Multiple Independent Retroelement Insertions in the Promoter of a Stress Response Gene Have Variable Molecular and Functional Effects in Drosophila

Abstract

[Abstract] Promoters are structurally and functionally diverse gene regulatory regions. The presence or absence of sequence motifs and the spacing between the motifs defines the properties of promoters. Recent alternative promoter usage analyses in Drosophila melanogaster revealed that transposable elements significantly contribute to promote diversity. In this work, we analyzed in detail one of the transposable element insertions, named FBti0019985, that has been co-opted to drive expression of CG18446, a candidate stress response gene. We analyzed strains from different natural populations and we found that besides FBti0019985, there are another eight independent transposable elements inserted in the proximal promoter region of CG18446. All nine insertions are solo-LTRs that belong to the roo family. We analyzed the sequence of the nine roo insertions and we investigated whether the different insertions were functionally equivalent by performing 5’-RACE, gene expression, and cold-stress survival experiments. We found that different insertions have different molecular and functional consequences. The exact position where the transposable elements are inserted matters, as they all showed highly conserved sequences but only two of the analyzed insertions provided alternative transcription start sites, and only the FBti0019985 insertion consistently affects CG18446 expression. The phenotypic consequences of the different insertions also vary: only FBti0019985 was associated with cold-stress tolerance. Interestingly, the only previous report of transposable elements inserting repeatedly and independently in a promoter region in D. melanogaster, were also located upstream of a stress response gene. Our results suggest that functional validation of individual structural variants is needed to resolve the complexity of insertion clusters.

[Author Summary] The presence of several transposable element insertions in the promoter region of a Drosophila melanogaster gene has only been described in heat shock protein genes. In this work, we have discovered and characterized in detail several naturally occurring independent transposable element insertions in the promoter region of a cold-stress response gene in the fruitfly Drosophila melanogaster. The nine transposable element insertions described are clustered in a small 368 bp region and all belong to the same family of transposable elements: the roo family. Each individual insertion is present at relatively low population frequencies, ranging from 1% to 17%. However, the majority of strains analyzed contain one of these nine roo insertions suggesting that this region might be evolving under positive selection. Although the sequence of these insertions is highly similar, their molecular and functional consequences are different. Only one of them, FBti0019985, is associated with increased viability in nonstress and in cold-stress conditions.