transposable element-host interactions:regulation of insertion and excision

P1: ARS/dat P2: MBL/ary QC: MBL/bs T1: MBL

October 25, 1997 18:1 Annual Reviews AR044-14

Annu. Rev. Genet. 1997. 31:381–404Copyright c© 1997 by Annual Reviews Inc. All rights reserved

TRANSPOSABLE ELEMENT-HOSTINTERACTIONS: Regulation ofInsertion and Excision

Mariano Labrador and Victor G. CorcesDepartment of Biology, The Johns Hopkins University, 3400 North Charles Street,Baltimore, Maryland 21218; e-mail: [email protected]

KEY WORDS: transposable element, retrotransposon, mutation, evolution, DNA repair

ABSTRACT

Transposable elements propagate by inserting into new locations in the genomesof the hosts they inhabit. Their transposition might thus negatively affect thefitness of the host, suggesting the requirement for a tight control in the regulationof transposable element mobilization. The nature of this control depends on thestructure of the transposable element. DNA elements encode a transposase thatis necessary, and in most cases sufficient, for mobilization. In general, regulationof these elements depends on intrinsic factors with little direct input from thehost. Retrotransposons require an RNA intermediate for transposition, and theirfrequency of mobilization is controlled at multiple steps by the host genomeby regulating both their expression levels and their insertional specificity. As aresult, a symbiotic relationship has developed between transposable elements andtheir host. Examples are now emerging showing that transposons can contributesignificantly to the well being of the organisms they populate.

CONTENTS

INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 382

DNA TRANSPOSONS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 382A Common Mechanism for Transposition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 383A Specific Case: Mobilization of Drosophila P Elements. . . . . . . . . . . . . . . . . . . . . . . . . . 384Gap Repair: The Other Side of Transposition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 387

RETROTRANSPOSONS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 389Mechanism of Integration of Poly(A)-Containing Retrotransposons. . . . . . . . . . . . . . . . . 389

3810066-4197/97/1215-0381$08.00

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382 LABRADOR & CORCES

Site-Specific Integration: Group II Introns and rDNA Insect Elements. . . . . . . . . . . . . . . 390Insertional Specificity: Yeast Elements Are Restricted in Where They Land. . . . . . . . . . . 392Host Factors Controlling Retrotransposon Expression and Mobilization. . . . . . . . . . . . . 393Retrotransposons Can Benefit the Host: Telomeres and Chromosome Repair. . . . . . . . . . 395Effects of Retrotransposon Insertions on Host Gene Expression. . . . . . . . . . . . . . . . . . . . 396

CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 398

INTRODUCTION

Transposable elements are major constituents of eukaryotic genomes, makingup to 10% of theDrosophilagenome and 35% of the human genome. Their mo-bilization must be under tight regulation, in both its frequency and insertionalspecificity, to avoid the accumulation of mutations that could be deleteriousto the host. But transposable elements must also maintain a certain level ofactivity to ensure their propagation and survival. This level of transpositionis probably the result of a balance between the interests of the transposableelements and those of the hosts they inhabit. One might think a priori that mo-bilization of transposable elements would be of little benefit to the host and thatit would be completely shut down. That this is not the case is manifested by theappearance of numerous transposable element-induced spontaneous mutationsin many organisms, including yeast,Drosophila, and humans. Here, we reviewthe current status of research on eukaryotic transposable elements, with an em-phasis on how these elements move and integrate into the genome, how the hostmaintains its transposition under control, and how transposable elements oftenget around this tight regulation to insert into new locations. We also discussexamples showing that in some cases transposable element mobilization mightbe advantageous to the host. We concentrate on eukaryotic transposons and, inparticular, on those cases for which a large body of evidence has accumulatedin recent years. Themariner/Tc1family of elements is reviewed elsewhere inthis volume and is not discussed here (see Hartl et al, this volume).

DNA TRANSPOSONS

DNA transposable elements have been found in all phyla: They are the mostcommon transposable elements in bacteria, and numerous families have beendescribed in fungi, ciliates, plants, worms, insects, fish, and humans (8). Thisclass of transposable elements is characterized by the presence of two invertedrepeats flanking a DNA sequence encoding a protein generically named trans-posase. This protein is involved in the processing of DNA at the donor andtarget sites by a “cut-and-paste” process. Transposase, in most instances, is theonly requirement for transposition. For this reason, the control of transpositionis often limited to the regulation of the expression of this protein.

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TRANSPOSON MOBILIZATION 383

A Common Mechanism for TranspositionThe mechanism of transposition appears to be essentially the same for mosttransposases and integrases (27). This similarity has been confirmed by theanalysis of three crystallographic structures of transposases and integrases frombacteriophage Mu, HIV, and ASV retroviruses (reviewed in 43). Crystal struc-ture comparisons show that the catalytic domain for all three proteins is verysimilar, bringing together the two aspartate and glutamate residues separatedby 50 to 70 (D-D) and 35 (D-E) residues in the primary structure. This cat-alytic domain is most likely responsible for a transphosphorylation necessary forDNA cleavage and strand transfer during the transposition process and is highlyconserved among integrases from very different elements (27). This process in-volves two sequential steps. Site-specific cleavage of the DNA takes place firstat the ends of the transposable element, and the complex of transposase-elementends is then brought to a DNA target, where the strand transfer is carried out bycovalently joining the 3′ ends of the element to the target DNA. A strand gap ofvariable size depending on the element is the result of the staggered phosphatesused in the reaction. This gap is later filled, probably by host-dependent repairmechanisms, and results in the characteristic direct duplications found at theends of all transposable elements.

Using in vitro transposition systems, it has been shown that transposase is theonly requirement for transposition of a variety of elements including bacterialtransposons,Tc1andP(46, 107). For this reason, the regulation of transpositionmust rely on cellular processes necessary to produce active transposase. Reg-ulation of transposition is specific for each element and includes regulation atthe levels of transcription, differential splicing, translation, and protein-proteininteractions. TheTc1 element ofC. elegansseems to represent the simplestcase analyzed so far. Transposase is the only protein required for mobilization,and regulation of transposition of this family appears to take place at the levelof transcription, as demonstrated by activation of transposition with increasingexpression levels in transgenic animals (108). Genetic factors of the host candetermine the transposition rate of theTc1element, but these factors probablycorrespond to particular active copies of theTc1element. This simple mecha-nism of regulation and the few constraints imposed onTc1mobilization mightexplain the relative success of this element and its widespread distribution.These elements have been found in many different species including ciliates,fungi, Drosophila, fish, and humans (81).

An additional level of complexity in the regulation of the mobilization of thisclass of transposons is represented by several transposable elements of maize(16, 35, 37). Ac or Activator is the full-length autonomously active element,a sequence of 4565 bp flanked by inverted repeats of 11 bp. The transposase

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gene has 5 exons encoding a single protein. No differential splicing has beenreported, and the promoter seems to be constitutively active at a very low tran-scription rate (51, 57). Binding of the Ac transposase to a series of subterminalrepeats is required for transposition. The direct relationship between transpo-sition rate and number of repeats suggests a role for cooperative interactionsbetween transposase molecules required for full transposition. Thus, control-ling the levels of transposase might be the primary mechanism of regulatingtransposition. The transposase protein is able to interact with itself to formoligomers that are inactive in the transposition process. This might represent anegative feedback mechanism to control transposition rates.

Regulation of theEn/Spmis yet more complex. This element encodes aseries of proteins that arise by alternative splicing. Two proteins, TnpA andTnpD, have been implicated in the transposition process (37, 66). Other proteinsproduced by alternative splicing, such as TnpB and TnpC, are not essentialbut appear to play a role in regulating transposition (66). TnpA recognizessequences of 180 bp at the 5′ end and of 300 bp at the 3′ end of En/Spm,which contain 6 and 8 copies, respectively, of a 12-bp repeat required fortransposition of these elements (106). The arrangement of these motifs in aspecific head-to-head and tail-to-tail organization at both ends of the elementsuggests that binding of several molecules of TnpA protein causes the bendingof the DNA, resulting in a specific conformation required for transposition.This conformation is necessary for cleavage of the DNA by TnpD, the actualtransposase (40).

Modification of the DNA by host methylases plays an important role in theinhibition of transposition of maize transposons, bringing to light a new strategyby which the host can regulate transposon mobilization. The binding propertiesof the transposase protein to the subterminal repeats of theAc/Dselements ismethylation sensitive, and methylation of the promoter region reduces the tran-scription of active elements almost completely (35, 51). In the case ofEn/Spm,methylation of two regions close to the transcription start site inactivates the pro-moter, and it also reduces the excision frequency even when transactivated byan activeEn/Spmelement. Interestingly, although TnpA acts as a repressor ofthe unmethylated En/Spm promoter, it can activate and promote demethylationof the methylated element. The transposition rate of the element is determinedby a trade-off between methylation, transcription, and levels of TnpA (34, 93).

