Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Transposable elements”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,225 records · Page 68Linked to original sources
PubMed1992

Transposable DNA elements and life history traits. I. Transposition of P DNA elements in somatic cells reduces the lifespan of Drosophila melanogaster.

As an initial study of the influence of transposable DNA elements on life history traits, and as a model system for estimating the impact of somatic genetic damage on longevity, the effect of P DNA element movement in somatic cells on adult lifespan was measured in Drosophila melanogaster males. Lifespan was significantly reduced in males that contained the somatically active P[ry+ delta 2-3](99B) element and 17, 4, 3, but not just a single P element. Furthermore, there appears to be a direct correlation between the number of transposing P elements and the amount of lifespan reduction. This reduction in lifespan observed in males with somatically active P elements is probably due to genetic damage in embryos, larvae and pupae from P-element excisions and insertions, leading to changes in gene structure and regulation, chromosome breakage, and subsequent cell death in adults. This hypothesis is supported in this study by a significant increase in recessive sex-linked lethal mutations in the same males that had reduced lifespans and by the previous observation of chromosome breakage in somatic cells of similar males. The evolutionary implications of these results are discussed, including the possible influence of somatic DNA transpositions on fitness and other life history traits.

Animals↗
PubMed2006

Very little intron loss/gain in Plasmodium: intron loss/gain mutation rates and intron number.

We compared intron positions in conserved regions of 3479 orthologous gene pairs from Plasmodium falciparum and Plasmodium yoelii, which likely diverged >or=100 million years ago (Mya). Only 27 out of 2212 positions were specific to one of the two species. Intron presence in related species shows that at least 19 and possibly 26 of the changes are due to intron loss, depending on phylogeny. The implied intron loss and gain rates are much lower than previously estimated for nematodes, arthropods, fungi, and plants, and are comparable only with the rates in vertebrates. That all observed changes were exact, occurring without loss or gain of flanking coding sequence, suggests intron loss via an mRNA intermediate, as does a nonsignificant trend toward loss of introns at adjacent positions. Many of the intron changes occurred in genes encoding proteins involved in nucleic acid-related processes, as previously found for intron gains in nematodes. Two changes occurred in the chloroquine resistance transporter, suggesting a role for positive selection in intron loss in Plasmodium. The dearth of intron loss and gain could be explained by the lack of known transposable elements in Plasmodium, since transposable elements and/or reverse transcriptase are thought to be necessary for both processes. The observed pattern suggests that the availability of stochastic intron loss and gain mutations can be a major determinant of changes in intron number.

Alternative Splicing↗
PubMed1997

Circularized Ac/Ds transposons: formation, structure and fate.

The maize Ac/Ds transposable elements are thought to transpose via a cut-and-paste mechanism, but the intermediates formed during transposition are still unknown. In this work we present evidence that circular Ac molecules are formed in plants containing actively transposing elements. In these circles, transposon ends are joined head-to-head. The sequence at the ends' junction is variable, containing small deletions or insertions. Circles containing deleted Ac ends are probably unable to successfully reintegrate. To test the ability of circles with intact transposon ends to integrate into the genome, an artificial Ds circle was constructed by cloning the joined ends of Ac into a plasmid carrying a plant selectable marker. When such a circular Ds was introduced into tobacco protoplasts in the presence of Ac-transposase, no efficient transposase-mediated integration was observed. Although a circular transposition intermediate cannot be ruled out, the findings of circles with deleted transposon ends and the absence of transposase-mediated integration of the circular Ds suggest that some of the joined-ends-carrying elements are not transposition intermediates, but rather abortive excision products. The formation of Ac circles might account for the previously described phenomenon of Ac-loss. The origin of Ac circles and the implications for models of Ac transposition are discussed.

Chromosomes↗
PubMed2003

Genetic variations of AA genome Oryza species measured by MITE-AFLP.

MITEs (miniature inverted-repeat transposable elements) are the major transposable elements in Oryza species. We have applied the MITE-AFLP technique to study the genetic variation and species relationship in the AA-genome Oryza species. High polymorphism was detected within and between species. The genetic variation in the cultivated species, Oryza sativa and Oryza glaberrima, was comparatively lower than in their ancestral wild species. In comparison between geographical lineages of the AA genome species, African taxa, O. glaberrima and Oryza barthii, showed lower variation than the Asian taxa, O. sativa, Oryza rufipogon, and Oryza nivara, and Australian taxon Oryza meridionalis. However, another African taxon, Oryza longistaminata, showed high genetic variation. Species relationships were analyzed by the pattern of presence or absence of homologous fragments, because nucleotide sequences of the detected MITE-AFLP fragments revealed that the same fragments in different species shared very high sequence homology. The clustering pattern of the AA-genome species matched well with the geographical origins (Asian, African and Australian), and with the Australian taxon being distant to the others. Therefore, this study demonstrated that the MITE-AFLP technique is amenable for studying the genetic variation and species relationship in rice.

