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Fitzgerald O, Wu B, Wang M, Maqbool R, Li W, Zhao W. Protocol for evaluating the E3 ligase activity of BRCA1-BARD1 and its variants by nucleosomal histone ubiquitylation. STAR Protoc 2024; 5:103294. [PMID: 39243377 PMCID: PMC11408276 DOI: 10.1016/j.xpro.2024.103294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 07/02/2024] [Accepted: 08/15/2024] [Indexed: 09/09/2024] Open
Abstract
The tumor suppressor breast cancer 1 (BRCA1) complexed with BRCA1-associated RING domain 1 (BARD1), a RING-type E3 ligase, facilitates the attachment of ubiquitin onto the substrate protein. Here, we present a protocol for evaluating the E3 ligase activity of BRCA1-BARD1 and its variants by nucleosomal histone ubiquitylation. We describe steps for isolating 147 bp Widom 601 DNA and assembling nucleosome core particles (NCPs). We then detail procedures for the in vitro ubiquitylation of nucleosome histone H2A by BRCA1-BARD1 and its variants. For complete details on the use and execution of this protocol, please refer to Wang et al.1.
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Affiliation(s)
- O'Taveon Fitzgerald
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Bo Wu
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Meiling Wang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Rouf Maqbool
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Wenjing Li
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
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2
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Ackermann BE, Debelouchina GT. Emerging Contributions of Solid-State NMR Spectroscopy to Chromatin Structural Biology. Front Mol Biosci 2021; 8:741581. [PMID: 34708075 PMCID: PMC8544521 DOI: 10.3389/fmolb.2021.741581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
The eukaryotic genome is packaged into chromatin, a polymer of DNA and histone proteins that regulates gene expression and the spatial organization of nuclear content. The repetitive character of chromatin is diversified into rich layers of complexity that encompass DNA sequence, histone variants and post-translational modifications. Subtle molecular changes in these variables can often lead to global chromatin rearrangements that dictate entire gene programs with far reaching implications for development and disease. Decades of structural biology advances have revealed the complex relationship between chromatin structure, dynamics, interactions, and gene expression. Here, we focus on the emerging contributions of magic-angle spinning solid-state nuclear magnetic resonance spectroscopy (MAS NMR), a relative newcomer on the chromatin structural biology stage. Unique among structural biology techniques, MAS NMR is ideally suited to provide atomic level information regarding both the rigid and dynamic components of this complex and heterogenous biological polymer. In this review, we highlight the advantages MAS NMR can offer to chromatin structural biologists, discuss sample preparation strategies for structural analysis, summarize recent MAS NMR studies of chromatin structure and dynamics, and close by discussing how MAS NMR can be combined with state-of-the-art chemical biology tools to reconstitute and dissect complex chromatin environments.
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Affiliation(s)
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
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3
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Nodelman IM, Patel A, Levendosky RF, Bowman GD. Reconstitution and Purification of Nucleosomes with Recombinant Histones and Purified DNA. ACTA ACUST UNITED AC 2021; 133:e130. [PMID: 33305911 DOI: 10.1002/cpmb.130] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleosomes are substrates for a broad range of factors, including those involved in transcription or chromosome maintenance/reorganization and enzymes that covalently modify histones. Given the heterogeneous nature of nucleosomes in vivo (i.e., varying histone composition, post-translational modifications, DNA sequence register), understanding the specificity and activities of chromatin-interacting factors has required in vitro studies using well-defined nucleosome substrates. Here, we provide detailed methods for large-scale PCR preparation of DNA, assembly of nucleosomes from purified DNA and histones, and purification of DNA and mononucleosomes. Such production of well-defined nucleosomes for biochemical and biophysical studies is key for studying numerous proteins and protein complexes that bind and/or alter nucleosomes and for revealing inherent characteristics of nucleosomes. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Large-scale PCR amplification of DNA Basic Protocol 2: DNA and nucleosome purification using a Bio-Rad Mini Prep Cell/Prep Cell Basic Protocol 3: Nucleosome reconstitution via linear gradient salt dialysis.
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Affiliation(s)
- Ilana M Nodelman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Ashok Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Robert F Levendosky
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.,Present address: Catalent Cell and Gene Therapy, Baltimore, Maryland
| | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
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4
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Sundaram R, Vasudevan D. Structural Basis of Nucleosome Recognition and Modulation. Bioessays 2020; 42:e1900234. [DOI: 10.1002/bies.201900234] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 05/05/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Rajivgandhi Sundaram
- Laboratory of Macromolecular Crystallography Institute of Life Sciences Bhubaneswar 751023 India
- Manipal Academy of Higher Education Manipal 576104 India
| | - Dileep Vasudevan
- Laboratory of Macromolecular Crystallography Institute of Life Sciences Bhubaneswar 751023 India
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Structural Basis for Recognition of Ubiquitylated Nucleosome by Dot1L Methyltransferase. Cell Rep 2020; 26:1681-1690.e5. [PMID: 30759380 PMCID: PMC6392056 DOI: 10.1016/j.celrep.2019.01.058] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/09/2019] [Accepted: 01/15/2019] [Indexed: 12/17/2022] Open
Abstract
Histone H3 lysine 79 (H3K79) methylation is enriched on actively transcribed genes, and its misregulation is a hallmark of leukemia. Methylation of H3K79, which resides on the structured disk face of the nucleosome, is mediated by the Dot1L methyltransferase. Dot1L activity is part of a trans-histone crosstalk pathway, requiring prior histone H2B ubiquitylation of lysine 120 (H2BK120ub) for optimal activity. However, the molecular details describing both how Dot1L binds to the nucleosome and why Dot1L is activated by H2BK120 ubiquitylation are unknown. Here, we present the cryoelectron microscopy (cryo-EM) structure of Dot1L bound to a nucleosome reconstituted with site-specifically ubiquitylated H2BK120. The structure reveals that Dot1L engages the nucleosome acidic patch using a variant arginine anchor and occupies a conformation poised for methylation. In this conformation, Dot1L and ubiquitin interact directly through complementary hydrophobic surfaces. This study establishes a path to better understand Dot1L function in normal and leukemia cells.
