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At least 829 records · Page 46Linked to original sources
PubMed1996

The Ty1-copia group retrotransposons of Allium cepa are distributed throughout the chromosomes but are enriched in the terminal heterochromatin.

The genomic organization and diversity of the Ty1-copia group retrotransposons has been investigated in a monocotyledonous plant, Allium cepa. We used the polymerase chain reaction (PCR) to generate sequences corresponding to a conserved domain of the reverse transcriptase gene of Ty1-copia retrotransposons in this plant. Sequence analysis of 27 of these PCR products shows that they are a highly heterogeneous population, a feature which is common in plants but not in yeast and Drosophila. Slot-blot analysis shows there are 100,000-200,000 copies of Ty1-copia group retrotransposons within the A. cepa genome (2C = 31.7 pg), indicating that they are a significant component of the genome of this plant. In situ hybridization to metaphase chromosomes reveals that Ty1-copia retrotransposons are distributed throughout the euchromatin of all chromosomes of A. cepa but are enriched in the terminal heterochromatic regions, which contain tandem arrays of satellite sequences. This is the first clear evidence for the presence of Ty1-copia retrotransposons in the terminal heterochromatin of plants and contrasts with the distribution of these elements in other plant species.

Allium↗
PubMed1996

Geographical variation in insertion site number of retrotransposon 412 in Drosophila simulans.

The insertion site number of the retrotransposable element 412 was analyzed in natural populations of Drosophila simulans of worldwide origin by in situ hybridization. We observe a gradient in copy number ranging from as high as 23 in Europe to 1-10 in South Africa, while populations in Madagascar and the Indian Islands, which are the cradle of D. simulans, have only 3-7 copies. We find very different copy numbers in some local populations of Australia and the Pacific Islands (with around 60 copies in 1 sample and only 5 in another), suggesting spontaneous transposition bursts in local populations. Such bursts occurring now and then in local natural populations followed by fly migration could lead to the progressive invasion of the entire species by the transposable element mobilized, explaining the gradient in 412 copy number between northern and southern hemispheres.

Animals↗
PubMed1994

Expression vectors for the construction of hybrid Ty-VLPs.

Purification of expressed proteins can be facilitated by expressing the recombinant protein as a fusion with a carrier protein that assembles into particulate structures. This article describes the use of expression vectors in producing a hybrid of the yeast retrotransposon Ty, which self-assembles into virus-like particles (VLPs). Hybrid VLPs can be used in such laboratory applications as the production of polyclonal and monoclonal antibodies, structure/function analyses, the detection of important antigenic determinants, and epitope mapping of monoclonal antibodies.

Biotechnology↗
PubMed1994

Production and purification of hybrid Ty-VLPs.

This article describes how pure Ty-VLPs (virus-like particles) can be prepared from hybrid Ty-VLPs. Many different hybrid Ty-VLPs have been produced and may be easily purified. Since the sedimentation properties of different hybrid Ty-VLPs are similar, a simple purification process can be used for any VLP. This fast, versatile, and easy process allows for the production of a variety of recombinant proteins.

Biotechnology↗
PubMed2006

Development of an efficient retrotransposon-based fingerprinting method for rapid pea variety identification.

Fast and efficient DNA fingerprinting of crop cultivars and individuals is frequently used in both theoretical population genetics and in practical breeding. Numerous DNA marker technologies exist and the ratio of speed, cost and accuracy are of importance. Therefore even in species where highly accurate and polymorphic marker systems are available, such as microsatellite SSR (simple sequence repeats), also alternative methods may be of interest. Thanks to their high abundance and ubiquity, temporary mobile retrotransposable elements come into recent focus. Their properties, such as genome wide distribution and well-defined origin of individual insertions by descent, predetermine them for use as molecular markers. In this study, several Ty3-gypsy type retrotransposons have been developed and adopted for the inter-retrotransposon amplified polymorphism (IRAP) method, which is suitable for fast and efficient pea cultivar fingerprinting. The method can easily distinguish even between genetically closely related pea cultivars and provide high polymorphic information content (PIC) in a single PCR analysis.

Breeding↗
PubMed1997

Analysis of orthologous retrovirus-like elements in the white-footed mouse, Peromyscus leucopus.

Three loci in the genome of the white-footed mouse, Peromyscus leucopus, were examined for the presence or absence of orthologous copies of the retrovirus-like element mys using polymerase chain reaction. We examined these loci in 28 mice collected throughout the P. leucopus species range. Mys insertions were present in only one of the individuals examined at the mys-1 and mys-7 loci. Conversely, the mys-6 element was found in several individuals, but the presence of this element was limited to northern latitudes. Because the long terminal repeats (LTRs) of a given element are expected to be identical at the time of retrotransposition into the genome, and to accumulate changes over evolutionary time, within-element LTR sequence comparisons can be used to estimate the relative age of insertions. Within-element LTR differences are greater in mys-6 than in mys-1 or mys-7. The LTRs from orthologous mys-6 elements of six mice were sequenced. The alignment revealed 13 of the 22 differences between the right and left LTRs that were shared by all orthologous mys-6 sites, suggesting that relative to its time of insertion into the genome, mys-6 has only recently spread across the northern part of the species range.

