A trithorax-group complex purified from Saccharomyces cerevisiae is required for methylation of histone H3

Abstract

Histone methylation has emerged as an important mechanism for regulating the transcriptional accessibility of chromatin. Several methyltransferases have been shown to target histone aminoterminal tails and mark nucleosomes associated with either euchromatic or heterochromatic states. However, the biochemical machinery responsible for regulating histone methylation and integrating it with other cellular events has not been well characterized. We report here the purification, molecular identification, and genetic and biochemical characterization of the Set1 protein complex that is necessary for methylation of histone H3 at lysine residue 4 in Saccharomyces cerevisiae. The seven-member 363-kDa complex contains homologs of Drosophila melanogaster proteins Ash2 and Trithorax and Caenorhabditis elegans protein DPY-30, which are implicated in the maintenance of Hox gene expression and regulation of X chromosome dosage compensation, respectively. Mutations of Set1 protein comparable to those that disrupt developmental function of its Drosophila homolog Trithorax abrogate histone methylation in yeast. These studies suggest that epigenetic regulation of developmental and sex-specific gene expression are species-specific readouts for a common chromatin remodeling machinery associated mechanistically with histone methylation.C ovalent modification of histone amino-terminal tails regulates access to the underlying DNA and thus serves an important role in fine tuning gene expression (1). Histone modifications such as acetylation and phosphorylation facilitate transitions between chromatin states that are permissive or restrictive for transcription (2). More recently, histone methylation has emerged as an additional modification for recruitment of chromatin-associated proteins that determine transcriptional accessibility of genes. Several methyltransferases have been shown to target histone amino-terminal tails and mark nucleosomes associated with either euchromatic or heterochromatic states (3-5).A subset of methyltransferases contains a highly conserved motif known as the SET domain. This motif was originally discovered in Drosophila proteins Su(var)3-9, Enhancer-of-zeste and Trithorax, which are involved in variegated or developmental gene expression (6). Although a functional role for the SET domain was not immediately evident, limited homology with plant methyltransferases prompted the discovery that Su(var)3-9 and its Schizosaccharomyces pombe homolog CLR4 are capable of transferring a methyl group onto Lys-9 of histone H3 (2). This methyl tag has subsequently been shown to mark nucleosomes that are associated with transcriptionally silenced genes in the Sch. pombe mating type locus (7), and the association of Su-(var)3-9 homologs with the Rb corepressor complex suggests that Lys-9 methylation may also play a role in transcriptional repression of euchromatic genes (8).Human SET domain-containing proteins such as MLL, a homolog of Drosophila Trithorax, NSD2, and NSD3 are essential for normal development and are also direc...

MLL: How complex does it get?

“…RBBP5 and WDR5, along with ASH2L, interact with the SET domain of MLL. This binding is also observed in other Set1 complexes and is required for the histone methyltranferase activity [Nagy et al, 2002]. It is of interest that a close MLL homolog, MLL2, was also shown to interact with ASH2L, RBBP5, and WDR5.…”

“…The Set1 protein contains a SET domain, which is highly homologous to the SET domain of MLL. Interestingly, just like the MLL protein, the Set1 complex was shown to methylate lysine 4 on histone H3 [Nagy et al, 2002]. This purified MLL complex is able to perform chromatin remodeling, histone methylation, acetylation, and deacetylation suggesting that all the associated proteins retain their enzymatic activities [Nakamura et al, 2002].…”

Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation

“…The first H3K4 methylase complex, COMPASS, was identified in the yeast S. cerevisiae and consists of Set1/KMT2 and seven other polypeptides (named Cps60-Cps15) [24]. Set1/KMT2 alone is not enzymatically active, but functions within COMPASS and is capable of mono-, di-, and trimethylating H3K4 [6,8,10,[24][25][26][27]. Following the identification of Set1/COMPASS as an H3K4 methylase, it was demonstrated that its mammalian homologues, the MLL proteins, MLL1-4 and hSet1A and B, are found in COMPASS-like complexes capable of methylating the fourth lysine of histone H3 [6,28,29] (Figure 2).…”

Matrix Metalloproteinase-9 gene induction by a truncated oncogenic NF-κB2 protein involves the recruitment of MLL1 and MLL2 H3K4 histone methyltransferase complexes

“…Thus, overexpressed p52 and Hut-78 induce MMP9 expression by tethering a H3K4 HMT complex. Whereas one multi-subunit complex (referred to as COMPASS and Set1 complex) that includes the Drosophila trithorax-related protein Set1 has been shown to trigger the mono-, di-and trimethylation of histone H3K4 in yeast (Briggs et al, 2001;Miller et al, 2001;Nagy et al, 2002;Noma and Grewal, 2002), multiple complexes harbouring robust H3K4 HMT activities have been isolated in mammalian cells and all of them contained one or two SET domain-containing homologues of yeast Set1 (Hughes et al, 2004;Glaser et al, 2006). As those distinct Set-1-like human H3K4 HMT complexes also share common subunits such as ASH2L, RBBP5 and WDR5, we determined whether those proteins interact with p52 by coimmunoprecipitation experiments.…”