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Khazaei S, Chen CCL, Andrade AF, Kabir N, Azarafshar P, Morcos SM, França JA, Lopes M, Lund PJ, Danieau G, Worme S, Adnani L, Nzirorera N, Chen X, Yogarajah G, Russo C, Zeinieh M, Wong CJ, Bryant L, Hébert S, Tong B, Sihota TS, Faury D, Puligandla E, Jawhar W, Sandy V, Cowan M, Nakada EM, Jerome-Majewska LA, Ellezam B, Gomes CC, Denecke J, Lessel D, McDonald MT, Pizoli CE, Taylor K, Cocanougher BT, Bhoj EJ, Gingras AC, Garcia BA, Lu C, Campos EI, Kleinman CL, Garzia L, Jabado N. Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration. Cell 2023; 186:1162-1178.e20. [PMID: 36931244 PMCID: PMC10112048 DOI: 10.1016/j.cell.2023.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 11/04/2022] [Accepted: 02/16/2023] [Indexed: 03/18/2023]
Abstract
Germline histone H3.3 amino acid substitutions, including H3.3G34R/V, cause severe neurodevelopmental syndromes. To understand how these mutations impact brain development, we generated H3.3G34R/V/W knock-in mice and identified strikingly distinct developmental defects for each mutation. H3.3G34R-mutants exhibited progressive microcephaly and neurodegeneration, with abnormal accumulation of disease-associated microglia and concurrent neuronal depletion. G34R severely decreased H3K36me2 on the mutant H3.3 tail, impairing recruitment of DNA methyltransferase DNMT3A and its redistribution on chromatin. These changes were concurrent with sustained expression of complement and other innate immune genes possibly through loss of non-CG (CH) methylation and silencing of neuronal gene promoters through aberrant CG methylation. Complement expression in G34R brains may lead to neuroinflammation possibly accounting for progressive neurodegeneration. Our study reveals that H3.3G34-substitutions have differential impact on the epigenome, which underlie the diverse phenotypes observed, and uncovers potential roles for H3K36me2 and DNMT3A-dependent CH-methylation in modulating synaptic pruning and neuroinflammation in post-natal brains.
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Affiliation(s)
- Sima Khazaei
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Carol C L Chen
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | | | - Nisha Kabir
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Pariya Azarafshar
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Shahir M Morcos
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Josiane Alves França
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Mariana Lopes
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Peder J Lund
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Geoffroy Danieau
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Orthopedic Surgery, Faculty of Surgery, McGill University, Montreal, QC H3G 1A4, Canada
| | - Samantha Worme
- Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Lata Adnani
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Nadine Nzirorera
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA; Marine College, Shandong University, Weihai 264209, China
| | - Gayathri Yogarajah
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Department of Biochemistry and Molecular Medicine, Université de Montreal, Research Center of the CHU Sainte-Justine, Montreal, QC H3T 1C5, Canada
| | - Caterina Russo
- Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Michele Zeinieh
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Cassandra J Wong
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Laura Bryant
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Steven Hébert
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Bethany Tong
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada
| | - Tianna S Sihota
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Damien Faury
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Evan Puligandla
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Wajih Jawhar
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Child Health and Human Development, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
| | - Veronica Sandy
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Mitra Cowan
- McGill Integrated Core for Animal Modeling (MICAM), McGill University, Montreal, QC, Canada
| | - Emily M Nakada
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Loydie A Jerome-Majewska
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Benjamin Ellezam
- Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Carolina Cavalieri Gomes
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Eppendorf, Hamburg, Germany
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Institute of Human Genetics, University Hospital of the Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Marie T McDonald
- Division of Medical Genetics, Duke University Hospital, Durham, NC, USA
| | - Carolyn E Pizoli
- Division of Pediatric Neurology, Duke University Hospital, Durham, NC, USA
| | - Kathryn Taylor
- Division of Medical Genetics, Duke University Hospital, Durham, NC, USA
| | | | | | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Eric I Campos
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Livia Garzia
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Orthopedic Surgery, Faculty of Surgery, McGill University, Montreal, QC H3G 1A4, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada.
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Siddaway R, Milos S, Coyaud É, Yun HY, Morcos SM, Pajovic S, Campos EI, Raught B, Hawkins C. The in vivo Interaction Landscape of Histones H3.1 and H3.3. Mol Cell Proteomics 2022; 21:100411. [PMID: 36089195 PMCID: PMC9540345 DOI: 10.1016/j.mcpro.2022.100411] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 08/10/2022] [Accepted: 09/06/2022] [Indexed: 01/18/2023] Open
Abstract
Chromatin structure, transcription, DNA replication, and repair are regulated via locus-specific incorporation of histone variants and posttranslational modifications that guide effector chromatin-binding proteins. Here we report unbiased, quantitative interactomes for the replication-coupled (H3.1) and replication-independent (H3.3) histone H3 variants based on BioID proximity labeling, which allows interactions in intact, living cells to be detected. Along with a significant proportion of previously reported interactions detected by affinity purification followed by mass spectrometry, three quarters of the 608 histone-associated proteins that we identified are new, uncharacterized histone associations. The data reveal important biological nuances not captured by traditional biochemical means. For example, we found that the chromatin assembly factor-1 histone chaperone not only deposits the replication-coupled H3.1 histone variant during S-phase but also associates with H3.3 throughout the cell cycle in vivo. We also identified other variant-specific associations, such as with transcription factors, chromatin regulators, and with the mitotic machinery. Our proximity-based analysis is thus a rich resource that extends the H3 interactome and reveals new sets of variant-specific associations.
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Affiliation(s)
- Robert Siddaway
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada,Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Scott Milos
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Étienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada,Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Université de Lille, Lille, France
| | - Hwa Young Yun
- Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Shahir M. Morcos
- Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sanja Pajovic
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Eric I. Campos
- Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Cynthia Hawkins
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada,Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada,For correspondence: Cynthia Hawkins
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