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Hsu PL, Shi H, Leonen C, Kang J, Chatterjee C, Zheng N. Structural Basis of H2B Ubiquitination-Dependent H3K4 Methylation by COMPASS. Mol Cell 2019; 76:712-723.e4. [PMID: 31733991 DOI: 10.1016/j.molcel.2019.10.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/03/2019] [Accepted: 10/10/2019] [Indexed: 12/20/2022]
Abstract
The COMPASS (complex of proteins associated with Set1) complex represents the prototype of the SET1/MLL family of methyltransferases that controls gene transcription by H3K4 methylation (H3K4me). Although H2B monoubiquitination (H2Bub) is well known as a prerequisite histone mark for COMPASS activity, how H2Bub activates COMPASS remains unclear. Here, we report the cryoelectron microscopy (cryo-EM) structures of an extended COMPASS catalytic module (CM) bound to the H2Bub and free nucleosome. The COMPASS CM clamps onto the nucleosome disk-face via an extensive interface to capture the flexible H3 N-terminal tail. The interface also sandwiches a critical Set1 arginine-rich motif (ARM) that autoinhibits COMPASS. Unexpectedly, without enhancing COMPASS-nucleosome interaction, H2Bub activates the enzymatic assembly by packing against Swd1 and alleviating the inhibitory effect of the Set1 ARM upon fastening it to the acidic patch. By delineating the spatial configuration of the COMPASS-H2Bub-nucleosome assembly, our studies establish the structural framework for understanding the long-studied H2Bub-H3K4me histone modification crosstalk.
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Affiliation(s)
- Peter L Hsu
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Hui Shi
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Calvin Leonen
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Jianming Kang
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - Ning Zheng
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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Colombo M, Pessey O, Marcia M. Topology and enzymatic properties of a canonical Polycomb repressive complex 1 isoform. FEBS Lett 2019; 593:1837-1848. [PMID: 31093962 PMCID: PMC6771824 DOI: 10.1002/1873-3468.13442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 11/28/2022]
Abstract
Polycomb repressive complex 1 (PRC1) catalyses monoubiquitination of histone H2A on Lys119, promoting gene silencing. Cells at different developmental stages and in different tissues express different PRC1 isoforms. The topology, subunit composition, structural architecture and molecular mechanism of most of these isoforms are still poorly characterized. Here, we have purified a PRC1 isoform comprising subunits RING1B, PCGF2, CBX2 and PHC2, two stable subcomplexes (RING1B‐PCGF2 and RING1B‐PHC2) and the catalytic subunit RING1B in isolation. By crosslinking mass spectrometry, we identified novel interactions between RING1B and the three non‐catalytic subunits. Biochemical, biophysical, and enzymatic data suggest that CBX2 and PHC2 play a structural role, whereas PCGF2 also modulates catalysis. Our data offer insights into the molecular architecture of PRC1 and its histone ubiquitination activity.
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Affiliation(s)
- Matteo Colombo
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France
| | - Ombeline Pessey
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France
| | - Marco Marcia
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France
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Crystal Structure of the COMPASS H3K4 Methyltransferase Catalytic Module. Cell 2018; 174:1106-1116.e9. [PMID: 30100181 PMCID: PMC6108940 DOI: 10.1016/j.cell.2018.06.038] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/08/2018] [Accepted: 06/20/2018] [Indexed: 01/07/2023]
Abstract
The SET1/MLL family of histone methyltransferases is conserved in eukaryotes and regulates transcription by catalyzing histone H3K4 mono-, di-, and tri-methylation. These enzymes form a common five-subunit catalytic core whose assembly is critical for their basal and regulated enzymatic activities through unknown mechanisms. Here, we present the crystal structure of the intact yeast COMPASS histone methyltransferase catalytic module consisting of Swd1, Swd3, Bre2, Sdc1, and Set1. The complex is organized by Swd1, whose conserved C-terminal tail not only nucleates Swd3 and a Bre2-Sdc1 subcomplex, but also joins Set1 to construct a regulatory pocket next to the catalytic site. This inter-subunit pocket is targeted by a previously unrecognized enzyme-modulating motif in Swd3 and features a doorstop-style mechanism dictating substrate selectivity among SET1/MLL family members. By spatially mapping the functional components of COMPASS, our results provide a structural framework for understanding the multifaceted functions and regulation of the H3K4 methyltransferase family.
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