1
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Orsetti A, van Oosten D, Vasarhelyi RG, Dănescu TM, Huertas J, van Ingen H, Cojocaru V. Structural dynamics in chromatin unraveling by pioneer transcription factors. Biophys Rev 2024; 16:365-382. [PMID: 39099839 PMCID: PMC11297019 DOI: 10.1007/s12551-024-01205-6] [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: 03/29/2024] [Accepted: 06/18/2024] [Indexed: 08/06/2024] Open
Abstract
Pioneer transcription factors are proteins with a dual function. First, they regulate transcription by binding to nucleosome-free DNA regulatory elements. Second, they bind to DNA while wrapped around histone proteins in the chromatin and mediate chromatin opening. The molecular mechanisms that connect the two functions are yet to be discovered. In recent years, pioneer factors received increased attention mainly because of their crucial role in promoting cell fate transitions that could be used for regenerative therapies. For example, the three factors required to induce pluripotency in somatic cells, Oct4, Sox2, and Klf4 were classified as pioneer factors and studied extensively. With this increased attention, several structures of complexes between pioneer factors and chromatin structural units (nucleosomes) have been resolved experimentally. Furthermore, experimental and computational approaches have been designed to study two unresolved, key scientific questions: First, do pioneer factors induce directly local opening of nucleosomes and chromatin fibers upon binding? And second, how do the unstructured tails of the histones impact the structural dynamics involved in such conformational transitions? Here we review the current knowledge about transcription factor-induced nucleosome dynamics and the role of the histone tails in this process. We discuss what is needed to bridge the gap between the static views obtained from the experimental structures and the key structural dynamic events in chromatin opening. Finally, we propose that integrating nuclear magnetic resonance spectroscopy with molecular dynamics simulations is a powerful approach to studying pioneer factor-mediated dynamics of nucleosomes and perhaps small chromatin fibers using native DNA sequences.
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Affiliation(s)
- Andrea Orsetti
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Daphne van Oosten
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | | | - Theodor-Marian Dănescu
- Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Jan Huertas
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, England
| | - Hugo van Ingen
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Vlad Cojocaru
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
- STAR-UBB Institute, Babeş-Bolyai University, Cluj-Napoca, Romania
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
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2
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Abasi LS, Elathram N, Movva M, Deep A, Corbett KD, Debelouchina GT. Phosphorylation regulates tau's phase separation behavior and interactions with chromatin. Commun Biol 2024; 7:251. [PMID: 38429335 PMCID: PMC10907630 DOI: 10.1038/s42003-024-05920-4] [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: 12/21/2023] [Accepted: 02/16/2024] [Indexed: 03/03/2024] Open
Abstract
Tau is a microtubule-associated protein often found in neurofibrillary tangles (NFTs) in the brains of patients with Alzheimer's disease. Beyond this context, mounting evidence suggests that tau localizes into the nucleus, where it may play a role in DNA protection and heterochromatin regulation. The molecular mechanisms behind these observations are currently unclear. Using in vitro biophysical experiments, here we demonstrate that tau can undergo liquid-liquid phase separation (LLPS) with DNA, mononucleosomes, and reconstituted nucleosome arrays under low salt conditions. Low concentrations of tau promote chromatin compaction and protect DNA from digestion. While the material state of samples at physiological salt is dominated by chromatin oligomerization, tau can still associate strongly and reversibly with nucleosome arrays. These properties are driven by tau's strong interactions with linker and nucleosomal DNA. In addition, tau co-localizes into droplets formed by nucleosome arrays and phosphorylated HP1α, a key heterochromatin constituent thought to function through an LLPS mechanism. Importantly, LLPS and chromatin interactions are disrupted by aberrant tau hyperphosphorylation. These biophysical properties suggest that tau may directly impact DNA and chromatin accessibility and that loss of these interactions could contribute to the aberrant nuclear effects seen in tau pathology.
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Affiliation(s)
- Lannah S Abasi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nesreen Elathram
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Manasi Movva
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Galia T Debelouchina
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
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3
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Marunde MR, Fuchs HA, Burg JM, Popova IK, Vaidya A, Hall NW, Weinzapfel EN, Meiners MJ, Watson R, Gillespie ZB, Taylor HF, Mukhsinova L, Onuoha UC, Howard SA, Novitzky K, McAnarney ET, Krajewski K, Cowles MW, Cheek MA, Sun ZW, Venters BJ, Keogh MC, Musselman CA. Nucleosome conformation dictates the histone code. eLife 2024; 13:e78866. [PMID: 38319148 PMCID: PMC10876215 DOI: 10.7554/elife.78866] [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: 03/22/2022] [Accepted: 02/05/2024] [Indexed: 02/07/2024] Open
Abstract
Histone post-translational modifications (PTMs) play a critical role in chromatin regulation. It has been proposed that these PTMs form localized 'codes' that are read by specialized regions (reader domains) in chromatin-associated proteins (CAPs) to regulate downstream function. Substantial effort has been made to define [CAP: histone PTM] specificities, and thus decipher the histone code and guide epigenetic therapies. However, this has largely been done using the reductive approach of isolated reader domains and histone peptides, which cannot account for any higher-order factors. Here, we show that the [BPTF PHD finger and bromodomain: histone PTM] interaction is dependent on nucleosome context. The tandem reader selectively associates with nucleosomal H3K4me3 and H3K14ac or H3K18ac, a combinatorial engagement that despite being in cis is not predicted by peptides. This in vitro specificity of the BPTF tandem reader for PTM-defined nucleosomes is recapitulated in a cellular context. We propose that regulatable histone tail accessibility and its impact on the binding potential of reader domains necessitates we refine the 'histone code' concept and interrogate it at the nucleosome level.