Cluster Analysis↗
PubMed2006

Interference with cell cycle progression by parasitic genetic elements: sleeping beauty joins the club.

Transposable elements are discrete segments of DNA that have the distinctive ability to move and replicate within genomes. Similar to viruses, transposons are best viewed as molecular parasites that propagate themselves using resources of the host cell. Many viruses have developed strategies to modulate the host cell cycle machinery and cellular self-destruct mechanisms to maximize the chance for successful infection and the production of virus progeny. Recent evidence shows that transposable elements have also evolved mechanisms to modulate cell cycle progression for their own benefit. Thus, interference with the cell cycle seems to be a shared strategy of parasitic selfish genetic elements.

Animals↗
PubMed1986

Repetitive DNA and chromosome evolution in plants.

Most higher plant genomes contain a high proportion of repeated sequences. Thus repetitive DNA is a major contributor to plant chromosome structure. The variation in total DNA content between species is due mostly to variation in repeated DNA content. Some repeats of the same family are arranged in tandem arrays, at the sites of heterochromatin. Examples from the Secale genus are described. Arrays of the same sequence are often present at many chromosomal sites. Heterochromatin often contains arrays of several unrelated sequences. The evolution of such arrays in populations is discussed. Other repeats are dispersed at many locations in the chromosomes. Many are likely to be or have evolved from transposable elements. The structures of some plant transposable elements, in particular the sequences of the terminal inverted repeats, are described. Some elements in soybean, antirrhinum and maize have the same inverted terminal repeat sequences. Other elements of maize and wheat share terminal homology with elements from yeast, Drosophila, man and mouse. The evolution of transposable elements in plant populations is discussed. The amplification, deletion and transposition of different repeated DNA sequences and the spread of the mutations in populations produces a turnover of repetitive DNA during evolution. This turnover process and the molecular mechanisms involved are discussed and shown to be responsible for divergence of chromosome structure between species. Turnover of repeated genes also occurs. The molecular processes affecting repeats imply that the older a repetitive DNA family the more likely it is to exist in different forms and in many locations within a species. Examples to support this hypothesis are provided from the Secale genus.

Animals↗
PubMed2004

siRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis.

Allelic variation in FLOWERING LOCUS C (FLC), a central repressor of flowering, contributes to natural differences in flowering behavior among Arabidopsis accessions. The weak nature of the FLC allele in the Ler accession is due to low levels of FLC RNA resulting, through an unknown mechanism, from a transposable element inserted in an intron of FLC. Here we show that the transposable element renders FLC-Ler subject to repressive chromatin modifications mediated by short interfering RNAs generated from homologous transposable elements in the genome. Our studies have general implications for the role of transposable elements in eukaryotic gene expression and evolution.

Arabidopsis↗
PubMed2003

[The distribution and origin of P elements in Drosophila melanogaster strains from northeast China].

Eukaryotic transposable elements, especially P transposable elements of Drosophla, are very important to study the evolution of biology. We collected 130 single--female lines of D. melanogaster from 13 places in Northeast China and 3 places nearby which are Beijing(BC), Yantai (YT), Huhehaote(HHT) in 1999 and 2000. We amplified the fragments from ORF2 to ORF3 of P elements using PCR and calculated the defective frequencies and defective parameters of P elements from different places. Basing on the distribution of defective P elements, we suggested the invasion route of P elements of D. melanogaster in Northeast China. The results indicate that the defective frequencies decrease from the frontier to the inland, and in the isolated places the frequencies are lower. It is proposed that P elements of D. melanogaster in Northeast China originate from Korea and Russia to the frontiers of P.R. China, then expand into the inland.

Animals↗
PubMed1983

Structural similarities between viroids and transposable genetic elements.

The primary structures of the tomato planta macho and tomato apical stunt viroids have been determined, and probable secondary structures are proposed. Both viroids can assume the rodlike conformation with extensive base-pairing characteristic of all known viroids. Sequence homologies between the two viroids (75%) and with members of the potato spindle tuber viroid group (73-83%) indicate that they both belong to this group. Comparative sequence analysis of all members of the group reveals striking similarities with the ends of transposable genetic elements. These similarities, the presence of inverted repeats often ending with the dinucleotides U-G and C-A, and flanking imperfect direct repeats suggest that viroids may have originated from transposable elements or retroviral proviruses by deletion of interior portions of the viral (or element) DNA.

Base Sequence↗
PubMed1991

The use of transgenic plants to understand transposition mechanisms and to develop transposon tagging strategies.

