Su et al. 2022 (PRJNA779461)
General Details
| Title | A dual-activity topoisomerase complex regulates mRNA translation and turnover |
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| Organism | |
| Number of Samples | 8 |
| Release Date | 2021/11/10 00:00 |
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Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP345494 |
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| ENA | SRP345494 |
| GEO | GSE188574 |
| BioProject | PRJNA779461 |
Publication
| Title | |
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| Authors | Su S, Xue Y, Sharov A, Zhang Y, Lee SK, Martindale JL, Li W, Ku WL, Zhao K, De S, Shen W, Sen P, Gorospe M, Xu D, Wang W |
| Journal | Nucleic acids research |
| Publication Date | 2022 Jul 8 |
| Abstract | Topoisomerase 3β (TOP3B) and TDRD3 form a dual-activity topoisomerase complex that interacts with FMRP and can change the topology of both DNA and RNA. Here, we investigated the post-transcriptional influence of TOP3B and associated proteins on mRNA translation and turnover. First, we discovered that in human HCT116 colon cancer cells, knock-out (KO) of TOP3B had similar effects on mRNA turnover and translation as did TDRD3-KO, while FMRP-KO resulted in rather distinct effects, indicating that TOP3B had stronger coordination with TDRD3 than FMRP in mRNA regulation. Second, we identified TOP3B-bound mRNAs in HCT116 cells; we found that while TOP3B did not directly influence the stability or translation of most TOP3B target mRNAs, it stabilized a subset of target mRNAs but had a more complex effect on translation-enhancing for some mRNAs whereas reducing for others. Interestingly, a point mutation that specifically disrupted TOP3B catalytic activity only partially recapitulated the effects of TOP3B-KO on mRNA stability and translation, suggesting that the impact of TOP3B on target mRNAs is partly linked to its ability to change topology of mRNAs. Collectively, our data suggest that TOP3B-TDRD3 can regulate mRNA translation and turnover by mechanisms that are dependent and independent of topoisomerase activity. Published by Oxford University Press on behalf of Nucleic Acids Research 2022. |
| PMC | PMC9262614 |
| PMID | 35748872 |
| 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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| SRR16913146 | PRJNA779461 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide |  |
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| SRR16913147 | PRJNA779461 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR16913148 | PRJNA779461 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR16913149 | PRJNA779461 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR16913150 | PRJNA779461 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR16913151 | PRJNA779461 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR16913152 | PRJNA779461 | Homo sapiens | HCT116 | Ribo-Seq | Cycloheximide | |
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| SRR16913153 | PRJNA779461 | 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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