Structure-function relationship of ASH1L and histone H3K36 and H3K4 methylation

The histone H3K36-specific methyltransferase ASH1L plays a critical role in development and is frequently dysregulated in human diseases, particularly cancer. Here, we report on the biological functions of the C-terminal region of ASH1L encompassing a bromodomain (ASH1L_BD), a plant homeodomain (ASH1L_PHD) finger, and a bromo-adjacent homology (ASH1L_BAH) domain, structurally characterize these domains, describe their mechanisms of action, and explore functional crosstalk between them. We find that ASH1L_PHD recognizes H3K4me2/3, whereas the neighboring ASH1L_BD and ASH1L_BAH have DNA binding activities. The DNA binding function of ASH1L_BAH is a driving force for the association of ASH1L with the linker DNA in the nucleosome, and the large interface with ASH1L_PHD stabilizes the ASH1L_BAH fold, merging two domains into a single module. We show that ASH1L is involved in embryonic stem cell differentiation and co-localizes with H3K4me3 but not with H3K36me2 at transcription start sites of target genes and genome wide, and that the interaction of ASH1L_PHD with H3K4me3 is inhibitory to the H3K36me2-specific catalytic activity of ASH1L. Our findings shed light on the mechanistic details by which the C-terminal domains of ASH1L associate with chromatin and regulate the enzymatic function of ASH1L.