title: Quantitative dissection and stoichiometry determination of the human SET1/MLL histone methyltransferase complexes.
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.
authors.affiliation: Molecular Cancer Research, Netherlands Proteomics Center, Utrecht, The Netherlands.
authors.forename: Rick
authors.initials: R
authors.lastname: van Nuland
authors.forename: Arne H
authors.initials: AH
authors.lastname: Smits
authors.forename: Paschalina
authors.initials: P
authors.lastname: Pallaki
authors.forename: Pascal W T C
authors.initials: PW
authors.lastname: Jansen
authors.forename: Michiel
authors.initials: M
authors.lastname: Vermeulen
authors.forename: H T Marc
authors.initials: HT
authors.lastname: Timmers
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000302:isolation & purification / Q000378:metabolism; D018797:Cell Cycle Proteins / Q000302:isolation & purification / Q000378:metabolism; D002467:Cell Nucleus / Q000378:metabolism; D002846:Chromatography, Affinity; D004268:DNA-Binding Proteins / Q000302:isolation & purification / Q000378:metabolism*; D006367:HeLa Cells; D011495:Histone-Lysine N-Methyltransferase / Q000302:isolation & purification / Q000378:metabolism*; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins; D051788:Myeloid-Lymphoid Leukemia Protein / Q000302:isolation & purification / Q000378:metabolism; D009363:Neoplasm Proteins / Q000302:isolation & purification / Q000378:metabolism*; D009687:Nuclear Proteins / Q000302:isolation & purification / Q000378:metabolism; D025941:Protein Interaction Mapping; D021122:Protein Subunits / Q000302:isolation & purification / Q000378:metabolism*; D011518:Proto-Oncogene Proteins / Q000302:isolation & purification / Q000378:metabolism; D014157:Transcription Factors / Q000302:isolation & purification / Q000378:metabolism
chemical_list: C485622:ASH2L protein, human; D048868:Adaptor Proteins, Signal Transducing; C524692:Bod1 protein, human; D018797:Cell Cycle Proteins; D004268:DNA-Binding Proteins; C507432:DPY30 protein, human; D047908:Intracellular Signaling Peptides and Proteins; C497422:KMT2A protein, human; C452979:KMT2C protein, human; C120898:KMT2D protein, human; C105373:MEN1 protein, human; D009363:Neoplasm Proteins; D009687:Nuclear Proteins; C504649:PSIP1 protein, human; D021122:Protein Subunits; D011518:Proto-Oncogene Proteins; C470552:RBBP5 protein, human; D014157:Transcription Factors; C502547:WDR5 protein, human; D051788:Myeloid-Lymphoid Leukemia Protein; D011495:Histone-Lysine N-Methyltransferase; C530816:MLL4 protein, human; C526068:Setd1A protein, human