Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.

E-GEOD-49197 - Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster

Status
Released on 5 December 2013, last updated on 3 June 2014
Organism
Drosophila melanogaster
Samples (12)
Protocols (1)
Description
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
Experiment types
other, RNA-seq of coding RNA 
Contacts
Joshua Griffin Dunn <joshua.g.dunn@gmail.com>, Jonathan S Weissman, Joshua G Dunn
Citation
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Links