The Saccharomyces retrotransposon Ty5 integrates preferentially into regions of silent chromatin at the telomeres and mating loci.

Abstract

The nonrandom integration of retrotransposons and retroviruses suggests that chromatin influences target choice. Targeted integration, in turn, likely affects genome organization. In Saccharomyces, native Ty5 retrotransposons are located near telomeres and the silent mating locus HMR. To determine whether this distribution is a consequence of targeted integration, we isolated a transposition-competent Ty5 element from S. paradoxus, a species closely related to S. cerevisiae. This Ty5 element was used to develop a transposition assay in S. cerevisiae to investigate target preference of de novo transposition events. Of 87 independent Ty5 insertions, -30% were located on chromosome III, indicating this small chromosome (-1/40 of the yeast genome) is a highly preferred target. Mapping of the exact location of 19 chromosome III insertions showed that 18 were within or adjacent to transcriptional silencers flanking HML and HMR or the type X subtelomeric repeat. We predict Ty5 target preference is attributable to interactions between transposition intermediates and constituents of silent chromatin assembled at these sites. Ty5 target preference extends the link between telomere structure and reverse transcription as carried out by telomerase and Drosophila retrotransposons.[Key Words: Retrotransposon; Ty5; integration; transposition; silent chromatin; telomere] Received November 17, 1995; revised version accepted January 19, 1996.Mobile genetic elements that replicate by reverse transcription are ubiquitous among eukaryotic genomes. These elements, collectively called retroelements, include the retroviruses and two classes of retrotransposons, which are distinguished by whether or not they are flanked by long terminal repeats [LTRs) (Xiong and Eickbush 1990). A common step in retroelement replication involves the integration of an element's cDNA into the host genome (Brown and Varmus 1989). For the retroviruses and LTR retrotransposons, this step is carried out by a nucleoprotein complex called the integration complex.

Integrase, LEDGF/p75 and HIV replication

“…Consider that the preference of HIV for active transcription units is an approximately two-fold effect, albeit one established with incontrovertible rigor due to the large number of independent events in the samples. In contrast, fully 90-95% of Ty5 retrotransposon insertions occur within confined heterochromatic regions at yeast telomeres or at the silent mating loci [180]. This process is mediated by a direct tethering interaction between Ty5 IN and a heterochromatinassociated protein, Sir4p [181].…”

Single-Nucleotide-Specific Targeting of the Tf1 Retrotransposon Promoted by the DNA-Binding Protein Sap1 of Schizosaccharomyces pombe

“…The ability of these elements to selectively integrate into specific target sequences has been paramount to their success because the employment of specific targeting mechanisms has allowed these retrotransposons to propagate within host genomes without disrupting genes and compromising the host's survival (Levin and Moran 2011). The long terminal repeat (LTR) retrotransposons Ty1, Ty3, and Ty5 of Saccharomyces cerevisiae avoid causing damage to the host by targeting noncoding genomic regions; Ty1 and Ty3 integrate upstream of RNA polemerase III-transcribed genes, while Ty5 integrates into heterochromatin (Chalker and Sandmeyer 1990;1992;Ji et al 1993;Kirchner et al 1995;Devine and Boeke 1996;Zou et al 1996;Zou and Voytas 1997;Yieh et al 2000;Sandmeyer 2003;Lesage and Todeschini 2005).In Schizosaccharomyces pombe, the LTR retrotransposon Tf1 has a unique targeting mechanism that directs integration to promoters of RNA polymerase II-transcribed genes with a bias for the promoters of stress-response genes (Behrens et al 2000;Singleton and Levin 2002;Bowen et al 2003;Leem et al 2008;Guo and Levin 2010). Surprisingly, insertion of Tf1 into promoters rarely reduces the expression of their downstream genes, and in approximately 40% of cases, it enhances it (Feng et al 2013).…”

“…The ability of these elements to selectively integrate into specific target sequences has been paramount to their success because the employment of specific targeting mechanisms has allowed these retrotransposons to propagate within host genomes without disrupting genes and compromising the host's survival (Levin and Moran 2011). The long terminal repeat (LTR) retrotransposons Ty1, Ty3, and Ty5 of Saccharomyces cerevisiae avoid causing damage to the host by targeting noncoding genomic regions; Ty1 and Ty3 integrate upstream of RNA polemerase III-transcribed genes, while Ty5 integrates into heterochromatin (Chalker and Sandmeyer 1990;1992;Ji et al 1993;Kirchner et al 1995;Devine and Boeke 1996;Zou et al 1996;Zou and Voytas 1997;Yieh et al 2000;Sandmeyer 2003;Lesage and Todeschini 2005).…”

Integration by design

“…As reported in this issue of PNAS, investigators have produced active retroviruslike elements with synthetic insertion specificities (2). Dan Voytas and colleagues at Iowa State University (Ames) study the Saccharomyces long terminal repeat (LTR)-retrotransposon Ty5, which targets heterochromatic regions (3). Now, in an elegant adaptation of the two-hybrid system, the 6-aa Ty5 targeting domain (TD) was exchanged for two heterologous domains shown to mediate interaction of their respective proteins with protein partners.…”