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Affiliation(s)
| | - Harrison A Fuchs
- Department of Biochemistry, University of Iowa Carver College of MedicineAuroraUnited States
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel HillChapel HillUnited States
| | | | | | | | | | | | - Catherine A Musselman
- Department of Biochemistry, University of Iowa Carver College of MedicineAuroraUnited States
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
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4
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Abasi LS, Elathram N, Movva M, Deep A, Corbett KD, Debelouchina GT. Phosphorylation regulates tau's phase separation behavior and interactions with chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572911. [PMID: 38187700 PMCID: PMC10769318 DOI: 10.1101/2023.12.21.572911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Tau is a microtubule-associated protein often found in neurofibrillary tangles (NFTs) in the brains of patients with Alzheimer's disease (AD). Beyond this context, mounting evidence suggests that tau localizes into the nucleus, where it may play a role in DNA protection and heterochromatin regulation. Models of tau depletion or pathology show loss of genetically silent heterochromatin, aberrant expression of heterochromatic genes, and transposable element activation. The molecular mechanisms behind these observations are currently unclear. Using in vitro biophysical experiments, here we demonstrate that tau can undergo liquid-liquid phase separation (LLPS) with DNA, mononucleosomes, and reconstituted nucleosome arrays under low salt conditions. Low concentrations of tau promote chromatin compaction and protect DNA from digestion. While the material state of samples at physiological salt is dominated by chromatin oligomerization, tau can still associate strongly and reversibly with nucleosome arrays. These properties are driven by tau's strong interactions with linker and nucleosomal DNA, while magic angle spinning (MAS) solid-state NMR experiments show that tau binding does not drastically alter nucleosome structure and dynamics. In addition, tau co-localizes into droplets formed by nucleosome arrays and phosphorylated HP1α, a key heterochromatin constituent thought to function through an LLPS mechanism. Importantly, LLPS and chromatin interactions are disrupted by aberrant tau hyperphosphorylation. These biophysical properties suggest that tau may directly impact DNA and chromatin accessibility and that loss of these interactions could contribute to the aberrant nuclear effects seen in tau pathology.
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Affiliation(s)
- Lannah S. Abasi
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nesreen Elathram
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Manasi Movva
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kevin D. Corbett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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5
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Sun W, Lebedenko OO, Salguero NG, Shannon MD, Zandian M, Poirier MG, Skrynnikov NR, Jaroniec CP. Conformational and Interaction Landscape of Histone H4 Tails in Nucleosomes Probed by Paramagnetic NMR Spectroscopy. J Am Chem Soc 2023; 145:25478-25485. [PMID: 37943892 PMCID: PMC10719895 DOI: 10.1021/jacs.3c10340] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The fundamental repeat unit of chromatin, the nucleosome, consists of approximately 147 base pairs of double-stranded DNA and a histone protein octamer containing two copies each of histones H2A, H2B, H3, and H4. Each histone possesses a dynamically disordered N-terminal tail domain, and it is well-established that the tails of histones H3 and H4 play key roles in chromatin compaction and regulation. Here we investigate the conformational ensemble and interactions of the H4 tail in nucleosomes by means of solution NMR measurements of paramagnetic relaxation enhancements (PREs) in recombinant samples reconstituted with 15N-enriched H4 and nitroxide spin-label tagged H3. The experimental PREs, which report on the proximities of individual H4 tail residues to the different H3 spin-label sites, are interpreted by using microsecond time-scale molecular dynamics simulations of the nucleosome core particle. Collectively, these data enable improved localization of histone H4 tails in nucleosomes and support the notion that H4 tails engage in a fuzzy complex interaction with nucleosomal DNA.
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Affiliation(s)
- Wenjun Sun
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Olga O. Lebedenko
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Nicole Gonzalez Salguero
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Matthew D. Shannon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mohamad Zandian
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Michael G. Poirier
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nikolai R. Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034, Russia
- Department of Chemistry, Purdue University, West Lafayette 47907, United States
| | - Christopher P. Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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6
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Elathram N, Ackermann BE, Clark ET, Dunn SR, Debelouchina GT. Phosphorylated HP1α-Nucleosome Interactions in Phase Separated Environments. J Am Chem Soc 2023; 145:23994-24004. [PMID: 37870432 PMCID: PMC10636758 DOI: 10.1021/jacs.3c06481] [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: 06/19/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023]
Abstract
In the nucleus, transcriptionally silent genes are sequestered into heterochromatin compartments comprising nucleosomes decorated with histone H3 Lys9 trimethylation and a protein called HP1α. This protein can form liquid-liquid droplets in vitro and potentially organize heterochromatin through a phase separation mechanism that is promoted by phosphorylation. Elucidating the molecular interactions that drive HP1α phase separation and its consequences on nucleosome structure and dynamics has been challenging due to the viscous and heterogeneous nature of such assemblies. Here, we tackle this problem by a combination of solution and solid-state NMR spectroscopy, which allows us to dissect the interactions of phosphorylated HP1α with nucleosomes in the context of phase separation. Our experiments indicate that phosphorylated human HP1α does not cause any major rearrangements to the nucleosome core, in contrast to the yeast homologue Swi6. Instead, HP1α interacts specifically with the methylated H3 tails and slows the dynamics of the H4 tails. Our results shed light on how phosphorylated HP1α proteins may regulate the heterochromatin landscape, while our approach provides an atomic resolution view of a heterogeneous and dynamic biological system regulated by a complex network of interactions and post-translational modifications.
