Uninvited guests: how transposable elements take advantage of Drosophila germline stem cells, and how stem cells fight back

•DNA and retrotransposons use different strategies to produce new insertions in germline stem cell genomes.•DNA damage from transposition threatens the establishment and maintenance of germline stem cells.•Transposition triggers DNA damage response pathways that lead to germline stem cell loss.•Germline stem cell loss may also reflect altered signaling for self-renewal or differentiation.•piRNA-mediated silencing defends germline stem cells and their progenitors from the harmful effects of transposable elements.