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Retrotransposon targeting to RNA polymerase III-transcribed genes Cheung, Stephanie; Manhas, Savrina; Measday, Vivien Apr 23, 2018

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REVIEW Open AccessRetrotransposon targeting to RNApolymerase III-transcribed genesStephanie Cheung1†, Savrina Manhas1† and Vivien Measday1,2*AbstractRetrotransposons are genetic elements that are similar in structure and life cycle to retroviruses by replicating via anRNA intermediate and inserting into a host genome. The Saccharomyces cerevisiae (S. cerevisiae) Ty1–5 elements arelong terminal repeat (LTR) retrotransposons that are members of the Ty1-copia (Pseudoviridae) or Ty3-gypsy (Metaviridae)families. Four of the five S. cerevisiae Ty elements are inserted into the genome upstream of RNA Polymerase (Pol)III-transcribed genes such as transfer RNA (tRNA) genes. This particular genomic locus provides a safe environment forTy element insertion without disruption of the host genome and is a targeting strategy used by retrotransposons thatinsert into compact genomes of hosts such as S. cerevisiae and the social amoeba Dictyostelium. The mechanism bywhich Ty1 targeting is achieved has been recently solved due to the discovery of an interaction between Ty1 Integrase(IN) and RNA Pol III subunits. We describe the methods used to identify the Ty1-IN interaction with Pol III and the Ty1targeting consequences if the interaction is perturbed. The details of Ty1 targeting are just beginning to emerge andmany unexplored areas remain including consideration of the 3-dimensional shape of genome. We present a variety ofother retrotransposon families that insert adjacent to Pol III-transcribed genes and the mechanism by which the hostmachinery has been hijacked to accomplish this targeting strategy. Finally, we discuss why retrotransposons selectedPol III-transcribed genes as a target during evolution and how retrotransposons have shaped genome architecture.Keywords: Retrotransposon, S. cerevisiae, Ty element, RNA polymerase III, tRNA, IntegraseBackgroundGenome evolution and plasticity are impacted by endogen-ous DNA sequences called transposable elements (TEs),that can mobilize within a genome [1]. TEs, which makeup a significant portion of eukaryotic genomes, are dividedinto two classes: class I retrotransposons that mobilize viaan RNA intermediate using a “copy and paste” mechanismand class II DNA transposons that use a “cut and paste”mechanism [2, 3]. Class I retrotransposons can be furtherdivided into five orders: LTR-retrotransposons, DIRS-likeelements, Penelope-like elements, long interspersed ele-ments (LINEs) and short interspersed elements (SINEs)[3]. LTR-retrotransposons carry characteristic flankingrepetitive sequences and are similar to retrovirusesin structure and replication but do not exit the cell.The S. cerevisiae genome contains five types of LTR-retrotransposon elements, known as Ty1–5, that trans-pose through an RNA intermediate and produce intracel-lular virus-like particles (VLPs) [4, 5]. The majority of theS. cerevisiae LTR retrotransposons belong to the copia(Pseudoviridiae) family (Ty1, 2, 4, 5) whereas Ty3 be-longs to the gypsy (Metaviridae) family [5]. Ty1–4elements enter the genome in the vicinity of Pol III-transcribed genes, whereas Ty5 elements insert into si-lent chromatin [5, 6] .Thirty-two copies of the Ty1 element, which is themost abundant S. cerevisiae TE, as well as 279 soloLTRs, are present in the genome of the commonly usedlaboratory strain S288C. Ty1 elements are 5.9 kb inlength and composed of GAG and POL open readingframes (ORFs) sandwiched in-between 334 bp LTRsequences [7, 8]. GAG encodes the structural protein ofthe VLP, while POL produces a polyprotein of protease(PR), IN, reverse transcriptase (RT) with ribonuclease Hactivity (RH) (Fig. 1) [7]. The copia and gypsy familiesdiffer in the order of RT/RH and IN such that the* Correspondence: vmeasday@mail.ubc.ca†Equal contributors1Department of Biochemistry and Molecular Biology, Faculty of Medicine,University of British Columbia, Vancouver, BC V6T 1Z4, Canada2Department of Food Science, Wine Research Centre, Faculty of Land andFood Systems, University of British Columbia, Room 325-2205 East Mall,Vancouver, British Columbia V6T 1Z4, Canada© The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, andreproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link tothe Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Cheung et al. Mobile DNA  (2018) 9:14 https://doi.org/10.1186/s13100-018-0119-2Ty3-gypsy element has RT/RH followed by IN (Fig. 1)[9]. Ty1 replication begins with transcription of a gen-omic Ty1 element using the host RNA Pol II machinery,translation of the Ty1 messenger RNA (mRNA) into theGag protein or the Gag-Pol fusion protein when a + 1ribosomal frameshift event places Gag and Pol in frame[7]. The Gag and Pol polypeptide, an initiator methioninetRNA (tRNAimet) and two Ty1 mRNA transcripts, areassembled into VLPs where Gag and Pol undergoprocessing and maturation by PR [10–12]. FollowingRT-mediated reverse transcription of the Ty1 mRNA inthe VLPs, a pre-integration complex composed minimallyof newly synthesized Ty1 cDNA and IN, called the inta-some, is generated. The intasome localizes to the nucleuswhere IN-mediated insertion of the Ty1 cDNA preferen-tially occurs in a ~ 1 kb window upstream of genes ac-tively transcribed by RNA Pol III including all 275 nucleartRNA genes and the 5S ribosomal RNA (rRNA) gene [13,14]. Ty1 cDNA can also enter the genome via homologousrecombination with a pre-existing Ty1 element [15, 16].baFig. 1 LTR and non-LTR retrotransposons that target to tRNA genes. a. LTR retrotransposons. Ty1, Ty3, DGLT-A and Tj1 elements are depicted indark green. The boxed black arrows represent the LTRs flanking the two ends of the elements. The first ORF of the Ty1 element encodes Gag andthe second ORF encodes a polypeptide (Pol) which is further processed into protease (PR), integrase (IN), and reverse transcriptase (RT)/ ribonuclease H(RH). Ty3 differs in structure from Ty1 by swapping positions of IN and RT/RH. For both Ty1 and Ty3, the Pol polypeptide is generated by a + 1 translationalframeshift 38 bp upstream of the 3’end of Gag [169–171]. The D. discoideum DGLT-A element contains one ORF that encodes for both Gag and Polproteins. DGLT-A belongs to the Ty3-gypsy clade, signified by the arrangement of pol with IN after RT/RH [172]. S. japonicas Tj1 has a similar structuralarrangement as Ty3 with GAG and POL as two separate ORFs. The GAG ORF has a stop codon that is thought to be translationally suppressedto allow for translation of the POL ORF which lacks a start codon [121]. The length of each element is depicted by the scale at the bottom inkb. b. non-LTR retrotransposons. D. discoideum TRE5-A and TRE3-A, D. purpureum NLTR-A and P. pallidum NLTR-B are depicted in dark orangeand all share a similar structural arrangement. All elements except NLTR-B have two ORFs flanked by untranslated regions (UTR), with TRE5-Aand TRE3-A ending with an oligo(A) tail. The 5′ and 3’UTR of TRE5-A are arranged into A- and B-modules, and B- and C-modules respectively.The protein domain arrangement of TRE5-A and TRE3-A ORF2 is the same and encodes a protein containing an apurinic/apyrimidinicendonuclease (APE), RT, and zinc-finger (ZF) domain. Both TRE5-A and TRE3-A require a − 1 frameshift for translation of ORF2 [137, 173].NLTR-A and NLTR-B have a similar arrangement to the TRE5-A and TRE3-A elements except that an RH domain substitutes for the ZF domain.In addition, NLTR-B has three separate ORFs for APE, RT and RH. It is not yet known if the 5′ and 3’ UTRs of NLTR-A and NLTR-B are arrangedinto modules. NLTR-A ORF1 overlaps with ORF2 by 13 bp but whether a frameshift occurs or not for translation of ORF2 is not yet known [124].NLTR-B does not contain overlapping ORFs, however RT does not contain a start codon [124]. The length of each element is depicted by the scale atthe bottom in kbCheung et al. Mobile DNA  (2018) 9:14 Page 2 of 15When Ty1 insertion assays are performed in vitro usingpurified VLPs and target DNA, targeting is random sug-gesting that S. cerevisiae host factors are required to targetTy1 elements to Pol III genes [17, 18]. As early as 1979, itwas observed that genomic copies of Ty1 are associatedwith tRNA genes [19]. By 1993, the 5′ region upstream oftRNA genes was defined as the preferred Ty1 elementinsertion site and the glycine tRNA gene SUF16 was iden-tified as a Ty1 insertion hotspot [20]. Upon completion ofthe S. cerevisiae genome sequence it was clear that themajority of Ty1–4 elements were located adjacent totRNA genes or other Pol III-transcribed genes [8, 21]. TheTy2 and Ty4 elements share the same insertion preferenceas Ty1 elements, whereas the Ty3 element integratesspecifically at the RNA Pol III transcription start site (TSS)[5]. To understand the mechanism of Ty insertion attRNA genes, it is important to briefly describe the RNAPol III transcription machinery.RNA Pol III transcription machineryRNA Pol III is a 17-subunit complex that, along withTFIIIB and TFIIIC transcription complexes, transcribesall tRNAs, and other essential RNAs including the U6small nuclear RNA [22, 23]. The 5S rRNA gene, which isalso transcribed by RNA Pol III requires the additionalTFIIIA transcription factor. For the purposes of this review,we briefly describe tRNA gene promoters because of thefrequent use of tRNA genes in Ty1 studies. tRNA genescontain an internal promoter with two highly conserved se-quence elements, a proximal box A and a more distal boxB, within the transcribed region. tRNA gene activation firstrequires association of TFIIIC with DNA, followed byTFIIIB, which then recruits RNA Pol III [22, 23]. TFIIIC isa 6-subunit complex with a τA subcomplex that recognizesbox A and a τB subcomplex that recognizes box B [24, 25].TFIIIB is assembled from three proteins in yeast – Brf1,TATA binding protein (TBP)/Spt15 and Bdp1 [26]. Brf1and TBP assemble first into the transcription complexfollowed by interaction with Bdp1 [27]. Once TFIIIB isbound, the RNA Pol III transcription complex can assem-ble onto the promoter [28]. The common features of alltypes of RNA Pol III promoters is that TFIIIC, TFIIIBand RNA Pol III are recruited to activate transcription.Mutation of the SUF16 tRNA promoter, such as a pointmutation in box B, that severely reduces transcription,also dramatically reduces Ty1 element insertion suggest-ing that active Pol III transcription is required for Ty1transposition [17].Mechanism for Ty1 insertion upstream of PolIII-transcribed genesTwo reports have demonstrated that Pol III subunits areessential host factors required for Ty1 intasometargeting upstream of Pol III-transcribed genes [29, 30].Below we outline the data presented in each study thatsupports a role for Pol III as the Ty1-IN host factor.Cheung et al. overexpressed the Ty1 element from aninducible plasmid in yeast cells, purified Ty1-IN usingthe 8b11 monoclonal anti-IN antibody, then performedmass spectrometry (MS) to identify Ty1-IN co-purifyingproteins [18, 30]. Five RNA Pol III subunits were identi-fied by MS (Rpc25, 34, 40, 53, 82) that co-purified withTy1-IN from two independent purifications [30]. The 17-subunit RNA Pol III complex consists of a ten-subunitcore with five subunits shared with all three Pols (Rpb5,Rpb6, Rpb8, Rpb10, Rpb12) and two others sharedbetween Pol I and III (Rpc40 and Rpc19) [31]. The sevenremaining subunits are the Rpc53/37 heterodimer, whichis the structural counterpart of TFIIF, the Rpc82/34/31heterotrimer which is related to TFIIE and the Rpc25/17dimer that is similar to Rpb4/7 [31]. GFP-tagged versionsof the two largest subunits of RNA Pol III (Rpc1 andRpc2) co-purified with Ty1-IN but the homologous Pol IIsubunits (Rpb1 and Rpb2, respectively) did not, suggestingthat Ty1-IN specifically interacts with the Pol III complex[30]. Pol III subunits tagged with either GFP or HA werepurified from yeast lysates and Rpc17, 19, 25, 34, 53, and82 all co-purified with Ty1-IN. However, since the Pol IIIcomplex is intact during these pull-downs, it is not pos-sible to pinpoint which Pol III subunit interacts directlywith Ty1-IN using this method. Therefore, in vitro bindingexperiments were also performed and demonstrated thatRpc31, 34 and 53 can interact directly with Ty1-IN usingbacterially expressed proteins [30].There are a few pieces of evidence to support the hy-pothesis that the Rpc53/37 heterodimer may be directlyinvolved in targeting Ty1-IN. Removal of the N-terminal280 amino acids from Rpc53 (rpc53Δ2–280) significantlyreduced Ty1 element targeting upstream of the SUF16gene [30]. However, Ty1 mobility in the rpc53Δ2–280mutant was not significantly impaired (~ 75% of wildtype levels) suggesting that the Ty1 element may betargeted elsewhere in the genome. When GFP pull-down experiments were performed with Rpc37-GFP inthe rpc53Δ2–280 strain background, Ty1-IN no longerco-purified with Rpc37 [30]. As well, a V5-tagged versionof rpc53D2-280 does not interact with Ty-IN in yeastlysates (S.C. and V.M. unpublished data). Since Rpc82-GFP, Rpc19-GFP and Rpc17-GFP interact with Ty1-INin the rpc53D2-280 mutant, the defect in Ty1 targetingmay be due to a loss of interaction between Ty1-INand the Rpc53/37 heterodimer. However, it is notknown which other Ty1-IN and Pol III subunit interac-tions may be compromised in the rpc53Δ2–280 mutant.Bridier-Nahmias et al., discovered an interaction be-tween Ty1-IN and the Rpc40 subunit of RNA Pol IIIusing a yeast two-hybrid assay that was confirmed byco-immunoprecipitation (IP) analysis between HA-taggedCheung et al. Mobile DNA  (2018) 9:14 Page 3 of 15Rpc40 and Ty1-IN [29]. Using the yeast two-hybridmethod, a specific interaction of Rpc40 was detected withonly the C-terminal 57 amino acids of Ty1-IN [29].Cheung et al. found that removal of 75 amino acidsfrom the C-terminus of Ty1-IN abrogated the inter-action of Ty1-IN with Rpc82-GFP in pull-down experi-ments [30]. Therefore, the data from both groupssuggests that the C-terminus of Ty1-IN is important forinteraction with Pol III. Interestingly, the C-terminusof Ty5-IN interacts with Sir4 to target Ty5 to silentchromatin [32, 33]. To disrupt the interaction of Ty1-INwith RNA Pol III without reducing Pol III transcrip-tion, Bridier-Nahmias et al., made clever use of a pre-vious observation that the Schizosaccharomyces pombe(S. pombe) Rpc40 subunit (Rpc40sp) can functionallyreplace the S. cerevisiae Rpc40 subunit [34]. WhenRpc40 was replaced with Rpc40sp, the interactionwith Ty1-IN and Ty1 element targeting upstream ofPol III genes was disrupted [29]. Interestingly, overallTy1 mobility was not impaired in the Rpc40sp strain andgenome-wide mapping revealed that Ty1 elements werepreferentially targeted to the last 20-30 kb at the ends ofeach chromosome [29]. This work reveals that Ty1-INmay interact with alternative host factors in the absenceof the Rpc40-Ty1-IN interaction. The Ty5 retrotrans-poson integrates preferentially into heterochromatin attelomeres and silent mating loci [35–37]. It would be in-teresting to test if Sir4, which targets Ty5-IN to hetero-chromatin, is able to interact with Ty1-IN in theabsence of Rpc40 [32, 33].Structures of retroviral intasomes, which are INs incomplex with their viral cDNA, have revealed thatintasomes can be a tetramer, an octamer or evenhigher order oligomers of IN protomers [38–43]. Thestructure of Ty1-IN has not been determined yet, norwhat type of oligomer structure it may form. SinceTy1-IN is a 636-amino acid protein (predicted molecu-lar weight of 71.5 kDa for a monomer or 286 kDa fora tetramer) it is possible that the Ty1-IN intasomecould interact with multiple Pol III subunits as the en-tire 17-subunit RNA Pol III complex is ~ 690 kDa. InFig. 2, we provide a structure of RNA Pol III based onrecent structural data that highlights the 2 largest PolIII subunits (Rpc1,2) the Pol III specific subunits(Rpc31/34/82 heterotrimer, Rpc53/37 dimer, Rpc17/25dimer) and Rpc40 [44]. Of the highlighted subunits inFig. 2, there is evidence that Rpc31, Rpc34, Rpc40 andRpc53 may interact directly with Ty1-IN [29, 30].Rpc40 is positioned in the Pol III complex facing theupstream DNA which may be relevant because Ty1 ele-ments are only inserted upstream of Pol III transcribedgenes [17, 21]. Future structural studies of Ty1-IN bindingto RNA Pol III will help determine precisely how thisinteraction takes place.Ty1 targeting into chromatinChromatin remodelingYeast tRNA genes have an open chromatin structure withstrongly ordered upstream nucleosomes and a nucleosome-depleted gene body [45–47]. Ty1 element genome-widemapping studies demonstrated that Ty1 insertions aretargeted to two DNA sites on the same surface of thenucleosome at the H2A/H2B interface [13, 14, 48].Structural studies of the prototype foamy virus (PFV)intasome, a homotetramer of PFV-IN, attached to a nucleo-some have revealed striking similarity to the nucleosomedata from the Ty1 genome-wide mapping studies [40, 49].The PFV intasome also interacts with one H2A/H2Bheterodimer and two DNA strands on the same surface ofbaFig. 2 Pol III structure highlighting subunits that may interact withTy1-IN. The Pol III surface view is based on the cryoelectron microscopystructure of the initially transcribing Pol III complex (Protein Data Bankcode 6f41) [44] with TBP, Brf1 and Bdp1 structures excluded. The arrowpoints to downstream DNA and the DNA template and non-templatestrands are coloured in light blue and dark blue, respectively. a Thehighlighted Pol III subunits are Rpc31 (dark green), Rpc34 (purple),Rpc82 (beige), Rpc1 (light pink), Rpc2 (light green), Rpc40 (magenta),Rpc53 (orange) and Rpc37 (red). The N-terminus of Rpc53 (amino acids1–270) is not depicted due to lack of structural data. b Same as in (a)except rotated 165oCheung et al. Mobile DNA  (2018) 9:14 Page 4 of 15the nucleosome [49]. Therefore, the interaction betweenhomotetramer INs and nucleosomes may be conserved.Chromatin remodeling complexes, which utilize ATPto mobilize nucleosomal DNA, impact Ty1 transcriptionand Ty1 genome integration. The SWI/SNF and SAGAchromatin-remodeling complexes are required for Ty1transcription whereas Isw1 and Isw2 (catalytic subunitsof three ISW1 chromatin remodeling enzymes) inhibitTy1 transcription [50–53]. Deletion of Isw2 disrupts theperiodic Ty1 integration pattern upstream of tRNAgenes likely because Isw2 is needed to maintain thenucleosome array upstream of all tRNA genes [46, 54, 55].Isw2 may be recruited by Bdp1, a component of TFIIIB,because removal of the Bdp1 N-terminus (bdp1-Δ240)also results in altered nucleosome positioning and Ty1insertion upstream of tRNA genes [54]. However, Ty1elements are still targeted to tRNA genes in the bdp1-Δ240mutant strain and Bdp1 does not interact with Ty1-IN inyeast lysates [30, 54]. This data suggests that the TFIIIBcomplex is not a Ty1-IN host targeting factor.Structural maintenance of chromosomes (Smc) com-plexes that are essential for chromosome condensation andsegregation localize to Pol III-transcribed genes. The Smc2/4 condensin complex, which is required for chromosomecompaction, binds to tRNA genes and physically interactswith TFIIIB and TFIIIC [56, 57]. A potential role forcondensin in Ty1 targeting has not yet been explored.The Smc1/3 cohesin complex, which holds sister-chromatids together, requires the Scc2/4 complex toload onto chromosomes [58, 59]. Notably, Scc2/4 bindsto the same chromosomal locations as condensin andmay be recruited by TFIIIC to bind box B sites [56].Once cohesin loads onto chromosomes at Scc2/4 bindingsites, it relocalizes to sites of active transcription [60]. Theseparation of sister chromatids in mitosis requires cleavageof the cohesin ring by a conserved cysteine protease calledseparase, or Esp1 in yeast [61]. Interestingly, Esp1 wasfound to physically interact with Ty1-IN and this inter-action is enriched in metaphase cells [62]. An esp1–1mutant with reduced cleavage activity has reduced Ty1 mo-bility and Ty1 insertion upstream of the SUF16 tRNA gene[62]. Consistently, mutations in cohesin proteins (includingScc1 which is cleaved by Esp1) cause enhanced Ty1 mobil-ity and increased Ty1 element insertion upstream of theSUF16 tRNA gene [62]. The simplest interpretation of whyincreased Ty1 mobility is observed upon removal of