The Saccharomyces Ty5 retrotransposon family is associated with origins of DNA replication at the telomeres and the silent mating locus HMR.

Abstract

We have characterized the genomic organization of the TyS retrotransposons among diverse strains of Saccharomyces cerevisiae and the related species Saccharomyces paradoxus. The S. cerevisiae strain S288C (or its derivatives) carries eight Ty5 insertions. Six of these are located near the telomeres, and five are found within 500 bp of autonomously replicating sequences present in the type X subtelomeric repeat. The remaining two S. cerevisiae elements are adjacent to the silent mating locus HMR and are located within 500 bp of the origin of replication present in the transcriptional silencer HMR-E. Although the S. cerevisiae TyS elements no longer appear capable of transposition, some strains of S. paradoxus have numerous Ty5 insertions, suggesting that transposition is occurring in this species. Most of these elements are adjacent to type X telomeric repeats, and regions flanking four of five characterized S. paradoxus insertions carry autonomously replicating sequences. The genomic organization of the Ty5 elements is in marked contrast to the other S. cerevisiae retrotransposon families (Tyl-4), which are typically located within 500 bp of tRNA genes. For Ty3, this association reflects an interaction between Ty3 and the RNA polymerase III transcription complex, which appears to direct integration [Chalker, D. L. & Sandmeyer, S. B. (1992) Genes Dev. 6, 117-128]. By analogy to Ty3, we predict that Ty5 target choice is specified by interactions with factors present at both the telomeres and HMR that are involved in DNA replication, transcriptional silencing, or the maintenance of the unique chromatin structure at these sites.Retrotransposons are mobile genetic elements that replicate by reverse transcription of an RNA intermediate. The final step in the retrotransposon life cycle is the integration of an element into a new site in the host genome. Integration may be deleterious to the host cell because it can cause mutations or lead to chromosome rearrangements. Mechanisms that minimize this damage preserve the host's genetic integrity and also allow retrotransposons to replicate and maintain viable populations. In the yeast, Saccharomyces cerevisiae mechanisms have evolved that limit the negative consequences of integration by directing transposition to specific sites in the genome.Target preference of the S. cerevisiae retrotransposons has been made strikingly evident by the recent genome sequencing efforts. Insertions of the four best-characterized retrotransposon families (Tyl-4) are found within the nucleotide sequences of chromosomes III and XI (chr III and chr XI, respectively)

HEED, the Product of the Human Homolog of the Murineeed Gene, Binds to the Matrix Protein of HIV-1

“…59), but the cellular and viral factors that control the reaction and the site(s) of integration remain elusive (60). The integration process is better understood at the molecular level for retrotransposons Ty1, Ty2, Ty3, and Ty4, which have been shown to specifically integrate upstream to genes that are transcribed by RNA polymerase III (61-63), and for Ty5, which integrates into regions of silent chromatin via yeast proteins Sir (64,65). Like Sir proteins in yeast, the products of Pc-G genes in upper eukaryotes are involved in the maintenance of the silent state of chromatin, possibly by recruitment of histone deacetylase enzymes (66,67).…”

Comparative Genomic Hybridization Provides New Insights Into the Molecular Taxonomy of the Saccharomyces Sensu Stricto Complex

“…The main regions of diversity of the strains and species of Saccharomyces are the telomeric regions and retrotransposons (Cohn et al 1998;Nakazato et al 1998;Rachidi et al 1999;Fischer et al 2000;Lockhart et al 2002;Winzeler et al 2003). Transposable (Ty) elements make up ∼3% of the total sequenced genome of S. cerevisiae S288c (Kim et al 1998), and the variation of these elements between different species of Saccharomyces is well reported (Zou et al 1995;Neuveglise et al 2002;Fingerman et al 2003). In addition to the variation between species, the varying distribution of Ty elements has also been identified within the strains of S. cerevisiae (Wicksteed et al 1994;Zou et al 1995;Codon et al 1998;Rachidi et al 1999).…”

“…Transposable (Ty) elements make up ∼3% of the total sequenced genome of S. cerevisiae S288c (Kim et al 1998), and the variation of these elements between different species of Saccharomyces is well reported (Zou et al 1995;Neuveglise et al 2002;Fingerman et al 2003). In addition to the variation between species, the varying distribution of Ty elements has also been identified within the strains of S. cerevisiae (Wicksteed et al 1994;Zou et al 1995;Codon et al 1998;Rachidi et al 1999). The rearrangements caused by recombination events between Ty elements or other repeated sequences have been shown to aid, if not cause, speciation events (Cohn et al 1998;Fischer et al 2000;Delneri et al 2003).…”

Hos2 and Set3 Promote Integration of Ty1 Retrotransposons at tRNA Genes in Saccharomyces cerevisiae

“…In vitro, position-specific integration results from tethering of the integration complex to the Brf and TATA-binding protein subunits of TFIIIB (Yiehet al 2000(Yiehet al , 2002. Ty5, in contrast to Ty3, displays a regional targeting preference, integrating into subtelomeric domains and the silent mating loci (Zou et al 1995(Zou et al , 1996. Recognition of the silencing protein Sir4 by the sixamino-acid targeting domain of Ty5 IN is the primary determinant in Ty5 target specificity (Gai and Voytas 1998;Zhu et al 1999Zhu et al , 2003Xie et al 2001).…”