Abstract
Methylation of lysine 4 on histone H3 (H3K4) at promoters is tightly linked to transcriptional regulation in human cells. At least six different COMPASS-like multisubunit (SET1/MLL) complexes that contain methyltransferase activity for H3K4 have been described, but a comprehensive and quantitative analysis of these SET1/MLL complexes is lacking. We applied label-free quantitative mass spectrometry to determine the subunit composition and stoichiometry of the human SET1/MLL complexes. We identified both known and novel, unique and shared interactors and determined their distribution and stoichiometry over the different SET1/MLL complexes. In addition to being a core COMPASS subunit, the Dpy30 protein is a genuine subunit of the NURF chromatin remodeling complex. Furthermore, we identified the Bod1 protein as a discriminator between the SET1B and SET1A complexes, and we show that the H3K36me-interactor Psip1 preferentially binds to the MLL2 complex. Finally, absolute protein quantification in crude lysates mirrors many of the observed SET1/MLL complex stoichiometries. Our findings provide a molecular framework for understanding the diversity and abundance of the different SET1/MLL complexes, which together establish the H3K4 methylation landscape in human cells.
Publication types
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Research Support, Non-U.S. Gov't
MeSH terms
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Adaptor Proteins, Signal Transducing / isolation & purification
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Adaptor Proteins, Signal Transducing / metabolism
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Cell Cycle Proteins / isolation & purification
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Cell Cycle Proteins / metabolism
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Cell Nucleus / metabolism
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Chromatography, Affinity
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DNA-Binding Proteins / isolation & purification
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DNA-Binding Proteins / metabolism*
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HeLa Cells
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Histone-Lysine N-Methyltransferase / isolation & purification
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Histone-Lysine N-Methyltransferase / metabolism*
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Humans
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Intracellular Signaling Peptides and Proteins
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Myeloid-Lymphoid Leukemia Protein / isolation & purification
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Myeloid-Lymphoid Leukemia Protein / metabolism
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Neoplasm Proteins / isolation & purification
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Neoplasm Proteins / metabolism*
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Nuclear Proteins / isolation & purification
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Nuclear Proteins / metabolism
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Protein Interaction Mapping
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Protein Subunits / isolation & purification
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Protein Subunits / metabolism*
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Proto-Oncogene Proteins / isolation & purification
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Proto-Oncogene Proteins / metabolism
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Transcription Factors / isolation & purification
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Transcription Factors / metabolism
Substances
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ASH2L protein, human
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Adaptor Proteins, Signal Transducing
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Bod1 protein, human
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Cell Cycle Proteins
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DNA-Binding Proteins
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DPY30 protein, human
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Intracellular Signaling Peptides and Proteins
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KMT2A protein, human
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KMT2C protein, human
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KMT2D protein, human
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MEN1 protein, human
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Neoplasm Proteins
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Nuclear Proteins
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PSIP1 protein, human
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Protein Subunits
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Proto-Oncogene Proteins
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RBBP5 protein, human
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Transcription Factors
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WDR5 protein, human
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Myeloid-Lymphoid Leukemia Protein
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Histone-Lysine N-Methyltransferase
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MLL4 protein, human
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Setd1A protein, human