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.

SourceResearch connectionFrom yearThrough year

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

At least 271 records · Page 15Linked to original sources

PubMed2003

Non-random association of transposable elements with duplicated genomic blocks in Arabidopsis thaliana.

The genome of Arabidopsis thaliana is known to contain numerous open reading frames apparently encoding transposases. In order to test the hypothesis that transposable elements have played a role in segmental duplication in this species, we compared the distribution of transposable elements with that of genomic windows that shared gene families to a greater extent than expected by chance. Phylogenetic analyses indicated that duplication of these segments occurred after the monocot-dicot divergence and probably after the eurosid I-eurosid II divergence. Known transposable elements were found to occur in putatively duplicated segments to a far greater extent than expected on the basis of their genome-wide distribution, suggesting that transposition may have played a role in segmental duplication in this species.

Arabidopsis↗

PubMed2002

Characterization of the repetitive sequences in a 200-kb region around the rice waxy locus: diversity of transposable elements and presence of veiled repetitive sequences.

Repetitive genomic sequences might have various structural features and properties distinct from those of the known transposable elements (TE). Here, the content and properties of the repetitive sequences present in a 200-kb region around the rice waxy locus were analyzed using the available rice genomic database. In our previous Southern blotting analysis, 70% of the segments in this region showed smeared patterns, but according to the present database analysis, the proportion of repetitive sequences in this region was only 15%. The repetitive segments in this 200-kb region comprised 75 repetitive sequences that we classified into 46 subfamilies: 21 subfamilies were known TEs or repetitive sequences and 25 subfamilies consisted of newly identified TEs or novel types of repetitive sequences. The region contains no long terminal repeat (LTR) retrotransposable elements, but miniature inverted repeat transposable elements (MITEs) constituted a major class among the elements identified. These MITEs showed remarkable structural divergence: 12 elements were found to be new members of known MITE superfamilies, while five elements had novel terminal structures, and did not belong to any known TE families. Interestingly, about 10% of the repetitive sequences, including virus-like sequences did not have any of the usual characteristics of TEs, suggesting that a certain proportion of repetitive sequences that might not share the transpositional mechanisms of known elements are dispersed in the compact rice genome.

Base Sequence↗

PubMed1995

A general method to isolate genes tagged by a high copy number transposable element.

The Petunia hybrida line W138 contains more than 200 copies of the transposable element dTph1. In W138 progeny these elements give rise to new unstable mutations at high frequency. With the aim of isolating these mutated genes a method was developed to isolate dTph1 flanking sequences unique for mutant plants. This method is based on differential screening of cloned inverse polymerase chain reaction (IPCR) products originating from the mutated plant. It directly yields a probe for the mutated gene which can be used to screen pre-existing cDNA and genomic libraries. This method may be generally applicable to isolate genes tagged by other high copy number transposable elements, like Mutator (Mu) or Dissociation (Ds) in Zea mays.

Alleles↗

PubMed1992

The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. I. Element frequencies and distribution.

Data were collected on the distribution of nine families of transposable elements among second and third chromosomes isolated from a natural population of Drosophila melanogaster, by means of in situ hybridization of element probes to polytene chromosomes. It was found that the copy numbers per chromosome in the distal sections of the chromosome arms followed a Poisson distribution. Elements appeared to be distributed randomly along the distal sections of the chromosome arms. There was no evidence for linkage disequilibrium in the distal sections of the chromosomes, but some significant disequilibrium was detected in proximal regions. There were many significant correlations between different element families with respect to the identity of the sites that were occupied in the sample. There were also significant correlations between families with respect to sites at which elements achieved relatively high frequencies. Element frequencies per chromosome band were generally low in the distal sections, but were higher proximally. These results are discussed in the light of models of the population dynamics of transposable elements. It is concluded that they provide strong evidence for the operation of a force or forces opposing transpositional increase in copy number. The data suggest that the rate of transposition per element per generation is of the order of 10(-4), for the elements included in this study.

Animals↗

PubMed1994

The evolutionary genetics of the hobo transposable element in the Drosophila melanogaster complex.

Hobo elements are a family of transposable elements found in Drosophila melanogaster and its three sibling species: D. simulans, D. mauritiana and D. sechellia. Studies in D. melanogaster have shown that hobo may be mobilized, and that the genetic effects of such mobilizations included the general features of hybrid dysgenesis: mutations, chromosomal rearrangements and gonadal dysgenis in F1 individuals. At the evolutionary level some hobo-hybridizing sequences have also been found in the other members of the melanogaster subgroup and in many members of the related montium subgroup. Surveys of older collected strains of D. melanogaster suggest that complete hobo elements were absent prior to 50 years ago and that they have recently been introduced into this species by horizontal transfer. In this paper we review our findings and those of others, in order to precisely describe the geographical distribution and the evolutionary history of hobo in the D. melanogaster complex. Studies of the DNA sequences reveal a different level of divergence between the group D. melanogaster, D. simulans and D. mauritiana and the fourth species D. sechellia. The hypothesis of multiple transfers in the recent past into the D. melanogaster complex from a common outside source is discussed.

