1
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Laeremans W, Segers M, Voorspoels A, Carlon E, Hooyberghs J. Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs cgDNA. J Chem Phys 2024; 160:144105. [PMID: 38591677 DOI: 10.1063/5.0197053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/19/2024] [Indexed: 04/10/2024] Open
Abstract
Coarse-grained models have emerged as valuable tools to simulate long DNA molecules while maintaining computational efficiency. These models aim at preserving interactions among coarse-grained variables in a manner that mirrors the underlying atomistic description. We explore here a method for testing coarse-grained vs all-atom models using stiffness matrices in Fourier space (q-stiffnesses), which are particularly suited to probe DNA elasticity at different length scales. We focus on a class of coarse-grained rigid base DNA models known as cgDNA and its most recent version, cgDNA+. Our analysis shows that while cgDNA+ closely follows the q-stiffnesses of the all-atom model, the original cgDNA shows some deviations for twist and bending variables, which are rather strong in the q → 0 (long length scale) limit. The consequence is that while both cgDNA and cgDNA+ give a suitable description of local elastic behavior, the former misses some effects that manifest themselves at longer length scales. In particular, cgDNA performs poorly on twist stiffness, with a value much lower than expected for long DNA molecules. Conversely, the all-atom and cgDNA+ twist are strongly length scale dependent: DNA is torsionally soft at a few base pair distances but becomes more rigid at distances of a few dozen base pairs. Our analysis shows that the bending persistence length in all-atom and cgDNA+ is somewhat overestimated.
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Affiliation(s)
- Wout Laeremans
- Soft Matter and Biological Physics, Department of Applied Physics, and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, Netherlands
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
- UHasselt, Faculty of Sciences, Data Science Institute, Theory Lab, Agoralaan, 3590 Diepenbeek, Belgium
| | - Midas Segers
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Aderik Voorspoels
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Enrico Carlon
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Jef Hooyberghs
- UHasselt, Faculty of Sciences, Data Science Institute, Theory Lab, Agoralaan, 3590 Diepenbeek, Belgium
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2
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Khatua P, Tang PK, Ghosh Moulick A, Patel R, Manandhar A, Loverde SM. Sequence Dependence in Nucleosome Dynamics. J Phys Chem B 2024; 128:3090-3101. [PMID: 38530903 DOI: 10.1021/acs.jpcb.3c07363] [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] [Indexed: 03/28/2024]
Abstract
The basic packaging unit of eukaryotic chromatin is the nucleosome that contains 145-147 base pair duplex DNA wrapped around an octameric histone protein. While the DNA sequence plays a crucial role in controlling the positioning of the nucleosome, the molecular details behind the interplay between DNA sequence and nucleosome dynamics remain relatively unexplored. This study analyzes this interplay in detail by performing all-atom molecular dynamics simulations of nucleosomes, comparing the human α-satellite palindromic (ASP) and the strong positioning "Widom-601" DNA sequence at time scales of 12 μs. The simulations are performed at salt concentrations 10-20 times higher than physiological salt concentrations to screen the electrostatic interactions and promote unwrapping. These microsecond-long simulations give insight into the molecular-level sequence-dependent events that dictate the pathway of DNA unwrapping. We find that the "ASP" sequence forms a loop around SHL ± 5 for three sets of simulations. Coincident with loop formation is a cooperative increase in contacts with the neighboring N-terminal H2B tail and C-terminal H2A tail and the release of neighboring counterions. We find that the Widom-601 sequence exhibits a strong breathing motion of the nucleic acid ends. Coincident with the breathing motion is the collapse of the full N-terminal H3 tail and formation of an α-helix that interacts with the H3 histone core. We postulate that the dynamics of these histone tails and their modification with post-translational modifications (PTMs) may play a key role in governing this dynamics.
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Affiliation(s)
- Prabir Khatua
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314, United States
| | - Phu K Tang
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Abhik Ghosh Moulick
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314, United States
| | - Rutika Patel
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Anjela Manandhar
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Sharon M Loverde
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Ph.D. Program in Physics, The Graduate Center of the City University of New York, New York, New York 10016, United States
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3
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Kapoor U, Kim YC, Mittal J. Coarse-Grained Models to Study Protein-DNA Interactions and Liquid-Liquid Phase Separation. J Chem Theory Comput 2024; 20:1717-1731. [PMID: 37988476 PMCID: PMC10911113 DOI: 10.1021/acs.jctc.3c00525] [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: 05/19/2023] [Revised: 10/20/2023] [Accepted: 10/27/2023] [Indexed: 11/23/2023]
Abstract
Recent advances in coarse-grained (CG) computational models for DNA have enabled molecular-level insights into the behavior of DNA in complex multiscale systems. However, most existing CG DNA models are not compatible with CG protein models, limiting their applications for emerging topics such as protein-nucleic acid assemblies. Here, we present a new computationally efficient CG DNA model. We first use experimental data to establish the model's ability to predict various aspects of DNA behavior, including melting thermodynamics and relevant local structural properties such as the major and minor grooves. We then employ an all-atom hydropathy scale to define nonbonded interactions between protein and DNA sites, to make our DNA model compatible with an existing CG protein model (HPS-Urry), which is extensively used to study protein phase separation, and show that our new model reasonably reproduces the experimental binding affinity for a prototypical protein-DNA system. To further demonstrate the capabilities of this new model, we simulate a full nucleosome with and without histone tails, on a microsecond time scale, generating conformational ensembles and provide molecular insights into the role of histone tails in influencing the liquid-liquid phase separation (LLPS) of HP1α proteins. We find that histone tails interact favorably with DNA, influencing the conformational ensemble of the DNA and antagonizing the contacts between HP1α and DNA, thus affecting the ability of DNA to promote LLPS of HP1α. These findings shed light on the complex molecular framework that fine-tunes the phase transition properties of heterochromatin proteins and contributes to heterochromatin regulation and function. Overall, the CG DNA model presented here is suitable to facilitate micrometer-scale studies with sub-nm resolution in many biological and engineering applications and can be used to investigate protein-DNA complexes, such as nucleosomes, or LLPS of proteins with DNA, enabling a mechanistic understanding of how molecular information may be propagated at the genome level.
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Affiliation(s)
- Utkarsh Kapoor
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 78743, United States
| | - Young C. Kim
- Center
for Materials Physics and Technology, Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Jeetain Mittal
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 78743, United States
- Department
of Chemistry, Texas A&M University, College Station, Texas 78743, United States
- Interdisciplinary
Graduate Program in Genetics in Genomics, Texas A&M University, College
Station, Texas 78743, United States
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4
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Chakraborty D, Mondal B, Thirumalai D. Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA-Protein Complexes. J Chem Theory Comput 2024; 20:1398-1413. [PMID: 38241144 DOI: 10.1021/acs.jctc.3c00833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
DNA-protein interactions are pervasive in a number of biophysical processes ranging from transcription and gene expression to chromosome folding. To describe the structural and dynamic properties underlying these processes accurately, it is important to create transferable computational models. Toward this end, we introduce Coarse-grained Force Field for Energy Estimation, COFFEE, a robust framework for simulating DNA-protein complexes. To brew COFFEE, we integrated the energy function in the self-organized polymer model with side-chains for proteins and the three interaction site model for DNA in a modular fashion, without recalibrating any of the parameters in the original force-fields. A unique feature of COFFEE is that it describes sequence-specific DNA-protein interactions using a statistical potential (SP) derived from a data set of high-resolution crystal structures. The only parameter in COFFEE is the strength (λDNAPRO) of the DNA-protein contact potential. For an optimal choice of λDNAPRO, the crystallographic B-factors for DNA-protein complexes with varying sizes and topologies are quantitatively reproduced. Without any further readjustments to the force-field parameters, COFFEE predicts scattering profiles that are in quantitative agreement with small-angle X-ray scattering experiments, as well as chemical shifts that are consistent with NMR. We also show that COFFEE accurately describes the salt-induced unraveling of nucleosomes. Strikingly, our nucleosome simulations explain the destabilization effect of ARG to LYS mutations, which do not alter the balance of electrostatic interactions but affect chemical interactions in subtle ways. The range of applications attests to the transferability of COFFEE, and we anticipate that it would be a promising framework for simulating DNA-protein complexes at the molecular length-scale.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
| | - Balaka Mondal
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
- Department of Physics, The University of Texas at Austin, 2515 Speedway, Austin 78712, Texas, United States
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5
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Chakraborty D, Mondal B, Thirumalai D. Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544064. [PMID: 37333386 PMCID: PMC10274755 DOI: 10.1101/2023.06.07.544064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
