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

Flynn, Ryan A.; Belk, Julia A.; Qi, Yanyan; Yasumoto, Yuki; Wei, Jin; Alfajaro, Mia Madel; Shi, Quanming; Mumbach, Maxwell R.; Limaye, Aditi; DeWeirdt, Peter C.; Schmitz, Cameron O.; Parker, Kevin R.; Woo, Elizabeth; Chang, Howard Y.; Horvath, Tamas L.; Carette, Jan E.; Bertozzi, Carolyn R.; Wilen, Craig B.; Satpathy, Ansuman T.

SARS-CoV-2 is the cause of a pandemic with growing global mortality. Using comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS), we identified 309 host proteins that bind the SARS-CoV-2 RNA during active infection. Integration of this data with ChIRP-MS data from three other RNA viruses defined viral specificity of RNA-host protein interactions. Targeted CRISPR screens revealed that the majority of functional RNA-binding proteins protect the host from virus-induced cell death, and comparative CRISPR screens across seven RNA viruses revealed shared and SARS-specific antiviral factors. Finally, by combining the RNA-centric approach and functional CRISPR screens, we demonstrated a physical and functional connection between SARS-CoV-2 and mitochondria, highlighting this organelle as a general platform for antiviral activity. Altogether, these data provide a comprehensive catalog of functional SARS-CoV-2 RNA-host protein interactions, which may inform studies to understand the host-virus interface and nominate host pathways that could be targeted for therapeutic benefit.