A Specific Case: Mobilization of Drosophila P ElementsTheDrosophila Pelement was discovered as the determinant of the P-M hybriddysgenesis system (30). TheP element is a 2.9-kb sequence flanked by 31-bpperfect inverted repeats and structured in 4 exons that encode a single 87-kDtransposase protein (30). Transposase does not bind to the terminal repeats;

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instead, two perfect 11-bp inverted subterminal repeats at the 5′ and 3′ ends areessential for transposition and are considered the binding sites for this protein(74). Transposase is the only requirement forPelement transposition, as shownafter the induction of transposition in an in vitro system (46). However, mobi-lization of P elements in vivo is a complex process controlled by interactionswith the host at many different levels.

GERM LINE VERSUS SOMATIC TRANSPOSITION This is the first clear-cutmechanism ofP element regulation indicative of a host-dependent control.Splicing of the third intron of theP element does not take place in somatic cellsof Drosophila, resulting in the production of an mRNA that encodes a 66-kDprotein as the consequence of a frameshift and a premature stop codon (53).The artificial removal of this intron eliminates the germ line specificity ofPtransposition and results in the production of transposase andP mobilizationin all tissues of the fly. Therefore the 66-kD protein normally produced in so-matic cells is defective for transposase activity; this explains why, even underhybrid dysgenesis conditions, somatic transposition is almost absent (reviewedin 30, 85, 86). When the third intron is placed in the context of a cellular gene,it is able to splice normally, suggesting the existence ofcis-acting sequences intheP element responsible for the splicing regulation through their interactionwith host proteins (19, 54). Two different proteins have been implicated in theformation of a multiprotein complex that binds to inhibitory sequences located5′ to the donor splice site (96). The 97-kDP element Somatic Inhibitor (PSI)protein was found to be responsible for the inhibition ofP mRNA splicingin the soma (95). It contains three KH RNA-binding domains characteristicof other RNA binding proteins, including the MER1 yeast splicing regulator(95). The expression of PSI is limited to somatic cells and could explain thesomatic inhibition of third intron processing in theP mRNA by stimulating anonconsensus, inactive pseudo 5′ splice site (96). A second protein involvedin the regulation ofP element splicing, hrp48, is a homolog of the mammalianhnRNP A1 implicated in nucleus-cytoplasm transport and could be responsiblefor the export of mRNAs to the cytoplasm (95).

COPY NUMBER REGULATION AND P CYTOTYPE The mobilization rate ofPelements is close to 25× 10−2 transpositions per element per generation un-der dysgenic conditions (99). Such a high transposition rate during prolongedperiods of time will be untenable to anyDrosophilapopulation, and in fact,extinction of hybrid dysgenic lines as a consequence ofP mobilization is afrequent phenomenon (31). However,P strains that carry ca 50 copies of theP element show very little or no transposition (29, 30). Although there aredifferences among naturally occurring populations, this number ofP elements

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represents the conditions at which transposition is repressed in natural popu-lations and laboratory strains. The control ofP element transposition shows astrong maternal effect: Dysgenic crosses with high levels of transposition in thegerm line of the F1 offspring are produced when females lackingP elements(M females) are crossed with males carryingP elements (P males), but notin the reciprocal cross. The repressor state in P females is called P cytotypebecause of its cytoplasmic nature. After a few generations of hybrid dysgeniccrosses, the repression of transposition is determined entirely by chromosomalP elements in the germ line of the zygote (30). Therefore, although maternallytransmitted P cytotype is ultimately determined by the presence of chromosomalP elements, this regulation is complex and not well understood.

Several lines of evidence suggest that theP element–encoded 66-kD pro-tein is a repressor of transposition. Naturally occurring P strains produce highlevels of the 66-kD protein during oogenesis. Defective elements frequentlyfound in natural populations, known as KP and Type I repressors, show internaldeletions and encode a defective 66-kD transposase. These elements have beencorrelated with the presence of repressor and are thought to be the natural deter-minants of the P cytotype (13, 42, 98). Other naturally occurringP elements atparticular chromosomal sites, and the full-length autonomousP elements, havealso been described as P cytotype determinants (42, 76, 89, 91). In addition, invitro–modified defectiveP elements capable of encoding a protein similar tothe 66-kD defective transposase are able to repress transposition in both germline and somatic tissues (70, 88). However, although single-copy transformantsare able to repress transposase activity zygotically, the same elements failed toshow a maternal inheritance of the P cytotype (69, 70). After mobilization ofthe initial defectivePelement transgenes that did not show maternal inheritanceto different locations in the genome, defectiveP elements inserted at some ofthe new positions were able to display strong maternal repression of transpo-sition (69). However, the presence of strong germ line–specific promoters atthe insertion site controllingP expression failed to correlate with maternal re-pression, indicating that although position effect is a determinant of P cytotype,factors other than an increase in repressor transcription must also be involved(69).

Several additional mechanisms for P cytotype repression have been sug-gested, including transcriptional regulation and multimer poisoning (30, 86),antisense RNA (84), and titration of transposase in the presence of manyPelement ends (97). Although P cytotype results in repression of theP ele-ment promoter in vivo (56, 91), this repression is not promoter specific, sinceheterologous promoters directingP expression are still partially or completelyrepressed (89). Moreover, inhibition of transposase transcription could not bethe only effect of P cytotype repression since some transcription is still observed

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in the germ line of repressed females (69, 89). It has been suggested recentlythat a multimer poisoning by the repressor protein could be the best explanationfor all phenomena associated with the establishment of the P cytotype. Singleamino acid mutations in the leucine zipper region of the KP repressor failed toinduce P cytotype, indicating the requirement for protein-protein interactionsand suggesting that the repressor might act by associating with transposase orother proteins involved in transposition to form inactive multimers (1). Analternative explanation of these results is based on the finding that purified KPrepressor binds to multiple sites inP element DNA, including the transposasebinding site, an enhancer of transposition and the 31-bp terminal inverted re-peat (55). The repressor may therefore inhibit transposition by competing withtransposase for the same binding sites in the genome. The leucine zipper re-gion actively participates in dimer formation, and this dimer has a higher DNAaffinity than the monomer. The DNA-binding activity of the repressor willresult in transcription inhibition due to partial overlap of the repressor bindingsite with the promoter region of theP element (55). Finally, this reduction oftranscription will increase the frequency of unspliced third intron sequences,increasing the repressive effect through the production of the 66-kD repressorby autonomousP elements, and creating a regulatory feedback loop that willshut down transcription completely and would explain the maternally inheritedproperties of P cytotype (89).

Gap Repair: The Other Side of TranspositionTwo different and general transposition strategies could be outlined for trans-posable elements: replicative and nonreplicative transposition. The first iscarried out by retrotransposons and DNA transposons like bacteriophage Mu.After transposition, the donor site is preserved intact and in the same posi-tion as the original copy. The second strategy is used by DNA transposonsthat move by a cut-and-paste mechanism. Double-strand breaks (DSBs) areproduced at the ends of the element during this process, and the donor copyphysically moves to the new target site. Nonreplicative transposition raisesan important question: How can nonreplicative transposable elements increasetheir copy number so quickly after a short number of generations? It is wellestablished that elements such asP can reach high copy number quickly afterhybrid dysgenesis events or following a short number of generations after germline transformation with a single element (23). Observations such as the highnumber of internally deleted elements with perfectly conserved inverted repeatsand the frequent footprints left by many elements at the donor site after appar-ently imperfect excisions are also difficult to rationalize (8). The explanationfor these observations first came from the work of Engels and coworkers (32),demonstrating that the frequency ofP element reversion increases hundreds of

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times when the chromosome homologous to that carrying theP element is wildtype for this insertion. The data fit a model in which a perfect reversion to wildtype is the result of a gene conversion event, with sequences in the homologouschromosome serving as template for repair of DSBs created after excision ofthe element. The results show that, although the homologous chromosome canact as a template, the template used most of the time is the sister chromatid,suggesting that repair must occur in late S or G2 phases of the cell cycle (32).Internal deletions arise when the repair process fails to be completed. The di-rect duplications inside theP element (74) serve as homology sites necessaryto complete DNA synthesis during the interrupted process of filling the gap.In fact, frequent deletion breakpoints in naturally occurring elements coincidewith these sequences (77). The same model could be applied toTc1, Ac, andto most transposable elements with frequent internally deleted copies (80, 90).In fact, it has been shown that the reversion frequency ofTc1insertion mutantsalso increases 100 times when the homologous chromosome is wild type. Dif-ferences in the footprints left after excision could be explained by differences inconcentration or activity of exonucleases in the germ line or to species-specificgap repair mechanisms (32, 90).

