|
| Status |
Public on Sep 12, 2018 |
| Title |
Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
Ribosome binding proteins function broadly in protein synthesis, gene regulation and cellular homeostasis but the complete complement of functional ribosome-bound proteins remains unknown. Using quantitative mass spectrometry we identified Late-annotated short open reading frame 2 (Lso2) as a ribosome-associated protein that is broadly conserved in eukaryotes. Genome-wide crosslinking and immunoprecipitation of Lso2 and its human ortholog CCDC124 recovered 25S rRNA in a region near the A site that overlaps the GTPase activating center. Consistent with this location, Lso2 also crosslinked to most tRNAs. Ribosome profiling of yeast lacking LSO2 (lso2Δ) revealed global translation defects during recovery from stationary phase with translation of most genes reduced more than 4-fold. Ribosomes accumulated at start codons, were depleted from stop codons, and showed codon-specific changes in occupancy in lso2Δ. These defects, and the conservation of the specific ribosome-binding activity of Lso2/CCDC124, indicate broadly important functions in translation and physiology.
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| |
|
| Overall design |
Enhanced crosslinking and immunoprecipitation (IP) followed by deep sequencing: 5 IP samples of Lso2 and CCDC124, 6 controls of size-matched input and untagged IP. Ribosome footprint profiling: 7 samples of wild-type and 7 samples of lso2 null mutants.
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| |
|
| Contributor(s) |
Wang Y, Gilbert W |
| Citation(s) |
30208026 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 GM094303 |
Functional Consequences of Ribosome Heterogeneity |
MASSACHUSETTS INSTITUTE OF TECHNOLOGY |
Wendy Victoria Gilbert |
|
| Submission date |
Jan 18, 2018 |
| Last update date |
May 20, 2019 |
| Contact name |
Yinuo Wang |
| Organization name |
Yale University
|
| Department |
Molecular Biophysics and Biochemistry
|
| Lab |
Dr. Wendy Gilbert
|
| Street address |
333 Cedar St C129
|
| City |
New Haven |
| ZIP/Postal code |
06510 |
| Country |
USA |
| |
|
| Platforms (3) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
| GPL17342 |
Illumina HiSeq 2500 (Saccharomyces cerevisiae) |
| GPL19756 |
Illumina NextSeq 500 (Saccharomyces cerevisiae) |
|
| Samples (25)
|
|
| Relations |
| BioProject |
PRJNA430526 |
| SRA |
SRP131127 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE109343_RAW.tar |
126.9 Mb |
(http)(custom) |
TAR (of BED, BEDGRAPH, TXT, WIG) |
| GSE109343_Riboseq.minus_glu.raw_counts.txt.gz |
63.2 Kb |
(ftp)(http) |
TXT |
| GSE109343_Riboseq.minus_glu.rpkms.txt.gz |
156.1 Kb |
(ftp)(http) |
TXT |
| GSE109343_Riboseq.recovery.raw_counts.txt.gz |
60.6 Kb |
(ftp)(http) |
TXT |
| GSE109343_Riboseq.recovery.rescaled_rpkms.txt.gz |
132.5 Kb |
(ftp)(http) |
TXT |
| GSE109343_Riboseq.replete.raw_counts.txt.gz |
82.9 Kb |
(ftp)(http) |
TXT |
| GSE109343_Riboseq.replete.rpkms.txt.gz |
210.9 Kb |
(ftp)(http) |
TXT |
| GSE109343_Sigma1278b.single_copy_tRNAs_rRNAs.annotations.gff.gz |
670.9 Kb |
(ftp)(http) |
GFF |
| GSE109343_Sigma1278b.single_copy_tRNAs_rRNAs.fasta.gz |
3.5 Mb |
(ftp)(http) |
FASTA |
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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