Amino Acid Sequence↗

PubMed2005

Deleterious transposable elements and the extinction of asexuals.

The genomes of virtually all sexually reproducing species contain transposable elements. Although active elements generally transpose more rapidly than they are inactivated by mutation or excision, their number can be kept in check by purifying selection if its effectiveness becomes disproportionately greater as their copy number increases. In sexually reproducing species, such synergistic selection can result from ectopic crossing-over or from homologous recombination under negative epistasis. In addition, there may be controls on transposon activity that are associated with meiosis. Because a sexual lineage that abandons sex must lack such mechanisms, it may be driven to extinction by the unchecked proliferation of deleterious transposons inherited from its sexual progenitor. An important component of the evolutionary advantage of sex over asex may therefore lie in the ability of sex, despite facilitating the spread of deleterious elements within interbreeding populations, also to restrain their intragenomic proliferation.

Biological Evolution↗

PubMed1999

Are chromosomal inversions induced by transposable elements? A paradigm from the malaria mosquito Anopheles gambiae.

Chromosomal rearrangements abound in nature and can be studied in detail in organisms with polytene chromosomes. In Drosophila and in Anopheline mosquitoes most speciation processes seem to be associated with the establishment of chromosomal rearrangements, particularly of paracentric inversions. It is not known what triggers inversions in natural populations. In the laboratory inversions are commonly generated by X-rays, mutagens or after the activity of certain transposable elements (TEs). The Anopheles gambiae complex is comprised of six sibling species, each one characterized by the presence of fixed paracentric inversions on their chromosomes. Two of these, An. gambiae s.s. and An. arabiensis, are the most important vectors of human malaria and are structured into sub-populations, each carrying a characteristic set of polymorphic chromosomal inversions. We have cloned the breakpoints of the naturally occurring polymorphic inversion In(2R)d' of An. arabiensis. Analysis of the surrounding sequences demonstrated that adjacent to the distal breakpoint lies a transposable element that we called Odysseus. Characteristics of Odysseus' terminal region and its cytological distribution in different strains as well as within the same strain indicate that Odysseus is an actively transposing element. The presence of Odysseus at the junction of the naturally occurring inversion In(2R)d' suggests that the inversion may be the result of the TEs activity. Cytological evidence from Drosophila melanogaster has also implicated the hobo transposable element in the generation of certain Hawaiian endemic inversions. This picture supports the hypothesis of the important role of TEs in generating natural inversions.

Animals↗

PubMed1988

Organization of the Tgm family of transposable elements in soybean.

We have compared the organization of six Tgm elements that were selected from a genomic library of soybean DNA on the basis of hybridization with subcloned regions of Tgm 1 (transposon, Glycine max) from the seed lectin gene. These elements ranged in size from 1.6 kbp to greater than 12 kbp. Tgm2, Tgm3, Tgm4 and Tgm5 represent partial isolates in which the genomic clone contained a 3' but not a 5' terminus of the element; while Tgm6 and Tgm7, like Tgm1, were small isolates flanked by both 5' and 3' nonelement sequences. Cross-hybridization studies between subcloned portions of these seven elements identified regions of homology which suggest that the Tgm transposable elements of soybean form a family of deletion derivatives. In addition to internal deletion events, numerous deletions and base substitutions are also present within the borders of these elements which are comprised of the same tandemly repeated sequence. The 39% amino acid homology between a 1 kb portion of an open reading frame in Tgm4 and Tgm5 and ORF1, an open frame from the first intron of the maize Enhancer (Suppressor-mutator) transposable element, suggests that both elements encode a common function that requires a high degree of protein conservation.

Base Sequence↗

PubMed1998

An active Ac-like transposable element in teleost fish.

The i4/i4 genotype of the medakafish, Oryzias latipes, exhibits a quasi albino phenotype due to insertion of a novel transposable element, Tol2, into the tyrosinase gene. Tol2 is 4681 bp in length, has short inverted terminal repeats, and contains four ORFs with the potential to encode a transposase protein. Excision activity of the element has been detected by PCR analysis. Genomic Southern of the Tol2 element revealed that about 20 copies are present in the diploid genome. Dot-matrix comparisons of amino acid sequences of ORFs show relatively high similarity with transposases from Ac of maize, hobo of Drosophila, and Tam3 of snapdragon, which are all active transposable elements. Tol2 is thus concluded to be an active Ac-like transposable element probably encoding a transposase protein. It should therefore find application as a unique material for establishing a gene tagging system in fish.

