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H3K27-me3 Inhibition Induces YTHDF2-Mediated Decay of m6A-Marked Severe Acute Respiratory Syndrome Coronavirus 2

Ram Kumar¹, Assim Verma¹, Himanshu Kamboj¹

¹National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India.

Journal of Medical Virology

|April 4, 2025

Abstract:

Emerging evidence highlights the role of epigenetic modification in virus infection. In this study, inhibition of H3K27-methylation (H3K27-me3) by UNC1999 (H3K27-methyltransferase inhibitor) was demonstrated to inhibit SARS-CoV-2 replication, as evidenced by reduced levels of viral RNA/protein. The m6A modifications of SARS-CoV-2 RNA were predominantly present on the 3' end, particularly the "N" gene. The methylated RNA immunoprecipitation (MeRIP) and western-blot analysis revealed a negative correlation between levels of cellular H3K27-me3 and m6A-modifications on the SARS-CoV-2 "N" gene. Moreover, m6A-modifications of the SARS-CoV-2 "N" gene were shown to promote the recruitment of YTHDF2, which eventually resulted in decay of the viral transcripts. The application of the H3K27-demethyltransferase or KDM6A/B inhibitor GSK-J4 can restore H3K27-me3 levels and mitigating the decay of viral mRNA in UNC1999-treated SARS-CoV-2-infected cells. Furthermore, long-term sequential passage (P = 50) of the virus in the presence of UNC1999 did not yield any UNC1999-resistant SARS-CoV-2 mutants. In conclusion, by integrating transcriptomics, molecular virology and functional analyses, we for the first time demonstrated that inhibition of H3K27-me3 induces m6A-mediated decay of SARS-CoV-2 transcripts, highlighting UNC1999 as novel antiviral candidate against SARS-CoV-2.

Insights

Inhibition of H3K27-methylation using UNC1999 reduces SARS-CoV-2 replication by promoting m6A-mediated RNA decay. This epigenetic strategy did not lead to resistant virus mutants, suggesting UNC1999 as a potential antiviral treatment.

Area of Science:

Epigenetics
Virology
Molecular Biology

Background:

Epigenetic modifications play a crucial role in viral infections.
Understanding these modifications can reveal novel therapeutic targets for antiviral strategies.

Purpose of the Study:

To investigate the effect of inhibiting H3K27-methylation on SARS-CoV-2 replication.
To explore the role of m6A RNA modification in SARS-CoV-2 transcript stability.
To identify potential antiviral agents targeting epigenetic pathways.

Main Methods:

Utilized UNC1999, an H3K27-methyltransferase inhibitor, to study SARS-CoV-2 replication.
Employed methylated RNA immunoprecipitation (MeRIP) and western-blot analysis to assess RNA modifications.
Performed long-term sequential passage to evaluate for viral resistance.

Main Results:

Inhibition of H3K27-methylation by UNC1999 significantly reduced SARS-CoV-2 RNA and protein levels.
SARS-CoV-2 RNA, particularly the "N" gene, showed predominant m6A modifications.
A negative correlation was observed between cellular H3K27-me3 levels and m6A modifications on the viral "N" gene.
m6A modification promoted YTHDF2 recruitment, leading to viral transcript decay.
GSK-J4, an H3K27-demethyltransferase inhibitor, restored H3K27-me3 levels and mitigated viral mRNA decay.
No UNC1999-resistant SARS-CoV-2 mutants were observed after 50 passages.

Conclusions:

Inhibition of H3K27-methylation induces m6A-mediated decay of SARS-CoV-2 transcripts.
UNC1999 demonstrates potential as a novel antiviral candidate against SARS-CoV-2.
The findings highlight the interplay between H3K27-methylation and m6A modification in controlling viral replication.

Read full analysis

Keywords:

GSK‐J4 H3K27‐me3 SARS‐CoV‐2 UNC1999 m6A stability viral transcript

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