An endogenous retroviral element co-opts an upstream regulatory sequence to achieve somatic expression and mobility

We characterize somatic retrotransposition in the Drosophila intestine using long-read DNA sequencing. We show that retroelement mobility does not change significantly upon aging and is limited to very few active sub-families of retrotransposons. Importantly, we identify a polymorphic donor locus of an endogenous LTR retroviral element rover, active in the intestinal tissue. We reveal that gut activity of the rover donor copy depends on its genomic environment. Without affecting local gene expression, the copy co-opts its upstream enhancer sequence, rich in transcription factor binding sites, for somatic expression. We further show that escargot, a snail-type transcription factor critical for gut progenitor cell function, can drive transcriptional activity of the active rover copy. These data provide new insights into how locus-specific features allow active retrotransposons to produce functional transcripts and mobilize in a somatic lineage. RNA-seq and direct ONT cDNA profiling of gut and head tissue in normal and Ago2 mutant conditions of the D. melanogaster strain with somatically active retrotransposon copies.