Mobilization of retrotransposon copia in the Drosophila melanogaster genome]

Considerable heterogeneity of retrotransposon copia sites of location on polytene chromosomes was revealed in one of the substocks of the inbred Drosophila melanogaster stock. Heterogeneity of copia sites of location was found in no other substocks analyzed. The heterogeneity was shown to be caused by copia insertions in new sites. The frequency of insertions is about 12% per haploid genome per generation. The retrotransposon excisions and somatic transpositions were not observed. The location of retrotransposons mdg1, mdg2, mdg3, mdg4, 297 and H.M.S. Beagle appeared to be stable in all the stocks analyzed. Thus, a model system allowing to study mechanisms of retrotransposon copia transpositions in D. melanogaster tissues as well as phenotypic effects of copia mobilization is described.     

Mutation accumulation and the effect of copia insertions in Drosophila melanogaster

Repeated efforts to estimate the genomic deleterious mutation rate per generation (U) in Drosophila melanogaster have yielded inconsistent estimates ranging from 0.01 to nearly 1. We carried out a mutation-accumulation experiment with a cryopreserved control population in hopes of resolving some of the uncertainties raised by these estimates. Mutation accumulation (MA) was carried out by brother sister mating of 150 sublines derived from two inbred lines. Fitness was measured under conditions chosen to mimic the ancestral laboratory environment of these genotypes. We monitored the insertions of a transposable element, copia, that proved to accumulate at the unusually high rate of 0.24 per genome per generation in one of our MA lines. Mutational variance in fitness increased at a rate consistent with previous studies, yielding a mutational coefficient of variation greater than 3%. The performance of the cryopreserved control relative to the MA lines was inconsistent, so estimates of mutation rate by the Bateman-Mukai method are suspect. Taken at face value, these data suggest a modest decline in fitness of about 0.3% per generation. The element number of copia was a significant predictor of fitness within generations; on average, insertions caused a 0.76% loss in fitness, although the confidence limits on this estimate are wide.     

Doc and copia instability in an isogenic Drosophila melanogaster stock

A high degree of heterogeneity and an overall increase in number of insertion sites of the mobile elements Doc and copia were revealed in one substock of an isogenic Drosophila melanogaster stock, while in two other substocks the distribution of copia sites was highly homogenous, but that of Doc sites was again heterogenous. We therefore concluded that copia was unstable in one of the substocks and Doc was unstable in all. Doc instability presumably arose earlier than copia instability. Doc and copia transpositions were directly observed in experiments with one substock. An abundance of copia insertions was revealed in the X chromosome where insertions with deleterious effects are exposed to selection in hemizygous condition. The locations of many other mobile elements (mdg1, mdg2, mdg3, mdg4, 297, B104, H.M.S. Beagle, I, P, BS, FB) were found to be conserved in each substock and did not differ between them, indicating that these mobile elements were stable. This homogeneity is a strong argument against any possibility of inadvertent contamination.     

Oncovirus-induced permanent genetic instability in Drosophila melanogaster

Mutant alleles of a system of genetic instability induced by oncoviral DNAs were shown to demonstrate an unstable manifestation 500 generations after their emergence. A cytogenetic analysis of oncovirus-induced unstable lines has revealed numerous chromosome rearrangements. For the Lobe alleles of this system, a specific chromosome rearrangement, Df(2L) = 35C-36B, was found on the left arm of chromosome 2. We used recessive lethal mutations involving DNA rearrangements in a successful construction of cross systems for "explosive" instability.     

Prolongation of MGE 412 transposition induction after gamma-irradiation in an isogenic line of Drosophila melanogaster]]

