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

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 3ʹ 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.