thecohesin complex is that the Ty1 intasome has increasedaccess to nucleosomes. However, the physical interactionbetween Ty1-IN and Esp1 could be one mechanism bywhich Ty1-IN is targeted to chromatin [62].Histone modificationChromatin-modifying enzymes, which add or removepost-translational modifications to the core histones,also impact Ty1 targeting. Hos2 and Set3, which areboth members of the Set3 histone deacetylase complex,are required for the efficient integration of Ty1 elementsupstream of tRNA genes [63]. Although Hos2 is requiredfor Ty1 integration, genome-wide Ty1 mapping studiesdid not find any difference in the Ty1 insertion pattern ofa hos2Δ mutant compared to a wild type strain [13].Deletion of the Rpd3 histone deacetylase caused reducedTy1 insertion upstream of the SUF16 tRNAGLY gene [64].Disruption of other types of complexes that interact withchromatin, such as the Paf1 complex that associates withelongating RNA Pol II, causes an increase in both Ty1mobility and Ty1 element insertion upstream of SUF16[64–66]. Paf1 stimulates the monoubiquitylation of histoneH2B (H2B K123Ub) by the Bre1-Rad6 ubiquitin ligasecomplex [67]. Interestingly, genome-wide Ty1 mapping in arad6Δ mutant demonstrated that Ty1 elements insert morefrequently into open reading frames compared to a wildtype strain [13]. An attractive hypothesis that emerges fromthese observations is that modification of nucleosomes byPaf1 associated Bre1-Rad6 restricts insertion of Ty1elements. A screen for mutants that negatively regulateTy1 transposition (rtt mutants) identified the Rtt109histone acetyltransferase and Rtt106 histone chaperone[68]. Rtt109 catalyzes the acetylation of Histone H3lysine 56 on newly synthesized H3-H4 dimers whichinteract with Rtt106 to promote replication couplednucleosome assembly [69]. Stalling of DNA replicationin the absence of either Rtt109 or Rtt106 may allow forincreased Ty1 mobility. However, genome-wide mappingof Ty1 element insertion in an rtt109Δ mutant strainrevealed a similar pattern to wild type strains suggestingthat Rtt109 does not directly affect Ty1 targeting [13]. Acomplete understanding of how chromatin remodellingand histone modifications may impact Ty1 targeting andmobility will be aided by histone mutant libraries. Forexample, a comprehensive library of H2A and H2Bmutants has been generated that could be used for testingTy1 targeting [70]. A systematic screen of Ty1 targeting inmutants of all chromatin-modifying complexes could alsobe performed. Ultimately, structural studies of the Ty1intasome in complex with nucleosomes is a criticalstep for understanding Ty1 element integration intothe genome.3-dimensional organization of tRNAs in the nucleusThe intranuclear positioning of tRNA genes could po-tentially affect the dynamics of Ty1 insertion. MultipleS. cerevisiae studies have assessed the localization oftRNA genes in the nucleus and different technical methodsreveal different localization patterns. Fluorescence in situhybridization demonstrated that yeast tRNA genes,although dispersed on linear chromosome maps, cluster inthe nucleolus in a condensin-dependant manner [57, 71].Cheung et al. Mobile DNA  (2018) 9:14 Page 5 of 15Chromosome conformation capture studies identified acluster of tRNA genes that co-localized with the nucle-olar ribosomal DNA (rDNA) repeats and another clusterthat co-localized with centromeres [72–75]. Live-cell im-aging of fluorescently labelled tRNA genes in S. cerevisiaedemonstrated that tRNA genes can reside at the nucleolus,the nuclear periphery and in the nucleoplasm [76, 77]. Inthe live-cell imaging studies, the frequency of tRNA asso-ciation with the nuclear periphery or nucleolus dependson how far the tRNA gene is from a tethering elementsuch as the centromere, telomere, or rDNA. For ex-ample, SNR6 is located close to the rDNA and exclu-sively localizes to the nucleolus whereas SUP53, whichis located 23 kb from CENIII, is excluded from the nu-cleolus [77]. A tRNA gene with no constraints maylocalize to the nucleolus, nucleolar periphery or nuclearperiphery [77]. Fluorescence microscopy and chromatinimmunoprecipitation (ChIP) studies demonstrated thattRNA genes are recruited to the nuclear pore complex(NPC) during G2/M phase which also happens to bethe peak of tRNA gene expression [78]. These studieshighlight the dynamic 3-dimensional positioning oftRNA genes in the nucleus during the yeast cell cycle.Furthermore, evidence is gathering that tRNA geneshave broad global effects on genome structure andorganization by providing tethers to cellular structuressuch as the nucleolus, nuclear periphery and mitoticspindle [77–79]. Our group has recently discoveredthat nuclear basket proteins, which are located on thenuclear side of the NPC, are required for targeting Ty1 el-ements upstream of tRNA genes [80]. In the absence ofthe nuclear basket proteins, Ty1 elements are targeted tosubtelomeric regions, similar to the Rpc40sp mutantstrain described above [80]. HIV-1 viral cDNA is pref-erentially inserted into transcriptionally active genesthat are localized near the nuclear envelope [81]. TheHIV-1 intasome also localizes near the nuclear periph-ery and the chromatin environment on the nuclear bas-ket side of the NPC is favourable for HIV-1 insertion[82, 83]. Chromatin that resides near the nuclear poremay therefore serve as a convenient site for intasomesto insert their cDNA immediately after passage throughthe NPC.Comparison of Ty1 and Ty3 targetingThe S. cerevisiae Ty3-gypsy retrotransposon also select-ively targets genes transcribed by RNA Pol III, however,unlike Ty1, it has a precise integration site that maps towithin 1–4 nucleotides of the Pol III TSS [84–86]. Thereare two full length Ty3 elements in the S288C S. cerevisiaegenome and only one is active [9]. Similar to Ty1, a func-tional Pol III promoter is required for Ty3 transpositionas mutation of the box A or box B promoter sequencesprevents insertion of the Ty3 element [85, 87]. However, atRNA gene with reduced transcriptional activity due tomutations in the transcription initiation region is still anactive Ty3 target [85]. The ability of TFIIIC and TFIIIB toload onto the tRNA promoter is essential for Ty3 target-ing but a wild type level of tRNA gene transcription is not.In vitro reconstitution with recombinant TFIIIB proteinsdemonstrated that Ty3-IN, TBP(Spt15) and Brf1 are re-quired for Ty3 insertion while addition of the third com-ponent of TFIIIB, Bdp1, enhances integration efficiency[88, 89]. The conserved domain of TBP inserted betweenthe N and C-terminal segments of Brf1, which can func-tion to initiate Pol III transcription, can also mediateTy3 insertion in vitro [90, 91]. Extra TFIIIC sites in theyeast genome that bind TFIIIC but not TFIIIB or PolIII, are not targeted by Ty3, further strengthening theargument that TFIIIB is the key Ty3 targeting factor[92, 93].Although TFIIIB is the host factor for Ty3-IN, TFIIICalso influences the Ty3 insertion pattern. The C-terminusof Tfc1 physically interacts with Ty3-IN and enables Ty3insertion in both orientations [88, 94]. By comparison, nophysical interaction was detected between Ty1-IN andTfc1, Tfc3 or Tfc7 in co-purification experiments fromyeast lysates [30]. Another interesting difference betweenTy1 and Ty3 targeting is that RNA Pol III, which isrequired for Ty1 element insertion, is inhibitory to Ty3insertion in vitro [87, 95]. Genome-wide Ty1 and Ty3insertion site mapping studies have also discoveredinteresting targeting differences between the two retro-transposons. For example, Ty3, unlike Ty1, does nottarget to nucleosomes [13, 14, 93]. Ty3 is capable ofinserting at the TSS of the tRNA relic gene ZOD1which is bound by the Pol III machinery whereas Ty1 isnot [13, 14, 93]. The lack of Ty1 targeting to ZOD1may be due to low ZOD1 transcription levels [13, 14].Interestingly, the ZOD1 locus is activated upon nucleo-some depletion which may also prevent Ty1 targeting [96].Finally, Ty3 elements only integrate at Pol III-transcribedgenes whereas Ty1 elements are capable of integrating atother genomic loci such as within silent mating cassettes,within or near Pol II-transcribed genes and at sub-telomeric regions [29, 97–102]. Ty1-IN may interactwith alternative host factors to achieve insertion intosuch a variety of genomic regions. Although Ty1 andTy3 are both targeted upstream of Pol III-transcribedgenes, they have devised different targeting mechanismsfor insertion into the genome.tRNA targeting TEs in other yeast speciesThe Saccharomyces sensu stricto genus includes sevennatural species: S. arboricolus, S. cerevisiae, S. eubayanus,S. kudriavzevii, S. mikatae, S. paradoxus, S. uvarum, andtwo hybrid species: S. pastorianus and S. bayanus[103–105]. There is variation in the presence or absence ofCheung et al. Mobile DNA  (2018) 9:14 Page 6 of 15Ty elements in these species and the abundance of a par-ticular element can vary widely between strains [106–108].For example, Ty3 and Ty5 elements do not occur in S.uvarum [109]. A novel Ty3-like element, called Ty3p, wasdiscovered in S. paradoxus that shares 82% nucleotide iden-tity with an S. cerevisiae Ty3 element (YGRWTy3–1) and isinserted ~ 6 bp upstream of a tRNA TSS (Table 1) [110].Degenerate solo LTRs of Ty3p are also present in the S.cerevisiae genome [111]. The targeting of Ty1, Ty2, Ty3,and Ty4 elements upstream of tRNA genes is conservedin the Saccharomyces sensu stricto genus.The rapid pace of whole genome sequencing in a varietyof fungal species has revealed the diversity of retrotran-sposons [112–114]. Interestingly, a subset of these newlydiscovered TEs in the fungal Ascomycota phylum aredistributed in the genome nearby tRNA genes (Table 1).The genome of the oleaginous yeast, Yarrowia lipolyticacontains three Ty3-gypsy-like elements (Tyl3, Ylt1, Tl6)located upstream of Pol-III transcribed genes (Table 1)[115–117]. Candida albicans (C. albicans) is an oppor-tunistic human fungal pathogen that contains 34 LTR-retrotransposon families (alpha, beta, gamma, etc.) inits genome that belong to the Ty1-copia and Ty3-gypsyfamilies [118]. The beta LTR of the Tca8 element, whichhas partial elements remaining in the genome, is localizedwithin 30 bp upstream of the