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Affiliation(s)
- Nesreen Elathram
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Bryce E. Ackermann
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Evan T. Clark
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Shelby R. Dunn
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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7
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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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8
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Low JYK, Shi X, Anandalakshmi V, Neo D, Peh GSL, Koh SK, Zhou L, Abdul Rahim MK, Boo K, Lee J, Mohanram H, Alag R, Mu Y, Mehta JS, Pervushin K. Release of frustration drives corneal amyloid disaggregation by brain chaperone. Commun Biol 2023; 6:348. [PMID: 36997596 PMCID: PMC10063603 DOI: 10.1038/s42003-023-04725-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/17/2023] [Indexed: 04/01/2023] Open
Abstract
TGFBI-related corneal dystrophy (CD) is characterized by the accumulation of insoluble protein deposits in the corneal tissues, eventually leading to progressive corneal opacity. Here we show that ATP-independent amyloid-β chaperone L-PGDS can effectively disaggregate corneal amyloids in surgically excised human cornea of TGFBI-CD patients and release trapped amyloid hallmark proteins. Since the mechanism of amyloid disassembly by ATP-independent chaperones is unknown, we reconstructed atomic models of the amyloids self-assembled from TGFBIp-derived peptides and their complex with L-PGDS using cryo-EM and NMR. We show that L-PGDS specifically recognizes structurally frustrated regions in the amyloids and releases those frustrations. The released free energy increases the chaperone's binding affinity to amyloids, resulting in local restructuring and breakage of amyloids to protofibrils. Our mechanistic model provides insights into the alternative source of energy utilized by ATP-independent disaggregases and highlights the possibility of using these chaperones as treatment strategies for different types of amyloid-related diseases.
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Affiliation(s)
- Jia Yi Kimberly Low
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Xiangyan Shi
- Department of Biology, Shenzhen MSU-BIT University, 518172, Shenzhen, China
| | | | - Dawn Neo
- Singapore Eye Research Institute, 11 Third Hospital Avenue, Singapore, 168751, Singapore
| | - Gary Swee Lim Peh
- Singapore Eye Research Institute, 11 Third Hospital Avenue, Singapore, 168751, Singapore
| | - Siew Kwan Koh
- Singapore Eye Research Institute, 11 Third Hospital Avenue, Singapore, 168751, Singapore
| | - Lei Zhou
- School of Optometry, Department of Applied Biology and Chemical Technology, Research Centre for SHARP Vision (RCSV), The Hong Kong Polytechnic University, Hong Kong, China
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - M K Abdul Rahim
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Ketti Boo
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - JiaXuan Lee
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Harini Mohanram
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Reema Alag
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Jodhbir S Mehta
- Singapore Eye Research Institute, 11 Third Hospital Avenue, Singapore, 168751, Singapore.
- Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Graduate Medical School, Singapore, 169857, Singapore.
- Singapore National Eye Centre, 11 Third Hospital Avenue, Singapore, 168751, Singapore.
| | - Konstantin Pervushin
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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9
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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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10
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Shi X, Nordenskiöld L, Sokolova OS, Shaytan AK. Editorial: Recent advances in molecular properties of DNA-protein interactions, chromatin and their biological roles. Front Mol Biosci 2023; 10:1171714. [PMID: 36959980 PMCID: PMC10029722 DOI: 10.3389/fmolb.2023.1171714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 02/27/2023] [Indexed: 03/09/2023] Open
Affiliation(s)
- Xiangyan Shi
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, Guangdong, China
- *Correspondence: Xiangyan Shi, ; Lars Nordenskiöld, ; Olga S. Sokolova, ; Alexey K. Shaytan,
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- *Correspondence: Xiangyan Shi, ; Lars Nordenskiöld, ; Olga S. Sokolova, ; Alexey K. Shaytan,
| | - Olga S. Sokolova
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, Guangdong, China
- *Correspondence: Xiangyan Shi, ; Lars Nordenskiöld, ; Olga S. Sokolova, ; Alexey K. Shaytan,
| | - Alexey K. Shaytan
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
- *Correspondence: Xiangyan Shi, ; Lars Nordenskiöld, ; Olga S. Sokolova, ; Alexey K. Shaytan,
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11
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Chen Q, Zhao L, Soman A, Arkhipova AY, Li J, Li H, Chen Y, Shi X, Nordenskiöld L. Chromatin Liquid-Liquid Phase Separation (LLPS) Is Regulated by Ionic Conditions and Fiber Length. Cells 2022; 11:cells11193145. [PMID: 36231107 PMCID: PMC9564186 DOI: 10.3390/cells11193145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/20/2022] [Accepted: 10/02/2022] [Indexed: 11/16/2022] Open
Abstract
The dynamic regulation of the physical states of chromatin in the cell nucleus is crucial for maintaining cellular homeostasis. Chromatin can exist in solid- or liquid-like forms depending on the surrounding ions, binding proteins, post-translational modifications and many other factors. Several recent studies suggested that chromatin undergoes liquid-liquid phase separation (LLPS) in vitro and also in vivo; yet, controversial conclusions about the nature of chromatin LLPS were also observed from the in vitro studies. These inconsistencies are partially due to deviations in the in vitro buffer conditions that induce the condensation/aggregation of chromatin as well as to differences in chromatin (nucleosome array) constructs used in the studies. In this work, we present a detailed characterization of the effects of K+, Mg2+ and nucleosome fiber length on the physical state and property of reconstituted nucleosome arrays. LLPS was generally observed for shorter nucleosome arrays (15-197-601, reconstituted from 15 repeats of the Widom 601 DNA with 197 bp nucleosome repeat length) at physiological ion concentrations. In contrast, gel- or solid-like condensates were detected for the considerably longer 62-202-601 and lambda DNA (~48.5 kbp) nucleosome arrays under the same conditions. In addition, we demonstrated that the presence of reduced BSA and acetate buffer is not essential for the chromatin LLPS process. Overall, this study provides a comprehensive understanding of several factors regarding chromatin physical states and sheds light on the mechanism and biological relevance of chromatin phase separation in vivo.
