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| Status |
Public on Dec 05, 2013 |
| Title |
Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
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.
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| Overall design |
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
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| Contributor(s) |
Dunn JG, Weissman JS |
| Citation(s) |
24302569 |
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| Submission date |
Jul 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Joshua Griffin Dunn |
| E-mail(s) |
joshua.g.dunn@gmail.com
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| Organization name |
UCSF / HHMI
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| Department |
Cellular & Molecular Pharmacology
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| Lab |
Weissman
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| Street address |
1700 4th Street, BH404
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| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94114 |
| Country |
USA |
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| Platforms (1) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
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| Samples (12)
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| GSM1195321 |
mRNA 0-2 hour embryo replicate B |
| GSM1195322 |
footprint 0-2 hour embryo cushion replicate A |
| GSM1195323 |
footprint 0-2 hour embryo cushion replicate B |
| GSM1195324 |
footprint 0-2 hour embryo gradient replicate A |
| GSM1195325 |
footprint 0-2 hour embryo gradient replicate B |
| GSM1195326 |
footprint S2 cell 150 replicate A |
| GSM1195327 |
footprint S2 cell 150 replicate B |
| GSM1195328 |
footprint S2 cell 250 replicate A |
| GSM1195329 |
footprint S2 cell 250 replicate B |
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| Relations |
| BioProject |
PRJNA213294 |
| SRA |
SRP028243 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE49197_RAW.tar |
726.3 Mb |
(http)(custom) |
TAR (of WIG) |
| GSE49197_fp_embryo_all_pooled_fw.wig.gz |
51.5 Mb |
(ftp)(http) |
WIG |
| GSE49197_fp_embryo_all_pooled_rc.wig.gz |
54.6 Mb |
(ftp)(http) |
WIG |
| GSE49197_fp_embryo_cd_pooled_fw.wig.gz |
44.9 Mb |
(ftp)(http) |
WIG |
| GSE49197_fp_embryo_cd_pooled_rc.wig.gz |
47.9 Mb |
(ftp)(http) |
WIG |
| GSE49197_mrna_embryo_pooled_fw.wig.gz |
63.9 Mb |
(ftp)(http) |
WIG |
| GSE49197_mrna_embryo_pooled_rc.wig.gz |
67.3 Mb |
(ftp)(http) |
WIG |
| GSE49197_s2_150ab_pooled_fw.wig.gz |
39.6 Mb |
(ftp)(http) |
WIG |
| GSE49197_s2_150ab_pooled_rc.wig.gz |
42.3 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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