mature coding sequence(MCS) of tRNA genes (Table 1) [119]. An investigation ofthe Pol III targets in C. albicans using Rpc82 ChIP-chiprevealed that Rpc82 bound tRNA genes at high occupancyand retrotransposon elements at low occupancy [120].The low occupancy binding of Rpc82 to elements such asTca8 is likely due to amplification of Rpc82 binding toTable 1 Retrotransposons that integrate adjacent to tRNA genesMobileelementClade Hosta Preferred integration site Host factors mediating this insertionpreferenceLTR RetrotransposonsTy1 Ty1-copia Saccharomycescerevisiae~ 1 kb window upstream of RNA PolIII-transcribed genes, including tRNAand 5S rRNA genes [13, 14, 21]Ty1-IN interaction with Rpc40 [29] and Ty1-INinteraction with Rpc53, Rpc34, Rpc31 [30]Ty2 Ty1-copia Saccharomycescerevisiae~ 1 kb window upstream of RNA PolIII-transcribed genes [21]Ty3 Ty3-gypsy Saccharomycescerevisiae1–4 bp upstream of tRNA TSSb [93] Ty3-IN interaction with TFIIIB [88, 89]Ty3p Ty3-gypsy Saccharomycesparadoxus~ 6 bp upstream of tRNA TSS [110]Ty4 Ty1-copia Saccharomycescerevisiae~ 1 kb window upstream of RNA PolIII-transcribed genes [21]Tj1 Ty3-gypsy Schizosaccharomycesjaponicus1–10 bp upstream of tRNA TSS [121]Beta/Tca8Ty3-gypsy Candida albicans 6-30 bp upstream of tRNA MCSc [119]Tyl3 Ty3-gypsy Yarrowia lipolytica ~ 5 bp upstream of tRNA TSS [116]Ylt1 Ty3-gypsy Yarrowia lipolytica ~ 5 bp upstream of tRNA TSS [117]Tyl6 Ty3-gypsy Yarrowia lipolytica ~ 5 bp upstream of tRNA TSS [115]DGLT-A Ty3-gypsy Dictyosteliumdiscoideum13–33 bp upstream of tRNA MCS [125]Skipper-2 Ty3-gypsy Dictyosteliumdiscoideum8–23 bp downstream of tRNAgene [124, 172]Non-LTR RetrotransposonsTRE5 L1 Dictyosteliumdiscoideum40–54 bp upstream of tRNA MCS; 37–41 bp upstreamof extrachromosomal 5S rRNA genes [125, 134, 135, 174]TRE5 ORF1 interaction with TFIIIB [132]TRE3 L1 Dictyosteliumdiscoideum40–150 bp downstream tRNA genes [137, 175]NLTR-A L1 Dictyosteliumpurpureum2–6 bp upstream of tRNA MCS [124]NLTR-B L1 Polysphondyliumpallidum39–64 bp upstream of tRNA MCS [124]aHost that retrotransposon was first identified inbTSS refers to the tRNA transcription start site which is ~ 10 bp upstream of the mature tRNAcMCS refers to the tRNA mature coding sequenceCheung et al. Mobile DNA  (2018) 9:14 Page 7 of 15tRNA genes located adjacent to retrotransposon elementsin the C. albicans genome [120].Whole genome sequencing and comparison of fissionyeast genomes revealed that the Schizosaccharomycesjaponicus (S. japonicus) genome contains 10 families (Tj1to Tj10) of Ty3-gypsy related retrotransposons clustered atthe centromeres and telomeres [121, 122]. Notably, retro-transposons were dramatically reduced or lost in the otherfission yeast genomes likely due to evolutionary change incontrol of centromere function [122]. Since tRNA genesare clustered at the centromere, the Levin lab hypothe-sized that the S. japonicus retrotransposons may bespecifically targeted to tRNA genes. They tested thishypothesis by cloning the S. japonicus Tj1 retrotransposonand analyzing its integration behaviour in the relatedfission yeast S. pombe [121]. As predicted, the Tj1transposon inserted 1–10 bp upstream of the TSS oftRNA genes and also at the Pol III-transcribed 5S rRNAgene (Fig. 1, Table 1) [121]. Therefore, S. japonicus Tj1targets Pol III-transcribed genes and has similar insertionbehaviour to Ty3 retrotransposons.The diversity of retrotransposons in fungal speciesnow includes Ty1-copia, Ty3-gypsy and LINE elements[112–114, 123]. The target specificity of each of theseretrotransposons has not been fully elucidated but it islikely that Pol III-targeting will feature prominently [123].TEs target RNA pol III transcribed genes inDictyosteliumMobile elements in other organisms with compact genomeshave also found a safe haven by inserting adjacent to tRNAgenes; the social amoeba model organism Dictyosteliumdiscoideum (D. discoideum) is one such organism. D. dis-coideum has tolerated an expansion of tRNA targetingretrotransposons to 3.8% of its genome whereas 0.9% or lessof the genomes of other social amoeba contain tRNA asso-ciated retrotransposons [124]. It is not known what selec-tion pressure may have allowed retroelement expansion inD. discoideum [124]. The Dictyostelium gypsy-like trans-poson (DGLT-A) belongs to the Ty3-gypsy clade of retro-transposons and preferentially inserts 13 to 33 bp upstreamof the tRNA MCS in either orientation (Fig. 1, Table 1)[125]. The lack of full length DGLT-A elements in the D.discoideum genome suggests that they are no longer active[124]. Skipper-1 is another LTR retrotransposon in the D.discoideum genome that is related to DGLT-A and theTy3-gypsy clade. Skipper elements, which accumulate at thecentromere, contain a characteristic chromo domain(CHD) in the C-terminus of the Skipper IN protein [126].The CHD may be important for targeting Skipper-1 intoheterochromatin at the centromere [127]. Skipper-2 (previ-ously named DGLT-P) has a diverged CHD and insteadof targeting to centromeres is targeted ~ 8-23 bp down-stream of tRNA genes (Fig. 3) [124]. Notably, Skipper-2has also been identified in other amoeba species, includingDictyostelium purpureum (D. purpureum), Dictyoste-lium fasciculatum (D. fasciculatum), and Polysphondyliumpallidum (P. pallidum), where it is located ~ 140 bp down-stream of tRNA genes (Table 1) [124]. Skipper-2 is the firstLTR retrotransposon that preferentially integrates down-stream of a tRNA gene [124]. It will be interesting to deter-mine if the diverged CHD is responsible for targetingSkipper-2 downstream of tRNA genes.The D. discoideum genome also contains non-LTR retro-transposons called TREs for tRNA gene-targeted retroele-ments. TRE5 elements preferentially integrate upstream (5′)of tRNA genes, whereas TRE3 elements are targeted down-stream (3′) of tRNA genes; the element names are a con-venient reminder of their integration preference (Figs. 1,3)[128–130]. There are three TRE5 elements (TRE5-A,B,C)and four TRE3 elements (TRE3-A,B,C,D) in the D. discoi-deum genome with TRE5-A and TRE3-A in the highestabundance [128]. TRE5 elements insert ~ 44-54 bp up-stream of the tRNA MCS in the opposite transcrip-tional orientation (Table 1, Fig. 3) [130]. The TRE5-Aretrotransposon has two ORFs - ORF1 encodes a 51kDprotein of unknown function and ORF2 encodes aprotein with an apurinic/apyrimidinic endonuclease (APE)domain, an RT domain, and a zinc-finger (ZF) domain(Fig. 1) [129, 131]. Interestingly, protein-protein interac-tions have been detected between the TRE5-A ORF1protein and the three D. discoideum TFIIIB proteins TBP,Brf1 and Bdp1 [132]. Despite the similarity to Ty3, whichalso interacts with TFIIIB, the molecular basis of TRE5-Atargeting may differ from Ty3 because of the mechanismby which TRE5-A elements integrate into the genome.Non-LTR retrotransposons such as TRE5-A elementsreplicate by target-primed reverse transcription wherebythe APE domain nicks the target DNA which allows forreverse transcription followed by integration of theelement [6]. However, similar to Ty3 elements, mutationsof the box B promoter that interfere with binding ofTFIIIC abolish the targeting of TRE5-A to the tRNAtarget gene [133]. TRE5-A insertion profiling demon-strated that TRE5-A can also integrate at the Pol III-transcribed ribosomal 5S gene which is located on amulti-copy extrachromosomal DNA element harboringthe rRNA genes [134, 135]. Unlike TRE5, TRE3 has abroader range of insertion that is 40–150 bp down-stream of tRNA genes in the same transcription orien-tation (Fig. 3) [130]. The broader insertion window isbecause TRE3 can target downstream of either thetRNA internal box B or an external box B (ex B) thatis positioned ~ 100 bp downstream of the internal boxB and present at ~ 80% of D. discoideum tRNA genes(Fig. 3) [136, 137]. New non-LTR retrotransposons(NLTR) were recently identified in the genomes ofD. purpureum (NTLR-A) and P. pallidum (NLTR-B) thatCheung et al. Mobile DNA  (2018) 9:14 Page 8 of 15are distantly related to TRE elements [124]. P. pallidumNLTR-B inserts upstream of tRNA genes in a similar man-ner to TRE5 elements however D. purpureum NLTR-Ahas a unique insertion specificity 2-6 bp upstream of thetRNA MCS (Fig. 3) [124].Evolutionary selection of pol III transcribed genesas a genomic target for insertionSurvival of mobile elements in the compact Saccharomy-ces and Dictyostelium genomes necessitated insertion ofthe element in a locus that minimized host genomedamage [138]. During evolution, retrotransposons haveindependently developed targeting to tRNA genes atleast six times in dictyostelids and at least four times(Ty1–4) in S. cerevisiae [124]. Insertion upstream of PolIII-transcribed genes has the advantage that most PolIII-transcribed genes exist in multiple copies, thereforethey are an abundant target and insertion into one locus isnot likely to be lethal. Furthermore, the promoter elementsof tRNA genes are embedded within the coding region andFig. 