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Affiliation(s)
- Qinming Chen
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (Q.C.); (A.S.)
| | - Lei Zhao
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China; (L.Z.); (A.Y.A.); (J.L.); (H.L.); (Y.C.)
| | - Aghil Soman
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (Q.C.); (A.S.)
| | - Anastasia Yu Arkhipova
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China; (L.Z.); (A.Y.A.); (J.L.); (H.L.); (Y.C.)
- Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Jindi Li
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China; (L.Z.); (A.Y.A.); (J.L.); (H.L.); (Y.C.)
| | - Hao Li
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China; (L.Z.); (A.Y.A.); (J.L.); (H.L.); (Y.C.)
| | - Yinglu Chen
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China; (L.Z.); (A.Y.A.); (J.L.); (H.L.); (Y.C.)
| | - Xiangyan Shi
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China; (L.Z.); (A.Y.A.); (J.L.); (H.L.); (Y.C.)
- Correspondence: (X.S.); (L.N.)
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (Q.C.); (A.S.)
- Correspondence: (X.S.); (L.N.)
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12
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Conroy DW, Xu Y, Shi H, Gonzalez Salguero N, Purusottam RN, Shannon MD, Al-Hashimi HM, Jaroniec CP. Probing Watson-Crick and Hoogsteen base pairing in duplex DNA using dynamic nuclear polarization solid-state NMR spectroscopy. Proc Natl Acad Sci U S A 2022; 119:e2200681119. [PMID: 35857870 PMCID: PMC9335254 DOI: 10.1073/pnas.2200681119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The majority of base pairs in double-stranded DNA exist in the canonical Watson-Crick geometry. However, they can also adopt alternate Hoogsteen conformations in various complexes of DNA with proteins and small molecules, which are key for biological function and mechanism. While detection of Hoogsteen base pairs in large DNA complexes and assemblies poses considerable challenges for traditional structural biology techniques, we show here that multidimensional dynamic nuclear polarization-enhanced solid-state NMR can serve as a unique spectroscopic tool for observing and distinguishing Watson-Crick and Hoogsteen base pairs in a broad range of DNA systems based on characteristic NMR chemical shifts and internuclear dipolar couplings. We illustrate this approach using a model 12-mer DNA duplex, free and in complex with the antibiotic echinomycin, which features two central adenine-thymine base pairs with Watson-Crick and Hoogsteen geometry, respectively, and subsequently extend it to the ∼200 kDa Widom 601 DNA nucleosome core particle.
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Affiliation(s)
- Daniel W. Conroy
- aDepartment of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Yu Xu
- bDepartment of Chemistry, Duke University, Durham, NC 27708
| | - Honglue Shi
- bDepartment of Chemistry, Duke University, Durham, NC 27708
| | | | - Rudra N. Purusottam
- aDepartment of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Matthew D. Shannon
- aDepartment of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Hashim M. Al-Hashimi
- bDepartment of Chemistry, Duke University, Durham, NC 27708
- cDepartment of Biochemistry, Duke University Medical Center, Durham, NC 27710
- dDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032
- 1To whom correspondence may be addressed. or
| | - Christopher P. Jaroniec
- aDepartment of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- 1To whom correspondence may be addressed. or
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13
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Elathram N, Ackermann BE, Debelouchina GT. DNP-enhanced solid-state NMR spectroscopy of chromatin polymers. JOURNAL OF MAGNETIC RESONANCE OPEN 2022; 10-11:100057. [PMID: 35707629 PMCID: PMC9191766 DOI: 10.1016/j.jmro.2022.100057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Chromatin is a DNA-protein polymer that represents the functional form of the genome. The main building block of chromatin is the nucleosome, a structure that contains 147 base pairs of DNA and two copies each of the histone proteins H2A, H2B, H3 and H4. Previous work has shown that magic angle spinning (MAS) NMR spectroscopy can capture the nucleosome at high resolution although studies have been challenging due to low sensitivity, the presence of dynamic and rigid components, and the complex interaction networks of nucleosomes within the chromatin polymer. Here, we use dynamic nuclear polarization (DNP) to enhance the sensitivity of MAS NMR experiments of nucleosome arrays at 100 K and show that well-resolved 13C-13C MAS NMR correlations can be obtained much more efficiently. We evaluate the effect of temperature on the chemical shifts and linewidths in the spectra and demonstrate that changes are relatively minimal and clustered in regions of histone-DNA or histone-histone contacts. We also compare samples prepared with and without DNA and show that the low temperature 13C-13C correlations exhibit sufficient resolution to detect chemical shift changes and line broadening for residues that form the DNA-histone interface. On the other hand, we show that the measurement of DNP-enhanced 15N-13C histone-histone interactions within the nucleosome core is complicated by the natural 13C abundance network in the sample. Nevertheless, the enhanced sensitivity afforded by DNP can be used to detect long-range correlations between histone residues and DNA. Overall, our experiments demonstrate that DNP-enhanced MAS NMR spectroscopy of chromatin samples yields spectra with high resolution and sensitivity and can be used to capture functionally relevant protein-DNA interactions that have implications for gene regulation and genome organization.
