CCR4/NOT complex associates with the proteasome and regulates histone methylation

Abstract

The proteasome regulates histone lysine methylation and gene transcription, but how it does so is poorly understood. To better understand this process, we used the epistatic miniarray profile (E-MAP) approach to identify factors that genetically interact with proteasomal subunits. In addition to members of the Set1 complex that mediate histone H3 lysine 4 methylation (H3K4me), we found that deleting members of the CCR4/NOT mRNA processing complex exhibit synthetic phenotypes when combined with proteasome mutants. Further biochemical analyses revealed physical associations between CCR4/NOT and the proteasome in vivo. Consistent with the genetic and biochemical interactions linking CCR4/NOT with proteasome and Set1-mediated methylation, we find that loss of Not4 decreases global and gene-specific H3K4 trimethylation (H3K4me3) and decreases 19S proteasome recruitment to the PMA1 gene. Similar to proteasome regulation of histone methylation, loss of CCR4/NOT members does not affect ubiquitinated H2B. Mapping of Not4 identified the RING finger domain as essential for H3K4me3, suggesting a role for ubiquitin in this process. Consistent with this idea, loss of the Not4-interacting protein Ubc4, a known ubiquitin-conjugating enzyme, decreases H3K4me3. These studies implicate CCR4/NOT in the regulation of H3K4me3 through a ubiquitin-dependent pathway that likely involves the proteasome.

The Ccr4-Pop2-NOT mRNA Deadenylase Contributes to Septin Organization in Saccharomyces cerevisiae

“…The NOT subunits of Ccr4-Pop2-NOT are thought to predominantly function in transcriptional control, affecting transcription initiation and chromatin modification (Collart 2003;Laribee et al 2007;Mulder et al 2007). Therefore, the morphogenesis and septin defects in the not mutants suggest that transcriptional functions of Ccr4-Pop2-NOT also contribute to septin assembly.…”

“…The Not proteins have overlapping, but also separate functional roles from Ccr4-Pop2 and they are thought to predominantly function in transcriptional control (Tucker et al 2002;Collart 2003;Traven et al 2005;Laribee et al 2007;Mulder et al 2007). We wanted to address if the NOT subunits of Ccr4-Pop2-NOT were also required for septin organization and cellular morphogenesis.…”

Intersection of nuclear receptors and the proteasome on the epigenetic landscape

“…The CCR4/NOT mRNA processing complex and 19S proteasome subunits physically interact and loss of the CCR4/NOT complex leads to a loss of proteasome subunit Rpt6 (SUG1) and a decrease in H3-K4 tri-methyl marks [Laribee et al, 2007]. In yeast the 19S seems to set up a ''trans histone tail'' regulatory pathway that modulates histone H3-K9/14 acetylation and H3-K4 methylation, associating the 19S at least with active transcription.…”

“…This is particularly relevant because histone lysine acetylation and methylation play a significant role in NR regulated gene expression and function [Metzger et al, 2005;Mo et al, 2006;Aoyagi and Archer, 2007;Garcia-Bassets et al, 2007;Kinyamu and Archer, 2007;Wang et al, 2007;Wissmann et al, 2007]. These histone modifications are also of special interest because of their established links to the proteasome and gene transcription [Ezhkova and Tansey, 2004;Lee et al, 2005;Kinyamu and Archer, 2007;Laribee et al, 2007].…”

Review of the Rpt3 Genes Encoding Part of the 26S Proteasome Associated with Loci Underlying Disease Resistance in Soybean

“…Thus, 19S ATPases might also function to regulate transcription of other genes contributing to SCN reaction. The 19S ATPases have been shown to play key roles in histone covalent modification in yeast and mammals (Lee et al, 2005;Ezhkova and Tansey, 2004;Laribee et al, 2007;Kinyamu et al, 2008;Koues et al, 2008Koues et al, , 2009. In yeast, inactivation of Rpt6/Sug1 leads to decreased dimethylated histone H3 lysine 4 (H3K4 di-me) and acetylated histone H3 (Lee et al, 2005).…”