3 tRNA targeted retrotransposon insertion site profiles. The insertion site preference for S. cerevisiae, Dictyostelium and P. pallidum are shownhere upstream and downstream of a tRNA gene. The tRNA gene (gray) contains box A (red) and box B (blue) internal promoters and the external box B(ex B, blue) for social amoeba. LTR-retrotransposons are in green and non-LTR retrotransposons are in orange. Inverted orange or green triangles denoteretrotransposon insertion windows ranging from 2 to ~ 1000 bp upstream or 7 to ~ 450 bp downstream of the tRNA gene (not drawn to scale).For the social amoeba, split orange and green inverted triangles denote overlapping insertion footprints for LTR (DGLT-A, Skipper-2) andnon-LTR (NLTR-A, NLTR-B, TRE5, TRE3) retrotransposons. For P. pallidum, a specific DLGT-A (DGLT-A.4) is indicated because DGLT-A.1–3 do not target totRNA genes in this organism [124]. The green triangle with a broader base represents the larger insertion window for S. cerevisiae Ty1 which can insert upto ~ 1 kb upstream of a Pol III-transcribed gene. Nucleosomes are depicted upstream of the S. cerevisiae tRNA gene as Ty1 inserts into nucleosomesCheung et al. Mobile DNA  (2018) 9:14 Page 9 of 15inserting upstream of tRNA genes will not damage pro-moter activity. The S. cerevisiae genome has 275 copiesof tRNA genes for decoding the 20 standard aminoacids, and the 5S rRNA exists in a tandem array consist-ing of 100–200 copies [8]. Therefore, there are plenty oftarget sites available for Ty1–4 retrotransposon integra-tion. D. discoideum and D. purpureum have an expansionin the number of their tRNA genes (418 and 353, respect-ively) compared to other dictyostelids [124]. The largenumber of tRNA genes has allowed amplification of theDGTL-A retrotransposon in D. discoideum but not theother dictyostelids, including D. purpureum [124]. There-fore, an increase in the target site, in this case a tRNAgene, does not always give a retrotransposon freedomto increase in abundance [124]. Insertion of retrotran-sposons downstream of tRNA genes is only found indictyostelid genomes (TRE3 and Skipper-2) but not inthe S. cerevisiae genome [124]. Integration of retrotran-sposons downstream of S. cerevisiae tRNA genes maynegatively impact tRNA or adjacent gene transcriptionand overall cell fitness. The insertion of Ty1 or Ty3 ele-ments upstream of tRNA genes does not appear tonegatively affect tRNA gene transcription in S. cerevi-siae. On the contrary, evidence shows that these ele-ments have a neutral or moderately stimulatory effect ontRNA gene transcription [139, 140]. It has not yet been in-vestigated if tRNA gene expression is affected in D. discoi-deum when retrotransposons insert nearby [131]. Theretrotransposon may benefit however from its targetingpreference because the promoter activity of the A modulein TRE5-A is enhanced if a tRNA gene is present up-stream [141].Whether or not Ty1 insertion events are advantageousor deleterious to the cell has no simple answer. Singlenovel Ty1 insertions upstream of Pol III-transcribed geneshave no growth advantage or disadvantage compared to aparental strain lacking Ty insertions [142]. This data isconsistent with the theory that the insertion site of Ty1elements has evolved to minimize deleterious effects onthe host genome [142]. Ty1 elements also have an internalmechanism of copy number control which likely evolvedto prevent retrotransposon bursts that decrease hostcell fitness due to genome instability. Expression froman internal promoter of a protein derived from theC-terminal half of Gag inhibits retrotransposition in adose-dependent manner [143, 144]. Ty1 transpositionmust be artificially induced to assess the effect ofincreased Ty1 copy number. As the copy number ofnovel Ty1 elements doubles, yeast strains develop awide range of growth phenotypes including insertionsthat do not affect strain growth, those that confer anegative fitness effect and those that confer a growthadvantage [145, 146]. Remarkably, Ty1 copy numbercan be increased as much as 10-fold and still only modestgrowth phenotypes are detected [147]. However, with a10-fold increase in Ty1 elements, the strains becomehighly sensitive to DNA damaging agents due to increasedectopic recombination [147].Mechanisms of Ty1-mediated genome evolutionTy elements can cause genome evolution by a variety ofmechanisms [148]. If transcription of the Ty1 element isinduced, for example in response to environmental stress(UV light, ionizing radiation) then Ty1-IN mediated inser-tion events may be a mechanism of genome evolution[149–151]. DNA replication stress, DNA damage andgenome damage due to telomere erosion can also activateTy1 mobility [152–154]. Increased Ty1 mobility is alsoresponsible for chromosome rearrangements in agingyeast populations [155]. Induction of Ty1 transcriptionand transposition under stress is thought to be a strategyto increase cell survival by inducing adaptive mutations.Ty1 predominantly inserts upstream of Pol III-transcribedgenes but can also insert into Pol II-transcribed genes orin subtelomeric regions [13, 14, 29, 80]. Insertion of Ty1into the URA3 gene can be detected when cells are grownon 5-Fluoroorotic acid which is toxic to cells unless theURA3 locus is mutated and cells are supplemented withuracil [98]. Another classic example of Ty1 insertion intoa Pol II-transcribed gene is mutation of the CAN1 locuswhich results in resistance to the arginine analoguecanavanine [102].Repetitive elements such as Ty retrotransposons andtRNA genes are fragile genomic sites because they areprone to genome rearrangement. Experimental evolutionof S. cerevisiae in a glucose-limited environment causedchromosomal rearrangements due to ectopic recombin-ation between tRNA genes, entire Ty elements or soloLTRs on different chromosomes [156]. Double-strandbreaks (DSBs) induced by ionizing radiation or perturba-tions of essential DNA replication proteins causechromosome breakage at repetitive Ty elements andchromosome translocations due to ectopic recombinationwith Ty elements on other chromosomes [157–161]. DSBscan also be repaired by ectopic recombination using Tyelements that are located up to ~ 50 kb away from thebreak site [162]. Interestingly, DSB repair has also beenshown to occur at NPCs, where active transcription tRNAgenes occurs [163, 164]. Pol III-transcribed genes are alsoprone to RNA:DNA hybrid formation (R-loops) that aresusceptible to DNA damage due to exposure of singlestranded DNA [165, 166]. In the absence of RNAse H,which removes RNA:DNA hybrids, Ty1 cDNA also formsR-loops likely during reverse transcription, and is elevated~ 3-fold resulting in increased Ty1 mobility [166]. Takentogether, tRNA and Ty repetitive elements are dynamicregions of genetic movement contributing to the evolu-tionary flux of the eukaryotic genome.Cheung et al. Mobile DNA  (2018) 9:14 Page 10 of 15ConclusionsRetrotransposons and retroviruses have successfullyutilized the Pol III transcription machinery and Pol III-transcribed genes to replicate in eukaryotic cells. Bothretrotransposons and retroviruses use a tRNA primingsystem for reverse transcription. SINE elements, whichconstitute ~ 11% of the human genome, evolved fromtRNA priming of retroviral genomes and contain box Aand box B elements in their 5′ regions [167, 168]. Bothyeast and social amoeba retrotransposons with differentstructures and ORFs have found a safe haven neartRNA genes (Fig. 3). The ongoing search for new TEsthat are targeted adjacent to Pol III-transcribed genesand the host factors required for their insertion willallow better understanding of the mechanisms used byretrotransposons and retroviruses to gain access to hostgenomes. Future studies on how mobile elements contrib-ute to the maintenance of the global architecture of thegenome will provide novel evolutionary insights into theimportance of these abundant elements.AbbreviationsAPE: Apurinic/apyrimidinic endonuclease; C. albicans: Candida albicans;ChIP: Chromatin immunoprecipitation; D. discoideum: Dictyosteliumdiscoideum; DGLT-A: Dictyostelium gypsy-like transposon; DSB: Double-strandbreak; ex B: External box B; IN: Integrase; IP: Immunoprecipitation; LINE: Longinterspersed element; LTR: Long terminal repeat; MCS: Mature codingsequence; mRNA: Messenger RNA; NLTR: Non-LTR retrotransposon;NPC: Nuclear pore complex; ORF: Open reading frame; P.pallidum: Polysphondylium pallidum; PFV: Prototype foamy virus;Pol: Polymerase; PR: Protease; rDNA: Ribosomal DNA; RH: Ribonuclease H;rRNA: Ribosomal RNA; RT: Reverse transcriptase; S.cerevisiae: Saccharomycescerevisiae; S.japonicus: Schizosaccharomyces japonicus;S.pombe: Schizosaccharomyces pombe; SINEs: Short interspersed elements;TBP: TATA binding protein; TE: Transposable elements; TOR: Target ofrapamycin; TRE: tRNA gene targeted retroelement; tRNA: Transfer RNA;TSS: Transcription start site; UTR: Untranslated region; VLP: Virus-like particle;ZF: Zinc-fingerAcknowledgementsWe would like to thank Dr. Hung-Ta Chen for generating Fig. 2.FundingSC holds a University of British Columbia 4-Year Fellowship. VM is supportedby a grant from the Natural Sciences and Engineering Research Council ofCanada (RGPIN-2016-04261) and the Canadian Institutes of Health Research(HOP-131559).Author’s contributionsSC, SM and VM shared equal roles in writing the manuscript. SC generated Fig. 1and Table 1, SM generated Fig. 3 and Dr. Hung-Ta Chen generated Fig. 2.Ethics approval and consent to participateNot applicable.Competing interestsThe authors declare that they have no competing interests.Publisher’s NoteSpringer Nature remains neutral with regard to jurisdictional claims inpublished maps and institutional affiliations.Received: 27 October 2017 Accepted: 16 April 2018References1. Huang CR, Burns KH, Boeke JD. Active transposition in genomes. Annu RevGenet. 2012;46:651–75.2. Finnegan DJ. Eukaryotic transposable elements and genome evolution.Trends Genet. 1989;5(4):103–7.3. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A,Leroy P, Morgante M, Panaud O, et al. A unified classification system foreukaryotic transposable elements. Nat Rev Genet. 2007;8(12):973–82.4. Boeke JD, Garfinkel DJ, Styles CA, Fink GR. Ty elements transpose throughan RNA intermediate. Cell. 1985;40(3):491–500.5. Lesage P, Todeschini AL. Happy together: the life and times of tyretrotransposons and their hosts. Cytogenet Genome Res. 2005;110(1–4):70–90.6. Sultana T, Zamborlini A, Cristofari G, Lesage P. Integration site selection byretroviruses and transposable elements in eukaryotes. Nat Rev Genet. 2017;18(5):292–308.7. Curcio MJ, Lutz S, Lesage P. The Ty1 LTR-retrotransposon of budding yeast,Saccharomyces cerevisiae. Microbiol Spectr. 2015;3(2):1–35.8. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F,Hoheisel JD, Jacq C, Johnston M, et al. Life with 6000 genes. Science. 1996;274(5287):546. 563-5479. Sandmeyer S, Patterson K, Bilanchone V. Ty3, a position-specificretrotransposon in budding yeast. Microbiol Spectr. 2015;3(2):1–29.10. Garfinkel DJ, Hedge AM, Youngren SD, Copeland TD. Proteolytic processingof pol-TYB proteins from the yeast retrotransposon Ty1. J Virol. 1991;65(9):4573–81.11. Merkulov GV, Lawler JF Jr, Eby Y, Boeke JD. Ty1 proteolytic cleavage sitesare required for transposition: all sites are not created equal. J Virol. 2001;75(2):638–44.12. Merkulov GV, Swiderek KM, Brachmann CB, Boeke JD. A critical proteolyticcleavage site near the C terminus of the yeast retrotransposon Ty1 gagprotein. J Virol. 