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Affiliation(s)
| | | | - Galia T. Debelouchina
- Corresponding author: Galia Debelouchina, University of California, San Diego, Natural Sciences Building 4322, 9500 Gilman Dr., La Jolla, CA 92093, 858-534-3038,
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14
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Shi X, Zhai Z, Chen Y, Li J, Nordenskiöld L. Recent Advances in Investigating Functional Dynamics of Chromatin. Front Genet 2022; 13:870640. [PMID: 35450211 PMCID: PMC9017861 DOI: 10.3389/fgene.2022.870640] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/11/2022] [Indexed: 11/26/2022] Open
Abstract
Dynamics spanning the picosecond-minute time domain and the atomic-subcellular spatial window have been observed for chromatin in vitro and in vivo. The condensed organization of chromatin in eukaryotic cells prevents regulatory factors from accessing genomic DNA, which requires dynamic stabilization and destabilization of structure to initiate downstream DNA activities. Those processes are achieved through altering conformational and dynamic properties of nucleosomes and nucleosome–protein complexes, of which delineating the atomistic pictures is essential to understand the mechanisms of chromatin regulation. In this review, we summarize recent progress in determining chromatin dynamics and their modulations by a number of factors including post-translational modifications (PTMs), incorporation of histone variants, and binding of effector proteins. We focus on experimental observations obtained using high-resolution techniques, primarily including nuclear magnetic resonance (NMR) spectroscopy, Förster (or fluorescence) resonance energy transfer (FRET) microscopy, and molecular dynamics (MD) simulations, and discuss the elucidated dynamics in the context of functional response and relevance.
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Affiliation(s)
- Xiangyan Shi
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Ziwei Zhai
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Yinglu Chen
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Jindi Li
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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15
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Liang L, Ji Y, Chen K, Gao P, Zhao Z, Hou G. Solid-State NMR Dipolar and Chemical Shift Anisotropy Recoupling Techniques for Structural and Dynamical Studies in Biological Systems. Chem Rev 2022; 122:9880-9942. [PMID: 35006680 DOI: 10.1021/acs.chemrev.1c00779] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With the development of NMR methodology and technology during the past decades, solid-state NMR (ssNMR) has become a particularly important tool for investigating structure and dynamics at atomic scale in biological systems, where the recoupling techniques play pivotal roles in modern high-resolution MAS NMR. In this review, following a brief introduction on the basic theory of recoupling in ssNMR, we highlight the recent advances in dipolar and chemical shift anisotropy recoupling methods, as well as their applications in structural determination and dynamical characterization at multiple time scales (i.e., fast-, intermediate-, and slow-motion). The performances of these prevalent recoupling techniques are compared and discussed in multiple aspects, together with the representative applications in biomolecules. Given the recent emerging advances in NMR technology, new challenges for recoupling methodology development and potential opportunities for biological systems are also discussed.
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Affiliation(s)
- Lixin Liang
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Ji
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuizhi Chen
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Pan Gao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Zhenchao Zhao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Guangjin Hou
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
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16
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Kanapeckaitė A, Burokienė N, Mažeikienė A, Cottrell GS, Widera D. Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies. BIOPHYSICAL REPORTS 2021; 1:100028. [PMID: 36425454 PMCID: PMC9680810 DOI: 10.1016/j.bpr.2021.100028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/24/2021] [Indexed: 06/16/2023]
Abstract
Epigenetic research holds great promise to advance our understanding of biomarkers and regulatory processes in health and disease. An increasing number of new approaches, ranging from molecular to biophysical analyses, enable identifying epigenetic changes on the level of a single gene or the whole epigenome. The aim of this review is to highlight how the field is shifting from completely molecular-biology-driven solutions to multidisciplinary strategies including more reliance on biophysical analysis tools. Biophysics not only offers technical advancements in imaging or structure analysis but also helps to explore regulatory interactions. New computational methods are also being developed to meet the demand of growing data volumes and their processing. Therefore, it is important to capture these new directions in epigenetics from a biophysical perspective and discuss current challenges as well as multiple applications of biophysical methods and tools. Specifically, we gradually introduce different biophysical research methods by first considering the DNA-level information and eventually higher-order chromatin structures. Moreover, we aim to highlight that the incorporation of bioinformatics, machine learning, and artificial intelligence into biophysical analysis allows gaining new insights into complex epigenetic processes. The gained understanding has already proven useful in translational and clinical research providing better patient stratification options or new therapeutic insights. Together, this offers a better readiness to transform bench-top experiments into industrial high-throughput applications with a possibility to employ developed methods in clinical practice and diagnostics.
