Characterizing the interactions that SARS-CoV-2 viral RNAs make with host cell proteins during infection can improve our understanding of viral RNA functions and the host innate immune response. Using RNA antisense purification and mass spectrometry, we identified up to 104 human proteins that directly and specifically bind to SARS-CoV-2 RNAs in infected human cells. We integrated the SARS-CoV-2 RNA interactome with changes in proteome abundance induced by viral infection and linked interactome proteins to cellular pathways relevant to SARS-CoV-2 infections. We demonstrated by genetic perturbation that cellular nucleic acid-binding protein (CNBP) and La-related protein 1 (LARP1), two of the most strongly enriched viral RNA binders, restrict SARS-CoV-2 replication in infected cells and provide a global map of their direct RNA contact sites. Pharmacological inhibition of three other RNA interactome members, PPIA, ATP1A1, and the ARP2/3 complex, reduced viral replication in two human cell lines. The identification of host dependency factors and defence strategies as presented in this work will improve the design of targeted therapeutics against SARS-CoV-2.

表征 SARS-CoV-2 病毒 RNA 在感染过程中与宿主细胞蛋白的相互作用可以提高我们对病毒 RNA 功能和宿主先天免疫反应的理解。使用 RNA 反义纯化和质谱分析，我们鉴定了多达 104 种直接和特异性结合受感染人体细胞中的 SARS-CoV-2 RNA 的人类蛋白质。我们将 SARS-CoV-2 RNA 相互作用组与病毒感染诱导的蛋白质组丰度变化相结合，并将相互作用组蛋白与与 SARS-CoV-2 感染相关的细胞通路联系起来。我们通过遗传扰动证明，细胞核酸结合蛋白 (CNBP) 和 La 相关蛋白 1 (LARP1) 是两种最富集的病毒 RNA 结合剂，可限制 SARS-CoV-2 在感染细胞中的复制并提供全球地图它们的直接 RNA 接触位点。对其他三个 RNA 相互作用组成员 PPIA、ATP1A1 和 ARP2/3 复合物的药理抑制减少了两种人类细胞系中的病毒复制。这项工作中提出的宿主依赖因素和防御策略的识别将改进针对 SARS-CoV-2 的靶向治疗的设计。