Genomic distribution of copia-like transposable elements in somatic tissues and during development of Drosophila melanogaster

Evolutionary pathways of the tirant LTR retrotransposon in the Drosophila melanogaster subgroup of species

Tirant, a LTR retrotransposon with copies scattered over the chromosome arms of Drosophila melanogaster, is in the process of being lost from the chromosome arms of most natural populations of the sister species D. simulans. In an attempt to clarify the dynamics and evolution of tirant, we have studied the regulatory and reverse transcriptase regions in copies of the nine closely related species of the D. melanogaster subgroup. We show that tirant is mainly vertically transmitted in these species, with the exception of a horizontal transfer event from an ancestor of D. melanogaster to D. teissieri. We propose that, in four of the species (D. melanogaster, D. simulans, D. sechellia, and D. mauritiana), the observed patterns of evolution of the regulatory region vary with genome constraints and with the history and biogeography of the species.

Direct determination of the influence of extreme temperature on transposition and structural mutation rates of Drosophila melanogaster mobile elements

Two sets of mutation accumulation lines, one reared at 28 degrees C and the other at 24 degrees C, were compared for their transposition and rearrangement rates of eleven transposable element families. The changes affecting mobile elements were analysed by the Southern technique and in situ hybridization. No differences were found between treated and control lines. The role of the host genotype in transposition control and the significance of structural mutations in transposable element dynamics are discussed.

Ongoing loss of the tirant transposable element in natural populations of Drosophila simulans

Tirant is a long terminal repeat (LTR) retrotransposon with an average of 11 insertion sites on the chromosome arms of Drosophila melanogaster flies collected from natural populations worldwide. In the sibling species Drosophila simulans, tirant is found only in African populations, which harbor a few insertion sites (1 to 5) on the chromosome arms, although some tirant sequences are present in the heterochromatin of most populations. This distribution in D. simulans reflects either the recent genomic invasion of African populations by a new variant of tirant, or a loss of tirant from the entire species apart from some sequence relics still present in Africa. In an attempt to clarify the situation, we focused on the LTR-UTR region of tirant copies from various populations of both D. melanogaster and D. simulans. We found two distinct types of regulatory region: one type was present in both D. melanogaster and D. simulans, and the other was present only in D. simulans. Copies of this latter type of tirant were transcriptionally inactive in gonads. Here we propose that the present day distribution of tirant in D. simulans populations reflects an ancient invasion of D. simulans by tirant copies followed by the loss of active copies from most populations, apart from the African ones, suggesting that this loss is still ongoing in this species.

Fixed and unstable I-related transposable elements in heterochromatin of Drosophila melanogaster

Transposable elements are disproportionately abundant in the heterochromatin of Drosophila melanogaster. Among the forces contributing to this bias in genomic distribution, fixation due to positive selection has been put forward. We have studied I-related elements which are located in pericentromeric heterochromatin and are believed to have a role in the control of active I elements. Flies straight from the wild have been studied where fixed elements are expected to emerge clearly over the highly polymorphic background in the genomic distribution of transposable elements. The results show that some restriction fragments due to I-related elements are conserved in size and are present in all individuals tested, consistent with a selective pressure for a role. Other fragments are polymorphic in presence/absence and intensity in individuals from the wild but appear homogeneous in laboratory stocks. Although the significance of this type of instability is unclear, the finding that these polymorphic bands are recurrent in populations from distant geographical locations is also suggestive of a selective pressure for a role.

Insertion polymorphism of retrotransposable elements in populations of the insular, endemic species Drosophila madeirensis

The insertion site numbers of the retrotransposable elements (TE) 412, gypsy and bilbo were determined in individuals of five distinct natural populations of the endemic species Drosophila madeirensis from the island of Madeira. The TE distributions were compared to those of the paleartic, widespread and phylogenetically closely related species, D. subobscura. In situ hybridization and Southern blots showed that in D. madeirensis the number of insertion sites ranged between 10 and 15, three and six, and 35 and 42 for elements 412, gypsy and bilbo, respectively. The corresponding values for D. subobscura were similar. Two of these elements, 412 and gypsy, had very few insertions in the heterochromatin, unlike bilbo, which displayed a high heterochromatic insertion number. The Southern band polymorphism was very high, leading to within-population variation of 97.2%, whatever the population and the TE concerned. Using the polymorphic TE insertion sites as markers to analyse population structure by AMOVA, adapted for RAPD (Randomly Amplified Polymorphic DNA) data, we found small but significant genetic differences between the populations on Madeira. This slight differentiation, coupled with similar copy numbers for each TE between populations, suggests that the D. madeirensis species consists of a single, only slightly subdivided population. These data also show that insular populations and endemic species of Drosophila can have as many copies of TEs as more widespread species.