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Affiliation(s)
- Austė Kanapeckaitė
- Algorithm379, Laisvės g. 7, LT 12007, Vilnius, Lithuania
- Reading School of Pharmacy, Whiteknights, Reading, UK, RG6 6UB
| | - Neringa Burokienė
- Clinics of Internal Diseases, Family Medicine and Oncology, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, M. K. Čiurlionio str. 21/27, LT-03101 Vilnius, Lithuania
| | - Asta Mažeikienė
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Institute of Biomedical Sciences, Faculty of Medicine, M. K. Čiurlionio str. 21/27, LT-03101 Vilnius, Lithuania
| | | | - Darius Widera
- Reading School of Pharmacy, Whiteknights, Reading, UK, RG6 6UB
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17
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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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18
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Shoaib M, Chen Q, Shi X, Nair N, Prasanna C, Yang R, Walter D, Frederiksen KS, Einarsson H, Svensson JP, Liu CF, Ekwall K, Lerdrup M, Nordenskiöld L, Sørensen CS. Histone H4 lysine 20 mono-methylation directly facilitates chromatin openness and promotes transcription of housekeeping genes. Nat Commun 2021; 12:4800. [PMID: 34417450 PMCID: PMC8379281 DOI: 10.1038/s41467-021-25051-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 07/15/2021] [Indexed: 12/26/2022] Open
Abstract
Histone lysine methylations have primarily been linked to selective recruitment of reader or effector proteins that subsequently modify chromatin regions and mediate genome functions. Here, we describe a divergent role for histone H4 lysine 20 mono-methylation (H4K20me1) and demonstrate that it directly facilitates chromatin openness and accessibility by disrupting chromatin folding. Thus, accumulation of H4K20me1 demarcates highly accessible chromatin at genes, and this is maintained throughout the cell cycle. In vitro, H4K20me1-containing nucleosomal arrays with nucleosome repeat lengths (NRL) of 187 and 197 are less compact than unmethylated (H4K20me0) or trimethylated (H4K20me3) arrays. Concordantly, and in contrast to trimethylated and unmethylated tails, solid-state NMR data shows that H4K20 mono-methylation changes the H4 conformational state and leads to more dynamic histone H4-tails. Notably, the increased chromatin accessibility mediated by H4K20me1 facilitates gene expression, particularly of housekeeping genes. Altogether, we show how the methylation state of a single histone H4 residue operates as a focal point in chromatin structure control. While H4K20me1 directly promotes chromatin openness at highly transcribed genes, it also serves as a stepping-stone for H4K20me3-dependent chromatin compaction. The effect of histone H4 lysine 20 methylation (H4K20me) on chromatin accessibility are not well established. Here the authors show how H4K20 methylation regulates chromatin structure and accessibility to ensure precise transcriptional outputs through the cell cycle using genome-wide approaches, in vitro biophysical assays, and NMR.
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Affiliation(s)
- Muhammad Shoaib
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Qinming Chen
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xiangyan Shi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nidhi Nair
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Chinmayi Prasanna
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Renliang Yang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Wilmar International Limited, Jurong Island, Singapore
| | - David Walter
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Hjorleifur Einarsson
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - J Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Chuan Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Mads Lerdrup
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Claus S Sørensen
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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19
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Ohtomo H, Kurita JI, Sakuraba S, Li Z, Arimura Y, Wakamori M, Tsunaka Y, Umehara T, Kurumizaka H, Kono H, Nishimura Y. The N-terminal Tails of Histones H2A and H2B Adopt Two Distinct Conformations in the Nucleosome with Contact and Reduced Contact to DNA. J Mol Biol 2021; 433:167110. [PMID: 34153285 DOI: 10.1016/j.jmb.2021.167110] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 11/28/2022]
Abstract
The nucleosome comprises two histone dimers of H2A-H2B and one histone tetramer of (H3-H4)2, wrapped around by ~145 bp of DNA. Detailed core structures of nucleosomes have been established by X-ray and cryo-EM, however, histone tails have not been visualized. Here, we have examined the dynamic structures of the H2A and H2B tails in 145-bp and 193-bp nucleosomes using NMR, and have compared them with those of the H2A and H2B tail peptides unbound and bound to DNA. Whereas the H2A C-tail adopts a single but different conformation in both nucleosomes, the N-tails of H2A and H2B adopt two distinct conformations in each nucleosome. To clarify these conformations, we conducted molecular dynamics (MD) simulations, which suggest that the H2A N-tail can locate stably in either the major or minor grooves of nucleosomal DNA. While the H2B N-tail, which sticks out between two DNA gyres in the nucleosome, was considered to adopt two different orientations, one toward the entry/exit side and one on the opposite side. Then, the H2A N-tail minor groove conformation was obtained in the H2B opposite side and the H2B N-tail interacts with DNA similarly in both sides, though more varied conformations are obtained in the entry/exit side. Collectively, the NMR findings and MD simulations suggest that the minor groove conformer of the H2A N-tail is likely to contact DNA more strongly than the major groove conformer, and the H2A N-tail reduces contact with DNA in the major groove when the H2B N-tail is located in the entry/exit side.
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Affiliation(s)
- Hideaki Ohtomo
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Jun-Ichi Kurita
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shun Sakuraba
- Institute for Quantum Life Science (iQLS), National Institutes for Quantum and Radiological Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Zhenhai Li
- Institute for Quantum Life Science (iQLS), National Institutes for Quantum and Radiological Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Yasuhiro Arimura
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Masatoshi Wakamori
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yasuo Tsunaka
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hidetoshi Kono
- Institute for Quantum Life Science (iQLS), National Institutes for Quantum and Radiological Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8258, Japan.
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20
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Rabdano SO, Shannon MD, Izmailov SA, Gonzalez Salguero N, Zandian M, Purusottam RN, Poirier MG, Skrynnikov NR, Jaroniec CP. Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Sevastyan O. Rabdano
- Laboratory of Biomolecular NMR St. Petersburg State University St. Petersburg 199034 Russian Federation
| | - Matthew D. Shannon
- Department of Chemistry and Biochemistry The Ohio State University Columbus OH 43210 USA
| | - Sergei A. Izmailov
- Laboratory of Biomolecular NMR St. Petersburg State University St. Petersburg 199034 Russian Federation
| | | | - Mohamad Zandian
- Department of Chemistry and Biochemistry The Ohio State University Columbus OH 43210 USA
| | - Rudra N. Purusottam
- Department of Chemistry and Biochemistry The Ohio State University Columbus OH 43210 USA
| | | | - Nikolai R. Skrynnikov
- Laboratory of Biomolecular NMR St. Petersburg State University St. Petersburg 199034 Russian Federation
- Department of Chemistry Purdue University West Lafayette IN 47906 USA
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21
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Rabdano SO, Shannon MD, Izmailov SA, Gonzalez Salguero N, Zandian M, Purusottam RN, Poirier MG, Skrynnikov NR, Jaroniec CP. Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA. Angew Chem Int Ed Engl 2021; 60:6480-6487. [PMID: 33522067 DOI: 10.1002/anie.202012046] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/15/2020] [Indexed: 12/21/2022]
Abstract
The interaction of positively charged N-terminal histone tails with nucleosomal DNA plays an important role in chromatin assembly and regulation, modulating their susceptibility to post-translational modifications and recognition by chromatin-binding proteins. Here, we report residue-specific 15 N NMR relaxation rates for histone H4 tails in reconstituted nucleosomes. These data indicate that H4 tails are strongly dynamically disordered, albeit with reduced conformational flexibility compared to a free peptide with the same sequence. Remarkably, the NMR observables were successfully reproduced in a 2-μs MD trajectory of the nucleosome. This is an important step toward resolving an apparent inconsistency where prior simulations were generally at odds with experimental evidence on conformational dynamics of histone tails. Our findings indicate that histone H4 tails engage in a fuzzy interaction with nucleosomal DNA, underpinned by a variable pattern of short-lived salt bridges and hydrogen bonds, which persists at low ionic strength (0-100 mM NaCl).
