Discovery and Functional Interrogation of the Virus and Host RNA Interactome of SARS-Cov-2 Proteins

The COVID-19 pandemic was caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral and host RNAs. SARS-CoV-2 proteins, NSP8 and NSP12, bind to specific regions in the RNA viral genome, providing evidence for their central and potential roles in replication, transcription and genome recombination. SARS-CoV-2 proteins expressed in human lung epithelial cells bind to 4,821 unique host RNAs. Nine SARS-CoV-2 proteins upregulate target gene expression, including NSP12 which upregulates mitochondrial and N-linked glycosylation proteins. Furthermore, siRNA knockdown of host genes targeted by the viral proteins in human lung organoid cells demonstrates substantial antiviral effects. Conversely, NSP9 inhibits host gene expression by blocking mRNA export and dampens inflammatory responses such as interleukin-1α/β production. Our extensive viral protein-RNA interactome provides a catalog of potential therapeutic targets and offers insight into the etiology of COVID-19 as a safeguard against future pandemics. Funding Information: The work has been supported by Emergency COVID-19 Research Seed Funding (#R00RG2636) from the University of California Office of the President. This publication includes data generated at the UC San Diego IGM Genomics Center utilizing an Illumina NovaSeq 6000 that was purchased with funding from a National Institutes of Health SIG grant (#S10 OD026929). J.S.X as a visiting fellow is partially supported by Agency for Science, Technology and Research (A*STAR) and Industrial Alignment Fund Pre-Positioning (IAF-PP) grant H17/01/a0/012. ELVN is supported by the NHGRI (R00HG009530). Declaration of Interests: J.S.X, F.E.T, J.C.S and G.W.Y declare a pending patent application. ELVN is co-founder, member of the Board of Directors, on the SAB, equity holder, and paid consultant for Eclipse BioInnovations. ELVN’s interests have been reviewed and approved by the Baylor College of Medicine in accordance with its conflict of interest policies. The authors declare no other competing interests Ethics Approval Statement: This study protocol was approved by the Institutional Review Board of UCSD's Human Research Protections Program (181180).