1996;70(8):5548–56.13. Baller JA, Gao J, Stamenova R, Curcio MJ, Voytas DF. A nucleosomal surfacedefines an integration hotspot for the Saccharomyces cerevisiae Ty1retrotransposon. Genome Res. 2012;22(4):704–13.14. Mularoni L, Zhou Y, Bowen T, Gangadharan S, Wheelan SJ, Boeke JD.Retrotransposon Ty1 integration targets specifically positioned asymmetricnucleosomal DNA segments in tRNA hotspots. Genome Res. 2012;22(4):693–703.15. Melamed C, Nevo Y, Kupiec M. Involvement of Cdna in homologousrecombination between ty elements in Saccharomyces-cerevisiae. Mol CellBiol. 1992;12(4):1613–20.16. Sharon G, Burkett TJ, Garfinkel DJ. Efficient homologous recombination ofTy1 element cDNA when integration is blocked. Mol Cell Biol. 1994;14(10):6540–51.17. Devine SE, Boeke JD. Integration of the yeast retrotransposon Ty1 istargeted to regions upstream of genes transcribed by RNA polymerase III.Genes Dev. 1996;10(5):620–33.18. Eichinger DJ, Boeke JD. The DNA intermediate in yeast Ty1 elementtransposition copurifies with virus-like particles: cell-free Ty1 transposition.Cell. 1988;54(7):955–66.19. Cameron JR, Loh EY, Davis RW. Evidence for transposition of dispersedrepetitive DNA families in yeast. Cell. 1979;16(4):739–51.20. Ji H, Moore DP, Blomberg MA, Braiterman LT, Voytas DF, Natsoulis G, BoekeJD. Hotspots for unselected Ty1 transposition events on yeast chromosomeIII are near tRNA genes and LTR sequences. Cell. 1993;73(5):1007–18.21. Kim JM, Vanguri S, Boeke JD, Gabriel A, Voytas DF. Transposable elementsand genome organization: a comprehensive survey of retrotransposonsrevealed by the complete Saccharomyces cerevisiae genome sequence.Genome Res. 1998;8(5):464–78.22. Acker J, Conesa C, Lefebvre O. Yeast RNA polymerase III transcription factorsand effectors. Biochim Biophys Acta. 2013;1829(3–4):283–95.23. Turowski TW, Tollervey D. Transcription by RNA polymerase III: insights intomechanism and regulation. Biochem Soc Trans. 2016;44(5):1367–75.24. Ducrot C, Lefebvre O, Landrieux E, Guirouilh-Barbat J, Sentenac A, Acker J.Reconstitution of the yeast RNA polymerase III transcription system with allrecombinant factors. J Biol Chem. 2006;281(17):11685–92.25. Male G, von Appen A, Glatt S, Taylor NM, Cristovao M, Groetsch H, Beck M,Muller CW. Architecture of TFIIIC and its role in RNA polymerase III pre-initiation complex assembly. Nat Commun. 2015;6:7387.Cheung et al. Mobile DNA  (2018) 9:14 Page 11 of 1526. Geiduschek EP, Kassavetis GA. The RNA polymerase III transcriptionapparatus. J Mol Biol. 2001;310(1):1–26.27. Kassavetis GA, Joazeiro CA, Pisano M, Geiduschek EP, Colbert T, Hahn S,Blanco JA. The role of the TATA-binding protein in the assembly andfunction of the multisubunit yeast RNA polymerase III transcription factor.TFIIIB Cell. 1992;71(6):1055–64.28. Kassavetis GA, Braun BR, Nguyen LH, Geiduschek EP. S. Cerevisiae TFIIIB isthe transcription initiation factor proper of RNA polymerase III, while TFIIIAand TFIIIC are assembly factors. Cell. 1990;60(2):235–45.29. Bridier-Nahmias A, Tchalikian-Cosson A, Baller JA, Menouni R, Fayol H, FloresA, Saib A, Werner M, Voytas DF, Lesage P. Retrotransposons. An RNApolymerase III subunit determines sites of retrotransposon integration.Science. 2015;348(6234):585–8.30. Cheung S, Ma L, Chan PH, Hu HL, Mayor T, Chen HT, Measday V. Ty1integrase interacts with RNA polymerase III-specific subcomplexes topromote insertion of Ty1 elements upstream of polymerase (pol) III-transcribed genes. J Biol Chem. 2016;291(12):6396–411.31. Cramer P, Armache KJ, Baumli S, Benkert S, Brueckner F, Buchen C, DamsmaGE, Dengl S, Geiger SR, Jasiak AJ, et al. Structure of eukaryotic RNApolymerases. Annu Rev Biophys. 2008;37:337–52.32. Gai X, Voytas DF. A single amino acid change in the yeast retrotransposonTy5 abolishes targeting to silent chromatin. Mol Cell. 1998;1(7):1051–5.33. Xie W, Gai X, Zhu Y, Zappulla DC, Sternglanz R, Voytas DF. Targeting of theyeast Ty5 retrotransposon to silent chromatin is mediated by interactionsbetween integrase and Sir4p. Mol Cell Biol. 2001;21(19):6606–14.34. Shpakovski GV, Shematorova EK. Rpc19 and Rpc40, two alpha-like subunitsshared by nuclear RNA polymerases I and III, are interchangeable betweenthe fission and budding yeasts. Curr Genet. 1999;36(4):208–14.35. Zou S, Ke N, Kim JM, Voytas DF. The Saccharomyces retrotransposon Ty5integrates preferentially into regions of silent chromatin at the telomeresand mating loci. Genes Dev. 1996;10(5):634–45.36. Zou S, Kim JM, Voytas DF. The Saccharomyces retrotransposon Ty5influences the organization of chromosome ends. Nucleic Acids Res. 1996;24(23):4825–31.37. Zou S, Voytas DF. Silent chromatin determines target preference of theSaccharomyces retrotransposon Ty5. Proc Natl Acad Sci U S A. 1997;94(14):7412–6.38. Ballandras-Colas A, Brown M, Cook NJ, Dewdney TG, Demeler B,Cherepanov P, Lyumkis D, Engelman AN. Cryo-EM reveals a novel octamericintegrase structure for betaretroviral intasome function. Nature. 2016;530(7590):358–61.39. Ballandras-Colas A, Maskell DP, Serrao E, Locke J, Swuec P, Jonsson SR,Kotecha A, Cook NJ, Pye VE, Taylor IA, et al. A supramolecular assemblymediates lentiviral DNA integration. Science. 2017;355(6320):93–5.40. Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov P. Retroviral intasomeassembly and inhibition of DNA strand transfer. Nature. 2010;464(7286):232–6.41. Maertens GN, Hare S, Cherepanov P. The mechanism of retroviralintegration from X-ray structures of its key intermediates. Nature. 2010;468(7321):326–9.42. Passos DO, Li M, Yang R, Rebensburg SV, Ghirlando R, Jeon Y, Shkriabai N,Kvaratskhelia M, Craigie R, Lyumkis D. Cryo-EM structures and atomic model ofthe HIV-1 strand transfer complex intasome. Science. 2017;355(6320):89–92.43. Yin Z, Shi K, Banerjee S, Pandey KK, Bera S, Grandgenett DP, Aihara H.Crystal structure of the Rous sarcoma virus intasome. Nature. 2016;530(7590):362–6.44. Vorlander MK, Khatter H, Wetzel R, Hagen WJH, Muller CW. Molecularmechanism of promoter opening by RNA polymerase III. Nature. 2018;553(7688):295–300.45. Brogaard K, Xi L, Wang JP, Widom J. A map of nucleosome positions inyeast at base-pair resolution. Nature. 2012;486(7404):496–501.46. Kumar Y, Bhargava P. A unique nucleosome arrangement, maintainedactively by chromatin remodelers facilitates transcription of yeast tRNAgenes. BMC Genomics. 2013;14:402.47. Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC,Albert I, Pugh BF. A barrier nucleosome model for statistical positioning ofnucleosomes throughout the yeast genome. Genome Res. 2008;18(7):1073–83.48. Bridier-Nahmias A, Lesage P. Two large-scale analyses of Ty1 LTR-retrotransposon de novo insertion events indicate that Ty1 targetsnucleosomal DNA near the H2A/H2B interface. Mob DNA. 2012;3(1):22.49. Maskell DP, Renault L, Serrao E, Lesbats P, Matadeen R, Hare S, LindemannD, Engelman AN, Costa A, Cherepanov P. Structural basis for retroviralintegration into nucleosomes. Nature. 2015;523(7560):366–9.50. Kent NA, Karabetsou N, Politis PK, Mellor J. In vivo chromatin remodeling byyeast ISWI homologs Isw1p and Isw2p. Genes Dev. 2001;15(5):619–26.51. Petty E, Pillus L. Balancing chromatin remodeling and histone modificationsin transcription. Trends Genet. 2013;29(11):621–9.52. Pollard KJ, Peterson CL. Role for ADA/GCN5 products in antagonizingchromatin-mediated transcriptional repression. Mol Cell Biol. 1997;17(11):6212–22.53. Winston F, Durbin KJ, Fink GR. The SPT3 gene is required for normaltranscription of ty elements in S. Cerevisiae. Cell. 1984;39(3 Pt 2):675–82.54. Bachman N, Gelbart ME, Tsukiyama T, Boeke JD. TFIIIB subunit Bdp1p isrequired for periodic integration of the Ty1 retrotransposon and targetingof Isw2p to S. Cerevisiae tDNAs. Genes Dev. 2005;19(8):955–64.55. Gelbart ME, Bachman N, Delrow J, Boeke JD, Tsukiyama T. Genome-wideidentification of Isw2 chromatin-remodeling targets by localization of acatalytically inactive mutant. Genes Dev. 2005;19(8):942–54.56. D'Ambrosio C, Schmidt CK, Katou Y, Kelly G, Itoh T, Shirahige K, Uhlmann F.Identification of cis-acting sites for condensin loading onto budding yeastchromosomes. Genes Dev. 2008;22(16):2215–27.57. Haeusler RA, Pratt-Hyatt M, Good PD, Gipson TA, Engelke DR. Clustering ofyeast tRNA genes is mediated by specific association of condensin withtRNA gene transcription complexes. Genes Dev. 2008;22(16):2204–14.58. Ciosk R, Shirayama M, Shevchenko A, Tanaka T, Toth A, Shevchenko A,Nasmyth K. Cohesin's binding to chromosomes depends on a separatecomplex consisting of Scc2 and Scc4 proteins. Mol Cell. 2000;5(2):243–54.59. Michaelis C, Ciosk R, Nasmyth K. Cohesins: chromosomal proteins thatprevent premature separation of sister chromatids. Cell. 1997;91(1):35–45.60. Lengronne A, Katou Y, Mori S, Yokobayashi S, Kelly GP, Itoh T, Watanabe Y,Shirahige K, Uhlmann F. Cohesin relocation from sites of chromosomalloading to places of convergent transcription. Nature. 2004;430(6999):573–8.61. Uhlmann F, Lottspeich F, Nasmyth K. Sister-chromatid separation atanaphase onset is promoted by cleavage of the cohesin subunit Scc1.Nature. 1999;400(6739):37–42.62. Ho KL, Ma L, Cheung S, Manhas S, Fang N, Wang K, Young B, Loewen C,Mayor T, Measday V. A role for the budding yeast separase, Esp1, in Ty1element retrotransposition. PLoS Genet. 2015;11(3):e1005109.63. Mou Z, Kenny AE, Curcio MJ. Hos2 and Set3 promote integration of Ty1retrotransposons at tRNA genes in Saccharomyces cerevisiae. Genetics.2006;172(4):2157–67.64. Nyswaner KM, Checkley MA, Yi M, Stephens RM, Garfinkel DJ. Chromatin-associated genes protect the yeast genome from Ty1 insertionalmutagenesis. Genetics. 2008;178(1):197–214.65. Jaehning JA. The Paf1 complex: platform or player in RNA polymerase IItranscription? Biochim Biophys Acta. 2010;1799(5–6):379–88.66. Tomson BN, Arndt KM. The many roles of the conserved eukaryotic Paf1complex in regulating transcription, histone modifications, and diseasestates. Biochim Biophys Acta. 2013;1829(1):116–26.67. Van Oss SB, Cucinotta CE, Arndt KM. Emerging insights into the roles of thePaf1 complex in gene regulation. Trends Biochem Sci. 2017;42(10):788–98.68. Scholes DT, Banerjee M, Bowen B, Curcio MJ. Multiple regulators of Ty1transposition in Saccharomyces cerevisiae have conserved roles in genomemaintenance. Genetics. 