RNA architecture of porcine deltacoronavirus genome inside virions detected by vRIC-seq

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 stu...

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Bibliographic Details
Published in:Scientific data 2024-10, Vol.11 (1), p.1124-11, Article 1124
Main Authors: Sun, Ju, Huang, Zhiyuan, Chen, Lei, Guo, Liangrong, Wang, Yuxiang, Deng, Yingxiang, Liu, Guoyue, Wen, Zi, Wei, Dengguo
Format: Article
Language:English
Subjects:
631/114/2163
631/326/596/2148
631/535/1267
Animals
Conformation
Coronaviruses
Data Descriptor
Deltacoronavirus - genetics
Evolution & development
Genome, Viral
Genomes
Humanities and Social Sciences
multidisciplinary
Nucleic Acid Conformation
Packaging
Protein structure
Ribonucleic acid
RNA
RNA viruses
RNA, Viral - genetics
Science
Science (multidisciplinary)
Secondary structure
Structure-function relationships
Swine
Virion - genetics
Virions
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Summary: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.
ISSN:2052-4463
2052-4463
DOI:10.1038/s41597-024-03975-w