Journal Article↗

PubMed1992

Control of excision frequency of maize transposable element Ds in Petunia protoplasts.

The complete coding region of maize transposable element Ac and truncated but active derivatives of it were placed under the control of promoters of different strength and tested for the ability to excise transposable element Ds from a beta-glucuronidase reporter gene in a cotransfection assay in Petunia protoplasts. The highest excision values (5% of the protoplasts able to express the beta-glucuronidase gene in a control experiment) were observed with a truncated version of the Ac coding region under the control of the 2' promoter. The weak Ac promoter is sufficient to give rise to excision values not much lower than those found with much stronger promoters such as the 2' and nos promoters. A decrease in excision frequency was observed when translation of the Ac coding region was hindered by out-of-frame ATG codons in addition to the use of weak promoters. Increasing the level of Ac transposase thus does not seem to be sufficient to raise the level of Ds excision observed in this system and possibly also in maize. Therefore another factor limits the excision of Ds elements. Previously, it was reported that in tobacco cells the deletion of Ds sequence between base pairs 186 and 245 led to a decrease of the Ds excision frequency by the full-length but not by the truncated Ac product. In the Petunia assay system, however, deletion of these sequences decreased the excision rate with both the full length and the truncated Ac coding region. A cDNA construct was found similarly active as the corresponding genomic DNA.

Journal Article↗

PubMed2003

Transposable elements: targets for early nutritional effects on epigenetic gene regulation.

Early nutrition affects adult metabolism in humans and other mammals, potentially via persistent alterations in DNA methylation. With viable yellow agouti (A(vy)) mice, which harbor a transposable element in the agouti gene, we tested the hypothesis that the metastable methylation status of specific transposable element insertion sites renders them epigenetically labile to early methyl donor nutrition. Our results show that dietary methyl supplementation of a/a dams with extra folic acid, vitamin B(12), choline, and betaine alter the phenotype of their A(vy)/a offspring via increased CpG methylation at the A(vy) locus and that the epigenetic metastability which confers this lability is due to the A(vy) transposable element. These findings suggest that dietary supplementation, long presumed to be purely beneficial, may have unintended deleterious influences on the establishment of epigenetic gene regulation in humans.

Alleles↗

PubMed1990

Characterization and purification of DNA-RNA complexes related with 1731 and copia-like transposable elements in a Drosophila cell line.

DNA-RNA complexes were characterized and purified in a Drosophila melanogaster cell line. Such duplexes were shown to be specific of 1731 and other "copia-like" transposable elements. DNA-RNA complexes were purified through a Sephadex G-75 column from a global nucleic acid preparation or from a total RNA fraction prior to DNA-A and RNA-A treatment. They incorporated both labelled thymidine and uridine and their resistance or sensibility to enzymes or chemicals was consistent with that being expected with such hybrid molecules. From that intermediate form of reverse transcription, the resulting labelled cDNAs were obtained and were shown to be homologous to different drosophila "copia-like" transposable elements. These results suggest that most of the "copia-like" transposable elements were amplified through a reverse transcription pathway in Drosophila melanogaster.

Animals↗

PubMed1998

The behaviour of the autonomous maize transposable element En/Spm in Arabidopsis thaliana allows efficient mutagenesis.

The behavior of the autonomous maize transposable element En/Spm of maize was studied in Arabidopsis. Transgenic Arabidopsis plants carrying En-1 elements were propagated for 12 generations using a single seed descent procedure. The distribution and activity of the En-1 element was monitored using Southern DNA hybridisations in generations 1, 6 and 12. In the first generation the highest number of En-1 insertions per line was 7, which increased to 20 in generation 12. The average number of En-1 insertions increased only slightly in the population, due to a gradual accumulation of segregants that lost the transposable element. During the development of the En-1 mutagenised population the element remained active even in the high-copy lines. In situ hybridisation demonstrated that multiple En-1 insertions were distributed over all Arabidopsis chromosomes. From the initial En-1 mutagenised populations many unstable gene mutations were recovered, indicating that En-1 can be used as a efficient tool for gene tagging in Arabidopsis.

Arabidopsis↗

PubMed1987

Developmental expression of Drosophila melanogaster retrovirus-like transposable elements.

