The architecture of the Porcine deltacoronavirus RNA genome inside virions by vRICseq
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ABSTRACT:
PROVIDER: PRJNA1072987 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27860506_1.fastq.gz | Fastqsanger.gz | |||
| SRR27860506_2.fastq.gz | Fastqsanger.gz | |||
| SRR27860507_1.fastq.gz | Fastqsanger.gz | |||
| SRR27860507_2.fastq.gz | Fastqsanger.gz |
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Project description:Porcine deltacoronavirus (PDCoV) is a newly emerging and special delta coronavirus, which infect mammals such as pigs, cattle and humans, as well as chickens and birds. Exploring RNA structures in the viral genome benefits the understanding of the role of RNA in the lifecycle of viruses. In this study, vRIC-seq is employed to analyze the RNA-RNA interaction in the whole genome structure of PDCoV in virions. About 12.87 and 13.52 million paired reads are obtained in two biological replicates, respectively, with 17.9% and 14.8% of them are identified as valid chimeric reads. These are employed to predict the RNA secondary structure, which is compact and highly structured. A twisted-cyclized conformation is observed in the RNA-RNA interaction map of PDCoV for the first time. 77 multi-way junctions are evenly distributed in the PDCoV genome. Our work provides fundamental structural insights that are essential for understanding the genomic structure and function, genetic evolution, and packaging characteristics of PDCoV.
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Project description:The coronavirus disease 2019 caused by SARS-CoV-2 has led to an unprecedented health crisis. However, to date, the architecture of the viral RNA genomes inside virions have not been observed because the interiors of viral particles are not visible, even using sophisticated Cryo-electron microscopy and tomography methods. Here, we devised a virion applicable RNA in situ conformation sequencing (RIC-seq) technology, named vRIC-seq, for probing viral RNA structures in intact virions. Using vRIC-seq, we successfully generated an RNA 3D interaction map for SARS-CoV-2 and observed many topologically isolated RNA domains. Based on the map, we reconstructed the whole genome structure of SARS-CoV-2, which revealed a fascinating “unentangled globule” conformation of this RNA genome. Our secondary structure model not only faithfully captured known RNA structural elements but also identified many previously unknown long-range duplexes and higher-order junctions with apparent biological impacts. Importantly, our structural model also enabled rapid screening of potent small interfering RNAs to target vulnerable regions of the SARS-CoV-2 RNA genome to against its infections in Vero cells. Thus, beyond illustrating an innovative method for characterizing the viral RNA structures present in intact virions of potentially any RNA virus and showing how this data can be quickly exploited to develop antiviral treatments, our work offers the first empirical-data-based look at how the SARS-CoV-2 RNA genome is organized inside virions.
2021-03-25 | GSE155733 | GEO
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Project description:Porcine deltacoronavirus (PDCoV) is an emerging pathogen of swine belonging to family Coronaviridae, genus Deltacoronavirus. PDCoV predominantly infects the porcine intestinal epithelial cells (IPECs) causing severe diarrhea and/or vomiting, dehydration, and death in piglets. However, there are no researches for clarifying the changes of proteins expression levels in the IPECs infected with PDCoV. To better understand the host response to PDCoV infection, in this study, an isobaric tags for relative and absolute quantification (iTRAQ) labeling combined with liquid chromatography-tandem mass spectrometry (LC-MS)-based quantitative proteomic analysis of PDCoV-infected IPEC-J2 cells were performed to investigate the differentially expressed cellular proteins in the PDCoV-infected IPEC-J2 cells. As a result, a total of 5,502 host proteins were quantified at 24 hours post-infection (hpi) in mock and infected cells, among which 78 cellular proteins were differentially expressed with 23 up-regulated proteins and 55 down-regulated proteins. Bioinformatics analysis demonstrated that most of these regulated proteins participated in immune system process and structural molecule activity. Further, expression levels of two representative proteins, ANAPC7 and IFIT1, were confirmed by relative real-time RT-PCR and western blot analysis. The data presented here will provide an overview of host cell response to PDCoV, which could benefit the development of potential antiviral research.
2020-10-19 | PXD019975 | Pride
Project description:Porcine deltacoronavirus (PDCoV) is one of the emerged coronaviruses posing a significant threat to the swine industry. Previous work showed the presence of a viral accessory protein NS6 in PDCoV-infected cells. In this study, we detected the expression of the NS6 protein in small intestinal tissues of PDCoV-infected piglets. In addition, SDS-PAGE and Western blot analysis of sucrose gradient-purified virions showed the presence of a 13-kDa NS6 protein. Further evidences of the presence of NS6 in the PDCoV virions were obtained by immunogold staining of purified virions with anti-NS6 antiserum, and by immunoprecipitation of NS6 from purified virions. Finally, the anti-NS6 antibody was not able to neutralize PDCoV in cultured cells. These data establish for the first time that the accessory protein NS6 is expressed during infection in vivo and incorporated into PDCoV virions.
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