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| Status |
Public on Apr 21, 2016 |
| Title |
Profiles of ribosome-associated mRNAs regulated by expression of wild-type (WT) or R534H variant of DDX3 with or without Sodium Arsenite treatment [Ribo-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
By using ribosome profiling, we demonstrate that catalytic activity of the RNA helicase DDX3 is generally required for mediating translation repression under stress. Intriguingly, however, a cancer-related DDX3 variant DDX3 R534H selectively preserves translation of genes encoding core nucleosome components. Additionally, DDX3 variants also shift ORF usage on select genes, such as RPLP1 and stress-response factors as an added mechanism of translation regulation during stress. Thus, DDX3 through both extensive and selective interactions with RNA and the ribosomal machinery helps to remodel the translational landscape under stress and in cancer.
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| Overall design |
Cells expressing either DDX3 WT or R534H variant were treated with or without sodium arsenite and lysed in the presence of cyclohexime. Ribosome-protected mRNA fragments after RNase I treatment were recovered and sequenced.
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| Contributor(s) |
Oh S, Cho Y |
| Citation(s) |
27058758 |
| Submission date |
Jul 11, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Sekyung Oh |
| E-mail(s) |
ohskjhmi@gmail.com
|
| Phone |
650-725-3354
|
| Organization name |
Stanford University School of Medicine
|
| Department |
Neurology and Neurological Sciences
|
| Street address |
1201 Welch Road, MSLS P224
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (12)
|
| GSM1819220 |
Rluc control ribosome profiling with sodium arsenite rep1 |
| GSM1819221 |
DDX3 WT ribosome profiling with sodium arsenite rep1 |
| GSM1819222 |
DDX3 R534H ribosome profiling with sodium arsenite rep1 |
| GSM1819223 |
Rluc control ribosome profiling rep2 |
| GSM1819224 |
DDX3 WT ribosome profiling rep2 |
| GSM1819225 |
DDX3 R534H ribosome profiling rep2 |
| GSM1819226 |
Rluc control ribosome profiling with sodium arsenite rep2 |
| GSM1819227 |
DDX3 WT ribosome profiling with sodium arsenite rep2 |
| GSM1819228 |
DDX3 R534H ribosome profiling with sodium arsenite rep2 |
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| This SubSeries is part of SuperSeries: |
| GSE70804 |
Profiles of ribosome-associated mRNAs regulated by expression of wild-type (WT) or R534H variant of DDX3 with or without Sodium Arsenite treatment |
|
| Relations |
| BioProject |
PRJNA289569 |
| SRA |
SRP060676 |
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