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Roy S, Adhikary H, D’Amours D. The SMC5/6 complex: folding chromosomes back into shape when genomes take a break. Nucleic Acids Res 2024; 52:2112-2129. [PMID: 38375830 PMCID: PMC10954462 DOI: 10.1093/nar/gkae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
High-level folding of chromatin is a key determinant of the shape and functional state of chromosomes. During cell division, structural maintenance of chromosome (SMC) complexes such as condensin and cohesin ensure large-scale folding of chromatin into visible chromosomes. In contrast, the SMC5/6 complex plays more local and context-specific roles in the structural organization of interphase chromosomes with important implications for health and disease. Recent advances in single-molecule biophysics and cryo-electron microscopy revealed key insights into the architecture of the SMC5/6 complex and how interactions connecting the complex to chromatin components give rise to its unique repertoire of interphase functions. In this review, we provide an integrative view of the features that differentiates the SMC5/6 complex from other SMC enzymes and how these enable dramatic reorganization of DNA folding in space during DNA repair reactions and other genome transactions. Finally, we explore the mechanistic basis for the dynamic targeting of the SMC5/6 complex to damaged chromatin and its crucial role in human health.
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Affiliation(s)
- Shamayita Roy
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
| | - Hemanta Adhikary
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
| | - Damien D’Amours
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
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Nosella ML, Kim TH, Huang SK, Harkness RW, Goncalves M, Pan A, Tereshchenko M, Vahidi S, Rubinstein JL, Lee HO, Forman-Kay JD, Kay LE. Poly(ADP-ribosyl)ation enhances nucleosome dynamics and organizes DNA damage repair components within biomolecular condensates. Mol Cell 2024; 84:429-446.e17. [PMID: 38215753 DOI: 10.1016/j.molcel.2023.12.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/30/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Nucleosomes, the basic structural units of chromatin, hinder recruitment and activity of various DNA repair proteins, necessitating modifications that enhance DNA accessibility. Poly(ADP-ribosyl)ation (PARylation) of proteins near damage sites is an essential initiation step in several DNA-repair pathways; however, its effects on nucleosome structural dynamics and organization are unclear. Using NMR, cryoelectron microscopy (cryo-EM), and biochemical assays, we show that PARylation enhances motions of the histone H3 tail and DNA, leaving the configuration of the core intact while also stimulating nuclease digestion and ligation of nicked nucleosomal DNA by LIG3. PARylation disrupted interactions between nucleosomes, preventing self-association. Addition of LIG3 and XRCC1 to PARylated nucleosomes generated condensates that selectively partition DNA repair-associated proteins in a PAR- and phosphorylation-dependent manner in vitro. Our results establish that PARylation influences nucleosomes across different length scales, extending from the atom-level motions of histone tails to the mesoscale formation of condensates with selective compositions.
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Affiliation(s)
- Michael L Nosella
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Tae Hun Kim
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shuya Kate Huang
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Robert W Harkness
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Monica Goncalves
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Alisia Pan
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Maria Tereshchenko
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Siavash Vahidi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Hyun O Lee
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Julie D Forman-Kay
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Lewis E Kay
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
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Shi X, Kannaian B, Prasanna C, Soman A, Nordenskiöld L. Structural and dynamical investigation of histone H2B in well-hydrated nucleosome core particles by solid-state NMR. Commun Biol 2023; 6:672. [PMID: 37355718 PMCID: PMC10290710 DOI: 10.1038/s42003-023-05050-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/16/2023] [Indexed: 06/26/2023] Open
Abstract
H2A-H2B dimer is a key component of nucleosomes and an important player in chromatin biology. Here, we characterized the structure and dynamics of H2B in precipitated nucleosome core particles (NCPs) with a physiologically relevant concentration using solid-state NMR. Our recent investigation of H3-H4 tetramer determined its unique dynamic properties and the present work provides a deeper understanding of the previously observed dynamic networks in NCP that is potentially functionally significant. Nearly complete 13C, 15N assignments were obtained for H2B R30-A121, which permit extracting unprecedented detailed structural and amino-acid site-specific dynamics. The derived structure of H2B in the well-hydrated NCP sample agrees well with that of X-ray crystals. Dynamics at different timescales were determined semi-quantitatively for H2B in a site-specific manner. Particularly, higher millisecond-microsecond dynamics are observed for H2B core regions including partial α1, L1, partial α2, and partial L3. The analysis of these regions in the context of the tertiary structure reveals the clustering of dynamical residues. Overall, this work fills a gap to a complete resonance assignment of all four histones in nucleosomes and delineates that the dynamic networks in NCP extend to H2B, which suggests a potential mechanism to couple histone core with distant DNA to modulate the DNA activities.
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Affiliation(s)
- Xiangyan Shi
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, Guangdong Province, China.
| | - Bhuvaneswari Kannaian
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chinmayi Prasanna
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Aghil Soman
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.
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Smrt ST, Gonzalez Salguero N, Thomas JK, Zandian M, Poirier MG, Jaroniec CP. Histone H3 core domain in chromatin with different DNA linker lengths studied by 1H-Detected solid-state NMR spectroscopy. Front Mol Biosci 2023; 9:1106588. [PMID: 36660422 PMCID: PMC9846530 DOI: 10.3389/fmolb.2022.1106588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Chromatin, a dynamic protein-DNA complex that regulates eukaryotic genome accessibility and essential functions, is composed of nucleosomes connected by linker DNA with each nucleosome consisting of DNA wrapped around an octamer of histones H2A, H2B, H3 and H4. Magic angle spinning solid-state nuclear magnetic resonance (NMR) spectroscopy can yield unique insights into histone structure and dynamics in condensed nucleosomes and nucleosome arrays representative of chromatin at physiological concentrations. Recently we used J-coupling-based solid-state NMR methods to investigate with residue-specific resolution the conformational dynamics of histone H3 N-terminal tails in 16-mer nucleosome arrays containing 15, 30 or 60 bp DNA linkers. Here, we probe the H3 core domain in the 16-mer arrays as a function of DNA linker length via dipolar coupling-based 1H-detected solid-state NMR techniques. Specifically, we established nearly complete assignments of backbone chemical shifts for H3 core residues in arrays with 15-60 bp DNA linkers reconstituted with 2H,13C,15N-labeled H3. Overall, these chemical shifts were similar irrespective of the DNA linker length indicating no major changes in H3 core conformation. Notably, however, multiple residues at the H3-nucleosomal DNA interface in arrays with 15 bp DNA linkers exhibited relatively pronounced differences in chemical shifts and line broadening compared to arrays with 30 and 60 bp linkers. These findings are consistent with increased heterogeneity in nucleosome packing and structural strain within arrays containing short DNA linkers that likely leads to side-chains of these interfacial residues experiencing alternate conformations or shifts in their rotamer populations relative to arrays with the longer DNA linkers.
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Affiliation(s)
- Sean T. Smrt
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Nicole Gonzalez Salguero
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Justin K. Thomas
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Mohamad Zandian
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Michael G. Poirier
- Department of Physics, The Ohio State University, Columbus, OH, United States
| | - Christopher P. Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States,*Correspondence: Christopher P. Jaroniec,
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