DNA-protein interactions are pervasive in a number of biophysical processes ranging from transcription, gene expression, to chromosome folding. To describe the structural and dynamic properties underlying these processes accurately, it is important to create transferable computational models. Toward this end, we introduce Coarse grained force field for energy estimation, COFFEE, a robust framework for simulating DNA-protein complexes. To brew COFFEE, we integrated the energy function in the Self-Organized Polymer model with Side Chains for proteins and the Three Interaction Site model for DNA in a modular fashion, without re-calibrating any of the parameters in the original force-fields. A unique feature of COFFEE is that it describes sequence-specific DNA-protein interactions using a statistical potential (SP) derived from a dataset of high-resolution crystal structures. The only parameter in COFFEE is the strength (λ D N A P R O ) of the DNA-protein contact potential. For an optimal choice of λ D N A P R O , the crystallographic B-factors for DNA-protein complexes, with varying sizes and topologies, are quantitatively reproduced. Without any further readjustments to the force-field parameters, COFFEE predicts the scattering profiles that are in quantitative agreement with SAXS experiments as well as chemical shifts that are consistent with NMR. We also show that COFFEE accurately describes the salt-induced unraveling of nucleosomes. Strikingly, our nucleosome simulations explain the destabilization effect of ARG to LYS mutations, which does not alter the balance of electrostatic interactions, but affects chemical interactions in subtle ways. The range of applications attests to the transferability of COFFEE, and we anticipate that it would be a promising framework for simulating DNA-protein complexes at the molecular length-scale.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA
| | - Balaka Mondal
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA
- Department of Physics, The University of Texas at Austin, 2515 Speedway,Austin TX 78712, USA
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6
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Portillo-Ledesma S, Li Z, Schlick T. Genome modeling: From chromatin fibers to genes. Curr Opin Struct Biol 2023; 78:102506. [PMID: 36577295 PMCID: PMC9908845 DOI: 10.1016/j.sbi.2022.102506] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/01/2022] [Accepted: 11/06/2022] [Indexed: 12/27/2022]
Abstract
The intricacies of the 3D hierarchical organization of the genome have been approached by many creative modeling studies. The specific model/simulation technique combination defines and restricts the system and phenomena that can be investigated. We present the latest modeling developments and studies of the genome, involving models ranging from nucleosome systems and small polynucleosome arrays to chromatin fibers in the kb-range, chromosomes, and whole genomes, while emphasizing gene folding from first principles. Clever combinations allow the exploration of many interesting phenomena involved in gene regulation, such as nucleosome structure and dynamics, nucleosome-nucleosome stacking, polynucleosome array folding, protein regulation of chromatin architecture, mechanisms of gene folding, loop formation, compartmentalization, and structural transitions at the chromosome and genome levels. Gene-level modeling with full details on nucleosome positions, epigenetic factors, and protein binding, in particular, can in principle be scaled up to model chromosomes and cells to study fundamental biological regulation.
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Affiliation(s)
- Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, 10003, NY, USA
| | - Zilong Li
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, 10003, NY, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, 10003, NY, USA; Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, 10012, NY, USA; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Room 340, Geography Building, 3663 North Zhongshan Road, Shanghai, 200122, China; Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, 10003, NY, USA.
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7
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Erkelens AM, Henneman B, van der Valk RA, Kirolos NCS, Dame RT. Specific DNA binding of archaeal histones HMfA and HMfB. Front Microbiol 2023; 14:1166608. [PMID: 37143534 PMCID: PMC10151503 DOI: 10.3389/fmicb.2023.1166608] [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: 02/15/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
In archaea, histones play a role in genome compaction and are involved in transcription regulation. Whereas archaeal histones bind DNA without sequence specificity, they bind preferentially to DNA containing repeats of alternating A/T and G/C motifs. These motifs are also present on the artificial sequence "Clone20," a high-affinity model sequence for binding of the histones from Methanothermus fervidus. Here, we investigate the binding of HMfA and HMfB to Clone20 DNA. We show that specific binding at low protein concentrations (<30 nM) yields a modest level of DNA compaction, attributed to tetrameric nucleosome formation, whereas nonspecific binding strongly compacts DNA. We also demonstrate that histones impaired in hypernucleosome formation are still able to recognize the Clone20 sequence. Histone tetramers indeed exhibit a higher binding affinity for Clone20 than nonspecific DNA. Our results indicate that a high-affinity DNA sequence does not act as a nucleation site, but is bound by a tetramer which we propose is geometrically different from the hypernucleosome. Such a mode of histone binding might permit sequence-driven modulation of hypernucleosome size. These findings might be extrapolated to histone variants that do not form hypernucleosomes. Versatile binding modes of histones could provide a platform for functional interplay between genome compaction and transcription.
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Affiliation(s)
| | - Bram Henneman
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | | | | | - Remus T. Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, Netherlands
- *Correspondence: Remus T. Dame,
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8
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Zuiddam M, Shakiba B, Schiessel H. Multiplexing mechanical and translational cues on genes. Biophys J 2022; 121:4311-4324. [PMID: 36230003 PMCID: PMC9703045 DOI: 10.1016/j.bpj.2022.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 07/06/2022] [Accepted: 10/07/2022] [Indexed: 12/14/2022] Open
Abstract
The genetic code gives precise instructions on how to translate codons into amino acids. Due to the degeneracy of the genetic code-18 out of 20 amino acids are encoded for by more than one codon-more information can be stored in a basepair sequence. Indeed, various types of additional information have been discussed in the literature, e.g., the positioning of nucleosomes along eukaryotic genomes and the modulation of the translating efficiency in ribosomes to influence cotranslational protein folding. The purpose of this study is to show that it is indeed possible to carry more than one additional layer of information on top of a gene. In particular, we show how much translation efficiency and nucleosome positioning can be adjusted simultaneously without changing the encoded protein. We achieve this by mapping genes on weighted graphs that contain all synonymous genes, and then finding shortest paths through these graphs. This enables us, for example, to readjust the disrupted translational efficiency profile after a gene has been introduced from one organism (e.g., human) into another (e.g., yeast) without greatly changing the nucleosome landscape intrinsically encoded by the DNA molecule.
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Affiliation(s)
- Martijn Zuiddam
- Institute Lorentz for Theoretical Physics, Leiden University, Leiden, the Netherlands
| | - Bahareh Shakiba
- Institute Lorentz for Theoretical Physics, Leiden University, Leiden, the Netherlands
| | - Helmut Schiessel
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany.
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9
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MacCarthy CM, Huertas J, Ortmeier C, Vom Bruch H, Tan DS, Reinke D, Sander A, Bergbrede T, Jauch R, Schöler HR, Cojocaru V. OCT4 interprets and enhances nucleosome flexibility. Nucleic Acids Res 2022; 50:10311-10327. [PMID: 36130732 PMCID: PMC9561370 DOI: 10.1093/nar/gkac755] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 07/28/2022] [Accepted: 08/24/2022] [Indexed: 01/06/2023] Open
Abstract
Pioneer transcription factors are proteins that induce cellular identity transitions by binding to inaccessible regions of DNA in nuclear chromatin. They contribute to chromatin opening and recruit other factors to regulatory DNA elements. The structural features and dynamics modulating their interaction with nucleosomes are still unresolved. From a combination of experiments and molecular simulations, we reveal here how the pioneer factor and master regulator of pluripotency, Oct4, interprets and enhances nucleosome structural flexibility. The magnitude of Oct4’s impact on nucleosome dynamics depends on the binding site position and the mobility of the unstructured tails of nucleosomal histone proteins. Oct4 uses both its DNA binding domains to propagate and stabilize open nucleosome conformations, one for specific sequence recognition and the other for nonspecific interactions with nearby regions of DNA. Our findings provide a structural basis for the versatility of transcription factors in engaging with nucleosomes and have implications for understanding how pioneer factors induce chromatin dynamics.
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Affiliation(s)
- Caitlin M MacCarthy
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Jan Huertas
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Yusuf Hamied Department of Chemistry, University of Cambridge, UK
| | - Claudia Ortmeier
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Hermann Vom Bruch
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Daisylyn Senna Tan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Deike Reinke
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Astrid Sander
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Hans R Schöler
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Medical Faculty, University of Münster, Germany
| | - Vlad Cojocaru
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Computational Structural Biology Group, University of Utrecht, The Netherlands.,STAR-UBB Institute, Babeş-Bolyai University, Cluj-Napoca, Romania
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10
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Korolev N, Zinchenko A, Soman A, Chen Q, Wong SY, Berezhnoy NV, Basak R, van der Maarel JRC, van Noort J, Nordenskiöld L. Reconstituted TAD-size chromatin fibers feature heterogeneous nucleosome clusters. Sci Rep 2022; 12:15558. [PMID: 36114220 PMCID: PMC9481575 DOI: 10.1038/s41598-022-19471-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/30/2022] [Indexed: 11/14/2022] Open
Abstract
Large topologically associated domains (TADs) contain irregularly spaced nucleosome clutches, and interactions between such clutches are thought to aid the compaction of these domains. Here, we reconstituted TAD-sized chromatin fibers containing hundreds of nucleosomes on native source human and lambda-phage DNA and compared their mechanical properties at the single-molecule level with shorter ‘601’ arrays with various nucleosome repeat lengths. Fluorescent imaging showed increased compaction upon saturation of the DNA with histones and increasing magnesium concentration. Nucleosome clusters and their structural fluctuations were visualized in confined nanochannels. Force spectroscopy revealed not only similar mechanical properties of the TAD-sized fibers as shorter fibers but also large rupture events, consistent with breaking the interactions between distant clutches of nucleosomes. Though the arrays of native human DNA, lambda-phage and ‘601’ DNA featured minor differences in reconstitution yield and nucleosome stability, the fibers’ global structural and mechanical properties were similar, including the interactions between nucleosome clutches. These single-molecule experiments quantify the mechanical forces that stabilize large TAD-sized chromatin domains consisting of disordered, dynamically interacting nucleosome clutches and their effect on the condensation of large chromatin domains.