The dose dependence of the rate of gamma-induced transpositions and consequent dynamics of the MGE 412 pattern after gamma-irradiation were investigated in isogenic line 49 in generations F1, F12, F140, and F170. It was shown that the results on dose dependence of transpositions was very similar with the corresponding results of the classic works by Timofeeff-Ressovsky et al. (1935). It is suggested that the transcribed copies of retrotransposon 412 "cure" gamma-radiation-induced double-strand DNA breaks. The phenomenon of prolongation of MGE transposition induction during early generations after treatment was shown. In this period (F1-F12), the maximum transposition rate (lambda approximately equal to 2 x 10(-2) events per MGE copy, per haploid genome, per generation) and the maximum number of heterozygous MGE copies were achieved. In the late generations (F140 and F170), the reduced induction level (lambda approximately 10(-3) was established. In the population of effective size Ne = 2000 individuals, this corresponds to the state when lambda > 1/4Ne, i.e., when the transposition flow prevails over the MGE copy loss by genetic drift. These data together with some indirect evidence argue for the hypothesis that the spontaneous transposition rate is proportional to the average number of heterozygous MGE copies per diploid genome.     

One of the copia genes is adjacent to satellite DNA in Drosophila melanogaster.

A method for purifying sequences adjacent to satellite DNA in the heterochromatin of D. melanogaster is described. A cloned DNA segment containing part of a copia gene adjacent to 1.688 g/cm3 satellite DNA has been isolated. The copia genes compose a repeated gene family which codes for abundant cytoplasmic poly(a)-containing RNA (Young and Hogness, 1977; Finnegan et al., 1978). We have identified two major poly (A)-containing RNA species [5.2 and 2.1 kilobases (kb)] produced by the copia gene family. The cloned segment contains copia sequences homologous to the 5' end of RNA within 0.65 kb of the 1.688 satellite DNA sequences. Seven different cloned copia genes from elsewhere in the genome have also been isolated, and a 5.2 kb region present in five of the clones was identified as copia by heteroduplex analysis. In addition, three ususual copies of copia were found: a "partial" copy of the gene (3.7 kb) which has one endpoint in common with the 5.2 kb unit; a copia gene flanked on one side by a 1.6 kb sequence and on the other by the same 1.6 kb sequence in the inverted orientation; and a copia gene flanked only on one side by the same sequence.     

Germ line transposition of the copia retrotransposon in Drosophila melanogaster is restricted to males by tissue-specific control of copia RNA levels

Germ line transposition rates of the retrotransposon copia were directly measured in males and females of an inbred Drosophila melanogaster line, 2b3, which is highly polymorphic for copia insertion sites. The elevated germ line transposition rate of copia in this line (3–8?×?10^?3 per generation per element) is confined to males, with transposition in females being undetectable under the conditions of the experiment but at most 50-fold lower than the rate for males. To determine the molecular basis of this effect, copia RNA levels were measured in whole bodies and germ lines of male and female flies of both the unstable 2b3 line and a stable line, Oregon RC-iso, which shows normal rates of copia transposition. Both male and female 2b3 flies contain much more copia RNA than flies of the stable line. However, 2b3 male germinal tissues contain much higher levels of copia RNA than the equivalent female tissues. The highest copia expression is detected in maturing primary spermatocytes. Our data show that high rates of germ line copia transposition are restricted to males by tissue-specific control of RNA levels and suggest that transposition of copia only occurs in fly tissues containing more than a relatively high threshold level of copia RNA.     

Structural instability of 297 element in Drosophila melanogaster

297 element Southern pattern modifications previously detected in mutation accumulation lines of Drosophila melanogaster were further investigated by in situ hybridisation, Southern blotting with different combinations of genomic digest-probe, and PCR. Only one out of the nine pattern modifications studied could be interpreted as an excision and was detectable by in situ hybridisation to polytene chromosomes. Results were consistent with most pattern modifications being small rearrangements within the body of the element. In agreement with the existence of spontaneous rearrangements of this kind is the observation that many genomic copies of element 297 are defective and these are not limited to heterochromatin. These findings have important implications for the models of transposable element (TE) number regulation as well as for the study of genome evolution. This revised version was published online in July 2006 with corrections to the Cover Date.     

