransposons, which currently make up roughly 17% of our DNA. (lu.se)
  • Two retrotransposons, belonging to the two major classes of LTR and non-LTR elements, were characterized trough a SCAR (Sequence Characterized Amplified Region) strategy. (sisef.it)
  • The cloning and sequencing of amplification products and a Cleaved Amplified Polymorphisms (CAPs) approach on the identified retrotransposons, showed a high level of diversity among the multiple copies of both elements. (sisef.it)
  • Non-LTR retrotransposons can be divided in several subclasses, such as LINE (Long INterspersed Elements) and SINE (Short INterspersed Elements - [44] ). (sisef.it)
Genetics1
  • This is a seminal paper not only in the history of the study of selfish genetic elements but in the history of genetics. (geneconvenevi.org)
Prokaryotes2
  • Most well-documented cases of horizontal gene transfer have been described in prokaryotes or in animals and they often involve transposable elements. (edu.sa)
  • These OMEGA systems are more ancestral to CRISPR and they are among the most abundant proteins on the planet, so it makes sense that they have been able to hop back and forth between prokaryotes and eukaryotes," says Saito. (mit.edu)
Proteins3
  • Different factors may be operating for the formation of this effect, such as the mobilization of transposable elements, effect of inbreeding and alteration of the heat-shock proteins functions. (scielo.br)
  • Here we report two groups of TnpB-like proteins (Fanzor1 and Fanzor2) that are widespread in diverse eukaryotic transposable elements (TEs), and in large double-stranded DNA (dsDNA) viruses infecting eukaryotes. (biomedcentral.com)
  • In contrast, Fanzor2 proteins appear only in some IS607 -type elements. (biomedcentral.com)
Superfamily1
  • We also analyze a new Helitron2 group from the Helitron superfamily, which contains elements with hairpin structures on both ends. (biomedcentral.com)
Copies2
Markers1
  • Furthermore, the high polymorphism of retrotransposable elements can represent a starting point for the development of new genetic variability markers. (sisef.it)
Repeat1
  • genome sequence did not include the interiors of highly similar repetitive elements and the extremely dense repeat regions near the centromeres. (wikipedia.org)
Intergenic1
  • We have determined globally the sites of initiation of intergenic lncRNAs in erythroid cells, allowing us to distinguish two similarly abundant classes of transcripts. (biomedcentral.com)
Widespread1
  • For a long time it wasn't appreciated how widespread those elements can be, but now it seems that patches of really important regulatory elements can be buried among the junk DNA. (evolverzone.com)
Class2
  • Among human TEs, LINE-1s is the most abundant class. (lu.se)
  • Fig. 1 - Schematic representation of the general structure of class I RNA mediated LTR TE (A), class I RNA mediated non-LTR elements (B) and class II DNA mediated elements (C) in their autonomous and non autonomous configurations. (sisef.it)
Promoter2
Proportion1
  • In chapter 3, we compared the proportion of TE across the Testudine clade, and we identified that the proportion of transposable elements within the clade is stable, regardless of the quality of the assemblies. (uni-potsdam.de)
Regulatory elements2
  • There's at least five regulatory elements for each [human] gene, probably many more," says gene control expert Robert Tjian of the University of California, Berkeley. (evolverzone.com)
  • An atlas of wheat epigenetic regulatory elements reveals subgenome-divergence in the regulation of development and stress responses. (fudan.edu.cn)
Molecular1
  • In this paper the molecular identification of retrotransposable elements in Fagus sylvatica L. is reported. (sisef.it)
Integrative1
  • To help explore the abundant information effectively, we built an integrative web portal for scientists to browse, search and perform analysis of all lincRNAs through an intuitive Web interface. (biomedcentral.com)
Human6
  • Among them, Alu is the most abundant element, constituting ~10% of the human genome. (genominfo.org)
  • Long interspersed nuclear element-1 (LINE-1 or L1) comprises 17% of the human genome. (biomedcentral.com)
  • Researchers at Lund University have discovered that a specific group of genetic elements in our DNA influence the development of the human brain, their study was published in Science Advances. (lu.se)
  • Researchers at Lund University offer new insights in their latest study, published in Science Advances, detailing how a specific group of genetic elements have influenced the development of the human brain over time. (lu.se)
  • These elements are suspected to have played a key role in shaping the development of the human brain. (lu.se)
  • The challenge has been to determine what these elements do and how they affect human tissues, given their abundant and repetitive presence in the human genome. (lu.se)
CRISPR1
  • We will then use CRISPR approaches to silence/activateLINE-1 elements in glioma cell lines and interrogate the consequences of LINE-1 modulation on tumor physiology. (lu.se)
Populations1
  • Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. (mbl.edu)
Upstream1
  • reported one THE1B element upstream of CRH gene alters gestation length by upregulating corticotropin-rele. (biomedcentral.com)
Important3
  • These elements, once considered "Junk DNA", are now providing important clues as to how our brain has evolved to differ from that of our closest living relative, the chimpanzee. (lu.se)
  • They discovered that LINE-1 elements play an important role in shaping the structural and functional complexity of our brains as we age. (lu.se)
  • Retrotransposable elements are important and peculiar genetic components derived from ancient retrovirus insertion inside plants genome. (sisef.it)
Genetic elements1
Highly1
  • For retrotransposon, a highly abundant element for this clade, we identify no correlation. (uni-potsdam.de)
Review2