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11
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Kim J, Sheu KM, Cheng QJ, Hoffmann A, Enciso G. Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling. Cell Rep 2022; 40:111076. [PMID: 35830792 PMCID: PMC10074953 DOI: 10.1016/j.celrep.2022.111076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 02/17/2022] [Accepted: 06/20/2022] [Indexed: 11/21/2022] Open
Abstract
The genomic positions of nucleosomes are a defining feature of the cell's epigenomic state, but signal-dependent transcription factors (SDTFs), upon activation, bind to specific genomic locations and modify nucleosome positioning. Here we leverage SDTFs as perturbation probes to learn about nucleosome dynamics in living cells. We develop Markov models of nucleosome dynamics and fit them to time course sequencing data of DNA accessibility. We find that (1) the dynamics of DNA unwrapping are significantly slower in cells than reported from cell-free experiments, (2) only models with cooperativity in wrapping and unwrapping fit the available data, (3) SDTF activity produces the highest eviction probability when its binding site is adjacent to but not on the nucleosome dyad, and (4) oscillatory SDTF activity results in high location variability. Our work uncovers the regulatory rules governing SDTF-induced nucleosome dynamics in live cells, which can predict chromatin accessibility alterations during inflammation at single-nucleosome resolution.
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Affiliation(s)
- Jinsu Kim
- Department of Mathematics, Pohang University of Science and Technology, Pohang, South Korea
| | - Katherine M Sheu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Quen J Cheng
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Medicine, Division of Infectious Diseases, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alexander Hoffmann
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA.
| | - German Enciso
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.
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12
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Sommer JU, Merlitz H, Schiessel H. Polymer-Assisted Condensation: A Mechanism for Hetero-Chromatin Formation and Epigenetic Memory. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00244] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Jens-Uwe Sommer
- Leibniz-Institut für Polymerforschung Dresden, Hohe Straße 6, 01069 Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, 01307 Dresden, Germany
| | - Holger Merlitz
- Leibniz-Institut für Polymerforschung Dresden, Hohe Straße 6, 01069 Dresden, Germany
| | - Helmut Schiessel
- Cluster of Excellence Physics of Life, TU Dresden, 01307 Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, Zellescher Weg 17, 01062 Dresden, Germany
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13
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Galaxy Dnpatterntools for Computational Analysis of Nucleosome Positioning Sequence Patterns. Int J Mol Sci 2022; 23:ijms23094869. [PMID: 35563261 PMCID: PMC9102330 DOI: 10.3390/ijms23094869] [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: 03/30/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 01/25/2023] Open
Abstract
Nucleosomes are basic units of DNA packing in eukaryotes. Their structure is well conserved from yeast to human and consists of the histone octamer core and 147 bp DNA wrapped around it. Nucleosomes are bound to a majority of the eukaryotic genomic DNA, including its regulatory regions. Hence, they also play a major role in gene regulation. For the latter, their precise positioning on DNA is essential. In the present paper, we describe Galaxy dnpatterntools—software package for nucleosome DNA sequence analysis and mapping. This software will be useful for computational biologists practitioners to conduct more profound studies of gene regulatory mechanisms.
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Huertas J, Woods EJ, Collepardo-Guevara R. Multiscale modelling of chromatin organisation: Resolving nucleosomes at near-atomistic resolution inside genes. Curr Opin Cell Biol 2022; 75:102067. [DOI: 10.1016/j.ceb.2022.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/24/2022] [Accepted: 02/04/2022] [Indexed: 12/15/2022]
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15
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Giniūnaitė R, Petkevičiūtė-Gerlach D. Predicting the configuration and energy of DNA in a nucleosome by coarse-grain modelling. Phys Chem Chem Phys 2022; 24:26124-26133. [DOI: 10.1039/d2cp03553g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We present a novel algorithm which uses a coarse-grained model and an energy minimisation procedure to predict the sequence-dependent DNA configuration in a nucleosome together with its energetic cost.
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Affiliation(s)
- Rasa Giniūnaitė
- Department of Applied Mathematics, Kaunas University of Technology, Studentų 50-318, 51368, Kaunas, Lithuania
- Institute of Applied Mathematics, Vilnius University, Naugarduko 24, 03225, Vilnius, Lithuania
| | - Daiva Petkevičiūtė-Gerlach
- Department of Applied Mathematics, Kaunas University of Technology, Studentų 50-318, 51368, Kaunas, Lithuania
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16
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Reddy G, Thirumalai D. Asymmetry in histone rotation in forced unwrapping and force quench rewrapping in a nucleosome. Nucleic Acids Res 2021; 49:4907-4918. [PMID: 33877361 PMCID: PMC8136794 DOI: 10.1093/nar/gkab263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/25/2021] [Accepted: 03/30/2021] [Indexed: 01/07/2023] Open
Abstract
Single molecule pulling experiments have shown that DNA in the nucleosomes unwraps in two stages from the histone protein core (HPC). The first stage, attributed to the rupture of the outer DNA turn, occurs between 3 and 5 pNs, and is reversible. The inner DNA turn ruptures irreversibly at forces between 9 and 15 pNs (or higher) in the second stage. Molecular simulations using the Self-Organized Polymer model capture the experimental findings. The unwrapping of the outer DNA turn is independent of the pulling direction. The rupture of the DNA inner turn depends on the pulling direction and involves overcoming substantial energetic (most likely electrostatic in origin) and kinetic barriers. They arise because the mechanical force has to generate sufficient torque to rotate the HPC by 180°. On the other hand, during the rewrapping process, HPC rotation is stochastic, with force playing no role. The assembly of the outer DNA wrap upon force quench nearly coincides with the unwrapping process, confirming the reversibility of the outer turn rupture. The asymmetry in HPC rotation during unwrapping and rewrapping explains the observed hysteresis in the stretch-release cycles in experiments. We propose experiments to test the prediction that HPC rotation produces kinetic barriers in the unwrapping process.
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Affiliation(s)
- Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - D Thirumalai
- Department of Chemistry, The University of Texas, Austin, TX 78712, USA
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Farr SE, Woods EJ, Joseph JA, Garaizar A, Collepardo-Guevara R. Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions. Nat Commun 2021; 12:2883. [PMID: 34001913 PMCID: PMC8129070 DOI: 10.1038/s41467-021-23090-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/23/2021] [Indexed: 12/19/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) is an important mechanism that helps explain the membraneless compartmentalization of the nucleus. Because chromatin compaction and LLPS are collective phenomena, linking their modulation to the physicochemical features of nucleosomes is challenging. Here, we develop an advanced multiscale chromatin model-integrating atomistic representations, a chemically-specific coarse-grained model, and a minimal model-to resolve individual nucleosomes within sub-Mb chromatin domains and phase-separated systems. To overcome the difficulty of sampling chromatin at high resolution, we devise a transferable enhanced-sampling Debye-length replica-exchange molecular dynamics approach. We find that nucleosome thermal fluctuations become significant at physiological salt concentrations and destabilize the 30-nm fiber. Our simulations show that nucleosome breathing favors stochastic folding of chromatin and promotes LLPS by simultaneously boosting the transient nature and heterogeneity of nucleosome-nucleosome contacts, and the effective nucleosome valency. Our work puts forward the intrinsic plasticity of nucleosomes as a key element in the liquid-like behavior of nucleosomes within chromatin, and the regulation of chromatin LLPS.
