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 631 records · Page 35Linked to original sources
PubMed1999

DEC: a new miniature inverted-repeat transposable element from the genome of the beetle Tenebrio molitor.

In this paper we describe a novel family of miniature inverted-repeat transposable elements (MITEs), named DEC, isolated from the genome of the beetle Tenebrio molitor. These elements are highly reiterated and their number is estimated to be around 3500 per haploid genome. Two of them have been isolated and the two sequences are 84% identical. Like other MITEs, they are characterized by their small size, their A + T richness, the presence of terminal inverted repeats and the absence of open reading frames. These data suggest that MITEs are probably widely distributed in arthropods.

Animals↗
PubMed2001

Population dynamics of an Ac-like transposable element in self- and cross-pollinating arabidopsis.

Theoretical models predict that the mating system should be an important factor driving the dynamics of transposable elements in natural populations due to differences in selective pressure on both element and host. We used a PCR-based approach to examine the abundance and levels of insertion polymorphism of Ac-III, a recently identified Ac-like transposon family, in natural populations of the selfing plant Arabidopsis thaliana and its close outcrossing relative, Arabidopsis lyrata. Although several insertions appeared to be ancient and shared between species, there is strong evidence for recent activity of this element family in both species. Sequences of the regions flanking insertions indicate that all Ac-III transposons segregating in natural populations are in noncoding regions and provide no evidence for local transposition events. Transposon display analysis suggests the presence of slightly higher numbers of insertion sites per individual but fewer total polymorphic insertions in the self-pollinating A. thaliana than A. lyrata. Element insertions appear to be segregating at significantly lower frequencies in A. lyrata than A. thaliana, which is consistent with a reduction in transposition rate, reduction in effective population size, or reduced efficacy of natural selection against element insertions in selfing populations.

Arabidopsis↗
PubMed2000

Distribution of the transposable element Minos in the genus Drosophila.

We analyzed 28 species of the genus Drosophila for the presence of the Tc1-like transposable element Minos using Southern blot hybridization under high stringency conditions. The Minos transposon was found in members of both the Drosophila and the Sophophora subgenus showing a distribution that is wider if compared to other well-studied Drosophila transposons such as the P element, hobo and mariner. The presence of Minos-hybridizing sequences was discontinuous in the Sophophora subgenus, especially in the melanogaster species group. Using the Polymerase Chain Reaction we amplified a portion corresponding to the putative Minos transposase from different Drosophila species. Cloning and sequence analysis of randomly selected Minos copies from D. mojavensisis, D. saltans and D. willistoni supports the idea that event(s) of horizontal transfer may have contributed to the spreading of this transposon in the Drosophila genus.

Animals↗
PubMed1998

Psl: a novel Spm-like transposable element from Petunia hybrida.

The identification of a spontaneous mutable Hf1 allele in Petunia hybrida provided an opportunity to isolate and characterize a novel transposable element. This 9.9 kb element has features in common with members of the Spm family, such as homologous terminal inverted repeats and a 3 bp target site direct duplication within the Hf1 gene. The element is named Petunia Spm-like (Psl). The footprints left by excising elements have been isolated from several germinal revertants and sequence analysis shows similarities to those left by other Spm family members. Southern analysis shows that the transposon is present at low copy number in the genome of different inbred lines and species of Petunia. The germinal excision frequency of Psl was 21-33% in outcross populations. The element appears to be very mobile somatically in the inbred line V26, with 38% of plants from an inbred population showing new Psl-hybridizing bands by Southern analysis. The high somatic and germinal excision frequency demonstrated by Psl suggests that this element may have utility for gene tagging in petunia.

Alleles↗
PubMed2003

Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions.

Nearly half of mammalian genomes are derived from ancient transposable elements (TEs). We analyzed the prevalence of TEs in untranslated regions of human and mouse mRNAs and found evidence suggesting that TEs affect the expression of many genes through the donation of transcriptional regulatory signals. Furthermore, we found that recently expanded gene classes, such as those involved in immunity or response to external stimuli, have transcripts enriched in TEs, whereas TEs are excluded from mRNAs of highly conserved genes with basic functions in development or metabolism. These results support the view that TEs have played a significant role in the diversification and evolution of mammalian genes.

Animals↗
PubMed2004

Transposable elements for transgenesis and insertional mutagenesis in vertebrates: a contemporary review of experimental strategies.

