Structures and mechanisms of tRNA methylation by METTL1–WDR4

Specific, regulated modification of RNAs is important for proper gene expression 1 , 2 . tRNAs are rich with various chemical modifications that affect their stability and function 3 , 4 . 7-Methylguanosine (m 7 G) at tRNA position 46 is a conserved modification that modulates steady-state tRNA levels to affect cell growth 5 , 6 . The METTL1–WDR4 complex generates m 7 G46 in humans, and dysregulation of METTL1–WDR4 has been linked to brain malformation and multiple cancers 7 – 22 . Here we show how METTL1 and WDR4 cooperate to recognize RNA substrates and catalyse methylation. A crystal structure of METTL1–WDR4 and cryo-electron microscopy structures of METTL1–WDR4–tRNA show that the composite protein surface recognizes the tRNA elbow through shape complementarity. The cryo-electron microscopy structures of METTL1–WDR4–tRNA with S -adenosylmethionine or S -adenosylhomocysteine along with METTL1 crystal structures provide additional insights into the catalytic mechanism by revealing the active site in multiple states. The METTL1 N terminus couples cofactor binding with conformational changes in the tRNA, the catalytic loop and the WDR4 C terminus, acting as the switch to activate m 7 G methylation. Thus, our structural models explain how post-translational modifications of the METTL1 N terminus can regulate methylation. Together, our work elucidates the core and regulatory mechanisms underlying m 7 G modification by METTL1, providing the framework to understand its contribution to biology and disease. Using cryo-electron microscopy, structural and mechanistic insights into how the METTL1–WDR4 complex catalyses methylation of tRNAs are shown.