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Affiliation(s)
- Stephen E Farr
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Esmae J Woods
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Jerelle A Joseph
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Adiran Garaizar
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
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18
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Brouwer T, Pham C, Kaczmarczyk A, de Voogd WJ, Botto M, Vizjak P, Mueller-Planitz F, van Noort J. A critical role for linker DNA in higher-order folding of chromatin fibers. Nucleic Acids Res 2021; 49:2537-2551. [PMID: 33589918 PMCID: PMC7969035 DOI: 10.1093/nar/gkab058] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 12/04/2020] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleosome-nucleosome interactions drive the folding of nucleosomal arrays into dense chromatin fibers. A better physical account of the folding of chromatin fibers is necessary to understand the role of chromatin in regulating DNA transactions. Here, we studied the unfolding pathway of regular chromatin fibers as a function of single base pair increments in linker length, using both rigid base-pair Monte Carlo simulations and single-molecule force spectroscopy. Both computational and experimental results reveal a periodic variation of the folding energies due to the limited flexibility of the linker DNA. We show that twist is more restrictive for nucleosome stacking than bend, and find the most stable stacking interactions for linker lengths of multiples of 10 bp. We analyzed nucleosomes stacking in both 1- and 2-start topologies and show that stacking preferences are determined by the length of the linker DNA. Moreover, we present evidence that the sequence of the linker DNA also modulates nucleosome stacking and that the effect of the deletion of the H4 tail depends on the linker length. Importantly, these results imply that nucleosome positioning in vivo not only affects the phasing of nucleosomes relative to DNA but also directs the higher-order structure of chromatin.
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Affiliation(s)
- Thomas Brouwer
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
| | - Chi Pham
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
| | - Artur Kaczmarczyk
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
| | - Willem-Jan de Voogd
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
| | - Margherita Botto
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
| | - Petra Vizjak
- Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Felix Mueller-Planitz
- Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany.,Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - John van Noort
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
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19
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Gutiérrez Fosado YA, Landuzzi F, Sakaue T. Twist dynamics and buckling instability of ring DNA: the effect of groove asymmetry and anisotropic bending. SOFT MATTER 2021; 17:1530-1537. [PMID: 33331374 DOI: 10.1039/d0sm01812k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
By combining analytical theory and Molecular Dynamics simulations we study the relaxation dynamics of DNA circular plasmids that initially undergo a local twist perturbation. In this process, the twist-bend coupling arising from the groove asymmetry in the DNA double helix clearly shows up. In the two scenarios explored, with/without this coupling, the initial perturbation relaxes diffusively. However, there are some marked differences in the value of the diffusion coefficient and the dynamics in both cases. These differences can be explained by assuming the existence of three distinctive time scales; a rapid relaxation of local bending, the slow twist spreading, and the buckling transition taking place in a much longer time scale. In particular, the separation of time scales allows deducing an effective diffusion equation in stage , with a diffusion coefficient influenced by the twist-bend coupling. We also discuss the mapping of the realistic DNA model to the simpler isotropic twistable worm-like chain using the renormalized bending and twist moduli; although useful in many cases, it fails to make a quantitative prediction on the instability mode of buckling transition.
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Affiliation(s)
- Yair Augusto Gutiérrez Fosado
- Department of Physics and Mathematics, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa 252-5258, Japan.
| | - Fabio Landuzzi
- Department of Physics and Mathematics, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa 252-5258, Japan.
| | - Takahiro Sakaue
- Department of Physics and Mathematics, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa 252-5258, Japan. and PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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20
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Doğan D, Arslan M, Uluçay T, Kalyoncu S, Dimitrov S, Kale S. CENP-A Nucleosome is a Sensitive Allosteric Scaffold for DNA and Chromatin Factors. J Mol Biol 2020; 433:166789. [PMID: 33387534 DOI: 10.1016/j.jmb.2020.166789] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 12/06/2020] [Accepted: 12/18/2020] [Indexed: 02/02/2023]
Abstract
Centromeric loci of chromosomes are defined by nucleosomes containing the histone H3 variant CENP-A, which bind their DNA termini more permissively than their canonical counterpart, a feature that is critical for the mitotic fidelity. A recent cryo-EM study demonstrated that the DNA termini of CENP-A nucleosomes, reconstituted with the Widom 601 DNA sequence, are asymmetrically flexible, meaning one terminus is more clearly resolved than the other. However, an earlier work claimed that both ends could be resolved in the presence of two stabilizing single chain variable fragment (scFv) antibodies per nucleosome, and thus are likely permanently bound to the histone octamer. This suggests that the binding of scFv antibodies to the histone octamer surface would be associated with CENP-A nucleosome conformational changes, including stable binding of the DNA termini. Here, we present computational evidence that allows to explain at atomistic level the structural rearrangements of CENP-A nucleosomes resulting from the antibody binding. The antibodies, while they only bind the octamer façades, are capable of altering the dynamics of the nucleosomal core, and indirectly also the surrounding DNA. This effect has more drastic implications for the structure and the dynamics of the CENP-A nucleosome in comparison to its canonical counterpart. Furthermore, we find evidence that the antibodies bind the left and the right octamer façades at different affinities, another manifestation of the DNA sequence. We speculate that the cells could use induction of similar allosteric effects to control centromere function.
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Affiliation(s)
- Deniz Doğan
- Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir 35330, Turkey
| | - Merve Arslan
- Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir 35330, Turkey; Izmir Biomedicine and Genome Institute, Dokuz Eylül University Health Campus, Balçova, Izmir 35330, Turkey
| | - Tuğçe Uluçay
- Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir 35330, Turkey
| | - Sibel Kalyoncu
- Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir 35330, Turkey
| | - Stefan Dimitrov
- Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir 35330, Turkey; Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Seyit Kale
- Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir 35330, Turkey.
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21
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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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22
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Kono H, Ishida H. Nucleosome unwrapping and unstacking. Curr Opin Struct Biol 2020; 64:119-125. [DOI: 10.1016/j.sbi.2020.06.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 05/31/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023]
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23
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Brouwer TB, Hermans N, van Noort J. Multiplexed Nanometric 3D Tracking of Microbeads Using an FFT-Phasor Algorithm. Biophys J 2020; 118:2245-2257. [PMID: 32053775 PMCID: PMC7202940 DOI: 10.1016/j.bpj.2020.01.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 01/23/2023] Open
Abstract
Many single-molecule biophysical techniques rely on nanometric tracking of microbeads to obtain quantitative information about the mechanical properties of biomolecules such as chromatin fibers. Their three-dimensional (3D) position can be resolved by holographic analysis of the diffraction pattern in wide-field imaging. Fitting this diffraction pattern to Lorenz-Mie scattering theory yields the bead's position with nanometer accuracy in three dimensions but is computationally expensive. Real-time multiplexed bead tracking therefore requires a more efficient tracking method, such as comparison with previously measured diffraction patterns, known as look-up tables. Here, we introduce an alternative 3D phasor algorithm that provides robust bead tracking with nanometric localization accuracy in a z range of over 10 μm under nonoptimal imaging conditions. The algorithm is based on a two-dimensional cross correlation using fast Fourier transforms with computer-generated reference images, yielding a processing rate of up to 10,000 regions of interest per second. We implemented the technique in magnetic tweezers and tracked the 3D position of over 100 beads in real time on a generic CPU. The accuracy of 3D phasor tracking was extensively tested and compared to a look-up table approach using Lorenz-Mie simulations, avoiding experimental uncertainties. Its easy implementation, efficiency, and robustness can improve multiplexed biophysical bead-tracking applications, especially when high throughput is required and image artifacts are difficult to avoid.
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Affiliation(s)
- Thomas B Brouwer
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, the Netherlands
| | - Nicolaas Hermans
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, the Netherlands
| | - John van Noort
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, the Netherlands.
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24
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Moller J, de Pablo JJ. Bottom-Up Meets Top-Down: The Crossroads of Multiscale Chromatin Modeling. Biophys J 2020; 118:2057-2065. [PMID: 32320675 DOI: 10.1016/j.bpj.2020.03.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/04/2020] [Accepted: 03/20/2020] [Indexed: 01/19/2023] Open
Abstract
Chromatin can be viewed as a hierarchically structured fiber that regulates gene expression. It consists of a complex network of DNA and proteins whose characteristic dynamical modes facilitate compaction and rearrangement in the cell nucleus. These modes stem from chromatin's fundamental unit, the nucleosome, and their effects are propagated across length scales. Understanding the effects of nucleosome dynamics on the chromatin fiber, primarily through post-translational modifications that occur on the histones, is of central importance to epigenetics. Within the last decade, imaging and chromosome conformation capture techniques have revealed a number of structural and statistical features of the packaged chromatin fiber at a hitherto unavailable level of resolution. Such experiments have led to increased efforts to develop polymer models that aim to reproduce, explain, and predict the contact probability scaling and density heterogeneity. At nanometer scales, available models have focused on the role of the nucleosome and epigenetic marks on local chromatin structure. At micrometer scales, existing models have sought to explain scaling laws and density heterogeneity. Less work, however, has been done to reconcile these two approaches: bottom-up and top-down models of chromatin. In this perspective, we highlight the multiscale simulation models that are driving toward an understanding of chromatin structure and function, from the nanometer to the micron scale, and we highlight areas of opportunity and some of the prospects for new frameworks that bridge these two scales. Taken together, experimental and modeling advances over the last few years have established a robust platform for the study of chromatin fiber structure and dynamics, which will be of considerable use to the chromatin community in developing an understanding of the interplay between epigenomic regulation and molecular structure.
