Host factors that promote retrotransposon integration are similar in distantly related eukaryotes

Abstract

Retroviruses and Long Terminal Repeat (LTR)-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs) encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration. We tested this hypothesis with a genome-wide screen of host factors that promote Tf1 integration. By combining an assay for transposition with a genetic assay that measures cDNA recombination we could identify factors that contribute differentially to integration. We utilized this assay to test a collection of 3,004 S. pombe strains with single gene deletions. Using these screens and immunoblot measures of Tf1 proteins, we identified a total of 61 genes that promote integration. The candidate integration factors participate in a range of processes including nuclear transport, transcription, mRNA processing, vesicle transport, chromatin structure and DNA repair. Two candidates, Rhp18 and the NineTeen complex were tested in two-hybrid assays and were found to interact with Tf1 IN. Surprisingly, a number of pathways we identified were found previously to promote integration of the LTR-retrotransposons Ty1 and Ty3 in Saccharomyces cerevisiae, indicating the contribution of host factors to integration are common in distantly related organisms. The DNA repair factors are of particular interest because they may identify the pathways that repair the single stranded gaps flanking the sites of strand transfer following integration of LTR retroelements.

Diverse transposable element landscapes in pathogenic and nonpathogenic yeast models: the value of a comparative perspective

“…The proteins of these genes contribute to diverse cellular functions, including chromatin structure, DNA repair, nuclear and vesicular transport, splicing and mRNA processing, transcription, and translation. While it is not immediately apparent how proteins involved in some of these activities contribute to integration, Tf1 IN interacts with at least two of these proteins in a twohybrid system: Cwf3, a subunit of a splicing complex, and the Rhp18 DNA repair protein [236]. Some of the proteins identified are homologs of proteins shown to regulate Ty1 and Ty3, supporting common aspects of retrotransposon regulation in Schizosaccharomyces pombe and Saccharomyces cerevisiae [236].…”

“…A large-scale screen for factors that specifically contribute to Tf1 integration identified 61 genes that promote integration [236]. The proteins of these genes contribute to diverse cellular functions, including chromatin structure, DNA repair, nuclear and vesicular transport, splicing and mRNA processing, transcription, and translation.…”

Transposable element insertions in fission yeast drive adaptation to environmental stress

“…Although stress-induced transcription of many TEs can be readily documented, it is difficult to determine whether this expression results in increased transposition events. We were able to measure transposition rates of the same four single-copy Tf1 elements using an assay that relies on a neo gene disrupted with an artificial intron (AI) (Atwood et al 1998;Rai et al 2017). We found three of the four single-copy Tf1 elements generated six-to 139fold higher rates of transposition when cells were exposed to CoCl 2 for 24 h (Fig.…”

Duplication and Transformation of the Schizosaccharomyces pombe Collection of Deletion Strains

“…1) into each deletion strain of the nonessential, haploid deletion library Version 2.0 (Bioneer, M2030H). The construction of pHL2282 has been described previously [4].…”

“…Often these screens require reporter or expression plasmids be introduced into each strain. We recently completed a screen of the Version 2.0 haploid set of deletions to identify genes that contribute to retrotransposition of Tf1 [4]. For this screen we introduced a Tf1 expression plasmid (Fig.…”