Polymorphism in structure of the retrotransposable element 412 in Drosophila simulans and D. melanogaster populations

The structure of the 412 retrotransposable element was investigated in various natural populations of D. melanogaster and D. simulans by a restriction enzyme analysis. We show that although the canonical structure of the 412 element was the same in both species, a high structural polymorphism existed with various rearranged elements. A 412 family was thus composed of heterogeneous copies of different sizes, with a large proportion of full-size copies. D. simulans had more rearranged copies than D. melanogaster, with some specific copies, such as a 5.6-kb BsrBI fragment, present in all populations of D. simulans. Full-size and rearranged copies were detected in both the euchromatin and the heterochromatin, with many rearranged copies in D. simulans, suggesting a recent mobilization of the 412 element in this species.

Morphological and molecular characterization of new Drosophila cell lines established from a strain permissive for gypsy transposition

The gypsy element of Drosophila melanogaster is the first retrovirus identified in invertebrates. Its transposition is controlled by a host gene called flamenco (flam): restrictive alleles of this gene maintain the retrovirus in a repressed state while permissive alleles allow high levels of transposition. To develop a cell system to study the gypsy element, we established four independent cell lines derived from the Drosophila strain SS, which contains a permissive allele of flamenco, and which is devoid of transposing copies of gypsy. The ultrastructural analysis of three SS cell lines revealed some remarkable characteristics, such as many nuclear virus-like particles, cytoplasmic dense particles, and massive cisternae filled with a fibrous material of unknown origin. Gypsy intragenomic distribution has been compared between the three cell lines and the original SS fly strain, and revealed in two of the cell lines an increase in copy number of a restriction fragment usually present in active gypsy elements. This multiplication seems to have occurred during the passage to the cell culture. Availability of SS cell lines should assist studies of gypsy transposition and infectivity and might be useful to produce high amounts of gypsy viral particles. These new lines already allowed us to show that the Envelope-like products of gypsy can be expressed as membrane proteins.

Potentially active copies of the gypsy retroelement are confined to the Y chromosome of some strains of Drosophila melanogaster possibly as the result of the female-specific effect of the flamenco gene

Gypsy is an endogenous retrovirus present in the genome of Drosophila melanogaster. This element is mobilized only in the progeny of females which contain active gypsy elements and which are homozygous for permissive alleles of a host gene called flamenco (flam). Some data strongly suggest that gypsy elements bearing a diagnostic HindIII site in the central region of the retrovirus body represent a subfamily that appears to be much more active than elements devoid of this site. We have taken advantage of this structural difference to assess by the Southern blotting technique the genomic distribution of active gypsy elements. In some of the laboratory Drosophila stocks tested, active gypsy elements were found to be restricted to the Y chromosome. Further analyses of 14 strains tested for the permissive vs. restrictive status of their flamenco alleles suggest that the presence of permissive alleles of flam in a stock tends to be associated with the confinement of active gypsy elements to the Y chromosome. This might be the result of the female-specific effect of flamenco on gypsy activity.

Intragenomic distribution and stability of transposable elements in euchromatin and heterochromatin of Drosophila melanogaster: non-LTR retrotransposon

The intragenomic location of the elements of the I, G, jockey, F, and Doc transposon families has been studied by the Southern blot analysis, in 12 laboratory Drosophila melanogaster stocks. Elements located in euchromatin, heterochromatin, and on the Y chromosome are identified, and their stability has been assessed by comparing the autoradiographs detected in different stocks and analysis of individual flies. Evidence is shown suggesting that preferential location in euchromatin or heterochromatin and the distribution within heterochromatin are distinctive of transposon families. Elements located in heterochromatin can be unstable. These results are discussed in the context of the relationship between transposable elements and the host genome.

Behaviour of the transposable elements copia and mdg1 in hybrids between the sibling species Drosophila melanogaster and D. simulans

The behaviour of the retrotransposons copia and mdg1 was analysed in hybrids between Drosophila melanogaster and D. simulans. Females of a highly inbred line of D. melanogaster were crossed with D. simulans males from three natural populations. The insertion site profiles for the two elements were determined in F1 hybrid larvae by in situ hybridization to polytene chromosomes, and were compared with that of their parents. No somatic transposition events were detected after this genomic stress of interspecific hybridization for the two transposable elements concerned.

Rates of movement of transposable elements in Drosophila melanogaster

Mobilization rates of nine families of transposable elements (P, hobo, FB, gypsy, 412, copia, blood, 297, and jockey) were estimated by using 182 lines. Lines were started from a completely isogenic population of Drosophila melanogaster, carrying the marker sepia as an indicator of possible contamination, and have been accumulating spontaneous mutations independently for 80 generations of brother-sister (or two double-first-cousin) matings. Transposable element movements have been analyzed in complete genomes by the Southern technique. Mobilization was a rare event, with an average rate of 10(-5) per site per generation. The most active element was FB. In contrast, the retroelements gypsy and blood did not move at all. Most changes in restriction patterns were consistent with rearrangements rather than with true transposition. The euchromatic or heterochromatic location of elements was tested by comparing insertion patterns from adults and salivary glands. Certain putative rearrangements involved heterochromatic copies of the retroelements 412, copia or 297. Clustering of movement across families was observed, suggesting that movement of different families may be non-independent. As association between modified insertion patterns and mutant effects on quantitative traits shows that spontaneous transposition events cause continuous variation.