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Affiliation(s)
- Joshua Moller
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Juan J de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois; Material Science Division, Argonne National Laboratory, Lemont, Illinois.
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25
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Schnepf M, Ludwig C, Bandilla P, Ceolin S, Unnerstall U, Jung C, Gaul U. Sensitive Automated Measurement of Histone-DNA Affinities in Nucleosomes. iScience 2020; 23:100824. [PMID: 31982782 PMCID: PMC6994541 DOI: 10.1016/j.isci.2020.100824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/12/2019] [Accepted: 01/06/2020] [Indexed: 11/06/2022] Open
Abstract
The DNA of eukaryotes is wrapped around histone octamers to form nucleosomes. Although it is well established that the DNA sequence significantly influences nucleosome formation, its precise contribution has remained controversial, partially owing to the lack of quantitative affinity data. Here, we present a method to measure DNA-histone binding free energies at medium throughput and with high sensitivity. Competitive nucleosome formation is achieved through automation, and a modified epifluorescence microscope is used to rapidly and accurately measure the fractions of bound/unbound DNA based on fluorescence anisotropy. The procedure allows us to obtain full titration curves with high reproducibility. We applied this technique to measure the histone-DNA affinities for 47 DNA sequences and analyzed how the affinities correlate with relevant DNA sequence features. We found that the GC content has a significant impact on nucleosome-forming preferences, but 10 bp dinucleotide periodicities and the presence of poly(dA:dT) stretches do not. Robotics permits full titration series to measure histone-DNA binding affinities Fluorescence anisotropy used as a fast, sensitive readout of bound/unbound DNA Free energies span three orders of magnitude, less for naturally occurring sequences GC content is a major determinant of measured binding free energies
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Affiliation(s)
- Max Schnepf
- Gene Center and Department of Biochemistry, Center for Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 München, Germany
| | - Claudia Ludwig
- Gene Center and Department of Biochemistry, Center for Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 München, Germany
| | - Peter Bandilla
- Gene Center and Department of Biochemistry, Center for Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 München, Germany
| | - Stefano Ceolin
- Gene Center and Department of Biochemistry, Center for Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 München, Germany
| | - Ulrich Unnerstall
- Gene Center and Department of Biochemistry, Center for Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 München, Germany
| | - Christophe Jung
- Gene Center and Department of Biochemistry, Center for Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 München, Germany.
| | - Ulrike Gaul
- Gene Center and Department of Biochemistry, Center for Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 München, Germany
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26
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Huertas J, MacCarthy CM, Schöler HR, Cojocaru V. Nucleosomal DNA Dynamics Mediate Oct4 Pioneer Factor Binding. Biophys J 2020; 118:2280-2296. [PMID: 32027821 PMCID: PMC7202942 DOI: 10.1016/j.bpj.2019.12.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/04/2019] [Accepted: 12/23/2019] [Indexed: 01/16/2023] Open
Abstract
Transcription factor (TF) proteins bind to DNA to regulate gene expression. Normally, accessibility to DNA is required for their function. However, in the nucleus, the DNA is often inaccessible, wrapped around histone proteins in nucleosomes forming the chromatin. Pioneer TFs are thought to induce chromatin opening by recognizing their DNA binding sites on nucleosomes. For example, Oct4, a master regulator and inducer of stem cell pluripotency, binds to DNA in nucleosomes in a sequence-specific manner. Here, we reveal the structural dynamics of nucleosomes that mediate Oct4 binding from molecular dynamics simulations. Nucleosome flexibility and the amplitude of nucleosome motions such as breathing and twisting are enhanced in nucleosomes with multiple TF binding sites. Moreover, the regions around the binding sites display higher local structural flexibility. Probing different structures of Oct4-nucleosome complexes, we show that alternative configurations in which Oct4 recognizes partial binding sites display stable TF-DNA interactions similar to those observed in complexes with free DNA and compatible with the DNA curvature and DNA-histone interactions. Therefore, we propose a structural basis for nucleosome recognition by a pioneer TF that is essential for understanding how chromatin is unraveled during cell fate conversions.
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Affiliation(s)
- Jan Huertas
- In Silico Biomolecular Structure and Dynamics Group, Hubrecht Institute, Utrecht, the Netherlands; Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany; Center for Multiscale Theory and Computation, Westfälische Wilhelms University, Münster, Germany; and
| | - Caitlin M MacCarthy
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Hans R Schöler
- Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany; Medical Faculty, University of Münster, Münster, Germany
| | - Vlad Cojocaru
- In Silico Biomolecular Structure and Dynamics Group, Hubrecht Institute, Utrecht, the Netherlands; Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany; Center for Multiscale Theory and Computation, Westfälische Wilhelms University, Münster, Germany; and.
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27
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Kaczmarczyk A, Meng H, Ordu O, Noort JV, Dekker NH. Chromatin fibers stabilize nucleosomes under torsional stress. Nat Commun 2020; 11:126. [PMID: 31913285 PMCID: PMC6949304 DOI: 10.1038/s41467-019-13891-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 11/25/2019] [Indexed: 01/11/2023] Open
Abstract
Torsional stress generated during DNA replication and transcription has been suggested to facilitate nucleosome unwrapping and thereby the progression of polymerases. However, the propagation of twist in condensed chromatin remains yet unresolved. Here, we measure how force and torque impact chromatin fibers with a nucleosome repeat length of 167 and 197. We find that both types of fibers fold into a left-handed superhelix that can be stabilized by positive torsion. We observe that the structural changes induced by twist were reversible, indicating that chromatin has a large degree of elasticity. Our direct measurements of torque confirmed the hypothesis of chromatin fibers as a twist buffer. Using a statistical mechanics-based torsional spring model, we extracted values of the chromatin twist modulus and the linking number per stacked nucleosome that were in good agreement with values measured here experimentally. Overall, our findings indicate that the supercoiling generated by DNA-processing enzymes, predicted by the twin-supercoiled domain model, can be largely accommodated by the higher-order structure of chromatin.
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Affiliation(s)
- Artur Kaczmarczyk
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
- Faculty of Medicine, Imperial College London, Du Cane Road, W12 0NN, London, United Kingdom
| | - He Meng
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands
| | - Orkide Ordu
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - John van Noort
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands.
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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28
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Ensembles of Breathing Nucleosomes: A Computational Study. Biophys J 2019; 118:2297-2308. [PMID: 31882248 DOI: 10.1016/j.bpj.2019.11.3395] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/15/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
About three-fourths of the human DNA molecules are wrapped into nucleosomes, protein spools with DNA. Nucleosomes are highly dynamic, transiently exposing their DNA through spontaneous unspooling. Recent experiments allowed to observe the DNA of an ensemble of such breathing nucleosomes through x-ray diffraction with contrast matching between the solvent and the protein core. In this study, we calculate such an ensemble through a Monte Carlo simulation of a coarse-grained nucleosome model with sequence-dependent DNA mechanics. Our analysis gives detailed insights into the sequence dependence of nucleosome breathing observed in the experiment and allows us to determine the adsorption energy of the DNA bound to the protein core as a function of the ionic strength. Moreover, we predict the breathing behavior of other potentially interesting sequences and compare the findings to earlier related experiments.
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29
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Ordu O, Lusser A, Dekker NH. DNA Sequence Is a Major Determinant of Tetrasome Dynamics. Biophys J 2019; 117:2217-2227. [PMID: 31521330 PMCID: PMC6895708 DOI: 10.1016/j.bpj.2019.07.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/13/2019] [Accepted: 07/30/2019] [Indexed: 10/26/2022] Open
Abstract
Eukaryotic genomes are hierarchically organized into protein-DNA assemblies for compaction into the nucleus. Nucleosomes, with the (H3-H4)2 tetrasome as a likely intermediate, are highly dynamic in nature by way of several different mechanisms. We have recently shown that tetrasomes spontaneously change the direction of their DNA wrapping between left- and right-handed conformations, which may prevent torque buildup in chromatin during active transcription or replication. DNA sequence has been shown to strongly affect nucleosome positioning throughout chromatin. It is not known, however, whether DNA sequence also impacts the dynamic properties of tetrasomes. To address this question, we examined tetrasomes assembled on a high-affinity DNA sequence using freely orbiting magnetic tweezers. In this context, we also studied the effects of mono- and divalent salts on the flipping dynamics. We found that neither DNA sequence nor altered buffer conditions affect overall tetrasome structure. In contrast, tetrasomes bound to high-affinity DNA sequences showed significantly altered flipping kinetics, predominantly via a reduction in the lifetime of the canonical state of left-handed wrapping. Increased mono- and divalent salt concentrations counteracted this behavior. Thus, our study indicates that high-affinity DNA sequences impact not only the positioning of the nucleosome but that they also endow the subnucleosomal tetrasome with enhanced conformational plasticity. This may provide a means to prevent histone loss upon exposure to torsional stress, thereby contributing to the integrity of chromatin at high-affinity sites.
