Hisaoka et al. 2022 (PRJNA701951)
General Details
| Title | Ribo-Seq experiments in HCT116 WT and TP53-/- cells upon neocarzinostatin treatment |
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| Organism | |
| Number of Samples | 16 |
| Release Date | 2021/02/15 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP306464 |
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| ENA | SRP306464 |
| GEO | GSE166783 |
| BioProject | PRJNA701951 |
Publication
| Title | |
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| Authors | Hisaoka M, Schott J, Bortecen T, Lindner D, Krijgsveld J, Stoecklin G |
| Journal | RNA biology |
| Publication Date | 2022 |
| Abstract | The transcription factor p53 exerts its tumour suppressive effect through transcriptional activation of numerous target genes controlling cell cycle arrest, apoptosis, cellular senescence and DNA repair. In addition, there is evidence that p53 influences the translation of specific mRNAs, including translational inhibition of ribosomal protein synthesis and translational activation of MDM2. A challenge in the analysis of translational control is that changes in mRNA abundance exert a kinetic (passive) effect on ribosome densities. In order to separate these passive effects from active regulation of translation efficiency in response to p53 activation, we conducted a comprehensive analysis of translational regulation by comparative analysis of mRNA levels and ribosome densities upon DNA damage induced by neocarzinostatin in wild-type and TP53 -/- HCT116 colorectal carcinoma cells. Thereby, we identified a specific group of mRNAs that are preferentially translated in response to p53 activation, many of which correspond to p53 target genes including MDM2, SESN1 and CDKN1A. By subsequent polysome profile analysis of SESN1 and CDKN1A mRNA, we could demonstrate that p53-dependent translational activation relies on a combination of inducing the expression of translationally advantageous isoforms and trans -acting mechanisms that further enhance the translation of these mRNAs. |
| PMC | PMC8993080 |
| PMID | 35388737 |
| DOI |
| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) | ||
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| SRR13712428 | PRJNA701951 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide |  |
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| SRR13712430 | PRJNA701951 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR13712432 | PRJNA701951 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR13712434 | PRJNA701951 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR13712439 | PRJNA701951 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR13712441 | PRJNA701951 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR13712443 | PRJNA701951 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR13712445 | PRJNA701951 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR13712447 | PRJNA701951 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR13712449 | PRJNA701951 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR13712451 | PRJNA701951 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR13712453 | PRJNA701951 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR13712416 | PRJNA701951 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR13712418 | PRJNA701951 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR13712420 | PRJNA701951 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR13712422 | PRJNA701951 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) |
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