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.
Publication types
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Research Support, N.I.H., Extramural
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Research Support, Non-U.S. Gov't
MeSH terms
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Chromosome Mapping
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Chromosomes, Fungal
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DNA-Binding Proteins / genetics
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DNA-Binding Proteins / metabolism
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Gene Deletion
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Gene Expression Regulation, Fungal*
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Histone-Lysine N-Methyltransferase
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Histones / analysis
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Histones / metabolism*
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Methylation
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Models, Genetic
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Proteasome Endopeptidase Complex / genetics
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Proteasome Endopeptidase Complex / metabolism*
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Protein Structure, Tertiary
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Proton-Translocating ATPases / genetics
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Proton-Translocating ATPases / metabolism
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RNA, Messenger / genetics
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RNA, Messenger / metabolism
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Repressor Proteins
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Ribonucleases / genetics
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Ribonucleases / metabolism*
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Saccharomyces cerevisiae / genetics
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Saccharomyces cerevisiae / metabolism
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Saccharomyces cerevisiae Proteins / genetics
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Saccharomyces cerevisiae Proteins / metabolism*
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Transcription Factors / genetics
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Transcription Factors / metabolism
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Ubiquitin-Conjugating Enzymes / genetics
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Ubiquitin-Conjugating Enzymes / metabolism
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Ubiquitin-Protein Ligases / chemistry
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Ubiquitin-Protein Ligases / genetics
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Ubiquitin-Protein Ligases / metabolism*
Substances
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DNA-Binding Proteins
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Histones
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RNA, Messenger
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Repressor Proteins
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Saccharomyces cerevisiae Proteins
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Transcription Factors
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Histone-Lysine N-Methyltransferase
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SET1 protein, S cerevisiae
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Ubc4 protein, S cerevisiae
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Ubiquitin-Conjugating Enzymes
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MOT2 protein, S cerevisiae
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Ubiquitin-Protein Ligases
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CCR4 protein, S cerevisiae
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Ribonucleases
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Proteasome Endopeptidase Complex
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PMA1 protein, S cerevisiae
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Proton-Translocating ATPases