Karasik et al. 2021 (PRJNA663848)
General Details
| Title | Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences |
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| Organism | |
| Number of Samples | 30 |
| Release Date | 2020/09/16 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP282584 |
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| ENA | SRP282584 |
| GEO | GSE158044 |
| BioProject | PRJNA663848 |
Publication
| Title | |
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| Authors | Karasik A,Jones GD,DePass AV,Guydosh NR |
| Journal | Nucleic acids research |
| Publication Date | 2021 Jun 21 |
| Abstract | Ribonuclease L (RNase L) is activated as part of the innate immune response and plays an important role in the clearance of viral infections. When activated, it endonucleolytically cleaves both viral and host RNAs, leading to a global reduction in protein synthesis. However, it remains unknown how widespread RNA decay, and consequent changes in the translatome, promote the elimination of viruses. To study how this altered transcriptome is translated, we assayed the global distribution of ribosomes in RNase L activated human cells with ribosome profiling. We found that RNase L activation leads to a substantial increase in the fraction of translating ribosomes in ORFs internal to coding sequences (iORFs) and ORFs within 5' and 3' UTRs (uORFs and dORFs). Translation of these alternative ORFs was dependent on RNase L's cleavage activity, suggesting that mRNA decay fragments are translated to produce short peptides that may be important for antiviral activity. Published by Oxford University Press on behalf of Nucleic Acids Research 2021. |
| PMC | PMC8216459 |
| PMID | 33556964 |
| 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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| SRR12651177 | PRJNA663848 | Homo sapiens | Hap1 | Ribo-Seq | untreated |  |
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| SRR12651178 | PRJNA663848 | Homo sapiens | Hap1 | Ribo-Seq | |
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| SRR12651179 | PRJNA663848 | Homo sapiens | Ribo-Seq | untreated | |
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| SRR12651180 | PRJNA663848 | Homo sapiens | Ribo-Seq | |
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| SRR12651181 | PRJNA663848 | Homo sapiens | Ribo-Seq | |
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| SRR12651182 | PRJNA663848 | Homo sapiens | Ribo-Seq | |
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| SRR12651183 | PRJNA663848 | Homo sapiens | Ribo-Seq | |
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| SRR12651184 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | untreated | |
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| SRR12651185 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | untreated | |
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| SRR12651186 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | |
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| SRR12651187 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | |
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| SRR12651188 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | |
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| SRR12651189 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | |
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| SRR12651190 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | |
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| SRR12651191 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | |
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| SRR12651192 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | untreated | |
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| SRR12651193 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | |
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| SRR12651194 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | untreated | |
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| SRR12651195 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | |
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| SRR12651196 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | |
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| SRR12651197 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | |
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| SRR12651198 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | |
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| SRR12651199 | PRJNA663848 | Homo sapiens | A549 | tRNA | untreated | |
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| SRR12651200 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | untreated | |
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| SRR12651201 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | |
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| SRR12651202 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | |
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| SRR12651203 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | |
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| SRR12651204 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | |
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| SRR12651205 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | |
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| SRR12651206 | PRJNA663848 | Homo sapiens | A549 | Ribo-Seq | |
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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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