Functional genomic analyses in vertebrate model systems, including fish, frogs, and mice, have greatly contributed to our understanding of embryonic development and human disease. However, new molecular tools and strategies are needed to meet the increasing demands of linking sequence information to gene function. Transposable elements (TEs) are very efficient at integrating into DNA, and are therefore useful vectors for transferring new genetic material into genomes. In particular, members of the Tc1/mariner superfamily of elements are able to transpose in species other than their hosts, and are therefore emerging tools for functional genomics in several organisms. This chapter describes strategies of using retrovirus vectors and DNA-based TEs for transgenesis and insertional mutagenesis in vertebrates, with special emphasis on the Sleeping Beauty (SB) element, a reconstructed Tc1/mariner-like transposon from fish. SB jumps efficiently in cells of diverse vertebrate species in culture, as well as in somatic and germline tissues of the mouse in vivo. Simple structure and easy laboratory handling of transposon vectors are coupled with efficient and stable transgene integration and persistent, long-term transgene expression by transposon-mediated gene transfer. These features all contribute to the usefulness of TEs as tools for vertebrate functional genomics, as well as for animal biotechnology and human gene therapy.

Animals↗
PubMed1997

What restricts the activity of mariner-like transposable elements.

A number of mechanisms have recently been described that might be important in restricting the level of activity of mariner-like transposable elements (MLEs) in natural populations. These mechanisms include overproduction inhibition, in which increasing the dose of transposase decreases net activity. Another mechanism is mediated by certain missense mutations, in which a mutant transposase protein impairs the activity of the wild-type transposase in heterozygous mutant/nonmutant genotypes. A further mechanism is the potential for transposase titration by defective elements that retain transposase binding activity. The issue of regulation is not only of theoretical importance in understanding the molecular and evolutionary genetics of MLEs, but also of practical significance in learning how best to use MLEs in the germline transformation of insect pests and disease vectors.

Animals↗
PubMed2001

Ikirara insertions reveal five new Anopheles gambiae transposable elements in islands of repetitious sequence.

Characterization of Anopheles gambiae genomic clones containing Ikirara inverted repeats revealed five novel sequences related to known transposable elements (TEs). One TE is related to the mariner/Tc1 superfamily of class II (DNA-to-DNA) transposons, while four are related to class I (RNA-mediated transposition) elements. Crusoe, the class II element; is most similar to the Caenorhabditis elegans transposon Tc1-like TEs. Vash elements, represented twice in our clones, are related to the Q/T1 family of A. gambiae non-LTR retrotransposable elements. Guildenstern is a member of the RT1 and RT2 non-LTR retrotransposon family. Although RT1 and RT2 elements normally have a highly stereotyped insertion preference for sequences within ribosomal genes, Guildenstern is not located in ribosomal sequence. JuanAg is the first anopheline member of the mosquito non-LTR retrotransposon family of Juan elements that previously had included just the culicine elements JuanA and JuanC. Approximately 753 bp is missing from the central portion of the JuanAg reverse transcriptase gene, where an Ikirara inverted repeat is found in its stead. Ozymandias, the only LTR retrotransposon found in the clones, is most similar to the Drosophila melanogaster 412 element. Single Ikirara inverted repeats were also found adjacent to nontransposable element repetitious sequences. Our analysis suggests that the A. gambiae genome organization could best be described as islands of short-period interspersion repetitious DNA in a sea of long-period interspersion, mostly unique sequence DNA.

Amino Acid Sequence↗
PubMedDate not supplied

Identification of the protein encoded by the transposable element Tn3 which is required for its transposition.

Protein products have now been identified which account for the entire coding capacity of the transposable element Tn3. Mutations in Tn3 have allowed us to map the genes encoding each of these peptides and to identify their role in transposition. We have found that only a single Tn3-encoded peptide is required for transposition. Expression of this peptide is repressed by the product of a second gene, which is itself autogenously regulated.

Bacterial Proteins↗
PubMed1987

Transposable element Ds2 of Zea mays influences polyadenylation and splice site selection.

In the allele adh1-2F11 of Zea mays the 1.3 kb transposable element Ds2 is inserted in the fourth exon of Adh1. Two major RNAs of 3.0 and 1.6 kb are transcribed from this allele. While the 3.0 kb transcript also contains the Ds2 sequences, the 1.6 kb transcript has lost the Ds2 sequences by an alternative splicing process. In this process, a normal 5' splice site is joined to a cryptic 3' splice site located within exon 4. This cryptic 3' splice site is not used in a wild-type Adh1F allele. Other minor transcripts of adh1-2F11 are prematurely terminated and polyadenylated.

