Genetic and epigenetic changes involving (retro)transposons in animal hybrids and polyploids.

Transposable elements (TEs) are discrete genetic units that have the ability to change their location within chromosomal DNA, and constitute a major and rapidly evolving component of eukaryotic genomes. They can be subdivided into 2 distinct types: retrotransposons, which use an RNA intermediate for transposition, and DNA transposons, which move only as DNA. Rapid advances in genome sequencing significantly improved our understanding of TE roles in genome shaping and restructuring, and studies of transcriptomes and epigenomes shed light on the previously unknown molecular mechanisms underlying genetic and epigenetic TE controls. Knowledge of these control systems may be important for better understanding of reticulate evolution and speciation in the context of bringing different genomes together by hybridization and perturbing the established regulatory balance by ploidy changes. See also sister article focusing on plants by Bento et al. in this themed issue.

Mobile genetic elements and sexual reproduction.

Transposable elements (TE) are prominent components of most eukaryotic genomes. In addition to their possible participation in the origin of sexual reproduction in eukaryotes, they may be also involved in its maintenance as important contributors to the deleterious mutation load. Comparative analyses of transposon content in the genomes of sexually reproducing and anciently asexual species may help to understand the contribution of different TE classes to the deleterious load. The apparent absence of deleterious retrotransposons from the genomes of ancient asexuals is in agreement with the hypothesis that they may play a special role in the maintenance of sexual reproduction and in early extinction for which most species are destined upon the abandonment of sex.

Penelope-like elements--a new class of retroelements: distribution, function and possible evolutionary significance.

Here we describe a new class of retroelements termed PLE (Penelope-like elements). The only transpositionally active representative of this lineage found so far has been isolated from Drosophila virilis. This element, Penelope, is responsible for the hybrid dysgenesis syndrome in this species, characterized by simultaneous mobilization of several unrelated TE families in the progeny of dysgenic crosses. Several lines of evidence favor the hypothesis of recent Penelope invasion into D. virilis. Moreover, when D. virilisPenelope was introduced by P element-mediated transformation into the genome of D. melanogaster, it underwent extensive amplification in the new host and induced several traits of the dysgenesis syndrome, including gonadal atrophy and numerous mutations. The single ORF encoded by PLE consists of two principal domains: reverse transcriptase (RT) and endonuclease (EN), which is similar to GIY-YIG intron-encoded endonucleases. With the appearance of a large number of PLEs in genome databases from diverse eukaryotes, including amoebae, fungi, cnidarians, rotifers, flatworms, roundworms, fish, amphibia, and reptilia, it becomes possible to resolve their phylogenetic relationships with other RT groups with a greater degree of confidence. On the basis of their peculiar structural features, distinct phylogenetic placement, and structure of transcripts, we conclude that PLE constitute a novel class of eukaryotic retroelements, different from non-LTR and LTR retrotransposons.

Three retrotransposon families in the genome of Giardia lamblia: two telomeric, one dead.

Transposable elements inhabiting eukaryotic genomes are generally regarded either as selfish DNA, which is selectively neutral to the host organism, or as parasitic DNA, deleterious to the host. Thus far, the only agreed-upon example of beneficial eukaryotic transposons is provided by Drosophila telomere-associated retrotransposons, which transpose directly to the chromosome ends and thereby protect them from degradation. This article reports the transposon content of the genome of the protozoan Giardia lamblia, one of the earliest-branching eukaryotes. A total of three non-long terminal repeat retrotransposon families have been identified, two of which are located at the ends of chromosomes, and the third one contains exclusively dead copies with multiple internal deletions, nucleotide substitutions, and frame shifts. No other reverse transcriptase- or transposase-related sequences were found. Thus, the entire genome of this protozoan, which is not known to reproduce sexually, contains only retrotransposons that are either confined to telomeric regions and possibly beneficial, or inactivated and completely nonfunctional.

[Transposable elements in the Animal Kingdom]. / Mobil'nye élementy v tsarstve zhivotnykh.

