Caenorhabditis elegans chromatin-associated proteins SET-2 and ASH-2 are differentially required for histone H3 Lys 4 methylation in embryos and adult germ cells

Abstract

Methylation of histone H3 lysine 4 (H3K4me), a mark associated with gene activation, is mediated by SET1 and the related mixed lineage leukemia (MLL) histone methyltransferases (HMTs) across species. Mammals contain seven H3K4 HMTs, Set1A, Set1B, and MLL1-MLL5. The activity of SET1 and MLL proteins relies on protein-protein interactions within large multisubunit complexes that include three core components: RbBP5, Ash2L, and WDR5. It remains unclear how the composition and specificity of these complexes varies between cell types and during development. Caenorhabditis elegans contains one SET1 protein, SET-2, one MLL-like protein, SET-16, and single homologs of RbBP5, Ash2L, and WDR5. Here we show that SET-2 is responsible for the majority of bulk H3K4 methylation at all developmental stages. However, SET-2 and absent, small, or homeotic discs 2 (ASH-2) are differentially required for tri-and dimethylation of H3K4 (H3K4me3 and -me2) in embryos and adult germ cells. In embryos, whereas efficient H3K4me3 requires both SET-2 and ASH-2, H3K4me2 relies mostly on ASH-2. In adult germ cells by contrast, SET-2 serves a major role whereas ASH-2 is dispensable for H3K4me3 and most H3K4me2. Loss of SET-2 results in progressive sterility over several generations, suggesting an important function in the maintenance of a functional germ line. This study demonstrates that individual subunits of SET1-related complexes can show tissue specificity and developmental regulation and establishes C. elegans as a model to study SET1-related complexes in a multicellular organism.chromatin | epigenetics | mortal germ line H istone H3 lysine 4 (H3K4) methylation and the proteins involved in its implementation are evolutionarily conserved marks of active and potentially active genes in all eukaryotes examined (1, 2). In yeast, Set1 is found in a multiprotein complex known as COMPASS, which is solely responsible for all histone H3K4 methylation (3-5). In mammalian cells, seven family members have been characterized: SET1a and SET1b (orthologs of yeast Set1) (6) and five mixed lineage leukemia (MLL) family members, MLL1-5, that share only limited similarity with yeast Set1 beyond the SET domain (7-11). Human SET1a/SET1b mediate the bulk of H3K4 trimethylation (H3K4me3) in mammalian cell extracts (12). Members of the MLL family of proteins do not appear to contribute significantly to bulk changes in H3K4 methylation, but serve both unique and overlapping tissue-and developmental stage-specific functions. Loss of either MLL1 or MLL2 results in embryonic lethality in mice (13, 14), whereas MLL3, -4, and -5 gene knockout mice are viable but have distinct developmental defects (15-18). Caenorhabditis elegans contains one SET1 protein, SET-2, and one MLL-like protein, 20). Whereas both SET-2 and SET-16 are required for global H3K4 methylation, SET-2 plays a predominant role (19-21).The enzymatic activity of SET1/MLL family members is regulated by interactions with a number of other proteins, including Swd3/WDR5, Swd1/RbBP5, Bre2/Ash2, and Sdc1/hDPY...

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