DNA Transposable Elements↗
PubMed2001

Perspective: transposable elements, parasitic DNA, and genome evolution.

The nature of the role played by mobile elements in host genome evolution is reassessed considering numerous recent developments in many areas of biology. It is argued that easy popular appellations such as "selfish DNA" and "junk DNA" may be either inaccurate or misleading and that a more enlightened view of the transposable element-host relationship encompasses a continuum from extreme parasitism to mutualism. Transposable elements are potent, broad spectrum, endogenous mutators that are subject to the influence of chance as well as selection at several levels of biological organization. Of particular interest are transposable element traits that early evolve neutrally at the host level but at a later stage of evolution are co-opted for new host functions.

Animals↗
PubMed1990

The effect of insertion of the maize transposable element mutator is dependent on genetic background.

A secondary mutant, derived from an allele of maize alcohol dehydrogenase 1 (Adh1) carrying a Mutator transposable element (Mu1) in its first intron, was reported to exhibit a threefold decrease in ADH enzymatic activity and steady-state RNA levels compared to the original mutant. The original mutant, Adh1-S3034 (abbreviated S3034), was previously characterized at the molecular level. The derivative, abbreviated S3034b, has now been cloned; at the DNA sequence level the insertion and surrounding Adh1 sequences are indistinguishable from S3034. Furthermore, in our lines there is no difference in relative ADH activities between products of the two putative alleles. A comparison of gene expression in heterozygotes obtained by crossing to different tester lines reveals a correlation between the measured decrease in levels of ADH polypeptide produced by the mutant allele and the background in which it is measured; this effect is distinct from any background-related variation in the expression of the progenitor allele. It does not appear to be attributable to alternative patterns of DNA modification. It appears to reflect a background-associated difference in the level of normal Adh1-RNA produced. Thus the previously reported distinction between S3034 and S3034b may be due to differences in the extent to which the mutant allele and a given genetic background interact to produce functional Adh1-RNA.

Alcohol Dehydrogenase↗
PubMed2025

Transposable elements create distinct genomic niches for effector evolution among Magnaporthe oryzae lineages.

BACKGROUND: Plant-pathogen interactions are characterized by evolutionary arms races. At the molecular level, fungal effectors can target important plant functions, while plants evolve to improve effector recognition. Rapid evolution in genes encoding effectors can be facilitated by transposable elements (TEs). In Magnaporthe oryzae, the causal agent of blast disease in several cereals and grasses, TEs play important roles in chromosomal evolution as well as the gain or loss of effector genes in host specialized lineages. However, a global understanding of TE dynamics driving effector evolution at population scale and across lineages is lacking. RESULTS: Here, we focus on 16 AVR effector loci assessed across a global sampling of 11 reference genomes and 447 newly generated draft genome assemblies from publicly available short-read sequencing data across all major M. oryzae lineages and outgroups. We classified each effector based on evidence for duplication, deletion and translocation processes among lineages. Next, we determined AVR gain and loss dynamics across lineages allowing for a broad categorization of effector dynamics. Each AVR was integrated in a distinct genomic niche determined by the TE activity profile contributing to the diversification at the locus. We quantified TE contributions to effector niches and found that TE identity helped diversify AVR loci. We used the large genomic dataset to recapitulate the evolution of the rice blast AVR1-CO39 locus. CONCLUSIONS: Taken together, our work demonstrates how TE dynamics are an integral component of M. oryzae effector evolution, likely facilitating escape from host recognition. In-depth tracking of effector loci is a valuable tool to predict the durability of host resistance.

Ascomycota↗
PubMed1999

Resident aliens: the Tc1/mariner superfamily of transposable elements.

Transgenic technology is currently applied to several animal species of agricultural or medical importance, such as fish, cattle, mosquitos and parasitic worms. However, the repertoire of genetic tools used for molecular analyses of mice and Drosophila is not always applicable to other species. For example, while retroviral enhancer-trap experiments in mice can be based on embryonic stem (ES) cell technology, this is not currently an option with other animals. Similarly, the germline transformation of Drosophila depends on the use of the P-element transposon, which does not jump in other genera. This article analyses the main characteristics of Tc1/mariner transposable elements, examines some of the factors that have contributed to their evolutionary success, and describes their potential, as well as their limitations, for transgenesis and insertional mutagenesis in diverse animals.

