H3.Y discriminates between HIRA and DAXX chaperone complexes and reveals unexpected insights into human DAXX-H3.3-H4 binding and deposition requirements.
Histone chaperones prevent promiscuous histone interactions before chromatin assembly. They guarantee faithful deposition of canonical histones and functionally specialized histone variants into chromatin in a spatial- and temporally-restricted manner. Here, we identify the binding partners of the primate-specific and H3.3-related histone variant H3.Y using several quantitative mass spectrometry approaches, and biochemical and cell biological assays. We find the HIRA, but not the DAXX/ATRX, complex to recognize H3.Y, explaining its presence in transcriptionally active euchromatic regions. Accordingly, H3.Y nucleosomes are enriched in the transcription-promoting FACT complex and depleted of repressive post-translational histone modifications. H3.Y mutational gain-of-function screens reveal an unexpected combinatorial amino acid sequence requirement for histone H3.3 interaction with DAXX but not HIRA, and for H3.3 recruitment to PML nuclear bodies. We demonstrate the importance and necessity of specific H3.3 core and C-terminal amino acids in discriminating between distinct chaperone complexes. Further, chromatin immunoprecipitation sequencing experiments reveal that in contrast to euchromatic HIRA-dependent deposition sites, human DAXX/ATRX-dependent regions of histone H3 variant incorporation are enriched in heterochromatic H3K9me3 and simple repeat sequences. These data demonstrate that H3.Y's unique amino acids allow a functional distinction between HIRA and DAXX binding and its consequent deposition into open chromatin.
Department of Molecular Biology, BioMedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.
Lisa-Maria
LM
Zink
Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway.
Erwan
E
Delbarre
Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany.
H Christian
HC
Eberl
Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany.
Eva C
EC
Keilhauer
Department of Molecular Biology, BioMedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.
Clemens
C
Bönisch
Department of Molecular Biology, BioMedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.
Sebastian
S
Pünzeler
Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany.
Marek
M
Bartkuhn
Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway.
Philippe
P
Collas
Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany.|Center for Integrated Protein Science Munich (CIPSM), 81377 Munich, Germany.
Matthias
M
Mann
Department of Molecular Biology, BioMedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.|Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany.|Center for Integrated Protein Science Munich (CIPSM), 81377 Munich, Germany.
Sandra B
SB
Hake
D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics* / Q000378:metabolism; D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D018797:Cell Cycle Proteins / Q000235:genetics* / Q000378:metabolism; D002461:Cell Line, Transformed; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism; D056970:Co-Repressor Proteins; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D004847:Epithelial Cells / Q000166:cytology / Q000378:metabolism; D006367:HeLa Cells; D006609:High Mobility Group Proteins / Q000235:genetics / Q000378:metabolism; D056488:Histone Chaperones / Q000235:genetics* / Q000378:metabolism; D042421:Histone Code; D006657:Histones / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D059630:Mesenchymal Stem Cells / Q000166:cytology / Q000378:metabolism; D018895:Microsatellite Repeats; D018832:Molecular Chaperones; D009687:Nuclear Proteins / Q000235:genetics* / Q000378:metabolism; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism; D061251:Primary Cell Culture; D011485:Protein Binding; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic; D035602:Transcriptional Elongation Factors / Q000235:genetics / Q000378:metabolism
D048868:Adaptor Proteins, Signal Transducing; D018797:Cell Cycle Proteins; D002843:Chromatin; D056970:Co-Repressor Proteins; C106985:DAXX protein, human; D004268:DNA-Binding Proteins; C086057:HIRA protein, human; D006609:High Mobility Group Proteins; D056488:Histone Chaperones; D006657:Histones; D018832:Molecular Chaperones; D009687:Nuclear Proteins; D009707:Nucleosomes; C073537:SSRP1 protein, human; D014157:Transcription Factors; D035602:Transcriptional Elongation Factors