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Affiliation(s)
- Orkide Ordu
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Alexandra Lusser
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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30
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Stormberg T, Stumme-Diers M, Lyubchenko YL. Sequence-dependent nucleosome nanoscale structure characterized by atomic force microscopy. FASEB J 2019; 33:10916-10923. [PMID: 31284760 PMCID: PMC6766637 DOI: 10.1096/fj.201901094r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/04/2019] [Indexed: 01/14/2023]
Abstract
DNA sequence plays an important role in the assembly of nucleosomes, and DNA motifs with high specificity to nucleosomes have been identified. At the same time, important questions such as how the DNA sequence changes DNA wrapping and how the DNA sequence contributes to the interaction between the nucleosomes remain unclear. Here, we addressed these questions by comparing nanoscale properties of nucleosomes assembled on the highest nucleosome positioning sequence, the 601 motif, and essentially random DNA sequences. We used atomic force microscopy to measure the nucleosome positions and the DNA wrapping. The studies showed that nucleosomes assemble on the nonspecific sequence without any preference for position on DNA, but they wrap the same DNA length as DNA of the same length with the 601 sequence. Experiments with longer DNA containing the 601 motif along with nonspecific DNA, capable of forming dinucleosomes, revealed that dinucleosomes assembled on hybrid sequences show a preference for positioning near each other, with one always assembling on the 601 motif. These findings point to the interaction between the nucleosomes and suggest that internucleosomal interactions may play a large role in nucleosome positioning.-Stormberg, T., Stumme-Diers, M., Lyubchenko, Y. L. Sequence-dependent nucleosome nanoscale structure characterized by atomic force microscopy.
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Affiliation(s)
- Tommy Stormberg
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Micah Stumme-Diers
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska, USA
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31
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Singh R, Bassett E, Chakravarti A, Parthun MR. Replication-dependent histone isoforms: a new source of complexity in chromatin structure and function. Nucleic Acids Res 2019; 46:8665-8678. [PMID: 30165676 PMCID: PMC6158624 DOI: 10.1093/nar/gky768] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/24/2018] [Indexed: 12/11/2022] Open
Abstract
Replication-dependent histones are expressed in a cell cycle regulated manner and supply the histones necessary to support DNA replication. In mammals, the replication-dependent histones are encoded by a family of genes that are located in several clusters. In humans, these include 16 genes for histone H2A, 22 genes for histone H2B, 14 genes for histone H3, 14 genes for histone H4 and 6 genes for histone H1. While the proteins encoded by these genes are highly similar, they are not identical. For many years, these genes were thought to encode functionally equivalent histone proteins. However, several lines of evidence have emerged that suggest that the replication-dependent histone genes can have specific functions and may constitute a novel layer of chromatin regulation. This Survey and Summary reviews the literature on replication-dependent histone isoforms and discusses potential mechanisms by which the small variations in primary sequence between the isoforms can alter chromatin function. In addition, we summarize the wealth of data implicating altered regulation of histone isoform expression in cancer.
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Affiliation(s)
- Rajbir Singh
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Emily Bassett
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Arnab Chakravarti
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Mark R Parthun
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
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32
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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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33
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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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34
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Caraglio M, Skoruppa E, Carlon E. Overtwisting induces polygonal shapes in bent DNA. J Chem Phys 2019; 150:135101. [PMID: 30954045 DOI: 10.1063/1.5084950] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
By combining analytical results and simulations of various coarse-grained models, we investigate the minimal energy shape of DNA minicircles which are torsionally constrained by an imposed over or undertwist. We show that twist-bend coupling, a cross interaction term discussed in the recent DNA literature, induces minimal energy shapes with a periodic alternation of parts with high and low curvature resembling rounded polygons. We briefly discuss the possible experimental relevance of these findings. We finally show that the twist and bending energies of minicircles are governed by renormalized stiffness constants, rather than the bare ones. This has important consequences for the analysis of experiments involving circular DNA meant to determine DNA elastic constants.
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Affiliation(s)
- Michele Caraglio
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Enrico Skoruppa
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Enrico Carlon
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
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35
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Shaytan AK, Xiao H, Armeev GA, Gaykalova DA, Komarova GA, Wu C, Studitsky VM, Landsman D, Panchenko AR. Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID. Nat Protoc 2018; 13:2535-2556. [PMID: 30341436 PMCID: PMC6322412 DOI: 10.1038/s41596-018-0048-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hydroxyl-radical footprinting (HRF) is a powerful method for probing structures of nucleic acid-protein complexes with single-nucleotide resolution in solution. To tap the full quantitative potential of HRF, we describe a protocol, hydroxyl-radical footprinting interpretation for DNA (HYDROID), to quantify HRF data and integrate them with atomistic structural models. The stages of the HYDROID protocol are extraction of the lane profiles from gel images, quantification of the DNA cleavage frequency at each nucleotide and theoretical estimation of the DNA cleavage frequency from atomistic structural models, followed by comparison of experimental and theoretical results. Example scripts for each step of HRF data analysis and interpretation are provided for several nucleosome systems; they can be easily adapted to analyze user data. As input, HYDROID requires polyacrylamide gel electrophoresis (PAGE) images of HRF products and optionally can use a molecular model of the DNA-protein complex. The HYDROID protocol can be used to quantify HRF over DNA regions of up to 100 nucleotides per gel image. In addition, it can be applied to the analysis of RNA-protein complexes and free RNA or DNA molecules in solution. Compared with other methods reported to date, HYDROID is unique in its ability to simultaneously integrate HRF data with the analysis of atomistic structural models. HYDROID is freely available. The complete protocol takes ~3 h. Users should be familiar with the command-line interface, the Python scripting language and Protein Data Bank (PDB) file formats. A graphical user interface (GUI) with basic functionality (HYDROID_GUI) is also available.
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Affiliation(s)
- Alexey K Shaytan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Grigoriy A Armeev
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Daria A Gaykalova
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Galina A Komarova
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vasily M Studitsky
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
- Fox Chase Cancer Center, Philadelphia, PA, USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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36
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Skoruppa E, Nomidis SK, Marko JF, Carlon E. Bend-Induced Twist Waves and the Structure of Nucleosomal DNA. PHYSICAL REVIEW LETTERS 2018; 121:088101. [PMID: 30192578 PMCID: PMC6132066 DOI: 10.1103/physrevlett.121.088101] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Indexed: 05/14/2023]
Abstract
Recent work indicates that twist-bend coupling plays an important role in DNA micromechanics. Here we investigate its effect on bent DNA. We provide an analytical solution of the minimum-energy shape of circular DNA, showing that twist-bend coupling induces sinusoidal twist waves. This solution is in excellent agreement with both coarse-grained simulations of minicircles and nucleosomal DNA data, which is bent and wrapped around histone proteins in a superhelical conformation. Our analysis shows that the observed twist oscillation in nucleosomal DNA, so far attributed to the interaction with the histone proteins, is an intrinsic feature of free bent DNA, and should be observable in other protein-DNA complexes.
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Affiliation(s)
- Enrico Skoruppa
- KU Leuven, Institute for Theoretical Physics, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Stefanos K Nomidis
- KU Leuven, Institute for Theoretical Physics, Celestijnenlaan 200D, 3001 Leuven, Belgium
- Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol, Belgium
| | - John F Marko
- Department of Physics and Astronomy, and Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Enrico Carlon
- KU Leuven, Institute for Theoretical Physics, Celestijnenlaan 200D, 3001 Leuven, Belgium
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37
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Schiessel H. Telling Left from Right in Breathing Nucleosomes. Biophys J 2018; 115:749-750. [PMID: 30119832 DOI: 10.1016/j.bpj.2018.07.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 07/26/2018] [Indexed: 11/16/2022] Open
Affiliation(s)
- Helmut Schiessel
- Institute Lorentz for Theoretical Physics, Leiden University, Leiden, the Netherlands.
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38
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D'Agostino L. Native DNA electronics: is it a matter of nanoscale assembly? NANOSCALE 2018; 10:12268-12275. [PMID: 29946628 DOI: 10.1039/c8nr03153c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The genomic DNA is enveloped by nanotubes formed by the nuclear aggregates of polyamines (NAPs) that induce DNA conformational changes and provide protection and increased interaction abilities for the double strands. In a physiological environment, the nanotube arrangement is initiated by spontaneous interaction among the terminal amino groups of the polyamines and the phosphate ions, with the consequent formation of cyclic monomers that hook at the DNA grooves. The polymer thus formed has the morphological features of an organic semiconductor and therefore, it can be considered to be able to conduct electric charges. Phosphate ions positioned on the NAP external surface could regulate, as in a physical electric circuit, both linear and rotational (histones) protein motion, in accordance with the basilar principles of the electronics. A model of a carrier system for protein motion along the polymer wrapping the DNA strands, based on the phosphate-phosphate complexation, is proposed.