Subsequent studies withP elements have shown that the gap repair processeffectively involves the copy of DNA alterations present in the homologouschromosome into the gap left byP excision (45). Repair of the gap could becarried out very effectively by copying sequences up to 8000 bp into the gap, andthis process works efficiently with ectopically introduced templates localized innonhomologous chromosomes (75), opening the use of the gap repair processfor targeted gene replacement inDrosophila (41, 45). The efficiency of gaprepair depends on the relative location of the template and on the particular locusunder study (33, 52). These results imply that after excision, the DSBs endsstart a search for homology throughout the genome. This search can target, andsubsequently use for gap repair, sequences harbored in nonintegrated plasmidsthat have been microinjected in theDrosophilaembryo (47).

The analysis of multiple conversion tracts in a recent study demonstrates thatthe repaired gaps retain part of the inverted repeat of theP element, suggestingthat a homology of 33 bp is sufficient to efficiently localize an ectopic homol-ogous sequence and carry out the repair process (47). The results also suggestthat if the inverted repeats are retained in the broken ends after excision, thesesequences are adequate to promote the search for homology and repair usingotherP elements present elsewhere in the genome. The inverted repeat bindingprotein (IRBP), which was initially shown to bind theP inverted repeats (87),is a good candidate to protect the broken ends of the gap against degradationand actively participate in the search for homology (47). The IRBP protein hasbeen characterized and shown to be related to the 70-kDa subunit of the human

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Ku protein involved in DSB repair and VDJ recombination (7). The IRBP/Kuprotein is functionally conserved betweenDrosophila, yeast, and humans (6),and it is encoded bymus309, a Drosophilamutation-sensitive gene involvedin DSB repair. Mutations in this gene result in reduced fly viability afterPelement mobilization (4).

RETROTRANSPOSONS

Retrotransposons are mobile elements that encode reverse transcriptase (seeReference 14 for a review). These elements can be divided into long ter-minal repeat (LTR)-containing and poly(A)-containing retransposons, basedon structural characteristics. LTR retrotransposons are similar to the proviralform of vertebrate retroviruses and usually contain two open reading frames(ORFs) encoding gag (capsid proteins) and pol (protease, integrase, reversetranscriptase, and RNase H) proteins. Some LTR retrotransposons such asgypsyandtomof Drosophilaencode a third ORF, which has been shown to bestructurally and functionally similar to the envelope protein of vertebrate retro-viruses. Poly(A)-type retroelements lack LTRs and contain an A-rich regionin the 3′ end. They usually contain two ORFs encoding gag and pol proteins.Key questions concerning the biology of these elements are the mechanismby which they are mobilized and integrated into the genome of their host, thenature of retroelement- and host-encoded factors that regulate this process, andthe details of the relationship between transposons and host that allows theirreproduction and persistence in the genome of all eukaryotes.

Mechanism of Integration of Poly(A)-ContainingRetrotransposonsThe mechanism of integration of LTR-containing retrotransposons is well un-derstood, thanks in part to the similarities to retroviral integration (14, 92). TheLTRs of these elements contain signals for initiation and termination of tran-scription of the full-length RNA. Reverse transcription of this RNA templatetakes place in the cytoplasm, where first-strand DNA synthesis is primed by aretroelement-specific tRNA and second-strand synthesis is primed by an oligo-purine RNA molecule. The synthesis of both strands is completed through strandtransfer events that involve terminal redundancies of the LTR sequences on theRNA template. This DNA intermediate then migrates to the nucleus wherea retroelement-encoded integrase bound to LTR sequences makes a double-stranded break at the target site and covalently joins the ends of the intermediateto the chromosome. This mechanism is not very different from that employedby DNA transposons. An interesting exception to this general mechanism is thatof the LTR-containing retrotransposonTf1of S. pombe. This element encodes a

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single ORF, and reverse transcription is independent of a tRNA primer (57, 59).Instead, reverse transcription is initiated by a self-priming event in which thefirst 11 nucleotides of theTf1RNA fold back and anneal to the primer bindingsite to initiate synthesis of the minus-strand strong-stop DNA; the RNase Hdomain of the reverse transcriptase then cleaves the RNA between nucleotides11 and 12 to generate the primer for reverse transcription (57, 58, 62).

Non-LTR or poly(A) retrotransposons, such as the humanLINE 1 (L1), andDrosophila I elements lack protease, RNase H, and integrase domains andmust therefore use a different strategy for inserting into the genome. BothL1andI elements have been shown to encode an active reverse transcriptase andmove by a retrotransposition mechanism in yeast andDrosophila, respectively(28, 67, 78). More recently, two humanL1 elements have been shown to retro-transpose in cultured mammalian HeLa cells (72). WhenL1 was expressedfrom an extrachromosomal episome under the control of the CMV promoter,the frequency of insertion into chromosomal sites was on the order of 5× 10−4.Proteins encoded by both ORF1 and ORF2 were found to be required for trans-position.L1 ORF1 encodes a 40-kD RNA-binding protein containing a leucinezipper motif that is essential for its function and participates in the formationof large complexes. This protein interacts with L1 RNA to form a high molec-ular weight complex found in the cytoplasm of various cell lines; this complexmight be an intermediate in the retrotransposition process (72). At least twodifferent domains ofL1 ORF2 are required for retrotransposition. One is thereverse transcriptase domain. A second one is located in the amino-terminalregion of ORF2 and is homologous to apurinic/apyrimidinic (AP) endonucle-ases such asE. coli Exo III (36). Interestingly, this domain is conserved inother poly(A)-type retroelements whose integration lacks sequence specificity,as well as in some sequence-specific elements such asR1Bmof Bombyx mori,but it is absent in group II introns and LTR retrotransposons. The endonucleaseactivity of L1 has been hypothesized to be responsible for the cleavage of thetarget DNA, leaving 5′-PO4 and 3′-OH termini that are then used for priming ofreverse transcription in a manner similar to that employed by sequence-specificretroelements. This therefore increases retrotransposition efficiency (36).

Site-Specific Integration: Group II Intronsand rDNA Insect ElementsThe details of the target site cleavage, reverse transcription, and integrationreactions of non-LTR retroelements have been studied in great detail in twodifferent systems: theR2Bmelement ofBombyx moriand yeast mitochondrialgroup II introns.R2 is a non-LTR retrotransposon that inserts preferentially inthe 28S ribosomal RNA genes of various insect species (44). InBombyx mori,it has been shown thatR2Bmcontains a single open reading frame encoding a

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highly specific endonuclease capable of nicking the 28S rRNA gene and thencleaving at a site 2 bp upstream, thus leaving a 2-bp stagger with 5′ overhangs.Interestingly, this protein also contains a reverse transcriptase activity. Thepresence of these two activities in the same protein suggests that the processesof target site cleavage and reverse transcription are linked. This is indeed thecase, and theR2protein has been shown to use the 3′ hydroxyl group exposedin the nicking reaction to prime reverse transcription ofR2 RNA templatesthat contain an A-rich sequence at the 3′ end (65). At least 250 bp at the 3′

untranslated region of the element are required for the reaction, and sequenceslocated in the downstream adjacent 28S gene aid in the accurate initiation ofreverse transcription at the 3′ end of theR2 element (63, 64). Thus, theR2reverse transcriptase can use the 3′ end of an RNA molecule to prime cDNAsynthesis in the absence of any sequence complementarity. Second-strandcleavage takes place after reverse transcription is complete (65). No details areknown on how the RNA template is removed and how second-strand synthesistakes place, although evidence suggests that it might be controlled by a cellularDNA repair mechanism.

