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PubMed2004

Evolution of the transposable element Pokey in the ribosomal DNA of species in the subgenus Daphnia (Crustacea: Cladocera).

Pokey is a member of the piggyBac (previously called the TTAA-specific) family of transposons and inserts into a conserved region of the large subunit ribosomal RNA gene. This location is a "hot spot" for insertional activity, as it is known to contain other arthropod transposable elements. However, Pokey is unique in that it is the first DNA transposon yet known to insert into this region. All other insertions are class I non-LTR retrotransposons. This study surveyed variation in Pokey elements through phylogenetic analysis of the 3' ends of Pokey elements from ribosomal DNA (rDNA) in species from the nominate subgenus of the genus Daphnia (Crustacea: Cladocera). The results suggest that Pokey has been stably, vertically inherited within rDNA over long periods of evolutionary time. No evidence was found to support horizontal transfer, which commonly occurs in other DNA transposons, such as P and mariner. Furthermore, Pokey has diverged into sublineages that have persisted across speciation events in some groups. In addition, a new highly divergent paralogous Pokey element was discovered in the rDNA of one species.

Animals↗
PubMed2004

Global heterochromatic colocalization of transposable elements with minisatellites in the compact genome of the pufferfish Tetraodon nigroviridis.

Because of its unusual high degree of compaction and paucity of repetitive sequences, the genome of the smooth pufferfish Tetraodon nigroviridis is the subject of a well-advanced sequencing project. An astonishing diversity of transposable elements not found in the human and the mouse has been observed in the genome of T. nigroviridis. Due to the difficulty of assembling repeat-rich regions, the whole genome shotgun sequencing approach will probably fail to reveal the general organisation of this compact vertebrate genome. Therefore, in order to gain new insights into the global distribution pattern of repeated DNA in the genome of T. nigroviridis, we have reconstructed partial/complete repetitive sequences from data generated by the genome project and performed double-colour fluorescent in situ hybridization (FISH) analysis for representatives of three major categories of repeated sequences including two minisatellites (ms100 and ms104), two DNA transposons (Tol2 and Buffy1) and two non-long terminal repeat (LTR) retrotransposons (Rex3 and Babar). We show that DNA transposons and retroelements very frequently colocalize with minisatellites and mostly accumulate within heterochromatic regions. These results, which have not been reported so far for the fugu Takifugu rubripes, show that repeated elements are generally excluded from gene-rich regions in T. nigroviridis and underline the extreme degree of compartmentalization of this compact genome. The genome organization of the pufferfish is clearly different from that observed in humans, where repeated sequences make up an important fraction of euchromatic DNA, and is more similar to that observed in the fruit fly Drosophila melanogaster.

Amino Acid Sequence↗
PubMed1988

Regulation of Mu element copy number in maize lines with an active or inactive Mutator transposable element system.

In the progeny of an active Mutator plant, the number of Mu elements increases on self-pollination and maintains the average parental Mu content on outcrossing to a non-Mutator line; both patterns of transmission require an increase in the absolute number of Mu elements from one generation to the next. The same average copy number of Mu elements is transmitted through the male and female, but there is wide variation in the absolute copy number among the progeny. In inactive Mutator plants-defined both by the loss of somatic instability at a reporter gene (bronze2-mu1) and by modification of the HinfI sites in the terminal inverted repeat sequences of Mu elements - the absolute copy number of Mu elements is fixed in the parent. Thus, in outcrosses Mu element number is halved, and on self-pollination Mu copy number is constant. Reactivation of somatic mutability at cryptic bz2-mu1 alleles in inactive individuals by crossing to an active line seems not to involve an increase in Mu element copy number transmitted by the inactive individual. These and other results suggest that increases in Mu copy number occur late in plant development or in the gametophyte rather than after fertilization.

DNA Transposable Elements↗
PubMed1990

Discovery of an insertion sequence, IS116, from Streptomyces clavuligerus and its relatedness to other transposable elements from actinomycetes.

We have identified an insertion sequence, IS116, present in Streptomyces clavuligerus at one copy per genome. The element was discovered as a 1.4 kb insertion into the multicopy plasmid pIJ702 after propagation in S. clavuligerus. The nucleotide sequence of IS116 and the flanking sequences from pIJ702 have been determined. The junctions with pIJ702 show no target site duplication and there are no inverted repeats at the ends of the element. One putative coding open reading frame of 1197 bp was identified which would code for a protein product of 399 amino acids. This protein resembles deduced integrase/transposase proteins specified by three other transposable elements of actinomycetes: IS110 and the mini-circle from Streptomyces coelicolor A3(2), and--most particularly--IS900 of Mycobacterium paratuberculosis. Two regions that are relatively conserved among these gene products show features found in similar positions in many reverse transcriptases. IS116 and IS900 are also closely similar in their general organization and (apparently) in their insertion site specificity, whereas IS110 and the mini-circle are quite different in these features.

