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Skrajna A, Bodrug T, Martinez-Chacin RC, Fisher CB, Welsh KA, Simmons HC, Arteaga EC, Simmons JM, Nasr MA, LaPak KM, Nguyen A, Huynh MT, Fargo I, Welfare JG, Zhao Y, Lawrence DS, Goldfarb D, Brown NG, McGinty RK. APC/C-mediated ubiquitylation of extranucleosomal histone complexes lacking canonical degrons. Nat Commun 2025; 16:2561. [PMID: 40089476 PMCID: PMC11910654 DOI: 10.1038/s41467-025-57384-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 02/20/2025] [Indexed: 03/17/2025] Open
Abstract
Non-degradative histone ubiquitylation plays a myriad of well-defined roles in the regulation of gene expression and choreographing DNA damage repair pathways. In contrast, the contributions of degradative histone ubiquitylation on genomic processes has remained elusive. Recently, the APC/C has been shown to ubiquitylate histones to regulate gene expression in pluripotent cells, but the molecular mechanism is unclear. Here we show that despite directly binding to the nucleosome through subunit APC3, the APC/C is unable to ubiquitylate nucleosomal histones. In contrast, extranucleosomal H2A/H2B and H3/H4 complexes are broadly ubiquitylated by the APC/C in an unexpected manner. Using a combination of cryo-electron microscopy (cryo-EM) and biophysical and enzymatic assays, we demonstrate that APC8 and histone tails direct APC/C-mediated polyubiquitylation of core histones in the absence of traditional APC/C substrate degron sequences. Taken together, our work implicates APC/C-nucleosome tethering in the degradation of diverse chromatin-associated proteins and extranucleosomal histones for the regulation of transcription and the cell cycle and for preventing toxicity due to excess histone levels.
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Affiliation(s)
- Aleksandra Skrajna
- Division of Chemical Biology and Medicinal Chemistry and Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Tatyana Bodrug
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, UNC School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Raquel C Martinez-Chacin
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Pharmacology, UNC School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Caleb B Fisher
- Department of Biochemistry and Biophysics, UNC School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Kaeli A Welsh
- Department of Pharmacology, UNC School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Holly C Simmons
- Division of Chemical Biology and Medicinal Chemistry and Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Eyla C Arteaga
- Division of Chemical Biology and Medicinal Chemistry and Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Jake M Simmons
- Division of Chemical Biology and Medicinal Chemistry and Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, UNC School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Mohamed A Nasr
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Kyle M LaPak
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Anh Nguyen
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Mai T Huynh
- Division of Chemical Biology and Medicinal Chemistry and Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Isabel Fargo
- Division of Chemical Biology and Medicinal Chemistry and Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Joshua G Welfare
- Division of Chemical Biology and Medicinal Chemistry and Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Yani Zhao
- Division of Chemical Biology and Medicinal Chemistry and Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - David S Lawrence
- Division of Chemical Biology and Medicinal Chemistry and Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
- Department of Pharmacology, UNC School of Medicine, University of North Carolina, Chapel Hill, NC, USA
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Dennis Goldfarb
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
- Institute for Informatics, Washington University School of Medicine, St. Louis, MO, USA
| | - Nicholas G Brown
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
- Department of Pharmacology, UNC School of Medicine, University of North Carolina, Chapel Hill, NC, USA.
| | - Robert K McGinty
- Division of Chemical Biology and Medicinal Chemistry and Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, UNC School of Medicine, University of North Carolina, Chapel Hill, NC, USA.
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Weinzapfel EN, Fedder-Semmes KN, Sun ZW, Keogh MC. Beyond the tail: the consequence of context in histone post-translational modification and chromatin research. Biochem J 2024; 481:219-244. [PMID: 38353483 PMCID: PMC10903488 DOI: 10.1042/bcj20230342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
The role of histone post-translational modifications (PTMs) in chromatin structure and genome function has been the subject of intense debate for more than 60 years. Though complex, the discourse can be summarized in two distinct - and deceptively simple - questions: What is the function of histone PTMs? And how should they be studied? Decades of research show these queries are intricately linked and far from straightforward. Here we provide a historical perspective, highlighting how the arrival of new technologies shaped discovery and insight. Despite their limitations, the tools available at each period had a profound impact on chromatin research, and provided essential clues that advanced our understanding of histone PTM function. Finally, we discuss recent advances in the application of defined nucleosome substrates, the study of multivalent chromatin interactions, and new technologies driving the next era of histone PTM research.
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