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Affiliation(s)
- Sevastyan O Rabdano
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russian Federation
| | - Matthew D Shannon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Sergei A Izmailov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russian Federation
| | | | - Mohamad Zandian
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Rudra N Purusottam
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Nikolai R Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russian Federation.,Department of Chemistry, Purdue University, West Lafayette, IN, 47906, USA
| | - Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
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22
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Linker histone defines structure and self-association behaviour of the 177 bp human chromatosome. Sci Rep 2021; 11:380. [PMID: 33432055 PMCID: PMC7801413 DOI: 10.1038/s41598-020-79654-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 12/08/2020] [Indexed: 01/02/2023] Open
Abstract
Linker histones play essential roles in the regulation and maintenance of the dynamic chromatin structure of higher eukaryotes. The influence of human histone H1.0 on the nucleosome structure and biophysical properties of the resulting chromatosome were investigated and compared with the 177-bp nucleosome using Cryo-EM and SAXS. The 4.5 Å Cryo-EM chromatosome structure showed that the linker histone binds at the nucleosome dyad interacting with both linker DNA arms but in a tilted manner leaning towards one of the linker sides. The chromatosome is laterally compacted and rigid in the dyad and linker DNA area, in comparison with the nucleosome where linker DNA region is more flexible and displays structural variability. In solution, the chromatosomes appear slightly larger than the nucleosomes, with the volume increase compared to the bound linker histone, according to solution SAXS measurements. SAXS X-ray diffraction characterisation of Mg-precipitated samples showed that the different shapes of the 177 chromatosome enabled the formation of a highly ordered lamello-columnar phase when precipitated by Mg2+, indicating the influence of linker histone on the nucleosome stacking. The biological significance of linker histone, therefore, may be affected by the change in the polyelectrolyte and DNA conformation properties of the chromatosomes, in comparison to nucleosomes.
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23
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le Paige UB, Xiang S, Hendrix MMRM, Zhang Y, Folkers GE, Weingarth M, Bonvin AMJJ, Kutateladze TG, Voets IK, Baldus M, van Ingen H. Characterization of nucleosome sediments for protein interaction studies by solid-state NMR spectroscopy. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:187-202. [PMID: 35647606 PMCID: PMC9135053 DOI: 10.5194/mr-2-187-2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Regulation of DNA-templated processes such as gene transcription and DNA repair depend on the interaction of a wide range of proteins with the nucleosome, the fundamental building block of chromatin. Both solution and solid-state NMR spectroscopy have become an attractive approach to study the dynamics and interactions of nucleosomes, despite their high molecular weight of ~ 200 kDa. For solid-state NMR (ssNMR) studies, dilute solutions of nucleosomes are converted to a dense phase by sedimentation or precipitation. Since nucleosomes are known to self-associate, these dense phases may induce extensive interactions between nucleosomes, which could interfere with protein-binding studies. Here, we characterized the packing of nucleosomes in the dense phase created by sedimentation using NMR and small-angle X-ray scattering (SAXS) experiments. We found that nucleosome sediments are gels with variable degrees of solidity, have nucleosome concentration close to that found in crystals, and are stable for weeks under high-speed magic angle spinning (MAS). Furthermore, SAXS data recorded on recovered sediments indicate that there is no pronounced long-range ordering of nucleosomes in the sediment. Finally, we show that the sedimentation approach can also be used to study low-affinity protein interactions with the nucleosome. Together, our results give new insights into the sample characteristics of nucleosome sediments for ssNMR studies and illustrate the broad applicability of sedimentation-based NMR studies.
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Affiliation(s)
- Ulric B. le Paige
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - ShengQi Xiang
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Marco M. R. M. Hendrix
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands
| | - Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Gert E. Folkers
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Markus Weingarth
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Alexandre M. J. J. Bonvin
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Tatiana G. Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Ilja K. Voets
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands
| | - Marc Baldus
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Hugo van Ingen
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
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Dynamic networks observed in the nucleosome core particles couple the histone globular domains with DNA. Commun Biol 2020; 3:639. [PMID: 33128005 PMCID: PMC7599221 DOI: 10.1038/s42003-020-01369-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022] Open
Abstract
The dynamics of eukaryotic nucleosomes are essential in gene activity and well regulated by various factors. Here, we elucidated the internal dynamics at multiple timescales for the human histones hH3 and hH4 in the Widom 601 nucleosome core particles (NCP), suggesting that four dynamic networks are formed by the residues exhibiting larger-scale μs-ms motions that extend from the NCP core to the histone tails and DNA. Furthermore, despite possessing highly conserved structural features, histones in the telomeric NCP exhibit enhanced μs-ms dynamics in the globular sites residing at the identified dynamic networks and in a neighboring region. In addition, higher mobility was observed for the N-terminal tails of hH3 and hH4 in the telomeric NCP. The results demonstrate the existence of dynamic networks in nucleosomes, through which the center of the core regions could interactively communicate with histone tails and DNA to potentially propagate epigenetic changes. Shi et al. use solid-state nuclear magnetic resonance spectroscopy to reveal the internal dynamics of human histones hH3 and hH4 in the Widom 601 and the telomeric nucleosome core particles. This work has implications for the propagation of epigenetic changes via the center of the nucleosome core communicating with histone tails and DNA.