A similar mechanism is employed by a second group of retroelements thatalso display site-specific integration. Group II introns present in some yeastmitochondrial genes are mobile elements that encode a protein with maturase,reverse transcriptase, and endonuclease activities. After splicing of the intronvia a lariat intermediate, the encoded protein promotes site-specific insertion(homing) of the intron into the double-stranded DNA corresponding to intron-less alleles of the same gene. Lambowitz and colleagues have studied in detailthe aI1 and aI2 introns of theCOX1gene. The premRNA transcribed fromCOX1serves as a template for the synthesis of aI1 and aI2 proteins that encodethree activities necessary for completion of the process: a maturase requiredfor splicing of the premRNA, an endonuclease necessary for cleavage of thenonsense strand in the target DNA, and a reverse transcriptase that copies thepremRNA into DNA (73). In the case of the aI2 intron, the aI2 protein formsa complex with the intron lariat, and this complex cleaves the target DNA inthe cognate intronless allele. The intron lariat is required for generating a nickin the sense strand of the DNA exactly at the junction of the two exons; thespecificity of this site is determined by interactions between intron and exonsequences. The cleavage takes place by a partial reverse-splicing reaction inwhich the intron lariat is covalently attached to the 5′ end of the nicked sensestrand. The cleavage of the nonsense strand is carried out by the endonucle-ase activity of the aI2 protein 10 bp downstream of the exon boundary. Thisreaction leaves a 3′ OH group that is used to initiate cDNA synthesis, usingthe reverse transcriptase activity of the aI2 protein, the antisense strand cleavedin the downstream exon as a primer, and the unsplicedCOX1premRNA as a

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template. Subsequent synthesis of the sense strand, and repair by conversionevents, generate the intron-containing gene (113, 114). Remarkably, in the caseof aI1, the intron RNA not only cleaves the sense strand but also completelyincorporates into the DNA by a two-step splicing reaction and then serves astemplate for reverse transcription (112). These findings are highly significantand provide explanations for intron dispersal and the evolution of nuclear splic-ing of mRNA. The similarities between the retrotransposition mechanisms ofgroup II introns and poly(A)-type retrotransposons, the close homology be-tween their reverse transcriptases, and the finding that group II introns can alsotranspose into nonallelic targets, point to an intimate evolutionary relationshipbetween these elements. This relationship is even more significant when oneconsiders the similarities between the DNA-primed reverse transcription reac-tion of the aI1 and aI2 proteins and that of telomerase, and the fact that, inDrosophila, the ends of chromosomes are kept intact by insertion of poly(A)-type retrotransposons instead of the standard telomerase reaction.

Insertional Specificity: Yeast Elements Are Restrictedin Where They LandAlthough vertebrate retroviruses appear to insert into regions with an open chro-matin structure, integration sites for most mammalian andDrosophilaretroele-ments appear to be distributed more or less randomly in the genome (110).Some retroelements, such asHeT-AandTART, insert preferentially into telo-meric regions, and theR1andR2elements ofB. mori insert solely in ribosomalRNA genes. A clear bias in the site selection choice has also been observed foryeast retrotransposons. TheTy1andTy3elements integrate preferentially, oralmost exclusively in the case ofTy3, upstream of genes transcribed by RNApolymerase III, including tRNA, 5S, and U6 genes (20); this seems to also bethe case forTy2andTy4, based on analyses of their genomic distribution. In-tegration ofTy3takes place within 1–3 nucleotides from the transcription startsite and requires a functional promoter. This observation suggests that targetsite selection might depend on the interaction between the integrase and Pol IIItranscription complexes. In vitro studies have demonstrated that transcriptionitself or Pol III are not required forTy3integration, and that the interaction takesplace with TFIIIB and TFIIIC, although the role of the latter might be only in-direct (50). Interestingly, althoughTy1 also inserts preferentially into tRNAgenes, target site selection is region specific rather than site specific. The targetsites forTy1are distributed over a region covering several hundreds of base pairsupstream of these genes. Contrary toTy3, active transcription by Pol III wasfound to greatly increase targeting ofTy1to tRNA genes (26). In contrast to theTy1-Ty4elements,Ty5is found at telomeres and the mating loci, suggesting thatthis element targets regions of silent chromatin (115, 116). The integration of

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yeast retroelements into specific sequences or regions of the chromosome mustreflect the interaction of components of the integration complex with specifichost factors, such as members of the transcription complex or heterochromatin-specific factors that mediate targeting to the integration site. Why do most orall yeast retroelements show target site–specificity, whereas mostDrosophilaand vertebrate elements appear to integrate randomly? The answer might liein the genomic organization of these various organisms.S. cerevisiaehas acompact genome and the elements that populate it might have learned to in-tegrate into specific sites that do not result in deleterious effects to the host.Drosophilaand mammalian retrotransposons might be able to insert randomlyowing to the higher proportion of intragenic sequences in which insertion wouldbe inconsequential to the host.

Host Factors Controlling Retrotransposon Expressionand MobilizationMost eukaryotic retrotransposons move only sporadically in the genome of theirhosts. Exceptions to this rule are the described cases of hybrid dysgenesis phe-nomena inDrosophilain which retrotransposons, such as theI element, movewith high frequency in the progeny of specific crosses (17). Other elementsmove rarely and unpredictably, suggesting the existence of a tight regulationon their transposition by the host genome. The nature of the mechanisms con-trolling retrotransposon mobilization is poorly understood. Possible steps atwhich the host genome might limit their mobilization are the overall levels oftranscription, tissue-specific expression (somatic versus germ line), processingof the RNA and encoded proteins, assembly of viral particles, reverse transcrip-tion, and integration of the double-stranded DNA. In yeast, although theTy1element is normally expressed at high levels, overexpression under the GAL4promoter is necessary and sufficient for high levels of transposition. This sug-gests the existence of a threshold in the levels ofTy1-encoded RNA and/orproteins necessary for mobilization of this element. It is not clear whetherthis could also be the case for other retrotransposons in higher eukaryotes, andperhaps high levels of germ line expression of the full-length RNA will en-sure the mobilization of any element. InDrosophila, several genes have beenfound to control the accumulation of the full-length RNA encoded by vari-ous retrotransposons. For example, thesuppressor of Hairy-winggene affectsgypsytranscription (39), whereasDarkener of apricotandWeakener of whiteaffect the accumulation ofcopiatranscripts (12, 83). The effect of these geneson the mobilization rate of transposable elements has not been tested, but arecently identifiedDrosophilagene namedflamenco( flam) has been found todramatically affect the mobilization rate of thegypsyretrotransposon.

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Gypsymoves infrequently in the genome ofD. melanogaster, but in theprogeny of females carrying the X-linkedflammutation,gypsytransposes withhigh frequency (for example, 10–15% of the progeny of these females willcontain agypsyelement in theovogene) (82).Gypsyis transcribed in varioussomatic tissues at different stages ofDrosophiladevelopment, including theovarian follicle cells, but its expression in the germ line is very low (39, 79).Inheritable transpositions ofgypsythat will be manifested in the form of newmutations are not possible without the presence ofgypsyRNA and proteins ingerm line cells. What is then the contribution of theflam mutation togypsymobilization? Levels of the full-lengthgypsyRNA increase 10–20-fold anda new ORF3-specific spliced RNA accumulates in the follicle cells offlamfemales (79). This RNA has been shown to encode a protein with the propertiesexpected for a retroviral envelope that is spliced into surface and transmembranecomponents (99, 100). Thus, assembly of viral particles could take place in thefollicle cells, where they have actually been observed by electron microscopy(100). Gypsyviral particles have also been visualized by immunogold electronmicroscopy after purification from ovary extracts offlam females (99). Thesegypsyparticles have been shown to be infectious after experiments in whichlarvae fed with particles gave rise to progeny containing de novogypsyinsertions(49, 99). Therefore, viral particles made in the somatic cells of the ovary mightbe able to infect the oocyte after budding out of the follicle cells. Once in theoocyte, these particles might be transported to the posterior end where theymight be taken up by the pole cells (100). Reverse transcription followed byintegration would then ensure inheritable transposition. This process requiresthatgypsyexpression and assembly of infectious particles take place before thevitelline membrane has surrounded the oocyte, posing an impenetrable barrierfor the virus. Coincidentally,gypsyRNAs and proteins are expressed beginningat stage 9 of oogenesis, allowing the particles to assemble and infect the oocytebefore the vitelline membrane forms at the end of stage 10. These particleshave in fact been found trapped in the vitelline membrane during late stages ofoogenesis by immunoelectron microscopy (100). The somatic expression andsubsequent infection of the germ line seems an ideal strategy to ensure a goodrelationship between a retrotransposon and its host:gypsyis normally expressedat low levels in somatic cells where infrequent mobilization might not causedamage to the host; only when a mutation in theflamgene arises doesgypsymove to the germ line cells and transpose to ensure its reproduction. What thenis the nature of theflamgene? This question can only be answered when thegene is cloned. Today we can only speculate. The flam protein is nonessential,mutations in the gene are viable (82), and they affect the accumulation ofboth thegypsyfull-length and spliced envelope transcripts (79). An intriguingpossibility is thatflam is a suppressor of nonsense mutations inDrosophila.

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ThegypsyRNA contains termination codons between the first and second, andsecond and third ORFs, causing it to be recognized by the cellular machinerythat shunts RNAs containing nonsense mutations for degradation (2). Ifflamis a component of this pathway,flammutants might allow the accumulation offull-length messages, and the presence of the envelope-specific transcript mightsimply be a consequence of higher levels of the precursor RNA.

