Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions
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Abstract
SARS-CoV-2 is a major threat to global health. Here, we investigate the RNA structure and RNA-RNA interactions of wildtype (WT) and a mutant (Δ382) SARS-CoV-2 in cells using Illumina and Nanopore platforms. We identify twelve potentially functional structural elements within the SARS-CoV-2 genome, observe that subgenomic RNAs can form different structures, and that WT and Δ382 virus genomes fold differently. Proximity ligation sequencing identify hundreds of RNA-RNA interactions within the virus genome and between the virus and host RNAs. SARS-CoV-2 genome binds strongly to mitochondrial and small nucleolar RNAs and is extensively 2’-O-methylated. 2’-O-methylation sites are enriched in viral untranslated regions, associated with increased virus pair-wise interactions, and are decreased in host mRNAs upon virus infection, suggesting that the virus sequesters methylation machinery from host RNAs towards its genome. These studies deepen our understanding of the molecular and cellular basis of SARS-CoV-2 pathogenicity and provide a platform for targeted therapy.
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SciScore for 10.1101/2021.01.17.427000: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization To reduce the amount of computing resources required, 20000 strands from each subgenomic transcripts in the unmodified libraries were randomly selected and used for the generation of models. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Cells and viruses: African green monkey kidney, clone E6 (Vero-E6) cells (ATCC# CRL-1586) were maintained in Dulbecco’s modified Eagle Medium (DMEM) supplemented with 5% fetal bovine serum (5% FBS). Vero-E6suggested: NoneTwo biological replicates of SARS-Cov-2 … SciScore for 10.1101/2021.01.17.427000: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization To reduce the amount of computing resources required, 20000 strands from each subgenomic transcripts in the unmodified libraries were randomly selected and used for the generation of models. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Cells and viruses: African green monkey kidney, clone E6 (Vero-E6) cells (ATCC# CRL-1586) were maintained in Dulbecco’s modified Eagle Medium (DMEM) supplemented with 5% fetal bovine serum (5% FBS). Vero-E6suggested: NoneTwo biological replicates of SARS-Cov-2 infected Vero E6 (total 4 replicates) and uninfected Vero E6 (total 2 replicates) were used to generate Nm-Seq libraries. Vero E6suggested: RRID:CVCL_XD71)Software and Algorithms Sentences Resources Protein-protein interaction network analysis by STRING: The top 25% of host RNA interactors with SARS-CoV-2 were used as input for STRING analysis35, a search tool for retrieval of interacting genes to acquire protein-protein interaction (PPI) networks. STRINGsuggested: (STRING, RRID:SCR_005223)The adaptors on raw reads were trimmed using Cutadapt and the reads without 3’ adaptors were discarded54. Cutadaptsuggested: (cutadapt, RRID:SCR_011841)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:While the structures along SARS-CoV-2 have also been probed using other short-read high throughput strategies such as DMS-sequencing29, these strategies have limitations in their ability to decipher sgRNA-specific structures due to extensive sequence similarity between the different sgRNAs. Using long-read sequencing, we identified both sgRNA-specific structures, as well as structure differences between WT and Δ382 genomes, that could serve as a basis for understanding sgRNA-specific functions in future. While existing literature has mostly focused on understanding SARS-CoV-2: host protein interactions, here we describe that the virus genomes bind directly to hundreds of host RNAs inside cells using SPLASH. In addition to a previous report that showed that SARS-CoV-2 binds to snRNAs that are involved in splicing46, we identified diverse, functionally related, host mRNA-virus interactions and found that SARS-CoV-2 binds particularly strongly to mitochondrial RNAs and snoRNAs. Our results are consistent with previous predictions of SARS-CoV-2 localization in the mitochondria and nucleolus38, and the observation that the mitochondria is dysregulated upon SARS-CoV-2 infection23. In addition, previous studies have also shown that SNORD27 and mitochondrial RNAs are enriched on SARS-CoV-2 using formaldehyde crosslinking, and sequencing23. However, it is unclear if these RNAs bind to the genome directly or indirectly through protein interactions. Our studies show that SARS-CoV-2 RNA ...
Results from TrialIdentifier: No clinical trial numbers were referenced.
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Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
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