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25
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Shi X, Prasanna C, Pervushin K, Nordenskiöld L. Solid-state NMR 13C, 15N assignments of human histone H3 in the nucleosome core particle. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:99-104. [PMID: 31907727 DOI: 10.1007/s12104-020-09927-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
Nucleosome core particle (NCP), the basic unit of chromatin in eukaryotic cells, consists of ~ 147 bp DNA wrapped around a histone octamer (HO) formed by two H2A-H2B dimers and one (H3-H4)2 tetramer. Histones undergo various post-translational modifications (PTMs), which regulates genomic activities in different cellular phases. High-resolution structures have been solved for many nucleosomes primarily including NCPs. However, the atomic-resolution structures of nucleosome arrays and chromatin fiber, as well as the dynamics of nucleosomes remain poorly understood. Solid-state NMR (SSNMR) is one of the premier techniques to answer these questions. In this study, we present the 13C and 15N chemical shifts assignments for the globular domain of human histone H3 (hH3) using multidimensional SSNMR experiments. The obtained spectra are of outstanding resolution and the assignments are nearly 100% complete for the backbone 13C and 15N spins of R42-G132 and ~ 80% when taking into account the side chains. The secondary structure derived from the chemical shifts agrees with the previously reported X-ray crystal structure. The reported chemical shifts can be carried over to future SSNMR studies of structure and dynamics of hH3 in NCPs, nucleosome array, chromatin fibers and nucleosome-protein complexes.
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Affiliation(s)
- Xiangyan Shi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.
| | - Chinmayi Prasanna
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Konstantin Pervushin
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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26
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Linking chromatin composition and structural dynamics at the nucleosome level. Curr Opin Struct Biol 2019; 56:46-55. [DOI: 10.1016/j.sbi.2018.11.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 01/31/2023]
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Abstract
Nucleosomes and chromatin control eukaryotic genome accessibility and thereby regulate DNA processes, including transcription, replication, and repair. Conformational dynamics within the nucleosome and chromatin structure play a key role in this regulatory function. Structural fluctuations continuously expose internal DNA sequences and nucleosome surfaces, thereby providing transient access for the nuclear machinery. Progress in structural studies of nucleosomes and chromatin has provided detailed insight into local chromatin organization and has set the stage for recent in-depth investigations of the structural dynamics of nucleosomes and chromatin fibers. Here, we discuss the dynamic processes observed in chromatin over different length scales and timescales and review current knowledge about the biophysics of distinct structural transitions.
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Affiliation(s)
- Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Michael G. Poirier
- Department of Physics, Biophysics Graduate Program, Ohio State Biochemistry Graduate Program, and Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210-1117, USA
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van Emmerik CL, van Ingen H. Unspinning chromatin: Revealing the dynamic nucleosome landscape by NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 110:1-19. [PMID: 30803691 DOI: 10.1016/j.pnmrs.2019.01.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 05/09/2023]
Abstract
NMR is an essential technique for obtaining information at atomic resolution on the structure, motions and interactions of biomolecules. Here, we review the contribution of NMR to our understanding of the fundamental unit of chromatin: the nucleosome. Nucleosomes compact the genome by wrapping the DNA around a protein core, the histone octamer, thereby protecting genomic integrity. Crucially, the imposed barrier also allows strict regulation of gene expression, DNA replication and DNA repair processes through an intricate system of histone and DNA modifications and a wide range of interactions between nucleosomes and chromatin factors. In this review, we describe how NMR has contributed to deciphering the molecular basis of nucleosome function. Starting from pioneering studies in the 1960s using natural abundance NMR studies, we focus on the progress in sample preparation and NMR methodology that has allowed high-resolution studies on the nucleosome and its subunits. We summarize the results and approaches of state-of-the-art NMR studies on nucleosomal DNA, histone complexes, nucleosomes and nucleosomal arrays. These studies highlight the particular strength of NMR in studying nucleosome dynamics and nucleosome-protein interactions. Finally, we look ahead to exciting new possibilities that will be afforded by on-going developments in solution and solid-state NMR. By increasing both the depth and breadth of nucleosome NMR studies, it will be possible to offer a unique perspective on the dynamic landscape of nucleosomes and its interacting proteins.
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Affiliation(s)
- Clara L van Emmerik
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.
| | - Hugo van Ingen
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.
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29
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Zhou K, Gaullier G, Luger K. Nucleosome structure and dynamics are coming of age. Nat Struct Mol Biol 2018; 26:3-13. [PMID: 30532059 DOI: 10.1038/s41594-018-0166-x] [Citation(s) in RCA: 180] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/07/2018] [Indexed: 11/09/2022]
Abstract
Since the first high-resolution structure of the nucleosome was reported in 1997, the available information on chromatin structure has increased very rapidly. Here, we review insights derived from cutting-edge biophysical and structural approaches applied to the study of nucleosome dynamics and nucleosome-binding factors, with a focus on the experimental advances driving the research. In addition, we highlight emerging challenges in nucleosome structural biology.
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Affiliation(s)
- Keda Zhou
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Guillaume Gaullier
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA. .,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA.
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