Retrotransposons Can Benefit the Host: Telomeres andChromosome RepairIn most cases, retrotransposons are deleterious to the host as a consequenceof their insertion into coding regions that lead to alterations of gene expres-sion. An interesting case in which the host uses retrotransposon mobilizationto its own benefit is that of telomere maintenance inDrosophila. Drosophilatelomeres lack the characteristic short tandem repeats found at the end of thechromosomes of most eukaryotes (9, 60). Instead,Drosophilachromosomescontain several copies of two transposable elements,HeT-AandTART, at theirends (11, 61). Both elements belong to the poly(A) family of retrotransposons.TARTcontains two open reading frames. ORF1 encodes a protein with threeCCHC repeats similar to those found in retroviral Gag proteins andLINE-likeelements, whereas ORF2 encodes a protein with homology to reverse transcrip-tase (61, 94). Some copies ofHeT-Acontain one ORF that is interrupted by oneor more stop codons in other copies of the element. This ORF encodes a Gag-like protein containing three CCHC motifs, but it lacks reverse transcriptase(10), suggesting that the RT necessary for its transposition might be providedin trans, perhaps byTART. TheHeT-Aelement encodes a 6-kb polyadenylatedRNA that has been found complexed with protein in what could be a trans-position intermediate (25).HeT-Aelements are found at telomeres in tandemarrays, with individual elements organized in a head-to-tail orientation. Thisarrangement appears to be a consequence of the presence of promoter sequencesfor this element in the 3′ rather than the 5′ region of the element. The synthesisof a completeHeT-ARNA thus requires that transcription initiated in the 3′

promoter of one element be continued through the downstream neighbor (24).This arrangement is reminiscent of the organization of transcription signals inthe long terminal repeats of retroviruses and LTR retrotransposons, in whichsequences necessary for transcription initiation and termination are presentboth in the 5′ and 3′ regions of the elements, suggesting thatHeT-Amight be anevolutionary intermediate between poly(A)-type and LTR-containing elements.Interestingly, this promoter is active in heterochromatin, as one might expectfrom its exclusive location within telomeric sequences, an important propertythat ensures the expression of this element and the accumulation of its RNA thatserves as a substrate for reverse transcription and subsequent integration (24).

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The mechanism of transposition ofHeT-AandTARTto the termini of chromo-somes has been proposed to be a variation of that employed by other poly(A)retroelements, using the 3′ DNA end at the terminus as the primer for reversetranscriptase (10, 61). This mechanism would account for the invariant orien-tation of these elements at the end of chromosomes and the lack of target siteduplications flanking them. Insertion of these elements at the termini in 1%of receding chromosomes per generation could replace the 50–100 nucleotidesthat are lost in the same period of time.

The healing of chromosome ends inDrosophilais not the only case of a ben-eficial role that retroelements bring to their hosts. Retrotransposon-encodedreverse transcriptase is also responsible for repairing double-strand breaks inyeast (71, 104). The HO endonuclease makes a unique double-strand cut at themating type locus, and this break is repaired by conversion, using sequencesfrom theHML or HMR loci. In rad52 mutants, homologous recombinationis blocked and HO-induced breaks are lethal. Overexpression of reverse tran-scriptase from various retroelements allows the isolation of survivors, whichcontain cDNAs orTy retrotransposon sequences at the site of the original break(71, 104). These results suggest that the ability to heal breaks, whether at theends or in the middle of chromosomes, might be an evolutionarily conservedrole for retrotransposons. This observation is also relevant in the context ofthe widespread distribution of retroelements in centromeric heterochromatin.Because heterochromatic sequences are late replicating, and replication forksmight be specially prone to breakage if the cell goes into G2 before replicationis complete, double-strand breaks might tend to accumulate in heterochromatin.Repair of these breaks by retroelement insertion might explain the abundanceof transposable elements in these regions of the chromosome.

Effects of Retrotransposon Insertions on Host Gene ExpressionMost retrotransposon insertions in or near the coding region of a gene affectits expression in a negative fashion by decreasing or abolishing transcription ofthe gene as a consequence of its effects on transcription initiation, termination,stability, or processing. But some retrotransposons have more sophisticatedeffects on the expression of host genes, altering their temporal or spatial patternof transcription. For example, inDrosophila, insertion of thegypsyretroele-ment affects gene expression controlled by enhancers located distal with respectto the promoter from the insertion site, whereas transcription from other en-hancers is normal (39). Thetom element causes over-expression of adjacentgenes in the eye imaginal discs (3, 103), and insertion of thebloodretrotranspo-son in exon 7 of the glycerol-3-phosphate dehydrogenase (GPDH) gene inducesisozyme GPDH-4 and alters the expression of isozymes GPDH-1 to GPDH-3(109). These examples show that insertion of retroelements is not necessarilydeleterious to the host and could result in new patterns of gene expression that, if

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fixed, might offer an advantage under specific selection conditions. It is tempt-ing to speculate that insertion of transposable elements could be an effector ofevolutionary change by giving rise to new patterns of gene expression. One ar-gument against this presumption is that remnants of retrotransposon sequencesare seldom found adjacent to eukaryotic genes. Although this might apply toanimals, recent analyses of plant transposable element insertion sites have re-vealed the presence of degenerate retrotransposon insertions adjacent to manynormal plant genes (111). These retrotransposon sequences, although vestigesof ancient insertions, still show recognizable similarities with various retro-transposon features such as LTRs, tRNA-binding sites, polypurine tracts, andthe coding regions of gag, protease, reverse transcriptase, and integrase. And inseveral instances in which sequences necessary for proper developmental regu-lation of a variety of plant genes had been previously identified, it is now evidentthat these regulatory elements were provided by retrotransposon sequences. Forexample, sequences that control expression of the maize polygalacturonase andthe tomato LAT59 genes during pollen development are provided by retro-transposon insertions. Sequences originating from a retrotransposon insertionin several gene family members encoding the small subunit of ribulose 1,5bisphosphate carboxylase in pea provide a negative regulator of transcriptionresponsible for their low levels of expression in leaves, petals, and seeds. Andone of the promoters in some maize zein genes is provided by the LTR of aretrotransposon insertion (111). In addition to retrotransposons, other DNA el-ements designated as miniature inverted repeat transposable elements (MITEs)are also present adjacent to many plant genes, where they provide regulatorysequences necessary for transcription (18). Thus, it appears that transposableelement insertions have been important contributors to the establishment ofnovel patterns of transcription for a variety (up to 100 found so far) of plantgenes, and could then be significant effectors of evolutionary change. Whetherthis is also the case in animals is a matter of controversy, since only a few ex-amples of transposable elements providing transcription signals toDrosophilaor vertebrate genes have been described (15). In mice, LTR sequences from anendogenous MMTV provirus contribute the androgen-responsive enhancer forthe expression of a sex-linked protein gene (101), and the LTR of an intracis-ternal A particle contributes to the expression of a placental gene (21). Similarregulatory sequences are responsible for the rat oncomodulin gene (5), and thehuman amylase gene is expressed in the parotid gland under the influence ofregulatory sequences present in an adjacent retroviral insertion (105). Finally,Alu sequences provide regulatory elements necessary for the expression of CD8gene in T lymphocytes, a human keratin gene, and the human parathyroid hor-mone, IgE gamma chain, myeloperoxidase, and Wilms tumor 1 genes (15).It has been proposed that the observed differences between plants and animalsmight be due to the different evolutionary histories of plant and animal genomes

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with respect to retroelement invasion (111). Reverse transcriptase sequencesfound in plant genomes are quite heterogeneous, suggesting inheritance throughvertical transmission from a progenitor that invaded the plant genome long ago.On the other hand, relationships amongDrosophilaretroelements support hor-izontal transmission as an important means of propagation, suggesting thatinvasion by these elements is a relatively recent event.

CONCLUSIONS

The debate on whether transposable elements are functional versus selfish DNAis not completely solved. Most transposable element features suggest a self-ish and parasitic nature of such elements, as corroborated by the populationgenetics of transposable elements, developed at the experimental level onlyin Drosophila (22). Figure 1 shows the determinant steps in the evolution

Figure 1 Schematic representation of transposable element evolution in relation to the host.Transposable elements invade new species by horizontal transmission. Then, a balance betweenforces increasing and those decreasing copy number (transposition and excision/negative selection,respectively) must be established. During the transition step, molecular and population mechanismscould bring the element to high copy numbers, like L1 in humans, or to low copy numbers, likemostDrosophilaelements. Eventually, an excessive transposition rate could bring the population toextinction, the elements could be lost from the population or species, or they could gain a selectivefunction that benefits the organism.

