Targeting Transposition: At Home in the Genome: Figure 1.

Sandmeyer, Suzanne

doi:10.1101/gr.8.5.416

Cited by 32 publications

(17 citation statements)

References 20 publications

(18 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Selection of integration sites by TRE5-A shows striking similarity with the pol III gene-targeted integration of yeast LTR retrotransposons. Ty3 elements integrate precisely at the transcription start of pol III genes, whereas Ty1 shows a preference to integrate within a window of about 700 bp upstream of tRNA genes (1,3,28,32). For Ty3 it is known that targeting of pol III genes by Ty3 is mediated by specific protein interactions of the Ty3 preintegration complex with the pol III-specific transcription factor TFIIIB subunit(s) TATA binding protein and/or Brf (41).…”

Section: Discussionmentioning

confidence: 99%

“…An intriguing example is integration in the vicinity of genes transcribed by RNA polymerase III (pol III), notably tRNA genes. Mobile elements that specifically target tRNA genes are found in both classes of retrotransposons, namely, the well-characterized long terminal repeat (LTR) retrotransposons Ty1 and Ty3 in yeast (3,32) and the non-LTR retrotransposon TRE5-A (formerly known as DRE) in D. discoideum (reviewed in reference 39).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Role of RNA Polymerase III Transcription Factors in the Selection of Integration Sites by the Dictyostelium Non-Long Terminal Repeat Retrotransposon TRE5-A

Siol

Boutliliss

Chung

et al. 2006

Molecular and Cellular Biology

View full text Add to dashboard Cite

In the compact Dictyostelium discoideum genome, non-long terminal repeat (non-LTR) retrotransposons known as TREs avoid accidental integration-mediated gene disruption by targeting the vicinity of tRNA genes. In this study we provide the first evidence that proteins of a non-LTR retrotransposon interact with a target-specific transcription factor to direct its integration. We applied an in vivo selection system that allows for the isolation of natural TRE5-A integrations into a known genomic location upstream of tRNA genes. TRE5-A frequently modified the integration site in a way characteristic of other non-LTR retrotransposons by adding nontemplated extra nucleotides and generating small and extended target site deletions. Mutations within the B-box promoter of the targeted tRNA genes interfered with both the in vitro binding of RNA polymerase III transcription factor TFIIIC and the ability of TRE5-A to target these genes. An isolated B box was sufficient to enhance TRE5-A integration in the absence of a surrounding tRNA gene. The RNA polymerase III-transcribed ribosomal 5S gene recruits TFIIIC in a B-box-independent manner, yet it was readily targeted by TRE5-A in our assay. These results suggest a direct role of an RNA polymerase III transcription factor in the targeting process.

show abstract

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Role of RNA Polymerase III Transcription Factors in the Selection of Integration Sites by the Dictyostelium Non-Long Terminal Repeat Retrotransposon TRE5-A

Siol

Boutliliss

Chung

et al. 2006

Molecular and Cellular Biology

View full text Add to dashboard Cite

show abstract

“…This inference is supported by the recent isolation of a Ty3 transposition-defective yeast strain, which was shown to have a mutation causing truncation of a TFIIIC subunit. 2 Our initial analysis of sites of Ty3 integration in the absence of TFIIIC also leaves open the possibility that TFIIIC refines the precision of Ty3 targeting, perhaps by interfering with integration a few base pairs downstream of the start site of transcription (cf. Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Similar to retroviruses, yeast Ty elements transpose through reverse transcription of an almost full-length RNA copy into a full-length DNA copy, which is integrated into the host genome. Despite very similar molecular mechanisms of integration, budding yeast elements (Tys), both gypsy-like (Ty3) and copialike (Ty1, 2, 4, and 5), differ from retroviruses in that they exhibit dramatic global integration site preferences (1)(2)(3)(4). Ty1 elements, for example, integrate preferentially within a window of 750 bp, 1 upstream of genes transcribed by RNA polymerase III (pol III).…”

mentioning

confidence: 99%

The Brf and TATA-binding Protein Subunits of the RNA Polymerase III Transcription Factor IIIB Mediate Position-specific Integration of the Gypsy-like Element, Ty3

