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

Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 05/2007; 104(14):5836-41. DOI: 10.1073/pnas.0607996104
Source: PubMed


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.

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Available from: R. Nicholas Laribee, Oct 04, 2015
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    • "Whole-cell extracts (WCE) were prepared and coimmunoprecipitations were performed as previously described using 750 µg of WCE (35). ChIP experiments were performed as described (35) with minor modifications. "
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    ABSTRACT: Epigenetic changes in chromatin through histone post-translational modifications are essential for altering gene transcription in response to environmental cues. How histone modifications are regulated by environmental stimuli remains poorly understood yet this process is critical for delineating how epigenetic pathways are influenced by the cellular environment. We have used the target of rapamycin (TOR) pathway, which transmits environmental nutrient signals to control cell growth, as a model to delineate mechanisms underlying this phenomenon. A chemical genomics screen using the TOR inhibitor rapamycin against a histone H3/H4 mutant library identified histone H3 lysine 56 acetylation (H3K56ac) as a chromatin modification regulated by TOR signaling. We demonstrate this acetylation pathway functions in TOR-dependent cell growth in part by contributing directly to ribosomal RNA (rRNA) biogenesis. Specifically, H3K56ac creates a chromatin environment permissive to RNA polymerase I transcription and nascent rRNA processing by regulating binding of the high mobility group protein Hmo1 and the small ribosomal subunit (SSU) processome complex. Overall, these studies identify a novel chromatin regulatory role for TOR signaling and support a specific function for H3K56ac in ribosomal DNA (rDNA) gene transcription and nascent rRNA processing essential for cell growth.
    Nucleic Acids Research 05/2012; 40(14):6534-46. DOI:10.1093/nar/gks345 · 9.11 Impact Factor
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    • "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., 2008, 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). "
    03/2012; 2(1):88-93. DOI:10.5147/ajb.2012.0063
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    • "binds to oestrogen receptor and thereby represses ligand-dependent transcriptional activation (31). In addition, studies in Saccharomyces cerevisiae showed that the Not subunits and Not4, in particular, are required to maintain normal levels of histone methylation (32,33). As for the cytoplasmic function of the Ccr4–Not complex, early studies in yeast identified Ccr4 and Caf1 (also termed Pop2) as major cytoplasmic deadenylases (34,35). "
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    ABSTRACT: The carbon catabolite repressor protein 4 (Ccr4)-Negative on TATA (Not) complex controls gene expression at two levels. In the nucleus, it regulates the basal transcription machinery, nuclear receptor-mediated transcription and histone modifications. In the cytoplasm, the complex is required for messenger RNA (mRNA) turnover through its two associated deadenylases, Ccr4 and Caf1. Not1 is the largest protein of the Ccr4-Not complex and serves as a scaffold for other subunits of the complex. Here, we provide evidence that human Not1 in the cytoplasm associates with the C-terminal domain of tristetraprolin (TTP), an RNA binding protein that mediates rapid degradation of mRNAs containing AU-rich elements (AREs). Not1 shows extensive interaction through its central region with TTP, whereas binding of Caf1 is restricted to a smaller central domain within Not1. Importantly, Not1 is required for the rapid decay of ARE-mRNAs, and TTP can recruit the Caf1 deadenylase only in presence of Not1. Thus, cytoplasmic Not1 provides a platform that allows a specific RNA binding protein to recruit the Caf1 deadenylase and thereby trigger decay of its target mRNAs.
    Nucleic Acids Research 05/2011; 39(10):4373-86. DOI:10.1093/nar/gkr011 · 9.11 Impact Factor
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