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of transposable elements. Understanding horizontal transmission and host-element interactions is crucial to grasp the biological significance of theseelements. TheDrosophila Pelement is a good example of how complex theseinteractions are and illustrates the benefits that the study of transposable ele-ments could bring to related areas of biological knowledge. DNA transposableelements, from bacteria to mammals, fit perfectly the selfish nature paradigm,excepting perhaps the clearly opportunistic but selectable role of transposableelements that provide chemical resistance to the hosts. However, the possibilitythat transposable elements, in particular retrotransposons, can actually serve thehost with a function cannot be completely ruled out. TheDrosophilatelomereis the only example of such a function, but the recent discoveries of the asso-ciation between established gene regulatory regions and transposable elementsin plants and other organisms suggest that they can also contribute significantlyto the establishment of new and evolutionarily advantageous gene regulatorypathways (68). The finding that retrotransposons could serve as repair systemsafter DSBs is directly connected to their role in healingDrosophilatelomeresand opens a new scenario over the classical question. Further work is necessaryto clarify if R2Bmelements or group II introns have similar selective functions.In addition, the possibility that transposable elements could contribute to themaintenance of heterochromatin, and consequently to chromosome structure,or even to the heterochromatinization processes of neo Y chromosomes duringchromosomal evolution (102) opens new and exciting avenues for experimen-tation on this field.

ACKNOWLEDGMENTS

Work in the authors’ lab is supported by Public Health Research Award GM35463 from the National Institutes of Health. M. Labrador was supported bya postdoctoral fellowship from Direccio General de Recerca, Generalitat deCatalunya, Spain.

Visit the Annual Reviews home pageathttp://www.annurev.org.

Literature Cited

1. Andrews JD, Gloor GB. 1995. A rolefor the KP leucine zipper in regulatingP element transposition inDrosophilamelanogaster. Genetics141:587–94

2. Aoufouchi S, Yelamos J, Milstein C.1996. Nonsense mutations inhibit RNAsplicing in a cell-free system: recognitionof mutant codon is independent of proteinsynthesis.Cell 85:415–22

3. Awasaki T, Juni N, Yoshida KM. 1996. Aneye imaginal disc-specific transcriptionalenhancer in the long terminal repeat ofthe tom retrotransposon is responsible foreye morphology mutations ofDrosophilaananassae. Mol. Gen. Genet.251:161–66

4. Banga SS, Velazquez A, Boyd JB. 1991.P transposition inDrosophila provides

Ann

u. R

ev. G

enet

. 199

7.31

:381

-404

. Dow

nloa

ded

from

ww

w.a

nnua

lrev

iew

s.or

gby

Uni

vers

ity o

f So

uth

Flor

ida

on 0

4/13

/13.

For

per

sona

l use

onl

y.




a new tool for analyzing postrepli-cation repair and double-strand breakrepair.Mutat. Res.255:79–88

5. Banville D, Boie Y. 1989. Retroviral longterminal repeat is the promoter of the geneencoding the tumor-associated calcium-binding protein oncomodulin in the rat.J.Mol. Biol. 207:481–90

6. Barnes G, Rio DC. 1997. DNA double-strand-break sensitivity, DNA replica-tion, and cell cycle arrest phenotypes ofKu-deficient Saccharomyces cerevisiae.Proc. Natl. Acad. Sci. USA94:867–72

7. Beall EL, Admon A, Rio DC. 1994. ADrosophilaprotein homologous to the hu-man p70 Ku autoimmune antigen inter-acts with theP transposable element in-verted repeats.Proc. Natl. Acad. Sci. USA91:12681–85

8. Berg DE, Howe MM, eds. 1989.MobileDNA.Washington, DC: Am. Soc. Micro-biol.

9. Biessmann H, Carter SB, Mason JM.1990. Chromosome ends inDrosophilawithout telomeric DNA sequences.Proc.Natl. Acad. Sci. USA87:1758–61

10. Biessmann H, Champion LE, O’Hair M,Ikenaga K, Kasravi B, Mason JM. 1992.Frequent transpositions ofDrosophilamelanogasterHeT-A transposable ele-ments to receding chromosome ends.EMBO J.11:4459–69

11. Biessmann H, Mason JM, Ferry K,d’Hulst M, Valgeirsdottir K, et al. 1990.Addition of telomere-associated HeT-ADNA sequences “heals” broken chromo-some ends inDrosophila. Cell61:663–73

12. Birchler JA, Bhadra U, Rabinow L, LinsR, Nguyen-Huynh AT. 1994. Weakenerof white Wow, a gene that modifies theexpression of the white eye color locusand that suppresses position effect varie-gation inDrosophila melanogaster. Ge-netics137:1057–70

13. Black DM, Jackson MS, Kidwell MG,Dover GA. 1987.KP elements repressP-induced hybrid dysgenesis inDrosophilamelanogaster. EMBO J.6:4125–35

14. Boeke JD, Corces VG. 1989. Transcrip-tion and reverse transcription in retro-transposons.Annu. Rev. Microbiol.43:403–33

15. Britten RJ. 1996. DNA sequence insertionand evolutionary variation in gene regula-tion.Proc. Natl. Acad. Sci. USA93:9274–77

16. Brown J, Sundaresan V. 1992. Geneticstudy of the loss and restoration ofMutator transposon activity in maize:evidence against dominant-negative reg-

ulator associated with loss of activity.Ge-netics130:889–98

17. Bucheton A. 1990. I transposable ele-ments and I-R hybrid dysgenesis inDro-sophila. Trends Genet.6:16–21

18. Bureau TE, Ronald PC, Wessler SR.1996. A computer-based systematic sur-vey reveals the predominance of smallinverted-repeat elements in wild-type ricegenes.Proc. Natl. Acad. Sci. USA93:8524–29

19. Chain AC, Zollman S, Tseng JC, LaskiFA. 1991. Identification of a cis-actingsequence required for germ line-specificsplicing of thePelement ORF2-ORF3 in-tron.Mol. Cell. Biol.11:1538–46

20. Chalker DL, Sandmeyer SB. 1992. Ty3integrates within the region of RNA poly-merase III transcription initiation.GenesDev.6:117–28

21. Chang-yeh A, Mold DE, Huang RCC.1991. Identification of a novel murineIAP-promoted placenta-expressed gene.Nucleic Acids Res.19:3667–72

22. Charlesworth B, Sniegowski P, StephanW. 1994. The evolutionary dynamics ofrepetitive DNA in eukaryotes.Nature371:215–20

23. Daniels SB, Clark SH, Kidwell MG,Chovnick A. 1987. Genetic transforma-tion of Drosophila melanogasterwith anautonomousP element: phenotypic andmolecular analyses of long-establishedtransformed lines.Genetics 115:711–23

24. Danilevskaya ON, Arkhipova IR, Tra-verse KL, Pardue ML. 1997. Promoting intandem: the promoter for telomere trans-poson HeT-A and implications for theevolution of retroviral LTRs.Cell88:647–55

25. Danilevskaya ON, Slot F, Traverse KL,Hogan NC, Pardue ML. 1994.Drosophilatelomere transposon HeT-A produces atranscript with tightly bound protein.Proc. Natl. Acad. Sci. USA91:6679–82

26. Devine SE, Boeke JD. 1996. Integrationof the yeast retrotransposon Ty1 is tar-geted to regions upstream of genes tran-scribed by RNA polymerase III.GenesDev.10:620–33

27. Doak TG, Doerder FP, Jahn CG, Her-rick AG. 1994. A proposed superfamilyof transposase genes: transposon-like el-ements in ciliated protozoa and a common“D35E” motif. Proc. Natl. Acad. Sci. USA91:942–46

28. Dombroski BA, Feng Q, Mathias SL,Sassaman DM, Scott AF, et al. 1994.An in vivo assay for the reverse tran-scriptase of human retrotransposon L1 in

Ann

u. R

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enet

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ida

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y.




