Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions

Xiang, J. S.; Mueller, J. R.; Luo, E.-C.; Yee, B. A.; Schafer, D.; Schmok, J. C.; Tan, F. E.; Rothamel, K.; McVicar, R. N.; Kwong, E. M.; Jones, K. L.; Her, H.-L.; Chen, C.-Y.; Vu, A. Q.; Jin, W.; Park, S. S.; Le, P.; Brannan, K. W.; Kofman, E. R.; Li, Y.; Tankka, A. T.; Dong, K. D.; Song, Y.; Carlin, A. F.; Van Nostrand, E. L.; Leibel, S. L.; Yeo, G. W.

doi:10.1101/2022.02.21.481223

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bioRxiv · 10.1101/2022.02.21.481223

Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions

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Abstract

The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral and host RNAs in authentic virus-infected cells. SARS-CoV-2 proteins, NSP8, NSP12, and nucleocapsid display distinct preferences to specific regions in the RNA viral genome, providing evidence for their shared and separate roles in replication, transcription, and viral packaging. SARS-CoV-2 proteins expressed in human lung epithelial cells bind to 4773 unique host coding RNAs. Nine SARS-CoV-2 proteins upregulate target gene expression, including NSP12 and ORF9c, whose RNA substrates are associated with pathways in protein N-linked glycosylation ER processing and mitochondrial processes. Furthermore, siRNA knockdown of host genes targeted by viral proteins in human lung organoid cells identify potential antiviral host targets across different SARS-CoV-2 variants. Conversely, NSP9 inhibits host gene expression by blocking mRNA export and dampens cytokine productions, including interleukin-1/{beta}. Our 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.

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Xiang, J. S., Mueller, J. R., Luo, E.-C., Yee, B. A., Schafer, D., Schmok, J. C., Tan, F. E., Rothamel, K., McVicar, R. N., Kwong, E. M., Jones, K. L., Her, H.-L., Chen, C.-Y., Vu, A. Q., Jin, W., Park, S. S., Le, P., Brannan, K. W., Kofman, E. R., Li, Y., Tankka, A. T., Dong, K. D., Song, Y., Carlin, A. F., Van Nostrand, E. L., Leibel, S. L., Yeo, G. W.. 2022-02-24. Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions. https://doi.org/10.1101/2022.02.21.481223

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