Histone H3 lysine 4 monomethylation (H3K4me1) is an evolutionarily conserved feature of enhancer chromatin catalyzed by the Trr/MLL3/4-COMPASS family1–3. Here we demonstrate that Drosophila embryos expressing catalytically deficient Trr-COMPASS eclose and develop to a productive adulthood. Parallel experiments with a Trr allele that augments enzyme product specificity reveal that conversion of H3K4me1 at enhancers to H3K4me2 and H3K4me3 is also compatible with life and results in minimal changes in gene expression. Similarly, loss of mammalian MLL3 and MLL4 catalytic SET domain in embryonic stem cells does not disrupt self-renewal capability of the ES cells. Trr catalytic mutant alleles manifest subtle developmental phenotypes when subjected to temperature stress or altered cohesin levels. Collectively, our findings suggest that metazoan development can occur in the context of Trr/COMPASS with H3K4me1 enzymatic deficiency, and points to a possible role for H3K4me1 on cis-regulatory elements in specific settings to fine-tune transcriptional regulation in response to environmental stress.

MLL3 (also named KMT2C) is a COMPASS subunit that implements H3K4 mono-methylation at gene enhancers. KMT2C frequently incurs point-mutations across a range of human tumors, nevertheless precisely how these lesions alter MLL3 function and contribute to oncogenesis is unclear. Here we report a cancer mutational hotspot in MLL3 within its Plant Homeo Domain (PHD) repeats and demonstrate that this domain mediates association with the histone H2A deubiquitinase and tumor suppressor BAP1. Cancer-associated MLL3 PHD mutations disrupt the interaction between MLL3 and BAP1 and correlate with poor patient survival. Cancer cells bearing MLL3 PHD mutations or lacking BAP1, exhibit reduced enhancer recruitment of MLL3 and the H3K27 demethylase UTX (KDM6A). As the result, inhibiting the H3K27 methyltransferase activity of polycomb repressor complex 2 (PRC2) in tumor cells harboring BAP1 or MLL3 mutations, restores normal gene expression patterns and impairs cell proliferation in vivo. This study provides mechanistic insight for the role of MLL3 PHD mutations in cancer and points to restoration of the balanced state of polycomb-COMPASS for the treatment of cancers resulting from mutations in these epigenetic factors.

assisted with the initial computational analyses. H.Z. helped with the mouse in vivo experiment. K.J. assisted with patient selection. P.R. performed the nested control study, and assisted with patient sample procurement and survival analyses. P.R. and C.S. also performed the patient clinical annotation. J.S.R. viewed the FFPE slides, performed the laser microdissection and provided intellectual support. C.K. supervised the SWI/SNF complex ChIP-seq, helped with the SWI/SNF complex ChIP-seq data interpretation and provided intellectual insights.