Regulatory landscape of widespread stop codon readthrough in Drosophila

In stop codon readthrough (SCR), ribosomes continue to translate past the stop. While programmed SCR is rare in mammals, it appears remarkably widespread in insects, yet its regulation and biological significance remain poorly understood. Here, we systematically characterize SCR in Drosophila melanogaster by integrating ribosome profiling, comparative genomics, proteomics, and functional screening. We identify ∼1,400 SCR genes, reveal sequence features associated with programmed SCR, and distinguish constitutive and tissue-restricted modes. We identify conserved cis -elements sufficient to stimulate constitutive SCR and demonstrate that many remain functional in mammalian cells. Unexpectedly, the major distinction between insect and mammalian cells was not termination efficiency, but insect responsiveness to SCR-promoting regulatory elements. SCR was further associated with increased overall protein output, suggesting a function beyond proteome diversification. Our results establish SCR as a pervasive regulatory mechanism in Drosophila and provide a new framework for its study through the Drosophila Stop Codon Readthrough Atlas.