Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster
Joshua G Dunn,
Catherine K Foo,
Nicolette G Belletier,
Elizabeth R Gavis,
Jonathan S Weissman
Affiliations
Joshua G Dunn
California Institute of Quantitative Biosciences, San Francisco, United States; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States; Center for RNA Systems Biology, Berkeley, United States
Catherine K Foo
California Institute of Quantitative Biosciences, San Francisco, United States; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
Nicolette G Belletier
Department of Molecular Biology, Princeton University, Princeton, United States
Elizabeth R Gavis
Department of Molecular Biology, Princeton University, Princeton, United States
Jonathan S Weissman
California Institute of Quantitative Biosciences, San Francisco, United States; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States; Center for RNA Systems Biology, Berkeley, United States
Ribosomes can read through stop codons in a regulated manner, elongating rather than terminating the nascent peptide. Stop codon readthrough is essential to diverse viruses, and phylogenetically predicted to occur in a few hundred genes in Drosophila melanogaster, but the importance of regulated readthrough in eukaryotes remains largely unexplored. Here, we present a ribosome profiling assay (deep sequencing of ribosome-protected mRNA fragments) for Drosophila melanogaster, and provide the first genome-wide experimental analysis of readthrough. Readthrough is far more pervasive than expected: the vast majority of readthrough events evolved within D. melanogaster and were not predicted phylogenetically. The resulting C-terminal protein extensions show evidence of selection, contain functional subcellular localization signals, and their readthrough is regulated, arguing for their importance. We further demonstrate that readthrough occurs in yeast and humans. Readthrough thus provides general mechanisms both to regulate gene expression and function, and to add plasticity to the proteome during evolution.