Amino Acid Sequence↗
PubMed1993

Maize Spm transposable element has an enhancer-insensitive promoter.

We have used a transient assay system to investigate the promoter region of the maize Suppressor-mutator (Spm) transposable element. All of the sequence required for constitutive promoter activity is confined to the 0.2-kb sequence upstream from the transcription start site of the element at nt 209 and designated the upstream control region. The element's promoter is weak, lacks a conventional TATA box, and depends on the presence of multiple, short repetitive sequence elements. The Spm promoter is quite insensitive to the enhancer sequence of the cauliflower mosaic virus 35S promoter. Enhancer sensitivity can be restored by providing a -30 TATA sequence and removing the G + C-rich sequence encoding the untranslated leader of the element, designated the downstream control region. Although the downstream control region is without effect on Spm promoter activity, it completely inhibits the 35S core promoter and markedly inhibits activity of the complete 35S promoter. The properties of the Spm element's promoter buffer it from both mutational and position-dependent changes in activity. We suggest that the inherent characteristics of the promoter are part of the genetic mechanism that controls the element's transposition frequency, ensuring it remains low and insertion-site independent.

Base Sequence↗
PubMed2000

Glider and Vision: two new families of miniature inverted-repeat transposable elements in Xenopus laevis genome.

We have characterised from Xenopus laevis two new short interspersed repetitive elements, we have named Glider and Vision, that belong to the family of miniature inverted-repeat transposable elements (MITEs). Glider was first characterised in an intronic region of the alpha-tropomyosin (alpha-TM) gene and database search has revealed the presence of this element in 10 other Xenopus laevis genes. Glider elements are about 150 bp long and for some of them, their terminal inverted repeats are flanked by potential target-site duplications. Evidence for the mobility of Glider element has been provided by the presence/absence of one element at corresponding location in duplicated alpha-TM genes. Vision element has been identified in the promoter region of the cyclin dependant kinase 2 gene (cdk2) where it is boxed in a Glider element. Vision is 284bp long and is framed by 14-bp terminal inverted repeats that are flanked by 7-bp direct repeats. We have estimated that there are about 20,000 and 300 copies of Glider and Vision respectively scattered throughout the Xenopus laevis genome. Every MITEs elements but two described in our study are found either in 5' or in 3' regulatory regions of genes suggesting a potential role in gene regulation.

Animals↗
PubMed1988

Retrovirus-like features and site specific insertions of a transposable element, tom, in Drosophila ananassae.

The tom element, putatively associated with optic morphology (Om) mutations in Drosophila ananassae, was identified as a retrovirus-like transposable element. The tom element was found to terminate with 475 (or 474) base pair direct repeats which are identical in sequence to each other. Southern blot and heteroduplex analyses showed the tom element to have high homology to 297 and 17.6, two retrotransposons found in D. melanogaster. As in the cases of 297 and 17.6, tom includes nucleotide sequences coding for a presumptive protease and reverse transcriptase, similar in amino acid sequence to those of the Moloney murine leukaemia virus. At the tom insertion site of the sn9g locus, a host DNA sequence (T)ATAT was found to be duplicated on each side of the tom insertion and all other tom elements examined were also flanked by (T)ATAT. In each of six cases, the 5' flanking host sequence was TATAT. These results indicate that the target sequence of the tom element may be TATAT and that the entire region or a part of this sequence was duplicated on insertion of the tom element.

Animals↗
PubMed1995

The role of subterminal sites of transposable element Ds of Zea mays in excision.

Transposition depends on DNA sequences located at or near the termini of the transposon. In the maize transposable element Ds, these sequences were studied by site-directed mutagenesis followed by a transient excision assay in Petunia protoplasts. The transposase-binding AAACGG motifs found in large numbers in the element are important, but none of them is in itself indispensable, for excision. However, mutation of an isolated motif at the 3' end considerably reduced excisability. The inverted termini were confirmed to be indispensable. Point mutations in regions outside the inverted termini of Ds and not located in the transposase-binding motifs had, in some cases, a pronounced effect on excision frequency. The implications of these findings are discussed.

Base Sequence↗