Molecular Mechanisms of the MLL4 Complex in H3K4 Methylation and p53-Dependent Transcription Activation [RNA-seq]

Here, we utilized a reconstituted MLL4 complex (MLL4C) containing a truncated MLL4 “fusion” protein (MLL4F) that retains its catalytic SET domain and N-terminal functional regions for comprehensive structural and functional analyses. In vitro H3K4 methyltransferase assays demonstrated that MLL4 catalytic activity is notably stimulated by p53 and CBP/p300.

Cryo-electron microscopy (cryo-EM) analysis revealed that the MLL4 fusion core complex engages the nucleosome in three major distinct conformational states, providing mechanistic insights into the regulation of MLL4 and other MLL family methyltransferases by two structurally rigid modules: the SET–ASH2L–DPY30 module and the RBBP5–WDR5 module. In addition, we delineated a third structurally rigid module within the functional region upstream of MLL4 SET domain, encompassing the tandem PHD4–6, PHD7, and FYR domains, which is essential for MLL4- and p53-dependent transcription.