Saccharomyces cerevisiae. Mol. Cell.Biol. 14:4485–92

29. Eggleston WB, Johnson-Schlitz D, En-gels WR. 1988. P-M hybrid dysgenesisdoes not mobilze other transposable ele-ment families inDrosophila melanogas-ter. Nature331:368–70

30. Engels WR. 1989.P elements inDroso-phila melanogaster.See Ref. 8, pp. 437–84

31. Engels WR. 1996.P elements inDro-sophila. Curr. Top. Microbiol. Immunol.204:104–23

32. Engels WR, Johnson-Schlitz DM, Eggel-ston WB, Sved J. 1990. High-frequencyP element loss inDrosophilais homologdependent.Cell 62:515–25

33. Engels WR, Preston CR, Johnson-SchlitzDM. 1994. Long-range cis preference inDNA homology search over the lengthof a Drosophila chromosome.Science263:1623–25

34. Fedoroff NV. 1995. DNA methylation andactivity of the maizeSpm transposableelement.Curr. Top. Microbiol. Immunol.197:143–64

35. Fedoroff NV, Wessler S, Shure M. 1983.Isolation of the transposable maize con-trolling elements Ac and Ds.Cell35:235–42

36. Feng Q, Moran JV, Kazazian HH Jr,Boeke JD. 1996. Human L1 retrotrans-poson encodes a conserved endonucleaserequired for retrotransposition.Cell 87:905–16

37. Frey M, Reinecke J, Grant S, Saedler H,Gierl A. 1990. Excision of theEn/Spmtransposable element ofZea maysre-quires two element-encoded proteins.EMBO J.9:4037–44

38. Fusswinkel H, Schein S, Courage U, Star-linger P, Kunze R. 1991. Detection andabundance of mRNA and protein en-coded by transposable elementactivatorAc in maize.Mol. Gen. Genet.25:186–92

39. Gdula DA, Gerasimova TI, Corces VG.1996. Genetic and molecular analysis ofthe gypsychromatin insulator ofDroso-phila. Proc. Natl. Acad. Sci. USA93:9378–83

40. Gierl A. 1996. The En/Spm transposableelement of maize.Curr. Top. Microbiol.Immunol.204:145–59

41. Gloor GB, Nassif NA, Johnson-SchlitzDM, Preston CR, Engels WR. 1991.Targeted replacement inDrosophila viaP element-induced gap repair.Science253:1110–17

42. Gloor GB, Preston CR, Johnson-SchlitzDM, Nassif NA, Phillis RW, et al. 1993.

Type I repressors ofP element mobility.Genetics135:81–95

43. Grindley NDF, Leschziner AE. 1995.DNA transposition: from black box tocolor monitor.Cell 83:1063–66

44. Jakubczak JL, Burke WD, Eickbush TH.1991. Retrotransposable elements R1 andR2 interrupt the rRNA genes of mostinsects.Proc. Natl. Acad. Sci. USA88:3295–99

45. Johnson-Schlitz DM, Engels WR. 1993.P-element-induced interallelic gene con-version of insertions and deletions inDrosophila melanogaster. Mol. Cell. Biol.13:7006–18

46. Kaufman PD, Rio DC. 1992.P elementtransposition in vitro proceeds by a cut-and-paste mechanism and uses GTP as acofactor.Cell 69:27–39

47. Keeler KJ, Dray T, Penney JE, Gloor GB.1996. Gene targeting of a plasmid-bornesequence to a double strand DNA breakin Drosophila melanogaster. Mol. Cell.Biol. 16:522–28

48. Keeler KJ, Gloor GB. 1997. Efficientgap repair inDrosophila melanogasterre-quires a maximun of 31 nucleotides of ho-mologous sequence at the searching ends.Mol. Cell. Biol.17:627–34

49. Kim A, Terzian C, Santamaria P, PelissonA, Prud’homme N, Bucheton A. 1994.Retroviruses in invertebrates: Thegypsyretrotransposon is apparently an infec-tious retrovirus ofDrosophila melano-gaster. Proc. Natl. Acad. Sci. USA91:1285–89

50. Kirchner J, Connolly CM, SandmeyerSB. 1995. Requirement of RNA poly-merase III transcription factors for in vitroposition-specific integration of a retro-viruslike element. Science 267:1488–91

51. Kunze R. 1996. The maize transposableelement activator Ac.Curr. Top. Micro-biol. Immunol.204:161–94

52. Lankenau DH, Corces VG, Engels WR.1996. Comparison of targeted-gene re-placement frequencies inDrosophilamelanogasterat the forked and white loci.Mol. Cell. Biol.16:3535–44

53. Laski FA, Rio DC, Rubin GM. 1986. Tis-sue specificity ofDrosophila Pelementtransposition is regulated at the level ofmRNA splicing.Cell 44:7–19

54. Laski FA, Rubin GM. 1989. Analysisof cis-acting requirements for germ line-specific splicing of theP element ORF2-ORF3 intron.Genes Dev.3:720–28

55. Lee CC, Mul YU, Rio DC. 1996. TheDrosophila P-element KP repressor pro-tein dimerizes and interacts with multiple

Ann

u. R

ev. G

enet

. 199

7.31

:381

-404

. Dow

nloa

ded

from

ww

w.a

nnua

lrev

iew

s.or

gby

Uni

vers

ity o

f So

uth

Flor

ida

on 0

4/13

/13.

For

per

sona

l use

onl

y.




sites onP-element DNA.Mol. Cell. Biol.16:5616–22

56. Lemaitre B, Ronsseray S, Coen D. 1993.Maternal repression of theP elementpromoter in the germline ofDrosophilamelanogaster: a model for the P cytotype.Genetics135:149–60

57. Levin HL. 1995. A novel mechanism ofself-primed reverse transcription definesa new family of retroelements.Mol. Cell.Biol. 15:3310–17

58. Levin HL. 1996. An unusual mechanismof self-primed reverse transcription re-quires the RNase H domain of reversetranscriptase to cleave an RNA duplex.Mol. Cell. Biol.16:5645–54

59. Levin HL, Weaver DC, Boeke JD. 1993.Novel gene expression in a fission yeastretroelement: Tf1 proteins are derivedfrom a single primary translation product.EMBO J.12:4885–95

60. Levis RW 1989. Viable deletions of atelomere from aDrosophilachromosome.Cell 58:791–801

61. Levis RW, Ganesan R, Houtchens K, To-lar LA, Sheen F-M. 1993. Transposons inplace of telomeric repeats at aDrosophilatelomere.Cell 17:1083–93

62. Lin J, Levin HL. 1997. A complex struc-ture in the mRNA of Tf1 is recognized andcleaved to generate the primer of reversetranscription.Genes Dev.11:270–85

63. Luan DD, Eickbush TH. 1995. RNAtemplate requirements for target DNA-primed reverse transcription by the R2retrotransposable element.Mol. Cell.Biol. 15:3882–91

64. Luan DD, Eickbush TH. 1996. Down-stream 28S gene sequences on the RNAtemplate affect the choice of primer andthe accuracy of initiation by the R2reverse transcriptase.Mol. Cell. Biol.16:4726–34

65. Luan DD, Korman MH, Jakubczak JL,Eickbush TH. 1993. Reverse transcriptionof R2Bm RNA is primed by a nick atthe chromosomal target site: A mecha-nism for nonLTR retrotransposition.Cell72:595–605

66. Masson P, Strem M, Fedoroff N. 1991.The tnpA and tnpD gene products of theSpm element are required for transposi-tion in tobacco.Plant Cell3:73–85

67. Mathias SL, Scott AF, Kazazian HH Jr,Boeke JD, Gabriel A. 1991. Reverse tran-scriptase encoded by a human retrotrans-poson.Science254:1808–10

68. McDonald JF. 1993. Evolution and con-sequences of transposable elements.Curr.Opin. Genet. Dev.3:855–64

69. Misra S, Buratowski RM, Ohkawa

T, Rio DC. 1993. Cytotype controlof Drosophila melanogaster Pelementtransposition: genomic position deter-mines maternal repression.Genetics135:785–800

70. Misra S, Rio DC. 1990. Cytotype con-trol of Drosophila Pelement transposi-tion: The 66 kd protein is a repressor oftransposase activity.Cell 62:269–84

71. Moore JK, Haber JE. 1996. Capture ofretrotransposon DNA at the sites of chro-mosomal double-strand breaks.Nature383:644–46

72. Moran JV, Zimmerly S, Eskes R, Ken-nell JC, Lambowitz AM, et al. 1995. Mo-bile group II introns of yeast mitochon-drial DNA are novel site-specific retroele-ments.Mol. Cell. Biol.15:2828–38

73. Moran JV, Holmes SE, Naas TP, De-Berardinis RJ, Boeke JD, Kazazian HHJr. 1996. High frequency retrotransposi-tion in cultured mammalian cells.Cell87:917–27

74. Mullins MC, Rio DC, Rubin GM. 1989.Cis-acting DNA sequence requirementsfor P-element transposition.Genes Dev.3:729–38

75. Nassif N, Penney J, Pal S, Engels WR,Gloor G. 1994. Efficient copying of non-homologous sequences from ectopic sitesvia P-element-induced gap repair.Mol.Cell. Biol.14:1613–25

76. O’Hare K, Driver A, Maggrath S, John-son-Schlitz DM. 1992. Distribution andstructure ofP elements from theDroso-phila melanogasterP strainπ2. Genet.Res.60:33–41

77. O’Hare K, Rubin GM. 1983 Structures ofP transposable elements and their sites ofinsertion and excision in theDrosophilamelanogastergenome.Cell 34:25–35

78. Pelisson A, Finnegan DJ, Bucheton A.1991. Evidence for retrotransposition ofthe I factor, a LINE element ofDrosophilamelanogaster. Proc. Natl. Acad. Sci. USA88:4907–10

79. Pelisson A, Song SU, Prud’homme N,Smith PA, Bucheton A, Corces VG. 1994.Gypsy transposition correlates with theproduction of a retroviral envelope-likeprotein under the tissue-specific controlof theDrosophila flamencogene.EMBOJ. 13:4401–11

80. Plasterk RH. 1991. The origin of foot-prints of theTc1 transposon ofCaeno-rhabditis elegans. EMBO J.10:1919–25

81. Plasterk RH. 1996. TheTc1/marinertransposon family.Curr. Top. Microbiol.Immunol.204:125–43

82. Prud’homme N, Gans M, Masson M,Terzian C, Bucheton A. 1995.Flamenco,

Ann

u. R

ev. G

enet

. 199

7.31

:381

-404

. Dow

nloa

ded

from

ww

w.a

nnua

lrev

iew

s.or

gby

Uni

vers

ity o

f So

uth

Flor

ida

on 0

4/13

/13.