2001;159(4):1449–65.69. Dahlin JL, Chen X, Walters MA, Zhang Z. Histone-modifying enzymes,histone modifications and histone chaperones in nucleosome assembly:lessons learned from Rtt109 histone acetyltransferases. Crit Rev BiochemMol Biol. 2015;50(1):31–53.70. Jiang S, Liu Y, Xu C, Wang Y, Gong J, Shen Y, Wu Q, Boeke JD, Dai J.Dissecting nucleosome function with a comprehensive histone H2A andH2B mutant library. G3 (Bethesda). 2017;7(12):3857–66.71. Thompson M, Haeusler RA, Good PD, Engelke DR. Nucleolar clustering ofdispersed tRNA genes. Science. 2003;302(5649):1399–401.72. Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, Shendure J,Fields S, Blau CA, Noble WS. A three-dimensional model of the yeastgenome. Nature. 2010;465(7296):363–7.73. Rodley CD, Bertels F, Jones B, O'Sullivan JM. Global identification of yeastchromosome interactions using genome conformation capture. FungalGenet Biol. 2009;46(11):879–86.74. Rodley CD, Pai DA, Mills TA, Engelke DR, O'Sullivan JM. tRNA gene identityaffects nuclear positioning. PLoS One. 2011;6(12):e29267.75. Rutledge MT, Russo M, Belton JM, Dekker J, Broach JR. The yeast genomeundergoes significant topological reorganization in quiescence. NucleicAcids Res. 2015;43(17):8299–313.Cheung et al. Mobile DNA  (2018) 9:14 Page 12 of 1576. Albert B, Mathon J, Shukla A, Saad H, Normand C, Leger-Silvestre I, Villa D,Kamgoue A, Mozziconacci J, Wong H, et al. Systematic characterization ofthe conformation and dynamics of budding yeast chromosome XII. J CellBiol. 2013;202(2):201–10.77. Belagal P, Normand C, Shukla A, Wang R, Leger-Silvestre I, Dez C, Bhargava P,Gadal O. Decoding the principles underlying the frequency of association withnucleoli for RNA polymerase III-transcribed genes in budding yeast. Mol BiolCell. 2016;27(20):3164–77.78. Chen M, Gartenberg MR. Coordination of tRNA transcription with export atnuclear pore complexes in budding yeast. Genes Dev. 2014;28(9):959–70.79. Snider CE, Stephens AD, Kirkland JG, Hamdani O, Kamakaka RT, Bloom K.Dyskerin, tRNA genes, and condensin tether pericentric chromatin to thespindle axis in mitosis. J Cell Biol. 2014;207(2):189–99.80. Manhas S, Ma L, Measday V. The yeast Ty1 retrotransposon requirescomponents of the nuclear pore complex for transcription and genomicintegration. Nucleic Acids Res. 2018;46(7):3552–78.81. Marini B, Kertesz-Farkas A, Ali H, Lucic B, Lisek K, Manganaro L, Pongor S,Luzzati R, Recchia A, Mavilio F, et al. Nuclear architecture dictates HIV-1integration site selection. Nature. 2015;521(7551):227–31.82. Albanese A, Arosio D, Terreni M, Cereseto A. HIV-1 pre-integrationcomplexes selectively target decondensed chromatin in the nuclearperiphery. PLoS One. 2008;3(6):e2413.83. Lelek M, Casartelli N, Pellin D, Rizzi E, Souque P, Severgnini M, Di Serio C,Fricke T, Diaz-Griffero F, Zimmer C, et al. Chromatin organization at thenuclear pore favours HIV replication. Nat Commun. 2015;6:6483.84. Chalker DL, Sandmeyer SB. Transfer RNA genes are genomic targets for de novotransposition of the yeast retrotransposon Ty3. Genetics. 1990;126(4):837–50.85. Chalker DL, Sandmeyer SB. Ty3 integrates within the region of RNApolymerase III transcription initiation. Genes Dev. 1992;6(1):117–28.86. Sandmeyer SB, Bilanchone VW, Clark DJ, Morcos P, Carle GF, Brodeur GM.Sigma elements are position-specific for many different yeast tRNA genes.Nucleic Acids Res. 1988;16(4):1499–515.87. Kirchner J, Connolly CM, Sandmeyer SB. Requirement of RNA polymerase IIItranscription factors for in vitro position-specific integration of aretroviruslike element. Science. 1995;267(5203):1488–91.88. Yieh L, Hatzis H, Kassavetis G, Sandmeyer SB. Mutational analysis of thetranscription factor IIIB-DNA target of Ty3 retroelement integration. J BiolChem. 2002;277(29):25920–8.89. Yieh L, Kassavetis G, Geiduschek EP, Sandmeyer SB. The Brf and TATA-binding protein subunits of the RNA polymerase III transcription factor IIIBmediate position-specific integration of the gypsy-like element, Ty3. J BiolChem. 2000;275(38):29800–7.90. Kassavetis GA, Soragni E, Driscoll R, Geiduschek EP. Reconfiguring theconnectivity of a multiprotein complex: fusions of yeast TATA-bindingprotein with Brf1, and the function of transcription factor IIIB. Proc NatlAcad Sci U S A. 2005;102(43):15406–11.91. Qi X, Sandmeyer S. In vitro targeting of strand transfer by the Ty3retroelement integrase. J Biol Chem. 2012;287(22):18589–95.92. Moqtaderi Z, Struhl K. Genome-wide occupancy profile of the RNApolymerase III machinery in Saccharomyces cerevisiae reveals loci withincomplete transcription complexes. Mol Cell Biol. 2004;24(10):4118–27.93. Qi X, Daily K, Nguyen K, Wang H, Mayhew D, Rigor P, Forouzan S, JohnstonM, Mitra RD, Baldi P, et al. Retrotransposon profiling of RNA polymerase IIIinitiation sites. Genome Res. 2012;22(4):681–92.94. Aye M, Dildine SL, Claypool JA, Jourdain S, Sandmeyer SB. A truncationmutant of the 95-kilodalton subunit of transcription factor IIIC revealsasymmetry in Ty3 integration. Mol Cell Biol. 2001;21(22):7839–51.95. Connolly CM, Sandmeyer SB. RNA polymerase III interferes with Ty3integration. FEBS Lett. 1997;405(3):305–11.96. Guffanti E, Percudani R, Harismendy O, Soutourina J, Werner M, IacovellaMG, Negri R, Dieci G. Nucleosome depletion activates poised RNApolymerase III at unconventional transcription sites in Saccharomycescerevisiae. J Biol Chem. 2006;281(39):29155–64.97. Eibel H, Philippsen P. Preferential integration of yeast transposable elementty into a promoter region. Nature. 1984;307(5949):386–8.98. Natsoulis G, Thomas W, Roghmann MC, Winston F, Boeke JD. Ty1transposition in Saccharomyces cerevisiae is nonrandom. Genetics. 1989;123(2):269–79.99. Rose M, Winston F. Identification of a ty insertion within the codingsequence of the S. Cerevisiae URA3 gene. Mol Gen Genet. 1984;193(3):557–60.100. Simchen G, Winston F, Styles CA, Fink GR. Ty-mediated gene expression ofthe LYS2 and HIS4 genes of Saccharomyces cerevisiae is controlled by thesame SPT genes. Proc Natl Acad Sci U S A. 1984;81(8):2431–4.101. Weinstock KG, Mastrangelo MF, Burkett TJ, Garfinkel DJ, Strathern JN.Multimeric arrays of the yeast retrotransposon ty. Mol Cell Biol. 1990;10(6):2882–92.102. Wilke CM, Heidler SH, Brown N, Liebman SW. Analysis of yeast retrotransposonty insertions at the CAN1 locus. Genetics. 1989;123(4):655–65.103. Borneman AR, Pretorius IS. Genomic insights into the Saccharomyces sensustricto complex. Genetics. 2015;199(2):281–91.104. Libkind D, Hittinger CT, Valerio E, Goncalves C, Dover J, Johnston M,Goncalves P, Sampaio JP. Microbe domestication and the identification ofthe wild genetic stock of lager-brewing yeast. Proc Natl Acad Sci U S A.2011;108(35):14539–44.105. Scannell DR, Zill OA, Rokas A, Payen C, Dunham MJ, Eisen MB, Rine J,Johnston M, Hittinger CT. The awesome power of yeast evolutionarygenetics: new genome sequences and strain resources for theSaccharomyces sensu stricto genus. G3 (Bethesda). 2011;1(1):11–25.106. Edwards-Ingram LC, Gent ME, Hoyle DC, Hayes A, Stateva LI, Oliver SG.Comparative genomic hybridization provides new insights into themolecular taxonomy of the Saccharomyces sensu stricto complex. GenomeRes. 2004;14(6):1043–51.107. Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP,Roberts IN, Burt A, Koufopanou V, et al. Population genomics of domesticand wild yeasts. Nature. 2009;458(7236):337–41.108. Liti G, Peruffo A, James SA, Roberts IN, Louis EJ. Inferences of evolutionaryrelationships from a population survey of LTR-retrotransposons andtelomeric-associated sequences in the Saccharomyces sensu strictocomplex. Yeast. 2005;22(3):177–92.109. Bon E, Neuveglise C, Casaregola S, Artiguenave F, Wincker P, Aigle M,Durrens P. Genomic exploration of the hemiascomycetous yeasts: 5.Saccharomyces bayanus var. uvarum. FEBS Lett. 2000;487(1):37–41.110. Fingerman EG, Dombrowski PG, Francis CA, Sniegowski PD. Distribution andsequence analysis of a novel Ty3-like element in natural Saccharomycesparadoxus isolates. Yeast. 2003;20(9):761–70.111. Carr M, Bensasson D, Bergman CM. Evolutionary genomics of transposableelements in Saccharomyces cerevisiae. PLoS One. 2012;7(11):e50978.112. Bleykasten-Grosshans C, Neuveglise C. Transposable elements in yeasts. C RBiol. 2011;334(8–9):679–86.113. Castanera R, Borgognone A, Pisabarro AG, Ramirez L. Biology, dynamics, andapplications of transposable elements in basidiomycete fungi. ApplMicrobiol Biotechnol. 2017;101(4):1337–50.114. Donnart T, Piednoel M, Higuet D, Bonnivard E. Filamentous ascomycetegenomes provide insights into Copia retrotransposon diversity in fungi.BMC Genomics. 2017;18(1):410.115. Kovalchuk A, Senam S, Mauersberger S, Barth G. Tyl6, a novel Ty3/gypsy-likeretrotransposon in the genome of the dimorphic fungus Yarrowia lipolytica.Yeast. 2005;22(12):979–91.116. Magnan C, Yu J, Chang I, Jahn E, Kanomata Y, Wu J, Zeller M, Oakes M, BaldiP, Sandmeyer S. Sequence assembly of Yarrowia lipolytica strain W29/CLIB89 shows transposable element diversity. PLoS One. 2016;11(9):e0162363.117. Schmid-Berger N, Schmid B, Barth G. Ylt1, a highly repetitiveretrotransposon in the genome of the dimorphic fungus Yarrowia lipolytica.J Bacteriol. 1994;176(9):2477–82.118. Zhang L, Yan L, Jiang J, Wang Y, Jiang Y, Yan T, Cao Y. The structure andretrotransposition mechanism of LTR-retrotransposons in the asexual yeastCandida albicans. Virulence. 2014;5(6):655–64.119. Perreau VM, Santos MA, Tuite MF. Beta, a novel repetitive DNA elementassociated with tRNA genes in the pathogenic yeast Candida albicans. MolMicrobiol. 1997;25(2):229–36.120. Sellam A, Hogues H, Askew C, Tebbji F, van Het Hoog M, Lavoie H,Kumamoto CA, Whiteway M, Nantel A. Experimental annotation of thehuman pathogen Candida albicans coding and noncoding transcribedregions using high-resolution tiling arrays. Genome Biol. 2010;11(7):R71.121. Guo Y, Singh PK, Levin HL. A long terminal repeat retrotransposon ofSchizosaccharomyces japonicus integrates upstream of RNA pol IIItranscribed genes. Mob DNA. 2015;6:19.122. Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I,Roy S, Lin MF, Heiman DI, et al. Comparative functional genomics of thefission yeasts. Science. 