DOI: 10.5061/dryad.6nr73
title: Data from: Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster

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.
description: Raw sequencing
 dataRaw and processed
 high-throughput sequencing data, including both ribosome profiling and
 mRNA-seq experiments, for 0-2 hour Drosophila embryos and S2 cells.
 Reduced genomic alignments are additionally supplied as Wiggle files. See
 sample description at GEO for additional
 information.Supplementary table 1 -
 gene expression measurements in 0-2 hour Drosophila embryos and S2
 cellsGene expression data
 including ribosome profiling and RNA-seq for 0-2 hour embryos and S2
 cells. Source data for Figures 1 and 2, as well as their supplements. Data
 are supplied as a tab-delimited text file. Descriptions of columns and
 units and other metadata are included in header lines which begin with
 "##". Column headings are included in a header line beginning
 with "#". Data follow belowtable_s1_gene_expression_data.txt.bz2Supplementary table 2 - readthrough statistics for Drosophlia melanogasterSource data for Figs. 3, 4, and 6, as well as their supplements. Includes annotations and measurements of readthrough events in Drosophila melanogaster, as well as conservation data (PhyloCSF scores), Z-curve scores, and all related summary statistics. Data are supplied as a tab-delimited text file. Descriptions of columns, units, and other metadata are included in header lines which begin with "##". Column headings are included in a header line beginning with "#". Data follow below the headers.table_s2_fly_readthrough_master.txt.bz2Supplementary table 3 - readthrough statistics for Saccharomyces cerevisiaeSource data for Fig. 5 and annotations of readthrough events in [psi-] W303 yeast. Data are supplied as a tab-delimited text file. Descriptions of columns and units and other metadata are included in header lines which begin with "##". Column headings are included in a header line beginning with "#". Data follow below the headers.table_s3_yeast_readthrough_master.txt.bz2Supplementary table 4 - readthrough statistics for human foreskin fibroblastsSource data for Fig. 5 and annotations of readthrough events in human foreskin fibroblasts. Data are supplied as a tab-delimited text file. Descriptions of columns and units and other metadata are included in header lines which begin with "##". Column headings are included in a header line beginning with "#". Data follow below the headers.table_s4_human_readthrough_master.txt.bz2