For

per

sona

l use

onl

y.




a gene controlling thegypsy retrovirusof Drosophila melanogaster. Genetics139:697–711

83. Rabinow L, Chiang SL, Birchler JA.1993. Mutations at the Darkener ofapricot locus modulate transcript lev-els of copia and copia-induced muta-tions inDrosophila melanogaster. Genet-ics134:1175–85

84. Rasmunson KE, Raymon JD, SimmonsMJ. 1993. Repression of hybrid dysgen-esis inDrosophila melanogasterby in-dividual naturally occurringP elements.Genetics133:605–22

85. Rio DC. 1990. Molecular mechanismsregulatingDrosophila P element trans-position. Annu. Rev. Genet.24:543–78

86. Rio DC. 1991. Regulation ofDrosophilaP element transposition.Trends Genet.7:282–87

87. Rio DC, Rubin GM. 1988. Identifica-tion and purification of aDrosophilaprotein that binds to the terminal 31-base-pair inverted repeats of theP transpos-able element.Proc. Natl. Acad. Sci. USA85:8929–33

88. Robertson HM, Engels WR. 1989. Mod-ified P elements that mimic the P cyto-type inDrosophila melanogaster. Genet-ics123:815–24

89. Roche SE, Schiff M, Rio DC. 1995P-element repressor autoregulation involvesgerm-line transcriptional repression andreduction of third intron splicing.GenesDev.9275:1278–88

90. Rommens CMT, van Haaren MJJ, Nij-kamp HJJ, Hille J. 1993. Differentialrapair of excision gaps generated by trans-posable elements of theAcfamily. BioEs-says15:507–12

91. Ronsseray S, Lemaitre B, Coen D. 1993.Maternal inheritance of P cytotype inDrosophila melanogaster: A “preP cy-totype” is strictly extra-chromosomallytransmitted.Mol. Gen. Genet.241:115–23

92. Sandmeyer SB, Hansen LJ, Chalker DL.1990. Integration specificity of retro-transposons and retroviruses.Annu. Rev.Genet.24:491–518

93. Schlappi M, Raina R, Fedoroff N. 1994.Epigenetic regulation of the maizeSpmtransposable element: novel activationof a methylated promoter by TnpA.Cell77:427–37

94. Sheen F-M, Levis RW. 1994. Trans-position of the LINE-like retrotranspo-son TART to Drosophila chromosometermini. Proc. Natl. Acad. Sci. USA91:12510–14

95. Siebel CW, Admon A, Rio DC. 1995.Soma-specific expression and cloning ofPSI, a negative regulator ofP elementpremRNA splicing.Genes Dev.9:269–83

96. Siebel CW, Fresco LD, Rio DC. 1992. Themechanism of somatic inhibition: Mul-tiprotein complexes at an exon pseudo-5′ splice site control U1 snRNP binding.Genes Dev.6:1386–401

97. Simmons MJ, Bucholz LM. 1985.Transposase titration inDrosophilamelanogaster: a model of cytotype in theP-M system of hybrid dysgenesis.Proc.Natl. Acad. Sci. USA82:8119–23

98. Simmons MJ, Raymond JD, Rasmun-son KE, Miller LM, McLaron CF, ZuntJR. 1990. Repression ofP element-mediated hybrid dysgenesis inDroso-phila melanogaster. Genetics124: 663–76

99. Song SU, Gerasimova TI, Kurkulos M,Boeke JD, Corces VG. 1994. An env-likeprotein encoded by aDrosophilaretroele-ment: evidence thatgypsyis an infectiousretrovirus.Genes Dev.8:2046–57

100. Song SU, Kurkulos M, Boeke JD, CorcesVG. 1997. Mobilization of thegypsyretrotransposon ofDrosophila requiresinfection of the germ line by retroviralparticles.Development124:2789–98

101. Stavenhagen JB, Robins DM. 1988. Anancient provirus has imposed androgenregulation on the adjacent mouse sex-limited protein gene.Cell 55:247–54

102. Steinman M, Steinman S. 1997. Theenigma of Y chromosome degeneration:TRAM, a novel retrotransposon is pref-erentially located in the neo-Y chromo-some ofDrosophila miranda. Genetics145:261–66

103. Tanda S, Corces VG. 1991. Retrotrans-poson-induced overexpression of a home-obox gene causes defects in eye morpho-genesis inDrosophila. EMBO J.10:407–17

104. Teng S-C, Kim B, Gabriel A. 1996.Retrotransposon reverse transcriptase-mediated repair of chromosomal breaks.Nature383:641–44

105. Ting CN, Rosenberg MP, Snow CM,Samuelson LC, Meisler MH. 1992. En-dogenous retroviral sequences are re-quired for tissue-specific expression of ahuman salivary amylase gene.Genes Dev.6:1457–65

106. Trentmann SM, Saedler H, Gierl A.1993. The transposable element En/Spm-encoded TNPA protein contains a DNAbinding and a dimerization domain.Mol.Gen. Genet.238:201–8

Ann

u. R

ev. G

enet

. 199

7.31

:381

-404

. Dow

nloa

ded

from

ww

w.a

nnua

lrev

iew

s.or

gby

Uni

vers

ity o

f So

uth

Flor

ida

on 0

4/13

/13.

For

per

sona

l use

onl

y.




107. Vos JC, Baere ID, Plasterk HA. 1996.Transposase is the only nematode proteinrequired for in vitro transposition ofTc1.Genes Dev.10:755–61

108. Vos JC, van Luenen HG, Plasterk RH.1993. Characterization of theCaenorhab-ditis elegans Tc1transposase in vivo andin vitro. Genes Dev.7:1244–53

109. Wilanowski TM, Gibson JB, SymondsJE. 1995. Retrotransposon insertion in-duces an isozyme of sn-glycerol-3-phosphate dehydrogenase inDrosophilamelanogaster. Proc. Natl. Acad. Sci. USA92:12065–69

110. Withers-Ward ES, Kitamura Y, Barnes JP,Coffin JM. 1994. Distribution of targetsfor avian retrovirus DNA integration invivo. Genes Dev.8:1473–87

111. White SE, Habera LF, Wessler SR. 1994.Retrotransposons in the flanking regionsof normal plant genes: a role for copia-like elements in the evolution of genestructure and expression.Proc. Natl.Acad. Sci. USA91:11792–96

112. Yang J, Zimmerly S, Perlman PS, Lam-

bowitz AM. 1996. Efficient integration ofan intron RNA into double-stranded DNAby reverse splicing.Nature 381:332–35

113. Zimmerly S, Guo H, Eskes R, YangJ, Perlman PS, Lambowitz AM. 1995.A group II intron RNA is a catalyticcomponent of a DNA endonuclease in-volved in intron mobility.Cell 83:529–38

114. Zimmerly S, Guo H, Perlman PS, Lam-bowitz AM. 1995. Group II intron mobil-ity occurs by target DNA-primed reversetranscription.Cell 82:545–54

115. Zou S, Ke N, Kim JM, Voytas DF. 1996.The Saccharomyces retrotransposon Ty5integrates preferentially into regions ofsilent chromatin at the telomeres and mat-ing loci. Genes Dev.10:634–45

116. Zou S, Wright DA, Voytas DF. 1995. TheSaccharomyces Ty5 retrotransposon fam-ily is associated with origins of DNAreplication at the telomeres and the silentmating locus HMR.Proc. Natl. Acad. Sci.USA92:920–24

Ann

u. R

ev. G

enet

. 199

7.31

:381

-404

. Dow

nloa

ded

from

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Uni

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transposable element-host interactions:regulation of insertion and excision

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