This review compares the activity of the plant transposable elements Ac, Tam3, En/Spm and Mu in heterologous plant species and in their original host. Mutational analysis of the autonomous transposable elements and two-element systems have supplied data that revealed some fundamental properties of the transposition mechanism. Functional parts of Ac and En/Spm were detected by in vitro binding studies of purified transposase protein and have been tested for their importance in the function of these transposable elements in heterologous plant species. Experiments that have been carried out to regulate the activity of the Ac transposable element are in progress and preliminary results have been compiled. Perspectives for manipulated transposable elements in transposon tagging strategies within heterologous plant species are discussed.

DNA Mutational Analysis↗
PubMed2000

Identification of new transposable genetic elements in Burkholderia pseudomallei using subtractive hybridisation.

A subtraction library of Burkholderia pseudomallei was constructed by subtractive hybridisation of B. pseudomallei genomic DNA with Burkholderia thailandensis genomic DNA. Two clones were found to have significant sequence similarity to insertion sequences which have previously not been found in B. pseudomallei (designated ISA and ISB); and two clones showed sequence similarity to different regions of Burkholderia cepacia IS407 that has recently been detected in B. pseudomallei. The former, though possibly non-functional, represents new transposable genetic elements of B. pseudomallei. All three sequences were found to be present in multi-copy in the genomes of a number of B. pseudomallei strains and in B. thailandensis, which are the first transposable elements identified in this species.

Amino Acid Sequence↗
PubMed2003

Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells.

The aim of this study was to identify in human cells common targets of histone H3 lysine 9 (H3-Lys9) methylation, a modification that is generally associated with gene silencing. After chromatin immunoprecipitation using an H3-Lys9 methylated antibody, we cloned the recovered DNA and sequenced 47 independent clones. Of these, 38 clones (81%) contained repetitive elements, either short interspersed transposable element (SINE or Alu elements), long terminal repeat (LTR), long interspersed transposable element (LINE), or satellite region (ALR/Alpha) DNA, and three additional clones were near Alu elements. Further characterization of these repetitive elements revealed that 32 clones (68%) were Alu repeats, corresponding to both old Alu (23 clones) and young Alu (9 clones) subfamilies. Association of H3-Lys9 methylation was confirmed by chromatin immunoprecipitation-PCR using conserved Alu primers. In addition, we randomly selected 5 Alu repeats from the recovered clones and confirmed association with H3-Lys9 by PCR using primer sets flanking the Alu elements. Treatment with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine rapidly decreased the level of H3-Lys9 methylation in the Alu elements, suggesting that H3-Lys9 methylation may be related to the suppression of Alu elements through DNA methylation. Thus H3-Lys9 methylation is enriched at human repetitive elements, particularly Alu elements, and may play a role in the suppression of recombination by these elements.

Alu Elements↗
PubMed1977

Transposable genetic elements as agents of gene instability and chromosomal rearrangements.

Transposable genetic elements in prokaryotes and eukaryotes, when inserted at a given locus, can control expression of the locus and cause large scale rearrangements of adjacent DNA sequences. Striking similarities in genetic behaviour between the two groups of elements have led to the proposal of a molecular model of eukaryotic controlling elements, and to suggestions about the part such elements may play in evolution and differentiation.

Base Sequence↗
PubMed2026

Helitrons are enriched in lichenized fungi with long generation lengths and small distribution sizes.

Transposable elements have the potential to drive genome evolution by introducing mutations and causing structural instability and chromosomal rearrangements, particularly under conditions like environmental or genetic stress. In this study, we generated 18 new long-read-based metagenomically assembled reference genomes for lichenized fungi, which form obligate mutualistic symbioses with algae or cyanobacteria. We used the new genomes and 10 publicly available genomes to investigate the relationships between species traits (i.e. dominant reproductive mode, distribution size, and generation length) and the abundance and spatial distribution of transposable elements using a phylogenetic comparative framework. We found that species with smaller distribution sizes and longer generation lengths had a higher genomic DNA transposon load. Specifically, their genomes were enriched with Rolling Circle transposons, which contradict previous research that has identified high proportions of retrotransposons in rare species. Disproportionate distributions of transposable elements in rare and range-restricted species may disrupt genomic stability, decrease fitness, and be reflective of species experiencing a greater degree of stress. Conversely, greater transposable element activity may be an important source of novel genetic diversity in isolated populations with limited gene flow. Further research is needed to understand the potential mechanisms driving transposable element proliferation in rare species' genomes and if transposable element content is predictive of increased extinction risk.

DNA Transposable Elements↗
PubMed1999

Intimate association of microsatellite repeats with retrotransposons and other dispersed repetitive elements in barley.