Transposable elements (TEs) are commonly thought to be of universal occurrence in eukaryotes. Analysis of complete higher eukaryotic genomes confirms TE status as substantial genome components and provides insights into their role in shaping the genome structure of extant eukaryotes. This review addresses several recently investigated problems in transposon biology, including potential roles of promoter organization in transposon function and evolution, the ubiquity of TEs in numerous phyla of the animal kingdom, and possible connections between transposon content and the mode of reproduction.

Promoting in tandem: the promoter for telomere transposon HeT-A and implications for the evolution of retroviral LTRs.

HeT-A elements are non-long terminal repeat (non-LTR) retrotransposons found in head-to-tail arrays on Drosophila chromosome ends, where they form telomeres. We report that HeT-A promoter activity is located in the 3' end of the element, unlike the 5' location seen for other non-LTR retrotransposons. In HeT-A arrays the 3' sequence of one element directs transcription of its downstream neighbor. Because the upstream promoter has the same sequence as the 3' end of the transcribed element, the HeT-A promoter is effectively equivalent to a 5' LTR in both structure and function. Retroviruses and LTR retrotransposons have their promoters and transcription initiation sites in their 5' LTRs. Thus HeT-A appears to have the structure of an evolutionary intermediate between non-LTR and LTR retrotransposons.

Complex patterns of transcription of a Drosophila retrotransposon in vivo and in vitro by RNA polymerases II and III.

The mdg1 retrovirus-like retrotransposon of Drosophila melanogaster was found to possess a complex promoter which can be transcribed by both RNA polymerases II and III (pol II and pol III). Pol III transcription, which is not typical of protein-coding genes, is driven by the sequences located in the long terminal repeat (LTR) of mdg1, predominantly within the transcribed region and is initiated 10 bp upstream from the regular pol II RNA start site. The pol III RNA start site is observed not only in in vitro transcription reactions, but also in total RNA isolated from tissue culture cells, larvae, pupae and adult flies. A possible role of pol III transcription in mechanisms controlling the expression of full-length mdg1-encoded transcripts in the developing fly, which are apparently relaxed in cell culture, is discussed.

Promoter elements in Drosophila melanogaster revealed by sequence analysis.

A Drosophila Promoter Database containing 252 independent Drosophila melanogaster promoter entries has been compiled. The database and its subsets have been searched for overrepresented sequences. The analysis reveals that the proximal promoter region displays the most dramatic nucleotide sequence irregularities and exhibits a tripartite structure, consisting of TATA at -25/-30 bp, initiator (Inr) at +/- 5 bp and a novel class of downstream elements at +20/+30 bp from the RNA start site. These latter elements are also strand-specific. However, they differ from TATA and Inr in several aspects: (1) they are represented not by a single, but by multiple sequences, (2) they are shorter, (3) their position is less strictly fixed with respect to the RNA start site, (4) they emerge as a characteristic feature of Drosophila promoters and (5) some of them are strongly overrepresented in the TATA-less, but not TATA-containing, subset. About one-half of known Drosophila promoters can be classified as TATA-less. The overall sequence organization of the promoter region is characterized by an extended region with an increase in GC-content and a decrease in A, which contains a number of binding sites for Drosophila transcription factors.

Transcription of Drosophila mobile element gypsy (mdg4) in heat-shocked cells.

Drosophila melanogaster Schneider 2 line cultured cells were subjected to stable transformation by co-transfection with two plasmids, one of which conferred G418 resistance and another which contained the Drosophila retrotransposon, gypsy (mdg4), under the control of the heat-shock protein 70 promoter. Transcription of the introduced constructs, as well as of endogenous gypsy, was examined under the condition of heat shock. Active degradation of pre-existing gypsy transcripts was observed. During recovery, gypsy transcription was restored, but its termination and/or 3'-end processing became aberrant.