Structure, translation, and metabolism of the cytoplasmic copia ribonucleic acid of Drosophila melanogaster

We have characterized the copia RNA in the cytoplasm of cultured Drosophila cells. Copia RNA was detected and purified by hybridization to DNA of the plasmid cDm 1142, which contains the copia sequence. A large fraction (2.2%) of the total cytoplasmic poly(A)+ RNA was found to be copia RNA. Cytoplasmic copia RNA displays all the characteristics expected for a messenger RNA. It possesses a poly(A) tract identical in length with that of total poly(A)+ cytoplasmic RNA. It is associated with polysomes and can be released from this association by treatment with EDTA. When purified copia RNA is added to an mRNA-dependent rabbit reticulocyte lysate, three polypeptides of 51000, 33000, and 21000 daltons are seen. We have not determined if these are different polypeptides or if the two smaller polypeptides are fragments of the 51000-dalton polypeptide. The half-life of copia cytoplasmic RNA was determined in pulse--chase experiments to be 9.5 h; this is 1.6 times longer than the half-life of the intermediate decay class of total poly(A)+ cytoplasmic RNA. These properties provide strong evidence that copia RNA functions in vivo as a messenger RNA.     

Comparative analysis of MGE 412 patterns in 18 isogenic lines of Drosophila melanogaster

Comparative analysis of patterns of mobile genetic element 412 was conducted in 18 isogenic lines of Drosophila melanogaster isolated in three isogenic experiments in 1987 through 1999. Twelve "extra-hot" isogenization sites (in 15-18 lines) and 23 "hot" isogenization sites (> or = 10 lines) were found; of these, 19 occurred in the original heterogeneous line. These sites virtually do not overlap with hot induction sites of transposition. Sites of the latter group generally retain their positions during isogenization. It was shown that no more than 20% of the new sites were brought from the balancer by double recombination, while inbreeding and outbreeding caused 80% of them. Different factors were shown to have different hot isogenization sites. A similarity tree was constructed for the patterns of 18 isogenic lines. The maximum peak of the tree was very low (< 0.25), i.e., the isogenic lines are more similar to than different from one another. The tree was subdivided into subtrees. The division was in good agreement with the isogenization groups corresponding to individual isogenization experiments. Significant correlation was found between the total fragment length and the number of new sites per lines.     

Age dependence of the level of copia retrotransposon expression in the testes of Drosophila melanogaster

Expression of the lacZ reporter gene controlled by various deletion derivatives of the regulatory region of the copia retrotransposon was studied in the testes of adult transgenic males of the Drosophila melanogaster y1W67c23(2) strain at the age of 3, 6-9, 12-15, 18-21, and 24-27 days. When the construct contained the full-length regulatory region, which included the 5'-long terminal repeat (LTR) and the 5'-untranslated region (UTR), expression was the lowest in males aged 12-15 days and the highest in males aged 3 or 24-27 days. A similar V-shaped age dependence was previously observed for the copia transposition rate and RNA content in a strain with a high rate of copia transposition. Thus, the V-shaped age dependence of expression, which is unusual for Drosophila, proved to be characteristic of copia regardless of its transposition rate. Deletion of the 5' or 3' end of the LTR, but not of the UTR, changed the age dependence of the level of reporter gene expression. In this case, expression was the highest in 3-day-old males and gradually decreased with age, as typical for many Drosophila genes. It was assumed that the 5'- and 3'-terminal regions of the copia LTR contain regulatory elements responsible for the V-shaped age dependence of expression, while the expression level depends to a greater extent on the regulatory elements of UTR.     

Induction of MGE 412 transposition in an isogenic strain of Drosophila melanogaster by different doses of ethanol fumes

The effect of treatment of males from an isogenic Drosophila melanogaster strain by limiting doses of ethanol fumes on transpositions of MGE 412 was examined. Validity of the phenomenon of transposition induction was demonstrated. We estimated rates of induced transposition (approximately 10(-2) events per site, per sperm, per generation versus < 10(-3) in control) and showed dose dependence of the rate on the exposure time of the males to ethanol fumes. Experiments with alcohol treatment at limiting doses must end either in death of the individuals or bursts of genetic variability in their progeny. In terms of genetics of an individual, this may mean loss of vital hereditary basis followed by mass degradation of the progeny of the "hard drinkers." In terms of populations genetics, this mode of MGE transposition induction can rapidly create a burst of novel genetic variation, which, apart of great losses, may generate a number of advantageous individuals, i.e., be significant for population survival in new, stressful environments.