Molecular mechanisms of the MLL4 complex in H3K4 methylation and p53-dependent transcription activation

Mammalian H3K4 mono-methyltransferase MLL4 plays a critical role in enhancer-mediated gene activation. Here, we utilized a reconstituted MLL4 “fusion” complex (MLL4^FC) for structural and functional analyses and revealed that MLL4 function is regulated by three structurally rigid modules, namely, SET-ASH2L-DPY30, RBBP5-WDR5, and PHD-FYR. Notably, the PHD-FYR module is evolutionarily conserved across MLL1-4 and is essential for MLL4- and p53-dependent transcription. Combining results from cryo-EM and crosslinking mass spectrometry, we obtained a complete model of MLL4^FC and elucidated its functional interactions with p53. Genomic analyses in HCT116 cells further showed that MLL4 colocalizes with p53 at p53 target genes and that MLL4 knockout results in a marked reduction in the expression of p53-regulated genes, accompanied by reduced p53 chromatin occupancy. These findings provide molecular insights into the catalytic and non-catalytic transcriptional functions of the MLL4 complex in establishing active enhancers and facilitating p53-dependent transcription activation.