[Long terminal repeats of drosophila mobile elements direct transcript ion in Escherichia coli cells]. / Dlinnye kontsevye povtory mobil'nykh élementov drozofily napravliaiut transkriptsiiu v kletkakh Escherichia coli.

Retrotransposons of D. melanogaster are similar to vertebrate retroviruses in their structure and function. Long terminal repeats (LTR) of retrotransposons contain specific eukaryotic promoters and transcriptional control sequences. Recently it has been shown that several retroviral LTRs contain in addition some promoter-like sequences that are functional in E. coli cells. Plasmid constructions containing the mdg1 and mdg4 LTR fragments and the standard reporter chloramphenicol acetyltransferase (cat) gene are also able to direct transcription and expression of the reporter cat gene in E. coli cells. Analysis of the primary structure of corresponding LTR fragments revealed sequences similar to conserved nucleotides of the putative prokaryotic promoter.

Control of transcription of Drosophila retrotransposons.

Studies of transcriptional control sequences responsible for regulated and basal-level RNA synthesis from promoters of Drosophila melanogaster retrotransposons reveal novel aspects of gene regulation and lead to identification of trans-acting factors that can be involved in RNA polymerase II transcription not only of retrotransposons, but of many other cellular genes. Comparisons between promoters of retrotransposons and some other Drosophila genes demonstrate that there is a greater variety in basal promoter structure than previously thought and that many promoters may contain essential sequences downstream from the RNA start site.

Properties of promoter regions of mdg1 Drosophila retrotransposon indicate that it belongs to a specific class of promoters.

A sequence 30 bp downstream from the start site of the Drosophila melanogaster retrotransposon mdg1 is shown to be responsible for correct and precise initiation of mdg1 RNA synthesis in combination with the RNA start-site sequence TCAGTT. A sequence-specific DNA binding protein is demonstrated to interact with the +30 sequence, and the efficient binding of this factor is necessary for in vivo transcriptional activity of the plasmid constructs containing mdg1 promoter fragments. The nucleotides -8/+34 of mdg1 represent a minimal promoter which is able to provide correct initiation of transcription by RNA polymerase II at basal levels. A comparison with properties of some other retrotransposable elements and several developmentally regulated cellular genes allows us to conclude that together they form a specific class of RNA polymerase II promoter. This promoter class characteristically lacks upstream sequences necessary for transcription initiation, such as TATA boxes, but requires a specific downstream promoter element within 40 bp downstream of the RNA start site. The level of transcription can, however, be modulated by upstream regulatory elements. The identified sequence-specific downstream initiation factor may be responsible for transcription initiation on promoters of some genes which belong to this class.

[Organization of promotor regions in Drosophila retrotransposons]. / Osobennosti organizatsii promotornykh oblastei retrotranspozonov drozofily.

The absence of TATA-box-like sequences and the presence of TCAGT sequences in the region of transcription initiation is the common feature of a number of Drosophila retrotransposons (e.g. mdg1, mdg3, mdg4). To reveal the LTR sequences, responsible for the transcription, a series of deletion mutants, containing a bacterial gene of chloramphenicholacetyltranspherase (CAT) under the control of different LTR fragments of these mdgs, was constructed. Such constructions were transfected into Drosophila Schneider2 cultured cells and the CAT-activity was analysed. The transcription of these constructions was also investigated by Northern blot hybridization and primer extention methods. The analysis of mdg1 promoter region showed, that it has two different elements. The distal one is responsible for the RNA synthesis level, while the proximal one is localized in the site of transcription origin and is responsible for the precision of transcription initiation. Therefore, a new type of RNA-polymerase II promoter elements, responsible for the accuracy of transcription initiation was revealed. The analysis of mdg3 and mdg4 promoters showed, that these retrotransposons also have such elements, but in contrast to mdg1, they have no promoter sequences analogous to the distal one in mdg1.

[Cloning and molecular analysis of retrotransposon mdg4 from two Drosophila melanogaster strains, differing in genetic instability]. / Klonirovanie i molekuliarnyi analiz retrotranspozona mdg4 iz dvukh linii Drosophila melanogaster, razlichaiushchikhsia po geneticheskoi nestabil'nosti.

