|
| Status |
Public on Aug 01, 2023 |
| Title |
The DEAD-box RNA helicase Ded1 is a translation-elongation factor |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
DEAD-box RNA helicases are ATP-dependent RNA binding proteins and RNA-dependent ATPases that possess weak, nonprocessive unwinding activity in vitro, but they can form long-lived complexes on RNAs when the ATPase activity is inhibited. Ded1 is a yeast DEAD-box protein, the functional ortholog of mammalian DDX3, that is considered important for the scanning efficiency of the 48S pre-initiation complex ribosomes to the AUG start codon. We used a modified PAR-CLIP technique, which we call quicktime PAR-CLIP (qtPAR-CLIP) to crosslink Ded1 to 4-thiouridine-incorported RNAs in vivo using UV light centered at 365 nm. The irradiation conditions are largely benign to the yeast cells and to Ded1, and we are able to obtain a high efficiency of crosslinking under physiological conditions. We find that Ded1 forms crosslinks on the open reading frames of many different mRNAs, but it forms the most extensive interactions on a relatively few mRNAs, and particularly on mRNAs encoding certain ribosomal proteins and translation factors. Under glucose-depletion conditions the crosslinking pattern shifts to mRNAs encoding metabolic and stress-related proteins, which reflects the altered translation. These data are consistent with Ded1 functioning in the regulation of translation elongation, perhaps by pausing or stabilizing the ribosomes through its ATP-dependent binding.
|
| |
|
| Overall design |
Identify the RNA substrates of the yeast DEAD-box helicase Ded1 using a modified PAR-CLIP protocol
|
| Web link |
https://doi.org/10.3390/genes14081566
|
| |
|
| Contributor(s) |
Hilal Y, Naïma B, Emmeline H, Josette B, N Kyle T |
| Citation(s) |
37628617 |
| |
| Submission date |
Apr 03, 2023 |
| Last update date |
Sep 14, 2023 |
| Contact name |
N. Kyle Tanner |
| E-mail(s) |
[email protected]
|
| Phone |
+33 1 58 41 52 37
|
| Organization name |
Université de Paris-Cité & CNRS
|
| Department |
Microbial Gene Expression
|
| Lab |
RNA Helicases
|
| Street address |
13 rue Pierre et Marie Curie
|
| City |
Paris |
| State/province |
Ile de France |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platforms (1) |
| GPL19756 |
Illumina NextSeq 500 (Saccharomyces cerevisiae) |
|
| Samples (6)
|
| GSM7139756 |
Rep1 Ded1-RNA X-link grown in SD+LEU medium |
| GSM7139757 |
Rep2 Ded1-RNA X-link grown in SD+LEU medium |
| GSM7139758 |
Rep3 Ded1-RNA X-link grown in SD+LEU medium |
| GSM7139759 |
Rep1 Ded1-RNA X-link grown with glucose depletion |
| GSM7139760 |
Rep2 Ded1-RNA X-link grown with glucose depletion |
| GSM7139761 |
Rep3 Ded1-RNA X-link grown with glucose depletion |
|
| Relations |
| BioProject |
PRJNA951699 |
Less...
More...