Actinomycetales↗
PubMedDate not supplied

DNA sequence of the maize transposable element Dissociation.

The DNA sequence of the terminal 4.2 kilobases (kb) of the 30-kb insertion in the endosperm sucrose synthase gene of maize mutant sh-m5933 shows that it comprises two identical 2,040-base pair (bp) segments, one inserted in the reverse direction into the other. We suggest that the 2,040-bp sequence is an example of the transposable element Dissociation described by Barbara McClintock.

Base Sequence↗
PubMed1989

Interaction of the Enhancer of white-apricot with transposable element alleles at the white locus in Drosophila melanogaster.

The Enhancer of wa [E(wa)] mutation was shown to interact strongly with 4 of 41 tested alleles of the white (w) eye color locus. All four of the affected w alleles result from the insertion of a transposable element. E(wa) was further localized cytogenetically. The locus lies between the breakpoints of T(Y;2)L11 and T(Y;2)H137 (section 60) in 2R. The original mutation was shown to be antimorphic on the basis of its action in the presence of additional normal copies and the ability to revert the original allele to one that mimics the effect of a deficiency for the locus. The RNA transcribed from wa was analyzed from flies segregating for E(wa) and normal. The low level of normal functional messenger RNA present in white-apricot is reduced further in Enhancer homozygotes. Total copia RNA was also examined on Northern analyses from the segregating population but no quantitative change in the major copia RNA was produced by E(wa) homozygotes compared to normal.

Alleles↗
PubMed1997

Evidence for a host role in regulating the activity of transposable elements in Drosophila melanogaster: the case of the persistent instability of Bari 1 elements in Charolles stock.

In most reports in which the activity of numerous Drosophila transposon families has been studied, only a subset of the families tested appears mobile. A comparison of these data shows that there are no transposons inherently more unstable than others and suggests that host factors regulate the activity of transposable elements. Consistent with this conclusion are the properties of Bari 1 elements, which are the only ones of the 14 families tested to be unstable in Charolles stock. Instability is persistent over 53 generations and appears to affect recurrent insertion sites.

Animals↗
PubMed1999

Transposable elements as a molecular evolutionary force.

This essay addresses the paradoxes of the complex and highly redundant genomes. The central theses developed are that: (1) the distinctive feature of complex genomes is the existence of epigenetic mechanisms that permit extremely high levels of both tandem and dispersed redundancy; (2) the special contribution of transposable elements is to modularize the genome; and (3) the labilizing forces of recombination and transposition are just barely contained, giving a dynamic genetic system of ever increasing complexity that verges on the chaotic.

Animals↗
PubMed2006

[Progress of Tol2 transposable element in Medaka fish].

As insertional mutagens or molecular tagging, transposons have been widely used for gene isolation, cloning and function study. Most of transposons are from microorganisms and plants. Medaka Tol2 is the only natural active transposon in vertebrate until now, which was found recently and is likely a peculiar transposon system of vertebrate. The structure of Tol2 transposable element, its transposition mechanism and application, are reviewed in this paper.

Animals↗
PubMed2005

Multiple events of horizontal transfer of the Minos transposable element between Drosophila species.

In this study the Minos element was analyzed in 26 species of the repleta group and seven species of the saltans group of the genus Drosophila. The PCR and Southern blot analysis showed a wide occurrence of the Minos transposable element among species of the repleta and the saltans groups and also a low number of insertions in both genomes. Three different analyses, nucleotide divergence, historical associations, and comparisons between substitution rates (d(N) and d(S)) of Minos and Adh host gene sequences, suggest the occurrence of horizontal transfer between repleta and saltans species. These data reinforce and extend the Arca and Savakis [Genetica 108 (2000) 263] results and suggest five events of horizontal transfer to explain the present Minos distribution: between D. saltans and the ancestor of the mulleri and the mojavensis clusters; between D. hydei and the ancestor of the mulleri and the mojavensis clusters; between D. mojavensis and D. aldrichi; between D. buzzatii and D. serido; and between D. spenceri and D. emarginata. An alternative explanation would be that repeated events of horizontal transfer involving D. hydei, which is a cosmopolitan species that diverged from the others repleta species as long as 14Mya, could have spread Minos within the repleta group and to D. saltans. The data presented in this article support a model in which distribution of Minos transposon among Drosophila species is determined by horizontal transmission balanced by vertical inactivation and extinction.

