Protein Interactions within the Set1 Complex and Their Roles in the Regulation of Histone 3 Lysine 4 Methylation

Abstract

Set1 is the catalytic subunit and the central component of the evolutionarily conserved Set1 complex (Set1C) that methylates histone 3 lysine 4 (H3K4). Here we have determined protein/protein interactions within the complex and related the substructure to function. The loss of individual Set1C subunits differentially affects Set1 stability, complex integrity, global H3K4 methylation, and distribution of H3K4 methylation along active genes. The complex requires Set1, Swd1, and Swd3 for integrity, and Set1 amount is greatly reduced in the absence of the Swd1-Swd3 heterodimer. Bre2 and Sdc1 also form a heteromeric subunit, which requires the SET domain for interaction with the complex, and Sdc1 strongly interacts with itself. Inactivation of either Bre2 or Sdc1 has very similar effects. Neither is required for complex integrity, and their removal results in an increase of H3K4 mono-and dimethylation and a severe decrease of trimethylation at the 5 end of active coding regions but a decrease of H3K4 dimethylation at the 3 end of coding regions. Cells lacking Spp1 have a reduced amount of Set1 and retain a fraction of trimethylated H3K4, whereas cells lacking Shg1 show slightly elevated levels of both di-and trimethylation. Set1C associates with both serine 5-and serine 2-phosphorylated forms of polymerase II, indicating that the association persists to the 3 end of transcribed genes. Taken together, our results suggest that Set1C subunits stimulate Set1 catalytic activity all along active genes.

The N-terminus of histone H3 is required for de novo DNA methylation in chromatin

“…The two proteins were therefore expressed in strains deleted for individual components of the COMPASS complex, the yeast analogue of mammalian MLL complex that catalyzes H3K4 methylation. The integrity and stability of COMPASS complex requires the heterodimer of Swd1/Swd3 (WD40 repeat protein), the catalytic subunit Set1, and the plant homeodomain finger protein Spp1 (18). As expected, deletion of SET1, SWD1, and SWD3 abolished mono-, di-, and trimethylation at H3K4, whereas deletion of SPP1 had no effect except for a decrease in trimethylation (Fig.…”

A phosphorylation switch on RbBP5 regulates histone H3 Lys4 methylation

“…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.Our molecular understanding of the protein complexes involved in H3K4 methylation stems from the isolation of COMPASS from Saccharomyces cerevisiae (Miller et al 2001;Roguev et al 2001;Krogan et al 2002;Dehe et al 2006). These studies demonstrated that regulatory subunits found within COMPASS and mammalian COMPASS-like complexes play key roles in stabilizing the enzyme and stimulating its methyltransferase activity as well as targeting the protein complex to specific genomic loci (Couture and Skiniotis 2013).…”

“…Our molecular understanding of the protein complexes involved in H3K4 methylation stems from the isolation of COMPASS from Saccharomyces cerevisiae (Miller et al 2001;Roguev et al 2001;Krogan et al 2002;Dehe et al 2006). These studies demonstrated that regulatory subunits found within COMPASS and mammalian COMPASS-like complexes play key roles in stabilizing the enzyme and stimulating its methyltransferase activity as well as targeting the protein complex to specific genomic loci (Couture and Skiniotis 2013).…”

Assembling a COMPASS

“…Using a TAP-tagging approach in combination with strains harboring genetic deletion of COMPASS components, Roguev et al determined that Cps30 and Cps50 remained bound upon deletion of S. cerevisiae (Sc) SET1 but lost interaction with the other COMPASS subunits, suggesting that these two β-propeller domain containing proteins formed a heterodimer. 8 Subsequent studies confirmed that this heterodimer was critical for maintaining global levels of H3K4 mono-di-and trimethylation in vivo, 24,[29][30][31] demonstrating the importance of the global organization of the ScSET1 complex for its function. Similar to the Cps30-Cps50 heterodimer, deletion of ScSET1 resulted in the dissociation of a Cps60-Cps25 heterodimer, 8 thus supporting previous genome wide yeast two-hybrid studies showing that Cps60 and Cps25 stably associated in budding yeast.…”

“…This is exemplified by the deletion of Cps50 and Cps30 which decreases the overall level of ScSET1. 2,29,31,37 To tackle these problems, in vitro reconstitution of protein complexes with purified components from a homologous or heterologous system, such as baculovirus-infected insect cells, have proven to be well-suited approaches.…”