猪德尔塔冠状病毒基因组在病毒粒子中的 RNA 结构通过 vRIC-seq 检测到。

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

机构信息

National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.

Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, Hubei, China.

出版信息

Sci Data. 2024 Oct 14;11(1):1124. doi: 10.1038/s41597-024-03975-w.

DOI:10.1038/s41597-024-03975-w

PMID:39402053

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11473776/

Abstract

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.

摘要

猪德尔塔冠状病毒（PDCoV）是一种新出现的特殊德尔塔冠状病毒，可感染猪、牛和人类等哺乳动物，以及鸡和鸟类。探索病毒基因组中的 RNA 结构有助于了解 RNA 在病毒生命周期中的作用。在这项研究中，采用 vRIC-seq 分析了 PDCoV 病毒粒子全基因组结构中的 RNA-RNA 相互作用。两个生物学重复分别获得了约 1287 万和 1352 万对reads，其中 17.9%和 14.8%被鉴定为有效的嵌合reads。这些被用于预测 RNA 二级结构，其结构紧凑且高度结构化。首次在 PDCoV 的 RNA-RNA 相互作用图谱中观察到扭曲的环化构象。77 个多向连接均匀分布在 PDCoV 基因组中。我们的工作提供了基本的结构见解，对于理解 PDCoV 的基因组结构和功能、遗传进化和包装特性至关重要。