2011;332(6032):930–6.Cheung et al. Mobile DNA  (2018) 9:14 Page 13 of 15123. Neuveglise C, Feldmann H, Bon E, Gaillardin C, Casaregola S. Genomicevolution of the long terminal repeat retrotransposons inhemiascomycetous yeasts. Genome Res. 2002;12(6):930–43.124. Spaller T, Kling E, Glockner G, Hillmann F, Winckler T. Convergent evolutionof tRNA gene targeting preferences in compact genomes. Mob DNA. 2016;7(1):17.125. Hofmann J, Schumann G, Borschet G, Gosseringer R, Bach M, Bertling WM,Marschalek R, Dingermann T. Transfer RNA genes from Dictyostelium discoideumare frequently associated with repetitive elements and contain consensus boxesin their 5′ and 3′-flanking regions. J Mol Biol. 1991;222(3):537–52.126. Glockner G, Heidel AJ. Centromere sequence and dynamics in Dictyosteliumdiscoideum. Nucleic Acids Res. 2009;37(6):1809–16.127. Gao X, Hou Y, Ebina H, Levin HL, Voytas DF. Chromodomains directintegration of retrotransposons to heterochromatin. Genome Res. 2008;18(3):359–69.128. Winckler T, Dingermann T, Glockner G. Dictyostelium mobile elements:strategies to amplify in a compact genome. Cell Mol Life Sci. 2002;59(12):2097–111.129. Winckler T, Schiefner J, Spaller T, Siol O. Dictyostelium transfer RNA gene-targeting retrotransposons: studying mobile element-host interactions in acompact genome. Mob Genet Elements. 2011;1(2):145–50.130. Winckler T, Szafranski K, Glockner G. Transfer RNA gene-targeted integration:an adaptation of retrotransposable elements to survive in the compactDictyostelium discoideum genome. Cytogenet Genome Res. 2005;110(1–4):288–98.131. Malicki M, Iliopoulou M, Hammann C. Retrotransposon domestication andcontrol in Dictyostelium discoideum. Front Microbiol. 2017;8:1869.132. Chung T, Siol O, Dingermann T, Winckler T. Protein interactions involved intRNA gene-specific integration of Dictyostelium discoideum non-longterminal repeat retrotransposon TRE5-a. Mol Cell Biol. 2007;27(24):8492–501.133. Siol O, Boutliliss M, Chung T, Glockner G, Dingermann T, Winckler T. Role ofRNA polymerase III transcription factors in the selection of integration sitesby the dictyostelium non-long terminal repeat retrotransposon TRE5-a. MolCell Biol. 2006;26(22):8242–51.134. Siol O, Spaller T, Schiefner J, Winckler T. Genetically tagged TRE5-aretrotransposons reveal high amplification rates and authentic target sitepreference in the Dictyostelium discoideum genome. Nucleic Acids Res.2011;39(15):6608–19.135. Spaller T, Groth M, Glockner G, Winckler T. TRE5-a retrotranspositionprofiling reveals putative RNA polymerase III transcription complex bindingsites on the Dictyostelium extrachromosomal rDNA element. PLoS One.2017;12(4):e0175729.136. Szafranski K, Glockner G, Dingermann T, Dannat K, Noegel AA, Eichinger L,Rosenthal A, Winckler T. Non-LTR retrotransposons with unique integrationpreferences downstream of Dictyostelium discoideum tRNA genes. Mol GenGenet. 1999;262(4–5):772–80.137. Winckler T, Tschepke C, de Hostos EL, Jendretzke A, Dingermann T. Tdd-3, atRNA gene-associated poly(a) retrotransposon from Dictyosteliumdiscoideum. Mol Gen Genet. 1998;257(6):655–61.138. Boeke JD, Devine SE. Yeast retrotransposons: finding a nice quietneighborhood. Cell. 1998;93(7):1087–9.139. Bolton EC, Boeke JD. Transcriptional interactions between yeast tRNA genes,flanking genes and ty elements: a genomic point of view. Genome Res.2003;13(2):254–63.140. Kinsey PT, Sandmeyer SB. Adjacent pol II and pol III promoters: transcriptionof the yeast retrotransposon Ty3 and a target tRNA gene. Nucleic Acids Res.1991;19(6):1317–24.141. Schumann G, Zundorf I, Hofmann J, Marschalek R, Dingermann T. Internallylocated and oppositely oriented polymerase II promoters direct convergenttranscription of a LINE-like retroelement, the Dictyostelium repetitiveelement, from Dictyostelium discoideum. Mol Cell Biol. 1994;14(5):3074–84.142. Blanc VM, Adams J. Ty1 insertions in intergenic regions of the genome ofSaccharomyces cerevisiae transcribed by RNA polymerase III have nodetectable selective effect. FEMS Yeast Res. 2004;4(4–5):487–91.143. Garfinkel DJ, Tucker JM, Saha A, Nishida Y, Pachulska-Wieczorek K, BlaszczykL, Purzycka KJ. A self-encoded capsid derivative restricts Ty1retrotransposition in Saccharomyces. Curr Genet. 2016;62(2):321–9.144. Pachulska-Wieczorek K, Blaszczyk L, Gumna J, Nishida Y, Saha A, Biesiada M,Garfinkel DJ, Purzycka KJ. Characterizing the functions of Ty1 gag and thegag-derived restriction factor p22/p18. Mob Genet Elements. 2016;6(2):e1154637.145. Boeke JD, Eichinger DJ, Natsoulis G. Doubling Ty1 element copy number inSaccharomyces cerevisiae: host genome stability and phenotypic effects.Genetics. 1991;129(4):1043–52.146. Wilke CM, Adams J. Fitness effects of ty transposition in Saccharomycescerevisiae. Genetics. 1992;131(1):31–42.147. Scheifele LZ, Cost GJ, Zupancic ML, Caputo EM, Boeke JD. Retrotransposonoverdose and genome integrity. Proc Natl Acad Sci U S A. 2009;106(33):13927–32.148. Garfinkel DJ. Genome evolution mediated by ty elements inSaccharomyces. Cytogenet Genome Res. 2005;110(1–4):63–9.149. McClanahan T, McEntee K. Specific transcripts are elevated inSaccharomyces cerevisiae in response to DNA damage. Mol Cell Biol. 1984;4(11):2356–63.150. Rolfe M, Spanos A, Banks G. Induction of yeast ty element transcription byultraviolet-light. Nature. 1986;319(6051):339–40.151. Sacerdot C, Mercier G, Todeschini AL, Dutreix M, Springer M, Lesage P.Impact of ionizing radiation on the life cycle of Saccharomyces cerevisiaeTy1 retrotransposon. Yeaste. 2005;22(6):441–55.152. Curcio MJ, Kenny AE, Moore S, Garfinkel DJ, Weintraub M, Gamache ER,Scholes DT. S-phase checkpoint pathways stimulate the mobility of theretrovirus-like transposon Ty1. Mol Cell Biol. 2007;27(24):8874–85.153. Maxwell PH, Coombes C, Kenny AE, Lawler JF, Boeke JD, Curcio MJ. Ty1mobilizes subtelomeric Y' elements in telomerase-negative Saccharomycescerevisiae survivors. Mol Cell Biol. 2004;24(22):9887–98.154. Scholes DT, Kenny AE, Gamache ER, Mou Z, Curcio MJ. Activation of a LTR-retrotransposon by telomere erosion. Proc Natl Acad Sci U S A. 2003;100(26):15736–41.155. Maxwell PH, Burhans WC, Curcio MJ. Retrotransposition is associated withgenome instability during chronological aging. Proc Natl Acad Sci U S A.2011;108(51):20376–81.156. Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO, Rosenzweig F,Botstein D. Characteristic genome rearrangements in experimentalevolution of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2002;99(25):16144–9.157. Argueso JL, Westmoreland J, Mieczkowski PA, Gawel M, Petes TD, ResnickMA. Double-strand breaks associated with repetitive DNA can reshape thegenome. Proc Natl Acad Sci U S A. 2008;105(33):11845–50.158. Casper AM, Greenwell PW, Tang W, Petes TD. Chromosome aberrationsresulting from double-strand DNA breaks at a naturally occurring yeastfragile site composed of inverted ty elements are independent of Mre11pand Sae2p. Genetics. 2009;183(2):423–39. 421SI-426SI159. Cheng E, Vaisica JA, Ou J, Baryshnikova A, Lu Y, Roth FP, Brown GW.Genome rearrangements caused by depletion of essential DNA replicationproteins in Saccharomyces cerevisiae. Genetics. 2012;192(1):147–60.160. Lemoine FJ, Degtyareva NP, Lobachev K, Petes TD. Chromosomaltranslocations in yeast induced by low levels of DNA polymerase a modelfor chromosome fragile sites. Cell. 2005;120(5):587–98.161. Song W, Dominska M, Greenwell PW, Petes TD. Genome-wide high-resolution mapping of chromosome fragile sites in Saccharomycescerevisiae. Proc Natl Acad Sci U S A. 2014;111(21):E2210–8.162. Hoang ML, Tan FJ, Lai DC, Celniker SE, Hoskins RA, Dunham MJ, Zheng Y,Koshland D. Competitive repair by naturally dispersed repetitive DNA duringnon-allelic homologous recombination. PLoS Genet. 2010;6(12):e1001228.163. Chung DK, Chan JN, Strecker J, Zhang W, Ebrahimi-Ardebili S, Lu T,Abraham KJ, Durocher D, Mekhail K. Perinuclear tethers license telomericDSBs for a broad kinesin- and NPC-dependent DNA repair process. NatCommun. 2015;6:7742.164. Freudenreich CH, Su XA. Relocalization of DNA lesions to the nuclear porecomplex. FEMS Yeast Res. 2016;16(8)165. Chan YA, Aristizabal MJ, Lu PY, Luo Z, Hamza A, Kobor MS, Stirling PC,Hieter P. Genome-wide profiling of yeast DNA:RNA hybrid prone sites withDRIP-chip. PLoS Genet. 2014;10(4):e1004288.166. El Hage A, Webb S, Kerr A, Tollervey D. Genome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes, retrotransposons andmitochondria. PLoS Genet. 2014;10(10):e1004716.167. Batzer MA, Deininger PL. Alu repeats and human genomic diversity. Nat RevGenet. 2002;3(5):370–9.168. Okada N, Ohshima K. A model for the mechanism of initial generation ofshort interspersed elements (SINEs). J Mol Evol. 1993;37(2):167–70.169. Clare J, Farabaugh P. Nucleotide sequence of a yeast ty element: evidencefor an unusual mechanism of gene expression. Proc Natl Acad Sci U S A.1985;82(9):2829–33.Cheung et al. Mobile DNA  (2018) 9:14 Page 14 of 15170. Farabaugh PJ, Zhao H, Vimaladithan A. A novel programed frameshiftexpresses the POL3 gene of retrotransposon Ty3 of yeast: frameshiftingwithout tRNA slippage. Cell. 1993;74(1):93–103.171. Mellor J, Fulton SM, Dobson MJ, Wilson W, Kingsman SM, Kingsman AJ. Aretrovirus-like strategy for expression of a fusion protein encoded by yeasttransposon Ty1. Nature. 1985;313(5999):243–6.172. Glockner G, Szafranski K, Winckler T, Dingermann T, Quail MA, Cox E,Eichinger L, Noegel AA, Rosenthal A. The complex repeats of Dictyosteliumdiscoideum. Genome Res. 2001;11(4):585–94.173. Marschalek R, Hofmann J, Schumann G, Gosseringer R, Dingermann T.Structure of DRE, a retrotransposable element which integrates withposition specificity upstream of Dictyostelium discoideum tRNA genes. MolCell Biol. 1992;12(1):229–39.174. Beck P, Dingermann T, Winckler T. Transfer RNA gene-targetedretrotransposition of Dictyostelium TRE5-a into a chromosomal UMPsynthase gene trap. J Mol Biol. 2002;318(2):273–85.175. Marschalek R, Borschet G, Dingermann T. Genomic organization of thetransposable element Tdd-3 from Dictyostelium discoideum. Nucleic AcidsRes. 1990;18(19):5751–7.Cheung et al. Mobile DNA  (2018) 9:14 Page 15 of 15

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