Transposable elements (TEs), one type of mobile genetic elements, often represent a large part of eukaryotic genomes and were long regarded only as selfish genomic parasites. We are now coming to understanding of the complex relationships between TEs and their host organisms -- not only in the germline but in the soma too.
The repetitive nature of TE has prevented to fully grasp the level of their activity with molecular biology and sequencing techniques so far. This is particularly true of somatic transposition in the healthy tissues on the whole-genome scale, as these events represent rare variants difficult to accurately detect with bulk short-read sequencing approaches.
I will give a brief overview of the field and present our ongoing study of transposable elements mobility in D. melanogaster with long-read sequencing techniques. We were able to identify an endogenous LTR retroelement rover that is somatically active in the healthy gut tissues by tracing back sequence variants of the inserted sequences to the fixed rover copies. We dissected the transcriptional landscape as well as the local sequence and chromatin environment of the fixed copies and hypothesize that its activity may be determined by the upstream locus-specific chromatin features.