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WTAP-VIRMA counteracts dsDNA binding of the m6A writer METTL3-METTL14 complex and maintains N6-adenosine methylation activity Therefore, the RGG of METTL14 helps METTL3-METTL14 bind to nucleic acids and supports the interaction between METTL3-METTL14 and WTAP-VIRMA. Upon addition of the unlabeled WTAP-VIRMA SP 381-1486 sp , ssRNA SB GGACU sb , ssRNA SB UUUUU sb , or dsDNA SB 50 sb to the SP 15 sp N-labeled RGG, a similar set of peaks were found to be perturbed, meaning that WTAP-VIRMA SP 381-1486 sp , dsDNA SB 50 sb , ssRNA SB GGACU sb , and ssRNA SB UUUUU sb interact with the RGG of METTL3-METTL14 via a similar interface, which may lead to their competitive binding to METTL3-METTL14. In METTL3-METTL14, two types of nucleic acid-binding domains were identified[2], including the zinc finger domain (ZFD) in METTL3 and the RGG motif (RGG) in METTL14. [Extracted from the article]

N6-methyldeoxyadenine (6mA) has recently been reported as a prevalent DNA modification in eukaryotes. The Tetrahymena thermophila MTA1 complex consisting of four subunits, namely MTA1, MTA9, p1, and p2, is the first identified eukaryotic 6mA methyltransferase (MTase) complex. Unlike the prokaryotic 6mA MTases which have been biochemically and structurally characterized, the operation mode of the MTA1 complex remains largely elusive. Here, we report the cryogenic electron microscopy structures of the quaternary MTA1 complex in S-adenosyl methionine (SAM)-bound (2.6 Å) and S-adenosyl homocysteine (SAH)-bound (2.8 Å) states. Using an AI-empowered integrative approach based on AlphaFold prediction and chemical cross-linking mass spectrometry, we further modeled a near-complete structure of the quaternary complex. Coupled with biochemical characterization, we revealed that MTA1 serves as the catalytic core, MTA1, MTA9, and p1 likely accommodate the substrate DNA, and p2 may facilitate the stabilization of MTA1. These results together offer insights into the molecular mechanism underpinning methylation by the MTA1 complex and the potential diversification of MTases for N6-adenine methylation. [ABSTRACT FROM AUTHOR]