PDF(Pubmed)
Abstract：
Virus-to-host RNA-RNA interactions directly regulate host mRNA stability and viral replication. However, globally profiling virus-to-host in situ RNA-RNA interactions remains challenging. Here, we present an RNA in situ conformation sequencing (RIC-seq)-based protocol for mapping high-confidence virus-to-host in situ RNA-RNA interactions in infected cells. We detail steps for formaldehyde crosslinking, pCp-biotin labeling, in situ proximity ligation, chimeric RNA enrichment, strand-specific library construction, and data analysis. This protocol allows unbiased identification of virus-to-host RNA-RNA interactions for various RNA viruses and is potentially applicable to DNA virus-derived transcripts. For complete details on the use and execution of this protocol, please refer to Zhao et al.1.
摘要：
病毒与宿主RNA-RNA相互作用直接调节宿主mRNA稳定性和病毒复制。然而,全球分析病毒与宿主的原位RNA-RNA相互作用仍然具有挑战性.这里,我们提出了一种基于RNA原位构象测序（RIC-seq）的方案，用于在感染细胞中绘制高置信度病毒与宿主的原位RNA-RNA相互作用。我们详细介绍了甲醛交联的步骤，pCp-生物素标记，原位邻近结扎，嵌合RNA富集，链特定库的构建，和数据分析。该方案允许无偏鉴定各种RNA病毒的病毒与宿主RNA-RNA相互作用，并且可能适用于DNA病毒衍生的转录本。有关此协议的使用和执行的完整详细信息，请参考赵等人1。