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39
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Elbahnsi A, Retureau R, Baaden M, Hartmann B, Oguey C. Holding the Nucleosome Together: A Quantitative Description of the DNA–Histone Interface in Solution. J Chem Theory Comput 2018; 14:1045-1058. [DOI: 10.1021/acs.jctc.7b00936] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ahmad Elbahnsi
- LBPA,
UMR 8113, ENS Paris-Saclay - CNRS, 61 avenue du Président Wilson, 94235 cedex Cachan, France
- LPTM,
UMR 8089, CNRS, Université de Cergy-Pontoise, 2 avenue Adolphe Chauvin, 95302 Cergy-Pontoise, France
| | - Romain Retureau
- LBPA,
UMR 8113, ENS Paris-Saclay - CNRS, 61 avenue du Président Wilson, 94235 cedex Cachan, France
| | - Marc Baaden
- Laboratoire
de Biochimie Théorique, CNRS, UPR9080, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Brigitte Hartmann
- LBPA,
UMR 8113, ENS Paris-Saclay - CNRS, 61 avenue du Président Wilson, 94235 cedex Cachan, France
| | - Christophe Oguey
- LPTM,
UMR 8089, CNRS, Université de Cergy-Pontoise, 2 avenue Adolphe Chauvin, 95302 Cergy-Pontoise, France
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40
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Blossey R, Schiessel H. The Latest Twists in Chromatin Remodeling. Biophys J 2018; 114:2255-2261. [PMID: 29310890 DOI: 10.1016/j.bpj.2017.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/09/2017] [Accepted: 12/12/2017] [Indexed: 02/03/2023] Open
Abstract
In its most restrictive interpretation, the notion of chromatin remodeling refers to the action of chromatin-remodeling enzymes on nucleosomes with the aim of displacing and removing them from the chromatin fiber (the effective polymer formed by a DNA molecule and proteins). This local modification of the fiber structure can have consequences for the initiation and repression of the transcription process, and when the remodeling process spreads along the fiber, it also results in long-range effects essential for fiber condensation. There are three regulatory levels of relevance that can be distinguished for this process: the intrinsic sequence preference of the histone octamer, which rules the positioning of the nucleosome along the DNA, notably in relation to the genetic information coded in DNA; the recognition or selection of nucleosomal substrates by remodeling complexes; and, finally, the motor action on the nucleosome exerted by the chromatin remodeler. Recent work has been able to provide crucial insights at each of these three levels that add new twists to this exciting and unfinished story, which we highlight in this perspective.
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Affiliation(s)
- Ralf Blossey
- University of Lille 1, Unité de Glycobiologie Structurale et Fonctionnelle, CNRS UMR8576, Lille, France.
| | - Helmut Schiessel
- Institute Lorentz for Theoretical Physics, Leiden University, Leiden, the Netherlands
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41
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Culkin J, de Bruin L, Tompitak M, Phillips R, Schiessel H. The role of DNA sequence in nucleosome breathing. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2017; 40:106. [PMID: 29185124 PMCID: PMC7001874 DOI: 10.1140/epje/i2017-11596-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/14/2017] [Indexed: 05/05/2023]
Abstract
Roughly 3/4 of human genomes are sequestered by nucleosomes, DNA spools with a protein core, dictating a broad range of biological processes, ranging from gene regulation, recombination, and replication, to chromosome condensation. Nucleosomes are dynamical structures and temporarily expose wrapped DNA through spontaneous unspooling from either end, a process called site exposure or nucleosome breathing. Here we ask how this process is influenced by the mechanical properties of the wrapped DNA, which is known to depend on the underlying base pair sequence. Using a coarse-grained nucleosome model we calculate the accessibility profiles for site exposure. We find that the process is very sensitive to sequence effects, so that evolution could potentially tune the accessibility of nucleosomal DNA and would only need a small number of mutations to do so.
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Affiliation(s)
- Jamie Culkin
- Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands
| | - Lennart de Bruin
- Laboratory for Computation and Visualization in Mathematics and Mechanics, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Marco Tompitak
- Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands
| | - Rob Phillips
- Department of Applied Physics and Division of Biology and Biological Engineering, California Institute of Technology, 91125, Pasadena, CA, USA
| | - Helmut Schiessel
- Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands.
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42
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Wondergem JAJ, Schiessel H, Tompitak M. Performing SELEX experimentsin silico. J Chem Phys 2017; 147:174101. [DOI: 10.1063/1.5001394] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- J. A. J. Wondergem
- Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
| | - H. Schiessel
- Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
| | - M. Tompitak
- Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
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43
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Lequieu J, Schwartz DC, de Pablo JJ. In silico evidence for sequence-dependent nucleosome sliding. Proc Natl Acad Sci U S A 2017; 114:E9197-E9205. [PMID: 29078285 PMCID: PMC5676884 DOI: 10.1073/pnas.1705685114] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nucleosomes represent the basic building block of chromatin and provide an important mechanism by which cellular processes are controlled. The locations of nucleosomes across the genome are not random but instead depend on both the underlying DNA sequence and the dynamic action of other proteins within the nucleus. These processes are central to cellular function, and the molecular details of the interplay between DNA sequence and nucleosome dynamics remain poorly understood. In this work, we investigate this interplay in detail by relying on a molecular model, which permits development of a comprehensive picture of the underlying free energy surfaces and the corresponding dynamics of nucleosome repositioning. The mechanism of nucleosome repositioning is shown to be strongly linked to DNA sequence and directly related to the binding energy of a given DNA sequence to the histone core. It is also demonstrated that chromatin remodelers can override DNA-sequence preferences by exerting torque, and the histone H4 tail is then identified as a key component by which DNA-sequence, histone modifications, and chromatin remodelers could in fact be coupled.
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Affiliation(s)
- Joshua Lequieu
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637
| | - David C Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706
- UW-Biotechnology Center, University of Wisconsin-Madison, Madison, WI 53706
| | - Juan J de Pablo
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637;
- Materials Science Division, Argonne National Laboratory, Argonne, IL 60439
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44
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Meng H, Li H, Zheng Y, Yang Z, Jia Y, Bo S. Evolutionary analysis of nucleosome positioning sequences based on New Symmetric Relative Entropy. Genomics 2017; 110:154-161. [PMID: 28917635 DOI: 10.1016/j.ygeno.2017.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/06/2017] [Accepted: 09/12/2017] [Indexed: 10/18/2022]
Abstract
New Symmetric Relative Entropy (NSRE) was applied innovatively to analyze the nucleosome sequences in S. cerevisiae, S. pombe and Drosophila. NSRE distributions could well reflect the characteristic differences of nucleosome sequences among three organisms, and the differences indicate a concerted evolution in the sequence usage of nucleosome. Further analysis about the nucleosomes around TSS shows that the constitutive property of +1/-1 nucleosomes in S. cerevisiae is different from that in S. pombe and Drosophila, which indicates that S. cerevisiae has a different transcription regulation mechanism based on nucleosome. However, in either case, the nucleosome dyad region is conserved and always has a higher NSRE. Base composition analysis shows that this conservative property in nucleosome dyad region is mainly determined by base A and T, and the dependence degrees on base A and T are consistent in three organisms.
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Affiliation(s)
- Hu Meng
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Hong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
| | - Yan Zheng
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Zhenhua Yang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Yun Jia
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Suling Bo
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
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Singh J, Purohit PK. Structural transitions in torsionally constrained DNA and their dependence on solution electrostatics. Acta Biomater 2017; 55:214-225. [PMID: 28365483 DOI: 10.1016/j.actbio.2017.03.052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/13/2017] [Accepted: 03/28/2017] [Indexed: 02/05/2023]
Abstract
Experimental studies on single molecules of DNA have reported a rich variety of structural transitions, including coexistence of three phases, in a torsionally constrained molecule. A comprehensive knowledge of these structural transitions is useful for unraveling the in vivo and in vitro behavior of DNA. Our objective is to understand the structural transitions in a torsionally constrained DNA molecule when it is pulled using optical or magnetic tweezers. We use foundational concepts from the Zimm-Bragg helix-coil transition theory and merge them with ideas from the theory of fluctuating elastic rods to model the mechanics of DNA. We also account for the electrostatic interactions between the ions and the negatively charged phosphate backbone of DNA. Using our model, we calculate the force and torque corresponding to the overstretching transition characterized by a 70% jump in the contour length of the molecule and examine the effect of salt concentration on this transition. We also deduce conditions under which the co-existence of B-, S- and P-DNA is possible. We examine how the cooperativity parameter for each transition affects the force-extension curve or torque-rotation curve. We attempt to rationalize the non-monotonic dependence of external work done on the ion concentration by connecting it to the electrostatic dependence of the interfacial energy between two phases of DNA. Our theoretical results are in agreement with multiple experiments documented in the literature and they generate falsifiable predictions that can be tested in new experiments. STATEMENT OF SIGNIFICANCE The overarching objective of this paper is to explore the implications of variation in ion concentration on the structural transitions driven by external forces in a torsionally constrained DNA molecule. A comprehensive understanding of the phase behavior of torsionally constrained DNA is useful because DNA in cells is tightly packaged and is acted upon by molecular machines in different ionic environments. We examine the mechanics of the overstretching transition, characterized by a 70% jump in contour length, wherein a mixture of B- and S-DNA converts into a mixture of S- and P-DNA through a triple point in the phase diagram. Our results are corroborated by experimental data at every step and we make predictions that are experimentally verifiable.
