Evidence for De Novo rearrangements of Drosophila transposable elements induced by the passage to the cell culture

Abstract

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.

Host RNAs, including transposons, are encapsidated by a eukaryotic single-stranded RNA virus

“…In the FHVvirion-RNAseq dataset, the mutation frequency was 8.7 × 10 −4 for FHV RNA 1 and 9.8 × 10 −4 for FHV RNA 2. These values are within the range of the estimated Transposon ′1731′ is known to be highly duplicated in cell lines (28). ‡ See Dataset S4 for further details.…”

“…Strikingly, 89,559 reads mapped to transposable elements, which corresponds to 0.1% of the total encapsidated RNA. Most of these are Class I LTR retrotransposons (Table 2), which are the most abundant transposons in the D. melanogaster genome (27,28). Interestingly, unlike the mRNAs, a number of the transposable elements are present in both positive and negative sense directions (e.g., Gypsy, Springer, and Diver).…”

What makes transposable elements move in the Drosophila genome?

“…In Drosophila, short-term cultured cells promote transposition of the copia-like elements 412, 1731 and 297 (Junakovic et al, 1988) and 1731 element (Maisonhaute et al, 2007). However, mobilization is not observed in long-term cultured cells (Junakovic et al, 1988) or in other experiments where the TE mobilization was only observed for most copia-like elements, whereas B104 (gypsy-like), G (non-long terminal repeat retrotransposon) and blood (copia-like) elements remain stable (Di Franco et al, 1992). In the case of 1731 mentioned above, all new copies seem to be derived from a unique master copy slightly active in Drosophila genome and strongly activated during the establishment of the cell culture.…”

Deleterious transposable elements and the extinction of asexuals

“…Although there are no relevant data from asexual species, transposition of DNA and RNA elements is known to occur pre-and postmeiotically and in somatic cells and is reflected in the significant increase in TE copy number during the establishment and propagation of tissue culture lines. (57)(58)(59)(60)(61)(62)(63)(64) Limitations on DTE copy number So long as DTEs within a genome engage in replicative transposition, their number can be stabilized only by mechanisms the effectiveness of which is an increasing function of their number. (65,66) That such mechanisms exist in sexually reproducing systems is self-evident, as otherwise, given the excess of transposition over decay and excision, DTEs would increase indefinitely.…”