Unraveling the features of somatic transposition in the Drosophila intestine

Abstract

Transposable elements (TEs) play a significant role in evolution, contributing to genetic variation. However, TE mobilization in somatic cells is not well understood. Here, we address the prevalence of transposition in a somatic tissue, exploiting the Drosophila midgut as a model. Using whole-genome sequencing of in vivo clonally expanded gut tissue, we have mapped hundreds of highconfidence somatic TE integration sites genome-wide. We show that somatic retrotransposon insertions are associated with inactivation of the tumor suppressor Notch, likely contributing to neoplasia formation. Moreover, applying Oxford Nanopore longread sequencing technology we provide evidence for tissue-specific differences in retrotransposition. Comparing somatic TE insertional activity with transcriptomic and small RNA sequencing data, we demonstrate that transposon mobility cannot be simply predicted by whole tissue TE expression levels or by small RNA pathway activity. Finally, we reveal that somatic TE insertions in the adult fly intestine are enriched in genic regions and in transcriptionally active chromatin. Together, our findings provide clear evidence of ongoing somatic transposition in Drosophila and delineate previously unknown features underlying somatic TE mobility in vivo.

Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells

“…To enable us to discern somatic events, we compared DNA from neoplasia to DNA from the head of the same fly as a direct matched control and, consistent with human cancer studies, we will refer to sequenced neoplasia and heads as "tumour" and "normal" samples, respectively (Supplemental Table S1). Three samples were re-analysed from a previously published dataset (Siudeja et al 2015), and the remaining samples are also described in (Siudeja et al 2021). Using this approach, we can exploit the clonal nature of the tumours to identify somatic mutations in ISCs that are difficult to detect in genetically mosaic adult tissues (Fig.…”

“…S2; Supplemental Tables S3-S6; Supplemental Methods for details). In addition, we used a tool that we recently developed, "readtagger", to tag paired-end reads that partially map to, or have mates that map to, non-reference DNA sequences (Supplemental Methods; (Siudeja et al 2021)). Here, we tagged reads associated with TEs as well as enteric bacterial and viral species.…”

“…In the remaining four samples for which we did not find support for a structural variant in Notch (P15, P47, P51, D5), we detected evidence supporting de novo transposable element insertion in Notch, likely causing its inactivation. A further investigation of somatic TE insertions in this system is described elsewhere (Siudeja et al 2021).…”

“…We then used the tool svParse v0.3.1 developed within the svParser suite of tools (https://github.com/bardin-lab/svParser) to filter variants, selecting for those in the mappable genome, supported by at least 3 reads, with a coverage of at least 10 in both the tumour and normal, and a ratio of coverage to supporting reads > 0.05. We did not generally consider somatic events of transposable element insertions, which is the subject of a companion paper (Siudeja et al 2021), though we did annotate those found associated with structural variants. In addition, we excluded several events that appeared to be false positive duplications called due to inconsistent coverage between the tumour and normal samples (Supplemental Table S2).…”

“…(B) A comprehensive bioinformatic pipeline was created in order to accurately detect and characterise structural variants from sequenced neoplasia. We have developed multiple packages to enable us to tag reads that map to multiple genomes(Siudeja et al 2021), and filter and annotate structural variant breakpoints (svParser, svSupport, freqIn; Methods; Supplemental Methods). Our pipeline utilises multiple approaches to detect structural variants, and applies stringent filtering steps before annotating variants.…”