Direct RNA sequencing reveals m6A modifications and isoform changes in SARS-CoV-2-infected HEK cells

Area of Science:

• Molecular Biology
• Virology
• Genomics
• Epitranscriptomics

Background:

• Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes significant host responses, including changes in RNA transcription and modification.
• Understanding these RNA alterations is vital for deciphering viral pathogenesis and discovering therapeutic strategies.

Purpose of the Study:

• To comprehensively profile the transcriptomic and epitranscriptomic landscape of SARS-CoV-2 infected human cells using direct RNA sequencing.
• To analyze viral and host RNA expression, isoform usage, and N6-methyladenosine (m6A) modifications.

Main Methods:

• Direct RNA sequencing of human HEK-AT cells infected with SARS-CoV-2 at 8 hours post-infection, compared to mock controls.
• Analysis of viral and host transcriptomes, including gene expression, transcript quantification, and m6A modification sites.
• Identification of novel isoforms and transcript switching events.

Main Results:

• SARS-CoV-2 infection led to subgenomic RNA synthesis, with high expression of the N gene.
• Sixteen m6A modification sites were found in the viral genome (ORF1ab and S genes).
• Human cells showed 254 positions with altered m6A rates (119 decreased, 135 increased), with decreased modifications enriched in neurotrophin signaling pathways.
• A novel isoform of HIST1H2BK was significantly upregulated in infected cells.
• 24 significant isoform switches were identified, involving mitochondrial reprogramming and immune pathways.

Conclusions:

• Direct RNA sequencing provides a detailed view of host-virus RNA interactions during SARS-CoV-2 infection.
• The study reveals key insights into viral RNA modifications and host transcriptomic/epitranscriptomic changes.
• Findings highlight potential therapeutic targets and mechanisms underlying SARS-CoV-2 pathogenesis.