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| Status |
Public on Jan 27, 2019 |
| Title |
Regulation of Translation Elongation Revealed by Ribosome Profiling [Dataset_2] |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Other
|
| Summary |
Ribosomes undergo substantial conformational changes during translation elongation to accommodate incoming aminoacyl-tRNAs and translocate along the mRNA template. We used multiple elongation inhibitors and chemical probing to define ribosome conformational states corresponding to different sized ribosome-protected mRNA fragments (RPFs) generated by ribosome profiling. We show using various genetic and environmental perturbations that the previously identified 20-22 nucleotide (nt) RPFs correspond predominantly to ribosomes in a pre-accommodation state with an open 40S ribosomal A site while the classical 27-29 nt fragments correspond to ribosomes in a pre-translocation state with an occupied 40S ribosomal A site. These distinct ribosome conformational states revealed by ribosome profiling are seen in all eukaryotes tested including fungi, worms and mammals. This high-resolution ribosome profiling approach reveals the anticipated Rck2-dependent inhibition of translocation through eEF2 phosphorylation during hyperosmotic stress. These same approaches reveal a strong translation elongation arrest during oxidative stress where the ribosomes are trapped in a pre-translocation state, but in this case the translational arrest is independent of Rck2-driven eEF2 phosphorylation. These results provide new insights and approaches for defining the molecular events that impact translation elongation throughout biology.
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| |
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| Overall design |
6 samples are included for TIG lysate DMS-MaPseq.
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| |
|
| Contributor(s) |
Wu C, Green R |
| Citation(s) |
31858614 |
|
Colin Chih-Chien Wu, Boris Zinshteyn, Karen A. Wehner, Rachel Green. High-Resolution Ribosome Profiling Defines Discrete Ribosome Elongation States and Translational Regulation during Cellular Stress. Molecular Cell 2019. doi:10.1016/j.molcel.2018.12.009
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| |
| Submission date |
May 31, 2018 |
| Last update date |
Aug 21, 2020 |
| Contact name |
Colin Wu |
| Organization name |
NCI
|
| Department |
RNA Biology Laboratory
|
| Street address |
1050 Boyles St, BG 560, RM21-102C
|
| City |
Frederick |
| State/province |
MD |
| ZIP/Postal code |
21702 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL17342 |
Illumina HiSeq 2500 (Saccharomyces cerevisiae) |
|
| Samples (6)
|
| GSM3168374 |
lysate dilute no_drug_NO_DMS, DMSMaP-seq |
| GSM3168375 |
lysate dilute no_drug_40mM_DMS, DMSMaP-seq |
| GSM3168376 |
lysate dilute no_drug_90mM_DMS, DMSMaP-seq |
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| This SubSeries is part of SuperSeries: |
| GSE115162 |
Regulation of Translation Elongation Revealed by Ribosome Profiling |
|
| Relations |
| BioProject |
PRJNA473988 |
| SRA |
SRP149444 |
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