Animals↗
PubMed1989

Interactions between transposable elements for insertion in the Drosophila melanogaster genome.

Using in situ hybridization to polytene salivary gland chromosomes, we have registered the co-occurrences of insertions of the four mobile elements, copia, mdg-1, I and P in the whole genomes of 17 highly-inbred lines of Drosophila melanogaster (the insertions in the centromeric regions were excluded); these elements differ in structure, DNA sequence and profile of developmental transcription. The mdg-1 and P elements tend to avoid each other on the X chromosomes but not on the autosomes; copia and mdg-1, two copia-like elements, show an excess of co-occurrences on the 2L and 3R chromosome arms but not on the X chromosomes. The pairs mdg-1/I, I/copia, I/P and copia/P do not show any kind of interaction. Populational studies are thus necessary to obtain complete accurate information on interactions between transposable elements for their sites of insertion in a genome.

Animals↗
PubMed1995

Strain evolution in Caenorhabditis elegans: transposable elements as markers of interstrain evolutionary history.

Evolutionary relationships across taxa can be deduced from sequence divergence of proteins, RNA, or DNA; sequences which diverge rapidly, such as those of mitochondrial genes, have been especially useful for comparisons of closely related species, and--within limits--of strains within a species. We have utilized the transposable element Tc1 as a polymorphic marker to evaluate the evolutionary relationships among nine Caenorhabditis elegans strains. For five low-Tc1-copy strains, we compared patterns of restriction fragments hybridizing to a cloned Tc1 probe. Twenty of the 40 Tc1 insertion sites thus characterized were common to all five strains, and so presumably preceded strain divergence; the 20 differential bands were used to construct a maximum-parsimony tree relating these strains. In four high-copy-number stocks (three wild-type strains and a subline), we determined occupancy of 35 individual Tc1 insertion sites by a polymerase chain reaction assay. Surprisingly, the high-copy strains share a common subset of these Tc1 insertions, and the chromosomal distribution of conserved Tc1 sites is "clustered" with respect to the other elements tested. These data imply a close evolutionary relationship among the high-copy strains, such that two of these strains appear to have been derived from the highest-copy-number lineage (represented by two stocks) through crossing with a low-Tc1 strain. Abundances of Tc1 elements were also estimated for the four high-copy-number stocks, at approximately 200-500 copies per haploid genome, by quantitative dot-blot hybridization relative to two low-copy strains. Annealing with 32P-labeled probes corresponding to full-length Tc1, an oligonucleotide within the Tc1 terminal inverted repeats, and an internal Tc1 oligonucleotide, gave essentially identical results--indicating that Tc1 termini exist in the genome primarily as components of full-length Tc1 elements. A composite evolutionary tree is proposed, based on the locations and numbers of Tc1 elements in these strains, which is consistent with a four-branch intraspecific tree deduced previously by maximum-parsimony analyses of mitochondrial sequence changes; it also serves to elucidate the evolutionary history of transposon mobility.

Animals↗
PubMed2004

Transposition mechanisms and biothechnology applications of the medaka fish tol2 transposable element.

The Tol2 element of the medaka fish is a member of the hAT (hobo/Activator/Tam3) transposable element family. About 20 copies are present in the medaka fish genome and, unlike many other hAT family elements, virtually all the copies are autonomous or potentially autonomous, containing an intact transposase gene. Excision of Tol2 is not precise at the nucleotide sequence level, excision footprints being heterogeneous. In more than half of excision events, however, breakage and rejoining of DNA molecules occur within the 8-bp target site duplication region, removing the entire Tol2 sequence and retaining parts of the target site duplications. In the reminder of the excision events, either the left or the right terminal region is left and the other end is lost together with its flanking region. Thus, there might be two different mechanisms of excision. Insertion of Tol2 occurs without detectable preference for target sequences and creates a target site duplication of exactly 8 bp. In addition to the medaka fish and related fish species, Tol2 transposes in mammalian cells in culture, including human and mouse examples. Autonomy is also retained in these cases. A gene transfer vector using Tol2 has already been established in fish. Foreign DNA fragements inserted in Tol2 can be efficiently delivered to the chromosomes by transposition. The latest version of the vector contains, between the Tol2 terminal regions, a bacterial drug-resistance gene and a plasmid replication origin. This allows simple recovery of insertion regions, as plasmid DNA, from genomic DNA of transformants. Modification of this system for other vertebrates, especially for mammals, are now in progress.

