Distinct pathways utilized by METTL3 to regulate antiviral innate immune response

Methyltransferase-like 3 (METTL3), the core methyltransferase for N ⁶-methyladenosine (m6A), plays a crucial role in innate immunity by introducing m6A modifications on viral or host RNAs. Despite its well-established catalytic function in m6A deposition, the broader role of METTL3 in immune regulation remains unclear. Here, we uncovered that EV71 infection enhanced METTL3 expression in interferon (IFN)-deficient Vero and IFN-proficient rhabdomyosarcoma (RD) cells by modulating transcription and post-translational modification, respectively. METTL3 was shown to regulate antiviral immune responses in both m6A-dependent and -independent manners. METTL3's catalytic motif impaired viral RNA recognition by retinoic-acid-inducible gene I (RIG-I) via m6A modification, whereas its non-catalytic motif recruited and stabilized DEAD-box helicase 3X (DDX3X) by preventing DDX3X ubiquitination, which all mediate immune inhibition. This study reveals an m6A-independent pathway through which METTL3 regulates immune responses, highlighting its potential as a target for antiviral therapy.