Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions

Siwy Ling Yang,Xin Ni Lim,Danielle E Anderson,Tong Zhang,Tanu Chawla,Andres Merits,Alexander Lezhava,Jong Ghut Ashley Aw,Su Ying Lim,Lin-Fa Wang,Louis Defalco,Yue Wan,Yu Zhang,Yan Su,Kiat Yee Tan,Roland G Huber

doi:10.1038/s41467-021-25357-1

Abstract

SARS-CoV-2 is a major threat to global health. Here, we investigate the RNA structure and RNA-RNA interactions of wildtype (WT) and a mutant (Δ382) SARS-CoV-2 in cells using Illumina and Nanopore platforms. We identify twelve potentially functional structural elements within the SARS-CoV-2 genome, observe that subgenomic RNAs can form different structures, and that WT and Δ382 virus genomes fold differently. Proximity ligation sequencing identify hundreds of RNA-RNA interactions within the virus genome and between the virus and host RNAs. SARS-CoV-2 genome binds strongly to mitochondrial and small nucleolar RNAs and is extensively 2’-O-methylated. 2’-O-methylation sites are enriched in viral untranslated regions, associated with increased virus pair-wise interactions, and are decreased in host mRNAs upon virus infection, suggesting that the virus sequesters methylation machinery from host RNAs towards its genome. These studies deepen our understanding of the molecular and cellular basis of SARS-CoV-2 pathogenicity and provide a platform for targeted therapy.

Highlights

SARS-CoV-2 is a major threat to global health
We further show that 2’-O-methylation of host RNAs is decreased in SARS-CoV-2 infected cells, and that virus-SNORD27 interaction could serve as a mechanism for SARS-CoV-2 to facilitate host RNA degradation
Biological replicates of SARS-CoV-2 SHAPE-MaP show that the reactivities across replicates are highly reproducible (Supplementary Fig. 1c), cover around 80% of the entire SARS-CoV-2 genome (Fig. 1b), and map to known structures in the 5’ and 3’ untranslated regions (UTRs) as expected (Supplementary Fig. 1d, Supplementary Data 2)

Summary

Introduction

SARS-CoV-2 is a major threat to global health. Here, we investigate the RNA structure and RNA-RNA interactions of wildtype (WT) and a mutant (Δ382) SARS-CoV-2 in cells using Illumina and Nanopore platforms. 2’-O-methylation sites are enriched in viral untranslated regions, associated with increased virus pair-wise interactions, and are decreased in host mRNAs upon virus infection, suggesting that the virus sequesters methylation machinery from host RNAs towards its genome These studies deepen our understanding of the molecular and cellular basis of SARS-CoV-2 pathogenicity and provide a platform for targeted therapy. Coronaviruses (CoVs) are enveloped viruses with positivesense single-stranded RNA genomes They are widespread in animals and can cause mild to severe respiratory or enteric disease in humans[1,2]. RNA replication that, in addition to new genomes, generate numerous subgenomic RNA (sgRNA) species using discontinuous transcription[9] These RNAs, together with the full genome, can interact with host cell proteins and RNAs to regulate virus infection. Like many other RNA viruses such as dengue virus (DENV) and Zika virus (ZIKV), the SARS-CoV-2 genomic

Methods

Results

Conclusion