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Affiliation(s)
- Jaspreet Singh
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Prashant K Purohit
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Tompitak M, de Bruin L, Eslami-Mossallam B, Schiessel H. Designing nucleosomal force sensors. Phys Rev E 2017; 95:052402. [PMID: 28618598 DOI: 10.1103/physreve.95.052402] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Indexed: 11/07/2022]
Abstract
About three quarters of our DNA is wrapped into nucleosomes: DNA spools with a protein core. It is well known that the affinity of a given DNA stretch to be incorporated into a nucleosome depends on the geometry and elasticity of the basepair sequence involved, causing the positioning of nucleosomes. Here we show that DNA elasticity can have a much deeper effect on nucleosomes than just their positioning: it affects their "identities". Employing a recently developed computational algorithm, the mutation Monte Carlo method, we design nucleosomes with surprising physical characteristics. Unlike any other nucleosomes studied so far, these nucleosomes are short-lived when put under mechanical tension whereas other physical properties are largely unaffected. This suggests that the nucleosome, the most abundant DNA-protein complex in our cells, might more properly be considered a class of complexes with a wide array of physical properties, and raises the possibility that evolution has shaped various nucleosome species according to their genomic context.
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Affiliation(s)
- M Tompitak
- Instituut-Lorentz for Theoretical Physics, Leiden University, P.O. Box 9506, 2300 RA Leiden, The Netherlands
| | - L de Bruin
- Section de Mathématiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - B Eslami-Mossallam
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - H Schiessel
- Instituut-Lorentz for Theoretical Physics, Leiden University, P.O. Box 9506, 2300 RA Leiden, The Netherlands
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Rudnizky S, Malik O, Bavly A, Pnueli L, Melamed P, Kaplan A. Nucleosome mobility and the regulation of gene expression: Insights from single-molecule studies. Protein Sci 2017; 26:1266-1277. [PMID: 28329910 DOI: 10.1002/pro.3159] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/11/2017] [Accepted: 03/13/2017] [Indexed: 12/31/2022]
Abstract
Nucleosomes at the promoters of genes regulate the accessibility of the transcription machinery to DNA, and function as a basic layer in the complex regulation of gene expression. Our understanding of the role of the nucleosome's spontaneous, thermally driven position changes in modulating expression is lacking. This is the result of the paucity of experimental data on these dynamics, at high-resolution, and for DNA sequences that belong to real, transcribed genes. We have developed an assay that uses partial, reversible unzipping of nucleosomes with optical tweezers to repeatedly probe a nucleosome's position over time. Using the nucleosomes at the promoters of two model genes, Cga and Lhb, we show that the mobility of nucleosomes is modulated by the sequence of DNA and by the use of alternative histone variants, and describe how the mobility can affect transcription, at the initiation and elongation phases.
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Affiliation(s)
- Sergei Rudnizky
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Omri Malik
- Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Adaiah Bavly
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Lilach Pnueli
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Philippa Melamed
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel.,Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Ariel Kaplan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel.,Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa, 32000, Israel
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Kubik S, Bruzzone MJ, Shore D. Establishing nucleosome architecture and stability at promoters: Roles of pioneer transcription factors and the RSC chromatin remodeler. Bioessays 2017; 39. [PMID: 28345796 DOI: 10.1002/bies.201600237] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Improvements in deep sequencing, together with methods to rapidly deplete essential transcription factors (TFs) and chromatin remodelers, have recently led to a more detailed picture of promoter nucleosome architecture in yeast and its relationship to transcriptional regulation. These studies revealed that ∼40% of all budding yeast protein-coding genes possess a unique promoter structure, where we propose that an unusually unstable nucleosome forms immediately upstream of the transcription start site (TSS). This "fragile" nucleosome (FN) promoter architecture relies on the combined action of the essential RSC (Remodels Structure of Chromatin) nucleosome remodeler and pioneer transcription factors (PTFs). FNs are associated with genes whose expression is high, coupled to cell growth, and characterized by low cell-to-cell variability (noise), suggesting that they may promote these features. Recent studies in metazoans suggest that the presence of dynamic nucleosomes upstream of the TSS at highly expressed genes may be conserved throughout evolution.
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Affiliation(s)
- Slawomir Kubik
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Maria Jessica Bruzzone
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - David Shore
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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Tompitak M, Barkema GT, Schiessel H. Benchmarking and refining probability-based models for nucleosome-DNA interaction. BMC Bioinformatics 2017; 18:157. [PMID: 28270095 PMCID: PMC5341481 DOI: 10.1186/s12859-017-1569-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 02/24/2017] [Indexed: 01/30/2023] Open
Abstract
Background In investigations of nucleosome positioning preferences, a model that assigns an affinity to a given sequence is necessary to make predictions. One important class of models, which treats a nucleosome sequence as a Markov chain, has been applied with success when informed with experimentally measured nucleosomal sequence preferences. Results We find that we can also use such models as a fast approximative scheme for computationally expensive biophysical models, vastly increasing their reach. Employing these models in this way also allows us to benchmark them for the first time. Doing so for the approximative in silico models indirectly tells us about the accuracy we can expect of them when applied to real data. Conclusion We find that models presented in the literature should perform well, but this performance depends on factors such as the order of the Markov model, the preprocessing of the probability distributions on which the model is based, and the size and quality of the sequence ensemble from which those distributions are calculated. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1569-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marco Tompitak
- Lorentz Institute, Leiden University, Niels Bohrweg 2, Leiden, 2333CA, The Netherlands.
| | - Gerard T Barkema
- Institute for Theoretical Physics, Utrecht University, Princetonplein 5, Utrecht, 3584CC, The Netherlands
| | - Helmut Schiessel
- Lorentz Institute, Leiden University, Niels Bohrweg 2, Leiden, 2333CA, The Netherlands
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Leung A, Cheema M, González-Romero R, Eirin-Lopez JM, Ausió J, Nelson CJ. Unique yeast histone sequences influence octamer and nucleosome stability. FEBS Lett 2016; 590:2629-38. [PMID: 27339085 DOI: 10.1002/1873-3468.12266] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/17/2016] [Accepted: 06/21/2016] [Indexed: 12/22/2022]
Abstract
Yeast nucleosomes are known to be intrinsically less stable than those from higher eukaryotes. This difference presents significant challenges for the production of yeast nucleosome core particles (NCPs) and chromatin for in vitro analyses. Using recombinant yeast, human, and chimeric histone proteins, we demonstrate that three divergent amino acids in histone H3 (Q120 K121 K125 ) are responsible for the poor reconstitution of yeast histones into octamers. This QKK motif is only found in Fungi, and is located at the nucleosome dyad axis. Yeast-to-human changes at these positions render yeast histones amenable to well-established octamer reconstitution and salt dialysis methods for generating nucleosomal and longer chromatin templates. By contrast, the most divergent yeast core histones, H2A and H2B, affect the biophysical properties of NCP but not their stability. An evolutionary analysis of H3 sequences shows that a gradual divergence in H3 sequences occurred in Fungi to yield QKK in budding yeast. This likely facilitates the highly euchromatic nature of yeast genomes. Our results provide an explanation for the long recognized difference in yeast nucleosome stability and they offer a simple method to generate yeast chromatin templates for in vitro studies.
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Affiliation(s)
- Andrew Leung
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
| | - Manjinder Cheema
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
| | - Rodrigo González-Romero
- Chromatin Structure and Evolution (Chromevol) Group, Department of Biological Sciences, Florida International University, North Miami, FL, USA
| | - Jose M Eirin-Lopez
- Chromatin Structure and Evolution (Chromevol) Group, Department of Biological Sciences, Florida International University, North Miami, FL, USA
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
| | - Christopher J Nelson
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
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