The MLL3/MLL4 Branches of the COMPASS Family Function as Major Histone H3K4 Monomethylases at Enhancers

Abstract

Histone H3 lysine 4 (H3K4) can be mono-, di-, and trimethylated by members of the COMPASS (complex of proteins associated with Set1) family from Saccharomyces cerevisiae to humans, and these modifications can be found at distinct regions of the genome. Monomethylation of histone H3K4 (H3K4me1) is relatively more enriched at metazoan enhancer regions compared to trimethylated histone H3K4 (H3K4me3), which is enriched at transcription start sites in all eukaryotes. Our recent studies of Drosophila melanogaster demonstrated that the Trithorax-related (Trr) branch of the COMPASS family regulates enhancer activity and is responsible for the implementation of H3K4me1 at these regions. There are six COMPASS family members in mammals, two of which, MLL3 (GeneID 58508) and MLL4 (GeneID 8085), are most closely related to Drosophila Trr. Here, we use chromatin immunoprecipitation-sequencing (ChIP-seq) of this class of COMPASS family members in both human HCT116 cells and mouse embryonic stem cells and find that MLL4 is preferentially found at enhancer regions. MLL3 and MLL4 are frequently mutated in cancer, and indeed, the widely used HCT116 cancer cell line contains inactivating mutations in the MLL3 gene. Using HCT116 cells in which MLL4 has also been knocked out, we demonstrate that MLL3 and MLL4 are major regulators of H3K4me1 in these cells, with the greatest loss of monomethylation at enhancer regions. Moreover, we find a redundant role between Mll3 (GeneID 231051) and Mll4 (GeneID 381022) in enhancer H3K4 monomethylation in mouse embryonic fibroblast (MEF) cells. These findings suggest that mammalian MLL3 and MLL4 function in the regulation of enhancer activity and that mutations of MLL3 and MLL4 that are found in cancers could exert their properties through malfunction of these Trr/MLL3/ MLL4-specific (Trrific) enhancers.

A phosphorylation switch on RbBP5 regulates histone H3 Lys4 methylation

“…These observations are consistent with recent studies showing that COMPASS-like MLL3/ MLL4 complexes predominantly monomethylate H3K4 at enhancer regions and specific promoter regions (Herz et al 2012;Hu et al 2013;Morgan and Shilatifard 2013;Cheng et al 2014). Interestingly, upon incubation of the MLL3 SET domain with the Ash2L/RbBP5 complex reconstituted with RbBP5 phos , peaks corresponding to H3K4me1 and H3K4me2 were observed.…”

“…MLL1/MLL2 di/trimethylate H3K4 (H3K4me2/3) and regulate Hox gene expression during embryonic development (Yu et al 1995;Dou et al 2006). MLL3/MLL4 regulate adipogenesis ) and primarily monomethylate H3K4 (H3K4me1) at both enhancer (Herz et al 2012;Hu et al 2013) and promoter (Cheng et al 2014) regions, while SET1A/B are the primary H3K4 trimethyltransferases (Wu et al 2008). However, despite divergence in catalytic activity and functional roles, enzymes of the KMT2/COMPASS family must assemble into multisubunit complexes to carry out their biological functions.…”

Dynamic Epigenetic Regulation by Menin During Pancreatic Islet Tumor Formation

“…Our finding is consistent with earlier studies demonstrating that in contrast to Set1a and Set1b, the major H3K4 trimethylases in mammalian cells (30), MLL1 and MLL4, the HMTs known to associate with menin, are responsible for H3K4 trimethylation of only a subset of loci (31). Our observations are also in line with studies showing that MLL1 loss decreased H3K4me3 levels in less than 5% of genes in mouse embryonic fibroblasts (MEFs) and that MLL4 knockdown had no impact on overall H3K4me3 levels in mouse embryonic stem cells (31,32). We previously reported that inactivation of Rbp2 could partially rescue the tumor phenotype in Men1-deficient mice (24).…”

Histone Methyltransferase hSETD1A Is a Novel Regulator of Metastasis in Breast Cancer

“…Nevertheless, our group and others have observed both global and local changes in H3K4me3 at promoters of genes with cancer-promoting activity, in cancer cells (14,25,26,53,54). Methylation of H3K4 is primarily catalyzed by TrxG members, with the modification of H3K4me3 chiefly catalyzed by hSETD1A (26,27,(55)(56)(57)(58). Here, we showed increase in both global H3K4me3 and hSETD1A protein levels in cultured breast cancer cell lines (Fig.…”