Animals↗
PubMed1997

Intragenomic distribution and stability of transposable elements in euchromatin and heterochromatin of Drosophila melanogaster: non-LTR retrotransposon.

The intragenomic location of the elements of the I, G, jockey, F, and Doc transposon families has been studied by the Southern blot analysis, in 12 laboratory Drosophila melanogaster stocks. Elements located in euchromatin, heterochromatin, and on the Y chromosome are identified, and their stability has been assessed by comparing the autoradiographs detected in different stocks and analysis of individual flies. Evidence is shown suggesting that preferential location in euchromatin or heterochromatin and the distribution within heterochromatin are distinctive of transposon families. Elements located in heterochromatin can be unstable. These results are discussed in the context of the relationship between transposable elements and the host genome.

Animals↗
PubMed1997

A major non-LTR retrotransposon of Bombyx mori, L1Bm.

Repetitive sequences with oligo A tails were observed in Dra1 fragments of Bombyx mori genomic DNA. The full sequence of the element, an abundant non-LTR retrotransposon of B. mori, was determined by assembling inner restriction fragments. This element, designated L1Bm, contained two ORFs encoding a gag-like protein and reverse transcriptase (RT), respectively. An endonuclease domain was identified at the N-terminus of the RT sequence. The homology search of the amino acid sequences revealed that L1Bm belongs evolutionally to the same family as various other non-LTR retrotransposons of Drosophila and Mosquito. On the other hand, L1Bm resembles the L1 element of human genome in its high copy number and its frequent truncation at the 5'-side. Some units of the histone gene repeat in B. mori possess complete L1Bm elements in a 3'-flanking region of H2b.

Amino Acid Sequence↗
PubMed1997

Rapid evolution of a young L1 (LINE-1) clade in recently speciated Rattus taxa.

L1 elements are retrotransposons that have been replicating and evolving in mammalian genomes since before the mammalian radiation. Rattus norvegicus shares the young L1mlvi2 clade only with its sister taxon, Rattus cf moluccarius. Here we compared the L1mlvi2 clade in these recently diverged species and found that it evolved rapidly into closely related but distinct clades: the L1mlvi2-rm clade (or subfamily), characterized here from R. cf moluccarius, and the L1mlvi2-rn clade, originally described in R. norvegicus. In addition to other differences, these clades are distinguished by a cluster of amino acid replacement substitutions in ORF I. Both rat species contain the L1mlvi2-rm clade, but the L1mlvi2-rn clade is restricted to R. norvegicus. Therefore, the L1mlvi2-rm clade arose prior to the divergence of R. norvegicus and R. cf moluccarius, and the L1mlvi2-rn clade amplified after their divergence. The total number of L1mlvi2-rm elements in R. cf moluccarius is about the same as the sum of the L1mlvi2-rm and L1mlvi2-rn elements in R. norvegicus. The possibility that L1 amplification is in some way limited so that the two clades compete for replicative supremacy as well as the implications of the other distinguishing characteristic of the L1mlvi2-rn and L1mlvi2-rm clades are discussed.

Amino Acid Sequence↗
PubMed1997

Determination of the evolutionary relationships in Rattus sensu lato (Rodentia : Muridae) using L1 (LINE-1) amplification events.

We determined approximately 215 bp of DNA sequence from the 3'-untranslated region (UTR) of 240 cloned L1 (LINE-1) elements isolated from 22 species of Rattus sensu lato and Rattus sensu stricto murine rodents. The sequences were sorted into different L1 subfamilies, and oligonucleotides cognate to them were hybridized to genomic DNA of various taxa. From the distribution of the L1 subfamilies in the various species, we inferred the partial phylogeny of Rattus sensu lato. The four Maxomys species comprise a well-defined clade separate from a monophyletic cluster that contains the two Leopoldamys and four Niviventer species. The Niviventer/Leopoldamys clade, in turn, shares a node with the clade that contains Berylmys, Sundamys, Bandicota, and Rattus sensu stricto. The evolutionary relationships that we deduced agree with and significantly extend the phylogeny of Rattus sensu lato established by other molecular criteria. Furthermore, the L1 amplification events scored here produced a unique phylogenetic tree, that is, in no case did a character (a given L1 amplification event) appear on more than one branch. The lack of homoplasy found in this study supports the robustness of L1 amplification events as phylogenetic markers for the study of mammalian evolution.

Animals↗
PubMed1998

Short retroposons of the B2 superfamily: evolution and application for the study of rodent phylogeny.

