Genomic organization of the transposable element Tdd-3 from Dictyostelium discoideum

Marschalek, Rolf; Borschet, Gabi; Dingermann, Theo

doi:10.1093/nar/18.19.5751

Cited by 14 publications

(19 citation statements)

References 18 publications

(17 reference statements)

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“…To gain insight into this interesting phenomenon, we analyzed the genomic organization of previously isolated tRNA genes (32). In the course of this study, we repeatedly identified the retrotransposable element DRE as well as the previously characterized transposable Tdd-3 element (30,38). Both elements were found associated with several unrelated tRNA genes in a characteristic position-specific manner.…”

mentioning

confidence: 76%

Structure of DRE, a retrotransposable element which integrates with position specificity upstream of Dictyostelium discoideum tRNA genes.

Marschalek¹,

Hofmann²,

Schumann³

et al. 1992

Mol. Cell. Biol.

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morphism (12, 13). To gain insight into this interesting phenomenon, we analyzed the genomic organization of previously isolated tRNA genes (32). In the course of this study, we repeatedly identified the retrotransposable element DRE as well as the previously characterized transposable Tdd-3 element (30,38). Both elements were found associated with several unrelated tRNA genes in a characteristic position-specific manner.Up to now, DRE has never been found other than in association with tRNA genes in D. discoideum. In all analyzed clones, tRNA genes are separated by 50 ± 3 nucleotides from the associated DRE element, and DRE always occurs in a constant orientation relative to tRNA genes. Since no sequence similarity is apparent at the DRE integration site, a mechanism other than sequence-specific integration must be responsible for this striking position-specific and orientation-specific integration of DRE elements in D. discoideum. Similar results with respect to position specificity but not with respect to orientation specificity were obtained for Ty3, a retrotransposon identified in S. cerevisiae. Ty3 elements or a remnant LTR, termed sigma, were also found in front of various tRNA genes, separated in this case by 16 to 19 nucleotides from the mature coding tDNA sequence (10, 41). Both Ty3 and DRE, therefore, are members of a family of retrotransposons which integrate by a position-specific rather than by sequence-specific or random mechanisms into the chromosome (8, 31). Sequence-specific recombination has been described for many retrotransposable elements in different organisms (1,5,15,21,22,50), but many retrotransposons and most retroviruses are thought to integrate more or less at random (for reviews, see references 3, 42, and 45). In the cases of Ty3 and DRE, a great number and variety of tRNA genes mark the specific integration sites. This is a remarkable fact which puts these elements into a different category from other retrotransposons and

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confidence: 76%

Structure of DRE, a retrotransposable element which integrates with position specificity upstream of Dictyostelium discoideum tRNA genes.

Marschalek¹,

Hofmann²,

Schumann³

et al. 1992

Mol. Cell. Biol.

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“…For example, two retrotransposons are associated with tRNA genes in Dictyostelium discoideum (Marschalek et al 1989(Marschalek et al , 1990. In Drosophila melanogaster, the HeT-A and TART elements transpose to chromosome ends and serve as telomeres (Biessmann et al 1990;Levis et al 1993), and telomeric retrotransposons have also been observed in the blue-green alga Chlorella (Higashiyama et al 1997).…”

Section: Ty Target Biasmentioning

confidence: 99%

Transposable Elements and Genome Organization: A Comprehensive Survey of Retrotransposons Revealed by the Complete Saccharomyces cerevisiae Genome Sequence

Kim¹,

Vanguri²,

Boeke³

et al. 1998

Genome Res.

499

563

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We conducted a genome-wide survey of Saccharomyces cerevisiae retrotransposons and identified a total of 331 insertions, including 217 Ty1, 34 Ty2, 41 Ty3, 32 Ty4, and 7 Ty5 elements. Eighty-five percent of insertions were solo long terminal repeats (LTRs) or LTR fragments. Overall, retrotransposon sequences constitute >377 kb or 3.1% of the genome. Independent evolution of retrotransposon sequences was evidenced by the identification of a single-base pair insertion/deletion that distinguishes the highly similar Ty1 and Ty2 LTRs and the identification of a distinct Ty1 subfamily (Ty1Ј). Whereas Ty1, Ty2, and Ty5 LTRs displayed a broad range of sequence diversity (typically ranging from 70%-99% identity), Ty3 and Ty4 LTRs were highly similar within each element family (most sharing >96% nucleotide identity). Therefore, Ty3 and Ty4 may be more recent additions to the S. cerevisiae genome and perhaps entered through horizontal transfer or past polyploidization events. Distribution of Ty elements is distinctly nonrandom: 90% of Ty1, 82% of Ty2, 95% of Ty3, and 88% of Ty4 insertions were found within 750 bases of tRNA genes or other genes transcribed by RNA polymerase III. tRNA genes are the principle determinant of retrotransposon distribution, and there is, on average, 1.2 insertions per tRNA gene. Evidence for recombination was found near many Ty elements, particularly those not associated with tRNA gene targets. For these insertions, 5Ј-and 3Ј-flanking sequences were often duplicated and rearranged among multiple chromosomes, indicating that recombination between retrotransposons can influence genome organization. S. cerevisiae offers the first opportunity to view organizational and evolutionary trends among retrotransposons at the genome level, and we hope our compiled data will serve as a starting point for further investigation and for comparison to other, more complex genomes.

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“…It appeared that a Tdd-3 element was inserted into a Tdd-2 element, which had previously inserted downstream of the coding region of a tRNA Met (CUA) gene. In subsequent studies it was shown that Tdd-3 elements insert independently of Tdd-2 into genomic loci downstream of tRNA genes [52,53,63]. Tdd-2 and Tdd-3 are highly diverged in DNA sequence except for a 22-bp DNA motif near the 5% end of the element that is almost identical [62,64].…”

Section: Tdd-3 and Red Elementsmentioning

confidence: 99%

“…Several isolated genomic DNA fragments contained Tdd-3 tandem arrays. Although only the borders of such tandems have been sequenced [63], it is plausible to assume that the 5% Tdd-3 elements of tandems are inserted downstream of tRNA genes. Analysis of the spacing DNA sequences between Tdd-3 elements in the tandems showed no conserved sequences.…”

Section: Tdd-3 and Red Elementsmentioning

confidence: 99%

Retrotransposable elements in the Dictyostelium discoideum genome

Winckler¹

1998

Cellular and Molecular Life Sciences (CMLS)

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Repetitive DNA is a major component of any living cell. In eukaryotes retrotransposable elements make up several percent of the genome size, and consequently, retroelements are often identified in experiments aimed at establishing physical maps and whole genome sequences. In this review, recent progress in the characterization of retrotransposable elements in the genome of the eukaryotic microorganism Dictyostelium discoideum is summarized with a focus on retroelements which integrate near transfer RNA genes with intriguing position specificity.

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Genomic organization of the transposable element Tdd-3 from Dictyostelium discoideum

Cited by 14 publications

References 18 publications

Structure of DRE, a retrotransposable element which integrates with position specificity upstream of Dictyostelium discoideum tRNA genes.

Structure of DRE, a retrotransposable element which integrates with position specificity upstream of Dictyostelium discoideum tRNA genes.

Transposable Elements and Genome Organization: A Comprehensive Survey of Retrotransposons Revealed by the Complete Saccharomyces cerevisiae Genome Sequence

Retrotransposable elements in the Dictyostelium discoideum genome

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