Figure 1. Mechanisms of how the m⁶A core enzyme and its associated regulatory protein domains get recruited to or excluded from different target sites.

(A) Structure of the m⁶A enzymatic core complex consisting of methyltransferase METTL3 and the critical adapter protein METTL14. Left panel: domain structure of the METTL3 and METTL14 core enzymes. Middle panel: crystal structure of the METTL3/METTL14 complex (MAC) bound to methyl-donor S-Adenosyl methionine (SAM) (gray). The crystal structure contains the METTL3 MTA-70 methyltransferase domain (pink) and the HM and MTA-70 domains of METTL14 (blue); PDB-ID: 5IL1 (Wang et al, 2016). Right panel: AlphaFold 2 model (Mirdita et al, 2022) of the full-length complex between METTL3 and METTL14. Parts of METTL3 and METTL14 that are also present in the X-ray structure are colored in pink and blue, respectively. The CCCH domains of METTL3 are illustrated in green. (B) Regulatory subunit m⁶A-METTL-associated complex (MACOM). Left panel: domain structures of adapter proteins WTAP, VIRMA, ZC3H13, and HAKAI. Right panel: Cryo-EM structure of the WTAP, VIRMA, and ZC3H13 complex fitted into a low-threshold cryo-EM density map; PDB-ID: 7VF2 (Su et al, 2022). The METTL3/METTL14 X-ray structure (PDB-ID: 5IL1 (Wang et al, 2016)) is fitted into an additional low-threshold density. A potential binding interface for an RNA substrate (black) is illustrated based on protein-RNA crosslinking data from Su et al (2022). The 5′ to 3′ directionality of the RNA is unknown. (C) Model of how the METTL3/METTL14 core enzyme is recruited to mRNA 3′UTRs by VIRMA-meditated interactions with polyadenylation factors CPSF5 and CPSF6; PDB-ID: 5IL1 and 7VF2 (Yue et al, 2018). (D) Model of how METTL3/METTL14 is recruited to DRACH motifs on Xist lncRNA, mediated by RBM15 binding to U-rich stretches; PDB-ID: 5IL1 and 7VF2 (Patil et al, 2016). (E) Model of the exclusion-based mechanism whereby the m⁶A methylation complex cannot bind if the EJC occludes sites; PDB-ID: 5IL1 and 7VF2 (He et al, 2023; Uzonyi et al, 2023). ChimeraX version 1.6 was used for the visualization of experimental and predicted structures (Goddard et al, 2018; Pettersen et al, 2021). Panel (B) was adapted from Su et al (2022) under the Creative Commons CC By license (license: https://creativecommons.org/licenses/by/4.0/).