Puray-Chavez et al. 2020 (PRJNA667051)
General Details
| Title | Translational landscape of SARS-CoV-2 and infected cells |
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| Organism | |
| Number of Samples | 78 |
| Release Date | 2020/10/02 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP286182 |
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| ENA | SRP286182 |
| GEO | GSE158930 |
| BioProject | PRJNA667051 |
Publication
| Title | |
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| Authors | Puray-Chavez M,Lee N,Tenneti K,Wang Y,Vuong HR,Liu Y,Horani A,Huang T,Gunsten SP,Case JB,Yang W,Diamond MS,Brody SL,Dougherty J,Kutluay SB |
| Journal | mBio |
| Publication Date | 2022 Jun 28 |
| Abstract | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes a number of strategies to modulate viral and host mRNA translation. Here, we used ribosome profiling in SARS-CoV-2-infected model cell lines and primary airway cells grown at an air-liquid interface to gain a deeper understanding of the translationally regulated events in response to virus replication. We found that SARS-CoV-2 mRNAs dominate the cellular mRNA pool but are not more efficiently translated than cellular mRNAs. SARS-CoV-2 utilized a highly efficient ribosomal frameshifting strategy despite notable accumulation of ribosomes within the slippery sequence on the frameshifting element. In a highly permissive cell line model, although SARS-CoV-2 infection induced the transcriptional upregulation of numerous chemokine, cytokine, and interferon-stimulated genes, many of these mRNAs were not translated efficiently. The impact of SARS-CoV-2 on host mRNA translation was more subtle in primary cells, with marked transcriptional and translational upregulation of inflammatory and innate immune responses and downregulation of processes involved in ciliated cell function. Together, these data reveal the key role of mRNA translation in SARS-CoV-2 replication and highlight unique mechanisms for therapeutic development. IMPORTANCE SARS-CoV-2 utilizes a number of strategies to modulate host responses to ensure efficient propagation. Here, we used ribosome profiling in SARS-CoV-2-infected cells to gain a deeper understanding of the translationally regulated events in infected cells. We found that although viral mRNAs are abundantly expressed, they are not more efficiently translated than cellular mRNAs. SARS-CoV-2 utilized a highly efficient ribosomal frameshifting strategy and alternative translation initiation sites that help increase the coding potential of its RNAs. In permissive cells, SARS-CoV-2 infection induced the translational repression of numerous innate immune mediators. Though the impact of SARS-CoV-2 on host mRNA translation was more subtle in primary airway cell cultures, we noted marked transcriptional and translational upregulation of inflammatory and innate immune responses and downregulation of processes involved in ciliated cell function. Together, these data provide new insight into how SARS-CoV-2 modulates innate host responses and highlight unique mechanisms for therapeutic intervention. |
| PMC | PMC9239271 |
| PMID | 35604092 |
| 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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| SRR12764729 | PRJNA667051 | Chlorocebus sabaeus | Vero | Ribo-Seq | Cycloheximide |  |
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| SRR12764730 | PRJNA667051 | Chlorocebus sabaeus | Vero | Ribo-Seq | Cycloheximide | |
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| SRR12764731 | PRJNA667051 | Chlorocebus sabaeus | Vero | Ribo-Seq | Cycloheximide | |
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| SRR12764732 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR12764733 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR12764734 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR12764735 | PRJNA667051 | Chlorocebus sabaeus | Vero | Ribo-Seq | Cycloheximide | |
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| SRR12764736 | PRJNA667051 | Chlorocebus sabaeus | Vero | Ribo-Seq | Cycloheximide | |
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| SRR12764737 | PRJNA667051 | Chlorocebus sabaeus | Vero | Ribo-Seq | Cycloheximide | |
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| SRR12764738 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR12764739 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR12764740 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR12764753 | PRJNA667051 | Chlorocebus sabaeus | Vero | Ribo-Seq | Cycloheximide | |
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| SRR12764754 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR12764755 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR12764756 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR12764757 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR12764758 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR12764759 | PRJNA667051 | Chlorocebus sabaeus | Vero | Ribo-Seq | Cycloheximide | |
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| SRR12764760 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR12764761 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR12764762 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR12764763 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR12764764 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR12764777 | PRJNA667051 | Chlorocebus sabaeus | Vero | Ribo-Seq | chx_harr | |
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| SRR12764778 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | chx_harr | |
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| SRR12764779 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | chx_harr | |
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| SRR12764780 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | chx_harr | |
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| SRR12764781 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | chx_harr | |
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| SRR12764782 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | chx_harr | |
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| SRR12764783 | PRJNA667051 | Chlorocebus sabaeus | Vero | Ribo-Seq | chx_harr | |
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| SRR12764784 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | chx_harr | |
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| SRR12764785 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | chx_harr | |
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| SRR12764786 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | chx_harr | |
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| SRR12764787 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | chx_harr | |
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| SRR12764788 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | chx_harr | |
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| SRR12764797 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR12764798 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR12764799 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR12764800 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR12764801 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR12764802 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR12764803 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR12764804 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR12764809 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR12764810 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR12764811 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR12764812 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324684 | PRJNA667051 | Chlorocebus sabaeus | Vero | Ribo-Seq | Cycloheximide | |
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| SRR15324685 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR15324686 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR15324687 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR15324688 | PRJNA667051 | Chlorocebus sabaeus | Ribo-Seq | Cycloheximide | |
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| SRR15324714 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324715 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324716 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324717 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324718 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324719 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324720 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324721 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324722 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324723 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324724 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324725 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324726 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324727 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324728 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324729 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324730 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324731 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324732 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324733 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324734 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324735 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324736 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324737 | PRJNA667051 | Homo sapiens | Ribo-Seq | Cycloheximide | |
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| SRR15324738 | PRJNA667051 | Homo sapiens | 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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