Journal Article↗
PubMed2025

Enhancer activation from transposable elements in extrachromosomal DNA.

Extrachromosomal DNA (ecDNA) drives oncogene amplification and intratumoral heterogeneity in aggressive cancers. While transposable element (TE) reactivation is common in cancer, its role on ecDNA remains unexplored. Here, we map the 3D architecture of MYC-amplified ecDNA in colorectal cancer cells and identify 68 ecDNA-interacting elements (EIEs)-genomic loci enriched for TEs that are frequently integrated onto ecDNA. We focus on an L1M4a1#LINE/L1 fragment co-amplified with MYC, which functions only in the ecDNA amplified context. Using CRISPR-CATCH, CRISPR interference, and reporter assays, we confirm its presence on ecDNA, enhancer activity, and essentiality for cancer cell fitness. These findings reveal that repetitive elements can be reactivated and co-opted as functional rather than inactive sequences on ecDNA, potentially driving oncogene expression and tumor evolution. Our study uncovers a mechanism by which ecDNA harnesses repetitive elements to shape cancer phenotypes, with implications for diagnosis and therapy.

Journal Article↗
PubMed1993

Aberrant transcription caused by the insertion of an early transposable element in an intron of the Fas antigen gene of lpr mice.

The mouse lpr (lymphoproliferation) mutation carries a rearrangement in the chromosomal gene for the Fas antigen, which mediates apoptosis. Isolation and characterization of mouse Fas antigen chromosomal gene from wild-type and lpr mice indicated an insertion of an early transposable element (ETn) in intron 2 of the Fas antigen gene of lpr mice. Hybrid transcripts carrying the Fas antigen and ETn sequences were expressed in the thymus and liver of the mutant. This indicated that premature termination and aberrant splicing of the Fas antigen transcript caused by the insertion of the ETn in the intron are responsible for the lymphoproliferation and autoimmune phenotype of the mutant mouse. On the other hand, an insertion of the ETn into an intron of a mammalian expression vector dramatically but not completely reduced the expression efficiency. These findings suggest that lpr mice are able to express a very low level of the Fas antigen.

Amino Acid Sequence↗
PubMed1980

Electron microscopic observation of new transposable elements inserted into P22 phage genome from R plasmids.

By using phage P22spl, a deletion mutant of phage P22, the structures of two new transposons on P22 genomes were studied by the electron microscopic heteroduplex method. One of these was the Cm (chloramphenicol) transposon derived from an R plasmid, NR1, and the other the Km (kanamycin) transposon frin obr502. the heteroduplex between P22 phage DNAs with and without the Cm transposon revealed that the Cm transposon was similar in structure to the Tn9 element, a well-known Cm transposon derived from the R plasmid pMS14. On the other hand, the Km transposon of pNR502 was quite different in structure from other Km transposons reported previously. This transposon consists of a 6.8 kilobase (kb) segment of DNA, in which a short inverted repeat is contained. The heteroduplex experiments showed that a 4.5 kb segment of DNA was deleted from the P22 genome in the P22spl genome. Because of a shorter unit length of the genome, phage P22spl is considered to be useful of assaying various kinds of transposable elements.

Chromosome Deletion↗
PubMed2002

Using the P[wHy] hybrid transposable element to disrupt genes in region 54D-55B in Drosophila melanogaster.

Understanding the function of each gene in the genome of a model organism such as Drosophila melanogaster is an important goal. The development of improved methods for uncovering the mutant phenotypes of specific genes can accelerate achievement of this goal. The P[wHy] hybrid transposable element can be used to generate nested sets of precisely mapped deletions in a given region of the Drosophila genome. Here we use the P[wHy] method to generate overlapping, molecularly defined deletions from a set of three P[wHy] insertions in the 54E-F region of chromosome 2. Deletions that span a total of 0.5 Mb were identified and molecularly mapped precisely. Using overlapping deletions, the mutant phenotypes of nine previously uncharacterized genes in a 101-kb region were determined, including identification of new loci required for viability and female fertility. In addition, the deletions were used to molecularly map previously isolated lethal mutations. Thus, the P[wHy] method provides an efficient method for systematically determining the phenotypes of genes in a given region of the fly genome.

Animals↗