Transcriptomics

Dataset Information

309

Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster


ABSTRACT: 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. 12 samples of Drosophila ribosome profiling and poly(A)+ mRNA-seq, including technical replicates in S2 cells, and biological replicates of 0-2 hour embryos

ORGANISM(S): Drosophila melanogaster  

SUBMITTER: Joshua G Dunn   Jonathan S Weissman  Joshua Griffin Dunn 

PROVIDER: E-GEOD-49197 | ArrayExpress | 2013-12-05

SECONDARY ACCESSION(S): SRP028243GSE49197PRJNA213294

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster.

Dunn Joshua G JG   Foo Catherine K CK   Belletier Nicolette G NG   Gavis Elizabeth R ER   Weissman Jonathan S JS  

eLife 20131203


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  ...[more]

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