The copies of mobile element mdg4 (gypsy) were cloned from two different D. melanogaster strains. The first strain (stable) is characterized by small number of mdg4 copies and their constant localization in chromosomes. The second strain (unstable), which was originated from the first one, is characterized by increased number of mdg4 copies and higher frequency of its transpositions. The two copies of mdg4, cloned from stable and unstable strains differ in their structure and represent two different types of mdg4. Southern blot-analysis of structural organization of mdg4 in these two strains showed, that in the stable strain there are mdg4 copies of one type, and in the unstable strain there are both, but only the mdg4 copies of another type were amplified. In was shown by transient-expression experiments, that in spite of the structural differences both types of mdg4 were able to be transcribed. Nevertheless, in flies of stable strain the mdg4 transcripts were not detected.

[Transcription of Drosophila MDG4 mobile element under hyperthermic conditions]. / Transcriptsiia mobil'nogo élementa Drozofily MDG4 v usloviiakh gipertermii.

The Drosophila melanogaster cultured cells were subjected to stable transformation by cotransfection with two plasmids, one of which conferred G418 resistance and the second contained the Drosophila retrotransposon MDG4 (gypsy) under control of different promoter fragments of the heat shock protein gene hsp70. Transcription of these constructs as well as of the endogenous gypsy was examined in the conditions of heat shock. Active degradation of preexisting MDG4 transcripts is observed after heat shock. Transcription of MDG4 is restored during recovery but its termination and/or 3' end processing becomes aberrant.

Molecular analysis of the gypsy (mdg4) retrotransposon in two Drosophila melanogaster strains differing by genetic instability.

The structural organization of the retrotransposon gypsy (mdg4) is investigated in two Drosophila melanogaster strains. One of them, the stable w strain (SS), is characterized by a small copy number and stable localization of gypsy. In the other, unstable mutator strain (MS) which is derived from SS, the gypsy copy number and the frequency of its transposition are greatly increased. Genomic gypsy copies cloned from both strains display structural differences allowing them to be divided into two subfamilies. At the nucleotide level, these differences involve single substitutions, deletions and insertions. Southern blot analysis revealed that SS possesses only gypsy elements that belong to one subfamily, while in MS only gypsy copies from the other subfamily were amplified and transposed. The transcriptional activity of gypsy was also studied. Despite the structural differences, plasmid-borne copies of each type of gypsy exhibit equal transcriptional activity in transfected tissue culture cells. Nevertheless, although a high level of gypsy transcription is observed in MS, gypsy poly(A)+RNA is not detected in SS.

[Structure of long terminal repeats of transcriptionally active and inactive copies of the mobile dispersed gene MDG3 in Drosophila melanogaster]. / Struktura dlinnykh kontsevykh povtorov transkriptsionno aktivnykh i neaktivnykh kopii mobil'nogo dispergirovannogo gena MDG3 Drosophila melanogaster.

The nucleotide sequences of long terminal repeats (LTRs) and adjacent regions are determined in the transcribed and non-transcribed variants of a mobile dispersed genetic element MDG3. MDG3 is similar to other mdg elements. A 4 bp duplication of the host DNA is generated upon its integration. MDG3 is flanked by a 5 bp inverted repeat. The length of the LTRs varies in different MDG3 variants, the difference being connected mainly with duplications of certain sequences in U3 and R regions. The copies with 267 bp LTR are the most abundant ones and perfectly conservative in their primary structure. They are transcribed in 67J25D cell culture and are not transcribed in Kc cell line, where another variant with LTR length 293 bp is transcriptionally active. S1-mapping of transcription initiation and termination sites has demonstrated that in both MDG3 variants they are situated in the same positions, and the LTR itself may be subdivided into U3, R and U5 regions, like retroviral LTRs. Possible factors involved in the regulation of mdg transcription are discussed.