Simple sequence repeat (SSR)-based genetic markers are being actively developed for the majority of crop plant species. In barley, characterization of 290 dinucleotide repeat-containing clones from SSR-enriched libraries has revealed that a high percentage are associated with cereal retrotransposon-like and other dispersed repetitive elements. Associations found were with BARE-1, WIS2-1A, PREM1 and the dispersed repetitive element R173. Additional similarities between different SSR clones, which have no matches in DNA sequence databases, indicate that this phenomenon is probably widespread in the barley genome. Sequence homologies to the non-coding regions of several cereal genes were also explained by homology to mobile genetic elements. The SSRs found can therefore be classified into two types: (1) those with unique sequences on either flank, and (2) those which are intimately associated with retro-transposons and other dispersed repetitive elements. As the cereal genome is thought to consist largely of this type of DNA, some random association would be expected. However, the conserved positions of the SSRs, relative to repetitive elements, indicate that they have arisen non-randomly. Furthermore, this class of SSRs can be classified into three subtypes: (1) those which are positioned 3' of a transposable element with unique sequence on the other flank, (2) those positioned 5' of a transposable element, and (3) those which have arisen from an internal sequence and so have transposable element sequence on both flanks. The first appear to be analogous to the class of SSRs in mammalian systems which are associated with Alu elements and SINEs (short interspersed elements) and which have been postulated to arise following integration of an extended and polyadenylated retro-transcript into the host genome, followed by mutation of the poly(A) tract and expansion into an SSR. For the second, we postulate that a proto-SSR (A-rich sequence) has acted as a 'landing pad' for transposable element insertion (rather than being the result of insertion), while the third includes those which have evolved as a component of an active transposable element which has spread throughout the genome during bursts of transposition activity. The implications of these associations for genome and SSR evolution in barley are discussed.

Base Sequence↗
PubMedDate not supplied

Genetic effects of injection of Rous sarcoma virus DNA into polar plasm of early Drosophila melanogaster embryos.

Retroviral proviruses and the transposable elements of eukaryotic genomes are structurally similar. The biological significance of eukaryotic transposable elements has not been examined extensively but it is known that, like prokaryotic transposons, these elements can induce mutations in adjacent genes and cause their transposition. It is of interest to determine whether retroviral proviruses have the same mutagenic and gene transposing ability as transposable elements, particularly because the retrovirus genome is assumed to have originated from transposable elements of lower eukaryotes. The transfer of DNA sequences into animal zygotes or embryos by microinjection is a promising experimental approach for eluxidating their functions: when foreign DNAs were introduced into a mouse germ line, mutations were induced and at least in some mice, the mutation was caused by the insertion of a retroviral sequence. We have introduced Rous sarcoma virus (RSV) DNA into a germ line of Drosophila melanogaster, and describe here the resultant genetic effects.

Animals↗
PubMed2006

Mutator-like elements identified in melon, Arabidopsis and rice contain ULP1 protease domains.

The transposon Mutator was first identified in maize, and is one of the most active mobile elements in plants. The Arabidopsis thaliana genome contains at least 200 Mutator-like elements (MULEs), which contain the Mutator-like transposase gene, and often additional genes. We have detected a novel type of MULEs in melon (CUMULE), which, besides the transposase, contains two ubiquitin-like specific protease-like sequences (ULP1). This element is not present in the observed location in some melon cultivars. Multiple copies of this element exist in the Cucumis melo genome, and it has been detected in other Cucurbitaceae species. Analysis of the A. thaliana genome revealed more than 90 CUMULE-like elements, containing one or two Ulp1-like sequences, although no evidence of mobility exists for these elements. We detected various putative transposable elements containing ULP1-like sequences in rice. The discovery of these MULEs in melon and Arabidopsis, and the existence of similar elements in rice and maize, suggest that a proteolytic function may be important for this subset of the MULE transposable elements.

Arabidopsis↗
PubMed1998

Factors contributing to the hybrid dysgenesis syndrome in Drosophila virilis.

A hybrid dysgenesis syndrome in Drosophila virilis is associated with the mobilization of at least four unrelated transposable elements designated Helena, Paris, Penelope and Ulysses. We carried out 42 crosses between eight strains differing in transposable element copy number in order to assess their contributions to hybrid dysgenesis. Linear regression and stepwise regression analysis was performed to estimate the correlation between the difference in euchromatic transposable element number between the parental flies of different strains involved in the crosses and the percentage, in the progeny of these crosses, of males with atrophic gonads. Male gonadal atrophy is a typical manifestation of the D. virilis hybrid dysgenesis syndrome. About half the variability in the level of male gonadal atrophy can be attributed to Penelope and Paris/Helena. Other factors also seem to play a significant role in hybrid dysgenesis in D. virilis, including maternally transmitted host factors and/or uncontrolled environmental variation. In the course of this work a novel transposable element named Telemac was found. Telemac is also mobilized in hybrid dysgenesis but does not appear to play a major causative role.

Animals↗