We have determined the pattern of temporal expression of several Drosophila retrovirus-like transposable elements. Some of these elements can be grouped into classes whose members show a similar profile of developmental transcription. The members of the 412 class, which includes 412, mdg1, 17.6 and 3S18, are transcribed mainly in the early larval and pupal stages of development, with small differences among the various members. HMS Beagle and Springer constitute another class where RNA accumulation in the larval stages is higher than in pupae and the adult flies accumulate more RNA than any other stage of development. Finally, the transcription of other elements such as copia, 297 and B104 follows a specific and individual pattern distinct from those described above. These results suggest the existence of evolutionary relationships among different transposable elements in Drosophila and the involvement of different cellular genes in the control of their expression.

Animals↗

PubMedDate not supplied

Mys, a family of mammalian transposable elements isolated by phylogenetic screening.

It has recently been demonstrated both emperically and mathematically that transposable elements may spread rapidly throughout a population once introduced even when they dramatically reduce the fitness of individuals that carry them. Such events result in pronounced differences in the phylogenetic distribution of genetic elements capable of rapid genome invasion. Using a simple and general procedure to screen the genome of the white-footed mouse Peromyscus leucopus, we have isolated a family of retrovirus-like elements which is apparently absent from the genome of the house mouse Mus domesticus. Here, we report this procedure and an analysis of the organization, phylogenetic distribution and sequence of this family of transposable elements.

Animals↗

PubMed1996

Identification of Tnr3, a suppressor-mutator/enhancer-like transposable element from rice.

We isolated members of the retroposon family p-SINE1 in rice and found that one member contained an insertion.Aa 3-bp sequence at the insertion site within p-SINE1 appeared duplicated. The insertion sequence, 1539 bp in length, carried imperfect inverted repeats of about 13 bp at its termini which begin with 5'-CACTA---3'; these repeats are similar to those found in members of the En/Spm transposable element family. These results indicate that the insertion sequence is a transposable element belonging to the En/Spm family and is thus named Tnr3 (transposable element in rice no. 3). In fact, Tnr carried long subterminal regions containing direct and inverted repeats of short DNA sequences of 15 bp, another characteristic of the En/Spm family. The subterminal repeat sequences in Tnr3 are, however, of two kinds, although they share homology with each other. Tnr3 and its relatives were present in multiple copies in rice. considering the length of Tnr3, it cannot represent an autonomous type element, but is a non-autonomous element probably derived by deletion from an autonomous transposon.

Base Sequence↗

PubMed1980

Insertion of the eukaryotic transposable element Ty1 creates a 5-base pair duplication.

The his4-912 mutation results from insertion of a transposable element into the 5'-non-coding region of the his4 gene of yeast. A duplication of 5 base pairs of wild-type his4 DNA flanks the inserted element. The major class of His+ revertants result from excision of most of the transposable element, leaving an inserted segment of 334 base pairs flanked by the 5-base pair repeats.

Base Sequence↗

PubMed1997

Selection on the protein-coding genes of the TBE1 family of transposable elements in the ciliates Oxytricha fallax and O. trifallax.

TBE1s are "cut-and-paste" transposable elements found in high copy number in the germline genomes of the ciliates Oxytricha fallax and O. trifallax. TBE1 "family" sequence (sequence of mixed polymerase chain reaction products generated using primers that match roughly half the TBE1s in host whole-cell DNA) was obtained from both host species. Although family sequence autoradiograms represent thousands of different elements, they are as legible as those representing corresponding sequences of a single TBE1, implying that ideal polymorphisms are rare within the genes examined. Nucleotide polymorphisms among TBE1s (indicated by ambiguities in family sequence) are far more common at third than at first or second positions of codons of genes, implying that selection has conserved the amino acid sequences of these genes in the majority of TBE1s. Portions of the transposase gene and another TBE1 gene have been sequenced from 10 individual TBE1s. None of these portions is interrupted by stop codons or frameshifts, and, for both genes, pairwise comparisons of these sequences show that nonsynonymous differences are significantly less common than synonymous differences, again implicating conservative selection Phylogenetic analysis shows that multiple divergent lineages of TBE1s have evolved under this selection within O. fallax. All these results are unexpected for cut-and-paste transposons in eukaryotic hosts: since transposase encoded by intact elements presumably acts in trans, it can duplicate mutant copies (those that do not encode functional transposase) found in the same genome, and thus no selection is expected to maintain the transposase gene. The selection demonstrated here could act at transposition (if functional TBE1s are preferentially transposed) or at the level of the host (if the host's fitness depends on functional TBE1 genes). TBE1-encoded proteins might be responsible for the precise excision of TBE1s that occurs during development of the host somatic nucleus; selection on hosts for uninterrupted somatic genes would then translate into selection for TBE1 protein-coding competence. We suggest a method for distinguishing between these two classes of explanations by finding and analyzing divergent alleles of ancestral transposable element insertions.

Animals↗