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| Status |
Public on Feb 10, 2016 |
| Title |
Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
Third-party reanalysis
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| Summary |
Ribosome-footprint profiling provides genome-wide snapshots of translation, but technical challenges can confound its analysis. Here, we use improved methods to obtain ribosome-footprint profiles and mRNA abundances that more faithfully reflect gene expression in Saccharomyces cerevisiae. Our results support proposals that both the beginning of coding regions and codons matching rare tRNAs are more slowly translated. They also indicate that emergent polypeptides with as few as three basic residues within a 10-residue window tend to slow translation. With the improved mRNA measurements, the variation attributable to translational control in exponentially growing yeast was less than previously reported, and most of this variation could be predicted with a simple model that considered mRNA abundance, upstream open reading frames, cap-proximal structure and nucleotide composition, and lengths of the coding and 5'-untranslated regions. Collectively, our results provide a framework for executing and interpreting ribosome-profiling studies and reveal key features of translational control in yeast.
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| Overall design |
Ribosome-footprint profiling and RNA-seq (total RNA, poly(A) selected, RiboMinus treated, or Ribo-Zero treated) from log-phase S. cerevisiae. The study includes a reanalysis of the two Samples from GSE53313. The reanalyzed data is linked to the Series record.
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| Contributor(s) |
Weinberg DE, Shah P, Eichhorn SW, Hussmann JA, Plotkin JB, Bartel DP |
| Citation(s) |
26876183, 27692069 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| DP5 OD017895 |
Formation and regulation of the translating mRNP |
University of California San Francisco |
Weinberg |
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| Submission date |
Dec 10, 2015 |
| Last update date |
Jul 16, 2019 |
| Contact name |
David Eric Weinberg |
| E-mail(s) |
[email protected]
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| Phone |
415-514-9723
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| Organization name |
University of California, San Francisco
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| Lab |
Weinberg
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| Street address |
600 16th Street, GH S572F
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (3) |
| GSM1969533 |
RNA-seq, unselected (total) RNA |
| GSM1969534 |
RNA-seq, poly(A) selected using Dynabeads oligo(dT) |
| GSM1969535 |
RNA-seq, rRNA depleted using RiboMinus |
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| Relations |
| Reanalysis of |
GSM1289256 |
| Reanalysis of |
GSM1289257 |
| BioProject |
PRJNA305643 |
| SRA |
SRP067237 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE75897_RAW.tar |
90.0 Kb |
(http)(custom) |
TAR (of TXT) |
| GSE75897_RPF_RPKMs.txt.gz |
27.8 Kb |
(ftp)(http) |
TXT |
| GSE75897_RiboZero_RPKMs.txt.gz |
28.1 Kb |
(ftp)(http) |
TXT |
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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