Yieh

Kassavetis

Geiduschek

et al. 2000

Journal of Biological Chemistry

View full text Add to dashboard Cite

Ty3 integrates into the transcription initiation sites of genes transcribed by RNA polymerase III. It is known that transcription factors (TF) IIIB and IIIC are important for recruiting Ty3 to its sites of integration upstream of tRNA genes, but that RNA polymerase III is not required. In order to investigate the respective roles of TFIIIB and TFIIIC, we have developed an in vitro integration assay in which Ty3 is targeted to the U6 small nuclear RNA gene, SNR6. Because TFIIIB can bind to the TATA box upstream of the U6 gene through contacts mediated by TATA-binding protein (TBP), TFIIIC is dispensable for in vitro transcription. Thus, this system offers an opportunity to test the role of TFIIIB independent of a requirement of TFIIIC. We demonstrate that the recombinant Brf and TBP subunits of TFIIIB, which interact over the SNR6 TATA box, direct integration at the SNR6 transcription initiation site in the absence of detectable TFIIIC or TFIIIB subunit B؆. These findings suggest that the minimal requirements for pol III transcription and Ty3 integration are very similar.Integration site selection is a key step in the retroelement life cycle, potentially influencing both the effect of the insertion on the host genome and the expression of the element itself. Similar to retroviruses, yeast Ty elements transpose through reverse transcription of an almost full-length RNA copy into a full-length DNA copy, which is integrated into the host genome. Despite very similar molecular mechanisms of integration, budding yeast elements (Tys), both gypsy-like (Ty3) and copialike (Ty1, 2, 4, and 5), differ from retroviruses in that they exhibit dramatic global integration site preferences (1-4). Ty1 elements, for example, integrate preferentially within a window of 750 bp, 1 upstream of genes transcribed by RNA polymerase III (pol III). Analysis of the yeast genome sequence shows that Ty2 and Ty4 also occupy this region upstream of a fraction of tRNA genes. Ty5 integrates into regions of silenced DNA, including the silent mating type loci and telomeres. Hence Ty1, Ty2, Ty4, and Ty5 exhibit regional integration specificity. Despite similarities with these other elements, Ty3 differs in that it integrates within a highly defined window, one or two base pairs (bp) upstream of pol III transcription initiation sites.Targeting of integration appears to be directed by the cooperative actions of Ty3 element-and cell-encoded factors. For example, in addition to the element-encoded integrase protein, Ty3 and Ty1 targeting requires the presence of a transcriptionally competent pol III promoter (5, 6), and Ty5 targeting requires factors involved in the establishment of silent chromatin (7).Class III genes, including plasmid-borne U6, 5S, and tRNA genes, are used in vivo for position-specific Ty3 integration. Comparison of integration sites suggests that Ty3 integration preference is not a direct function of specific local sequences. Each class of pol III-transcribed genes differs from the others in composition of promoter elements (8) and d...

show abstract

“…Similarly, because transposable elements are, in general, only rarely transmitted across species boundaries, their continued existence is usually dependent upon the continued survival of their hosts. As a result, the elements themselves often appear to have evolved mechanisms, such as directing their integration to specific parts of the genome, which keep the damage they cause to a minimum (Sandmeyer, 1998).…”

Section: Introductionmentioning

confidence: 99%

The diversity of retrotransposons in the yeast Cryptococcus neoformans

Goodwin

Poulter

2001

Yeast

View full text Add to dashboard Cite

We have undertaken an analysis of the retrotransposons in the medically important basidiomycetous fungus Cryptococcus neoformans. Using the data generated by a C. neoformans genome sequencing project at the Stanford Genome Technology Center, 15 distinct families of LTR retrotransposons and several families of non-LTR retrotransposons were identified. Members of at least seven families have transposed recently and are probably still active. For several families, only partial elements could be identified and these are quite diverse in sequence, suggesting that they are ancient components of the C. neoformans genome. Most C. neoformans elements are not closely related to previously identified fungal retrotransposons, suggesting that the diversity of fungal retrotransposons has been only sparsely sampled to date. C. neoformans has fewer distinct retrotransposon families than Candida albicans (37 or more), in particular fewer families represented solely by ancient and inactive elements, but it has considerably more families than either Saccharomyces cerevisiae (five) or Schizosaccharomyces pombe (two). The findings suggest that elimination of retrotransposons is faster in C. neoformans than in C. albicans, but perhaps not as rapid as in S. cerevisiae or Sz. pombe. The identification of the retrotransposons of C. neoformans should assist in the molecular characterization of this important pathogen, and also further our understanding of the role played by retroelements in genome evolution.

show abstract

Targeting Transposition: At Home in the Genome: Figure 1.

Cited by 32 publications

References 20 publications

Role of RNA Polymerase III Transcription Factors in the Selection of Integration Sites by the Dictyostelium Non-Long Terminal Repeat Retrotransposon TRE5-A

Role of RNA Polymerase III Transcription Factors in the Selection of Integration Sites by the Dictyostelium Non-Long Terminal Repeat Retrotransposon TRE5-A

The Brf and TATA-binding Protein Subunits of the RNA Polymerase III Transcription Factor IIIB Mediate Position-specific Integration of the Gypsy-like Element, Ty3

The diversity of retrotransposons in the yeast Cryptococcus neoformans

Contact Info

Product

Resources

About