Short retroposons can be used as natural phylogenetic markers. By means of hybridization and PCR analysis, we demonstrate that B2 retroposon copies are present only in the three rodent families: Muridae, Cricetidae, and Spalacidae. This observation highlights the close phylogenetic relation between these families. Two novel B2-related retroposon families, named DIP and MEN elements, are described. DIP elements are found only in the genomes of jerboas (family Dipodidae) and birch mice (family Zapodidae), demonstrating the close relationship between these rodents. MEN element copies were isolated from the squirrel, Menetes berdmorei, but were not detected in three other species from the family Sciuridae. The MEN element has an unusual dimeric structure: the left and right monomers are B2- and B1-related sequences, respectively. Comparison of the B2, DIP, MEN, and 4.5S1 RNA elements revealed an 80-bp core sequence located at the beginning of the B2 superfamily retroposons. This observation suggests that these retroposon families descended from a common progenitor. A likely candidate for this direct progenitor could be the ID retroposon.

Animals↗
PubMed1998

Accumulation of transposable elements in the heterochromatin and on the Y chromosome of Drosophila simulans and Drosophila melanogaster.

The elements of the transposon families G, copia, mdg 1, 412, and gypsy that are located in the heterochromatin and on the Y chromosome have been identified by the Southern blotting technique in Drosophila simulans and D. melanogaster populations. Within species, the abundance of such elements differs between transposon families. Between species, the abundance in the heterochromatin and on the Y chromosome of the elements of the same family can differ greatly suggesting that differences within a species are unrelated to structural features of elements. By shedding some new light on the mechanism of accumulation of transposable elements in the heterochromatin, these data appear relevant to the understanding of the long-term interaction between transposable elements and the host genome.

Animals↗
PubMed1998

Evidence for the role of recombination in the regulatory evolution of Saccharomyces cerevisiae Ty elements.

The recent completion of the sequencing of the Saccharomyces cerevisiae genome provides a unique opportunity to analyze the evolutionary relationships existing among the entire complement of retrotransposons residing within a single genome. In this article we report the results of such an analysis of two closely related families of yeast long terminal repeat (LTR) retrotransposons, Ty1 and Ty2. In our study, we analyzed the molecular variation existing among the 32 Ty1 and 13 Ty2 elements present within the S. cerevisiae genome recently sequenced within the context of the yeast genome project. Our results indicate that while the Ty1 family is most likely ancestral to Ty2 elements, both families of elements are relatively recent components of the S. cerevisiae genome. Our results also indicate that both families of elements have been subject to purifying selection within their protein coding regions. Finally, and perhaps most interestingly, our results indicate that a relatively recent recombination event has occurred between Ty2 and a subclass of Ty1 elements involving the LTR regulatory region. We discuss the possible biological significance of these findings and, in particular, how they contribute to a better overall understanding of LTR retrotransposon evolution.

DNA, Fungal↗
PubMed1998

The mouse gene encoding the testis-specific isoform of Poly(A) binding protein (Pabp2) is an expressed retroposon: intimations that gene expression in spermatogenic cells facilitates the creation of new genes.

The gene encoding the testis-specific isoform of mouse poly(A) binding protein (Pabp2) has been isolated and sequenced. Unexpectedly, comparison of the sequence of genomic and cDNAs demonstrated that the Pabp2 gene lacks introns, whereas all other functional Pabp genes in plants, amphibians, and mammals contain introns. Thus, the mouse Pabp2 gene is a retroposon, created by synthesizing a reverse transcriptase copy of a processed mRNA and inserting the copy into the genome. The Pabp2 retroposon is unusual because it is functional: previous work demonstrates that its promoter drives the accumulation of Pabp2 mRNA in meiotic and early haploid spermatogenic cells, and the Pabp2 mRNA encodes a protein whose size and RNA-binding specificities are characteristic of PABP in plants, yeast, and mammals (Kleene et al. 1994). Two novel factors can be implicated in the retention of function of the Pabp2 retroposon. First, the promoter of the Pabp2 gene is not derived from its intron-containing progenitor, Pabp1. Second, mRNAs encoding somatic PABP isoform, PABP1, are present at high levels in meiotic and haploid spermatogenic cells. Both features contrast with the phosphoglycerate kinase 2 retroposon, which is believed to compensate for the depletion of the somatic isoform due to X-chromosome inactivation in meiotic spermatogenic cells. We also document that more functional retroposons are expressed in meiotic and haploid spermatogenic cells than in any other tissue and speculate that transcriptional derepression in spermatogenic cells favors the creation of expressed retroposons.

Amino Acid Sequence↗
PubMed1998

Full-length L1 elements have arisen recently in the same 1-kb region of the gorilla and human genomes.