DNA representation of variegating heterochromatic P-element inserts in diploid and polytene tissues of Drosophila melanogaster

Position-effect variegation (PEV) is the mosaic expression of a euchromatic gene brought into juxtaposition with heterochromatin. Fourteen different transformed Drosophila melanogaster lines with variegating P-element inserts were used to examine the DNA levels of these transgenes. Insert sites include pericentric, telomeric and fourth chromosome regions. Southern blot analyses showed that the heterochromatic hsp26 transgenes are underrepresented 1.3- to 33-fold in polytene tissue relative to the endogenous euchromatic hsp26 gene. In contrast, the heterochromatic hsp26 transgenes are present in approximately the same copy number as the endogenous euchromatic hsp26 gene in diploid tissue. It appears unlikely that DNA loss could account for the lack of gene expression in diploid tissues seen with these examples of PEV.

High transposition rates of Osvaldo, a new Drosophila buzzatii retrotransposon

Transposition of a new Drosophila retrotransposon was investigated. Total genomic Southern analysis and polytene in situ hybridizations in D. buzzatii strains and other related species using a 6 kb D. buzzatii clone (cDb314) showed a dispersed, repetitive DNA pattern, suggesting that this clone contains a transposable element (TE). We have sequenced the cDb314 clone and demonstrated that it contains all the conserved protein sequences and motifs typical of retrovirus-related sequences. Although cDb314 does not include the complete TE, the protein sequence alignment demonstrates that it includes a defective copy of a new long terminal repeat (LTR) retrotransposon, related to the gypsy family, which we have named Osvaldo. Using a D. buzzatii inbred line in which all insertion sites are known, we have measured Osvaldo transposition rates in hybrids between this D. buzzatii line and its sibling species D. koepferae. The results show that Osvaldo transposes in bursts at high rate, both in the D. buzzatii inbred line and in species hybrids.

LINE-related elements in Drosophila melanogaster

Mobile elements known as LINEs are members of a superfamily of repeated DNA conserved from protozoa to man. These sequences propagate by the retrotranscription of RNA intermediates and differ in many respects from retroviruses. Whereas most eukaryotic genomes host a single LINE family, several families of LINE-like sequences or type II retrotransposons coexist in the fruit fly Drosophila melanogaster. Properties and features of these elements are discussed in this work.

Genomic distribution of transposable elements among individuals of an inbred Drosophila line

The stability of the elements of eleven transposon families (412, B 104, blood, 297, 1731, G, copia, mdg 4, hobo, jockey and I) has been compared by the Southern technique among individuals of a Drosophila line that has been subjected to 30 generations of sister sib matings. The 412, B104, blood, 297, 1731 and G elements appear stable. Heterochromatic copia and hobo elements and euchromatic I elements appear highly polymorphic. In addition, copia, mdg 4, jockey and I elements undergo an instability resulting in significant variations in relative intensity among autoradiographic bands. The extent of the polymorphisms detected strongly suggests de novo rearrangements of transposable elements.

Evidence for de novo rearrangements of Drosophila transposable elements induced by the passage to the cell culture

The genomic distribution and the number of elements of eleven transposon families have been compared by the Southern technique between permanent cultured cells, larval salivary glands and the brains and whole flies of an inbred Drosophila line (inb-c) from which the cells were established. In cultured cells, changes in restriction patterns consistent with various types of rearrangements such as amplification, transposition and excision of the elements of copia, 1731, 412, 297 and mdg-4 transposon families are detected whereas B 104, G and blood elements appear stable. In previous reports these rearrangements were not detected among individuals of the inb-c line or among samples of somatic tissues, or in samples spanning years of maintenance of cultured cells. Hence, we believe that they have been induced de novo during the passage to the cell culture.

Preferential Y chromosomal location of TRIM, a novel transposable element of Drosophila miranda, obscura group

We have isolated a novel transposable element from the Y chromosome of Drosophila miranda (obscura group) which shows an organization intermediate between that of typical retroviruses and the I factor of Drosophila melanogaster. The site of integration of this element, TRIM, is an inverted repeat. On the 5' side the central region of TRIM is bordered by a sequence homologous to the tRNA primer binding site (PBS) and on the 3' side by a sequence homologous to the polypurine tract (PPT). The 5' LTR (long terminal repeat) contains transcription signals, such as a TATA box and a polyadenylation sequence. Three long open reading frames (ORFs) are found within the central region of the transposon. ORF1 and ORF2 show amino acid homology to the I factor of D. melanogaster and to conserved amino acid residues of retroviral reverse transcriptases. When used as a probe for in situ hybridization the TRIM element labels about 25 euchromatic sites and the chromocenter in polytene nuclei of D. miranda females. In the chromosome complement of males the polytenized part of the Y chromosome shows about the same number of additional TRIM homologous elements. Thus, as a result of this enrichment of TRIM elements in the Y chromosome, the genomic size of the TRIM population in D. miranda males is approximately doubled.