Dunn et al. 2015 (PRJNA213294)

General Details

Title Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster
Organism
Number of Samples 12
Release Date 2013/07/25 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP028243
ENA SRP028243
GEO
BioProject PRJNA213294

Publication

Title
Authors Dunn JG,Foo CK,Belletier NG,Gavis ER,Weissman JS
Journal eLife
Publication Date 2013 Dec 3
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. DOI: http://dx.doi.org/10.7554/eLife.01179.001.
PMC PMC3840789
PMID 24302569
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR942868 PRJNA213294 Drosophila melanogaster Ribo-Seq
SRR942869 PRJNA213294 Drosophila melanogaster Ribo-Seq
SRR942870 PRJNA213294 Drosophila melanogaster Ribo-Seq
SRR942871 PRJNA213294 Drosophila melanogaster Ribo-Seq
SRR942874 PRJNA213294 Drosophila melanogaster Ribo-Seq
SRR942875 PRJNA213294 Drosophila melanogaster Ribo-Seq
SRR942876 PRJNA213294 Drosophila melanogaster S2 Ribo-Seq
SRR942877 PRJNA213294 Drosophila melanogaster S2 Ribo-Seq
SRR942878 PRJNA213294 Drosophila melanogaster S2 Ribo-Seq
SRR942879 PRJNA213294 Drosophila melanogaster S2 Ribo-Seq
SRR942880 PRJNA213294 Drosophila melanogaster S2 Ribo-Seq
SRR942881 PRJNA213294 Drosophila melanogaster S2 Ribo-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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