Patterns of Isoform Variation for N Gene Subgenomic mRNAs in Betacoronavirus Transcriptomes

Area of Science:

• Virology
• Molecular Biology
• Genomics

Background:

• The nucleocapsid (N) protein is highly expressed in SARS-CoV-2 infection.
• N protein is translated from subgenomic mRNA (sgmRNA) via template switching.
• A leader sequence translation initiation site (TIS-L) is often out of frame with the N gene.

Purpose of the Study:

• To investigate the isoforms of N sgmRNA produced by SARS-CoV-2.
• To explore the potential regulatory role of these isoforms in N protein production.
• To compare N sgmRNA production mechanisms across different coronaviruses.

Main Methods:

• Analysis of multiple sequenced samples infected by SARS-CoV-2.
• Comparative analysis of sequenced samples from other coronavirus infections (SARS-CoV, OC43, MERS-CoV).
• Examination of junction breakpoint positions relative to the 5'-UTR stem loop 3.

Main Results:

• SARS-CoV-2 produces multiple N sgmRNA isoforms from a single variant.
• A dominant TIS-L isoform is out of frame, but two secondary isoforms restore the reading frame.
• Similar out-of-frame and in-frame isoforms are found in SARS-CoV, OC43, and SARS-CoV transcriptomes.
• Evidence suggests conserved mechanisms for N sgmRNA production in some coronaviruses.

Conclusions:

• The identified N sgmRNA isoforms likely play a role in regulating N protein production.
• Conserved mechanisms for N sgmRNA isoform generation exist across related coronaviruses.
• These findings may inform the development of antisense-based antiviral strategies.