Macroautophagy (autophagy) is a bulk degradation system for cytoplasmic 
components and is ubiquitously found in eukaryotic cells. Autophagy is induced 
under starvation conditions and plays a cytoprotective role by degrading 
unwanted cytoplasmic materials. The Ty1 transposon, a member of the Ty1/copia 
superfamily, is the most abundant retrotransposon in the yeast Saccharomyces 
cerevisiae and acts to introduce mutations in the host genome via Ty1 virus-like 
particles (VLPs) localized in the cytoplasm. Here we show that selective 
autophagy downregulates Ty1 transposition by eliminating Ty1 VLPs from the 
cytoplasm under nutrient-limited conditions. Ty1 VLPs are targeted to 
autophagosomes by an interaction with Atg19. We propose that selective autophagy 
safeguards genome integrity against excessive insertional mutagenesis caused 
during nutrient starvation by transposable elements in eukaryotic cells.