New copies of the mammalian retrotransposon L1 arise in the germline at an undetermined rate. Each new L1 copy appears at a specific evolutionary time point that can be estimated by phylogenetic analysis. In humans, the active L1 sequence L1.2 resides at the genomic locus LRE1. Here we analyzed the region surrounding the LRE1 locus in humans and gorillas to determine the evolutionary history of the region and to estimate the age of L1.2. We found that the region was composed of an ancient L1, L1Hs-Lrg, which was significantly divergent from all other L1 sequences available in the databases. We also determined that L1.2 was absent from the gorilla genome and arose in humans after the divergence of gorilla and human lineages. In the gorilla LRE1 region, we discovered a different full-length L1 element, L1Gg-1, which was allelic and present at a high gene frequency in gorillas but absent from other primates. We determined the nucleotide sequence of L1Gg-1 and found that it was 98% identical to L1.2, suggesting a close relationship between active L1s in gorillas and humans.

Alleles↗
PubMed1998

Similar target site selection occurs in integration of plant and mammalian retroposons.

The reverse transcription of RNA in DNA is responsible for the generation of large families of repetitive sequences called retroposons or non-LTR retrotransposons. Recent reports established that the integration of mammalian SINE and LINE retroposons occurs at nonrandom staggered breaks, probably resulting from the action of a LINE-encoded endonuclease (Feng et al. 1996; Jurka 1997; Jurka et al. 1998). We report here that plant SINE S1 retroposons also integrate at nonrandom staggered breaks. One of the two nicks involved in S1 integration is associated mainly with the 5'-Y/AAANNNG-3' motif. The other nick at opposite DNA strand occurs preferably within 14-16 bp, a situation also observed for mammalian retroposons, but is not associated with any specific motif. Further studies on the distribution of dinucleotides surrounding the two nicking sites showed that, as for mammalian retroposons, S1 retroposons integrate at sites rich in TA, CA, and TG dinucleotides. These dinucleotides were reported as specific DNA sites where special DNA structures called "kinks" may occur under bending constraints. Nicking sites are preceded by peaks in frequency of di-pyrimidine followed by peaks of di-purine. These results suggest that the general A/T richness of a given DNA region and the presence of short runs of pyrimidines followed by short runs of purines could represent a favorable context for the integration of retroposons. In such a context, an endonuclease upon fixation could be able to generate the kink at the pyrimidine/purine transition and to nick the DNA. The similarities in target site selection observed for plant and mammalian retroposons suggest that retroposition is a surprisingly well conserved process.

Animals↗
PubMed1998

Interelement selection in the regulatory region of the copia retrotransposon.

We report the results of an analysis of naturally occurring cis-regulatory variation within and between two families of the copia Drosophila long terminal repeat (LTR) retrotransposon. The copia 5' LTR and adjacent untranslated leader region (ULR) consists of a number of well-characterized sequence motifs which play a role in regulating expression of the element. In order to understand the evolutionary forces which may be responsible for generating and maintaining copia regulatory sequence variation, we have quantified levels of naturally occurring copia LTR-ULR nucleotide variation and subjected the data to a series of tests of neutrality. Our analysis indicates that the copia LTR-ULR has been subject to negative purifying selection within families and positive adaptive selection between families. We discuss these findings with respect to the regulatory evolution of retrotransposons and the phenomenon of interelement selection.

5' Untranslated Regions↗
PubMed1999

Evolution of tandemly repeated sequences: What happens at the end of an array?

Tandemly repeated sequences are a major component of the eukaryotic genome. Although the general characteristics of tandem repeats have been well documented, the processes involved in their origin and maintenance remain unknown. In this study, a region on the paternal sex ratio (PSR) chromosome was analyzed to investigate the mechanisms of tandem repeat evolution. The region contains a junction between a tandem array of PSR2 repeats and a copy of the retrotransposon NATE, with other dispersed repeats (putative mobile elements) on the other side of the element. Little similarity was detected between the sequence of PSR2 and the region of NATE flanking the array, indicating that the PSR2 repeat did not originate from the underlying NATE sequence. However, a short region of sequence similarity (11/15 bp) and an inverted region of sequence identity (8 bp) are present on either side of the junction. These short sequences may have facilitated nonhomologous recombination between NATE and PSR2, resulting in the formation of the junction. Adjacent to the junction, the three most terminal repeats in the PSR2 array exhibited a higher sequence divergence relative to internal repeats, which is consistent with a theoretical prediction of the unequal exchange model for tandem repeat evolution. Other NATE insertion sites were characterized which show proximity to both tandem repeats and complex DNAs containing additional dispersed repeats. An "accretion model" is proposed to account for this association by the accumulation of mobile elements at the ends of tandem arrays and into "islands" within arrays. Mobile elements inserting into arrays will tend to migrate into islands and to array ends, due to the turnover in the number of intervening repeats.

Base Sequence↗