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

Abstract

Transposable elements (TEs) constitute a substantial fraction of the eukaryotic genome and, as a result, have a complex relationship with their host that is both adversarial and dependent. To minimize damage to cellular genes, TEs possess mechanisms that target integration to sequences of low importance. However, the retrotransposon Tf1 of Schizosaccharomyces pombe integrates with a surprising bias for promoter sequences of stress-response genes. The clustering of integration in specific promoters suggests that Tf1 possesses a targeting mechanism that is important for evolutionary adaptation to changes in environment. We report here that Sap1, an essential DNA-binding protein, plays an important role in Tf1 integration. A mutation in Sap1 resulted in a 10-fold drop in Tf1 transposition, and measures of transposon intermediates support the argument that the defect occurred in the process of integration. Published ChIP-Seq data on Sap1 binding combined with high-density maps of Tf1 integration that measure independent insertions at single-nucleotide positions show that 73.4% of all integration occurs at genomic sequences bound by Sap1. This represents high selectivity because Sap1 binds just 6.8% of the genome. A genome-wide analysis of promoter sequences revealed that Sap1 binding and amounts of integration correlate strongly. More important, an alignment of the DNA-binding motif of Sap1 revealed integration clustered on both sides of the motif and showed high levels specifically at positions +19 and 29. These data indicate that Sap1 contributes to the efficiency and position of Tf1 integration. KEYWORDS Sap1; Tf1; integration; transposition; Schizosaccharomyces pombe R ETROTRANSPOSONS are pervasive among eukaryotes and, in many cases, account for a substantial portion of the host genome (Moore et al. 2004;Scheifele et al. 2009;Levin and Moran 2011). 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 rarel...

Cross-Regulation between Transposable Elements and Host DNA Replication

“…Genome-wide analysis showed that Sap1 binding is highly predictive of Tf1 insertion [36,56]. However, Sap1 binding is not sufficient for insertion, as some very strong Sap1 binding sites are cold spots for transposition.…”

“…Additionally, Sap1 binding sites constitute insertion hotspots but only if they exhibit RFB activity, and their insertion competence depends on the orientation with respect to the advancing fork. However, other programmed RFB that are independent of Sap1 are not targeted for insertion [36,53,56]. These observations indicate that Sap1 binding and RFB activity are both necessary but neither is sufficient for target site selection.…”

“…Could the arrested fork be the real tethering factor? Sap1-INT interaction is only detectable by yeast two-hybrid [36,56]. Weak intasome tethering can be detected at Sap1-independent RFB when in the blocking orientation with respect to fork progression, although these are not insertion targets [36,53].…”

The Ty1 integrase nuclear localization signal is necessary and sufficient for retrotransposon targeting to tRNA genes

“…These LTR retrotransposons integrate at the transcription start site of Pol IIItranscribed genes and in subtelomeric regions, respectively (Kirchner et al, 1995;Xie et al, 2001). The Tf1 LTR retrotransposon of Schyzosaccharomyces pombe and the MLV retrovirus both target the promoter region of Pol II-transcribed genes (Gupta et al, 2013;Hickey et al, 2015;Jacobs et al, 2015;De Rijck et al, 2013;Sharma et al, 2013), and the HIV-1 retrovirus targets the gene body of Pol II-transcribed genes (Cherepanov et al, 2003;Llano et al, 2006).…”

Genome-Wide Mapping of Yeast Retrotransposon Integration Target Sites

“…In S. pombe, Tf1 preferentially integrates into nucleosome-free promoters of Pol II-transcribed genes with an enrichment of stress-responsive genes (Chatterjee et al, 2014;Guo & Levin, 2010). The DNA-binding factor Sap1 and its replication fork barrier activity collaborate to determine Tf1 target site selection (Hickey et al, 2015;Jacobs et al, 2015). In S. cerevisiae, Ty5 integrates into nucleosome-free regions at subtelomeres and silent mating-type loci (HM) through an interaction between its integrase and the Sir4 heterochromatin protein (Baller et al, 2011;Xie et al, 2001).…”