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.
Raw sequencing data
Raw 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 cells
Gene 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 below
table_s1_gene_expression_data.txt.bz2
Supplementary table 2 - readthrough statistics for Drosophlia melanogaster
Source 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.bz2
Supplementary table 3 - readthrough statistics for Saccharomyces cerevisiae
Source 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.bz2
Supplementary table 4 - readthrough statistics for human foreskin fibroblasts
Source 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