Cell Rep . Characterization and functional interrogation of the SARS-CoV-2 RNA interactome

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Cell Rep


. 2022 Apr 26;39(4):110744.
doi: 10.1016/j.celrep.2022.110744.
Characterization and functional interrogation of the SARS-CoV-2 RNA interactome


Athéna Labeau ¹ , Luc Fery-Simonian ¹ , Alain Lefevre-Utile ² , Marie Pourcelot ¹ , Lucie Bonnet-Madin ¹ , Vassili Soumelis ² , Vincent Lotteau ³ , Pierre-Olivier Vidalain ³ , Ali Amara ⁴ , Laurent Meertens ⁵



Affiliations

• PMID: 35477000
• DOI: 10.1016/j.celrep.2022.110744

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic, which has led to a devastating global health crisis. The emergence of variants that escape neutralizing responses emphasizes the urgent need to deepen our understanding of SARS-CoV-2 biology. Using a comprehensive identification of RNA-binding proteins (RBPs) by mass spectrometry (ChIRP-MS) approach, we identify 107 high-confidence cellular factors that interact with the SARS-CoV-2 genome during infection. By systematically knocking down their expression in human lung epithelial cells, we find that the majority of the identified RBPs are SARS-CoV-2 proviral factors. In particular, we show that HNRNPA2B1, ILF3, QKI, and SFPQ interact with the SARS-CoV-2 genome and promote viral RNA amplification. Our study provides valuable resources for future investigations into the mechanisms of SARS-CoV-2 replication and the identification of host-centered antiviral therapies.

Keywords: CP: Microbiology; SARS-CoV-2 RNA interactome; SARS-CoV-2 infection inhibitors; comprehensive identification of RNA binding proteins by mass spectrometry, ChIRP-MS; host RNA binding proteins; host-dependency factors; severe acute respiratory syndrome coronavirus 2; siRNA screen.