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Sun R, Bishop T. The nucleosome reference frame and standard geometries for octasomes. Biophys Rev 2024; 16:315-330. [PMID: 39099844 PMCID: PMC11297230 DOI: 10.1007/s12551-024-01206-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 06/21/2024] [Indexed: 08/06/2024] Open
Abstract
There are over 533 nucleosome structures in the Research Collaboratory for Structural Bioinformatics (RCSB). Collectively, numerous variants and species are present, as are sub-nucleosomal and super-nucleosomal assemblies within the nucleosome family. The organization of the histones and DNA is highly conserved in all standard octasomes containing 145, 146, or 147 base pairs. This observation is used to establish a nucleosome reference frame that enables us to describe and compare the gross structure and organization of all nucleosomes. We observe that cumulative sums of Rise, Twist, and DNA arc length are linear functions of the base pair index withR 2 values exceeding 0.999 for almost all octasome structures. These relationships enable us to readily compare the location and orientation of DNA director frames extracted from the crystal structures to ideal superhelix values. Such comparisons reveal that the DNA superhelix extracted from X-ray structures exhibits a sinusoidal variation with an amplitude of approximately 5Å about a constant superhelix radius of ∼ 42 Å, in agreement with early descriptions of nucleosome organization as tripartite. There is also a distinct straightening of the nucleosomal DNA over the outermost turn of DNA's double helix. The straightening of the DNA superhelix marks the transition to linker DNA and is easily recognized as a rapid increase in superhelix radius and is concomitant with a change in pitch. This provides a rigorous means of separating nucleosomal DNA from linker DNA. For all X-ray structures, we find that near the dyad, there exists a set of DNA director frames for which the spatial location and orientation are highly conserved. Away from the dyad, the DNA superhelix exhibits "singletrack" and "multipath" regions. In the singletrack region, all structures exhibit a single highly conserved pathway along which all base pairs must track, but at varying rates. In the multipath regions, the base pairs are allowed to map out a limited number of different pathways along the surface of the histone octamer. To demonstrate the utility of the proposed reference geometries, standard and distorted octasome structures, super-nucleosomal structures, nucleosomes with linker DNA, and nucleosomes in closed circular DNA are analyzed. Supplementary Information The online version contains supplementary material available at 10.1007/s12551-024-01206-5.
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Affiliation(s)
- Ran Sun
- College of Engineering and Science, Louisiana Tech University, 600 Dan Reneau Dr., Ruston, LA 71272 USA
| | - Thomas Bishop
- Departments of Chemistry and Physics, Louisiana Tech University, 600 Dan Reneau Dr, Ruston, LA 71272 USA
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2
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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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3
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Liu G, Liu GJ, Tan JX, Lin H. DNA physical properties outperform sequence compositional information in classifying nucleosome-enriched and -depleted regions. Genomics 2018; 111:1167-1175. [PMID: 30055231 DOI: 10.1016/j.ygeno.2018.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/07/2018] [Accepted: 07/15/2018] [Indexed: 12/15/2022]
Abstract
The nucleosome is the fundamental structural unit of eukaryotic chromatin and plays an essential role in the epigenetic regulation of cellular processes, such as DNA replication, recombination, and transcription. Hence, it is important to identify nucleosome positions in the genome. Our previous model based on DNA deformation energy, in which a set of DNA physical descriptors was used, performed well in predicting nucleosome dyad positions and occupancy. In this study, we established a machine-learning model for predicting nucleosome occupancy in order to further verify the physical descriptors. Results showed that (1) our model outperformed several other sequence compositional information-based models, indicating a stronger dependence of nucleosome positioning on DNA physical properties; (2) nucleosome-enriched and -depleted regions have distinct features in terms of DNA physical descriptors like sequence-dependent flexibility and equilibrium structure parameters; (3) gene transcription start sites and termination sites can be well characterized with the distribution patterns of the physical descriptors, indicating the regulatory role of DNA physical properties in gene transcription. In addition, we developed a web server for the model, which is freely accessible at http://lin-group.cn/server/iNuc-force/.
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Affiliation(s)
- Guoqing Liu
- The School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China.
| | - Guo-Jun Liu
- School of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620000, Russia
| | - Jiu-Xin Tan
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hao Lin
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
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4
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Liu G, Ma Q, Xu Y. Physical properties of DNA may direct the binding of nucleoid-associated proteins along the E. coli genome. Math Biosci 2018; 301:50-58. [PMID: 29625128 DOI: 10.1016/j.mbs.2018.03.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 02/22/2018] [Accepted: 03/28/2018] [Indexed: 11/26/2022]
Abstract
Nucleoid-associated proteins (NAPs) play important roles in both chromosome packaging and gene regulation in bacteria. The underlying mechanisms, however, remain elusive particularly for how NAPs contribute to chromosome packaging. We report here a characterization of the binding sites for several major NAPs in E. coli, namely HNS, IHF, Fis, Dps and a non-NAP protein, FNR, in terms of the physical properties of their binding DNA. Our study shows that (i) as compared with flanking regions, the binding sites for IHF, Fis and FNR tend to have high intrinsic curvature, while no characterized pattern of intrinsic curvature distribution around those of HNS and Dps; (ii) all the binding sites analyzed in this study except those of HNS are characterized by high structural flexibility; (iii) the intrinsic curvature and flexibility at the binding sites for Fis and IHF are found to be coupled with the sequence specificity required in their binding, while the physical properties of the binding regions for both Dps and FNR are independent of sequence specificity. Our data suggest that physical properties of DNA sequence may contribute to binding of NAPs and mediate genome packaging and transcriptional regulation of the downstream genes. Our results should be informative for prediction of NAPs binding sites and understanding of the bacterial chromosome packaging.
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Affiliation(s)
- Guoqing Liu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China; Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, the University of Georgia, Athens, GA 30602, USA.
| | - Qin Ma
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, the University of Georgia, Athens, GA 30602, USA; Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture and Plant Science, South Dakot State University, SD 57007, USA
| | - Ying Xu
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, the University of Georgia, Athens, GA 30602, USA; College of Computer Science and Technology, Jilin University, Changchun 130012, China.
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5
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Villota-Salazar NA, Mendoza-Mendoza A, González-Prieto JM. Epigenetics: from the past to the present. FRONTIERS IN LIFE SCIENCE 2016. [DOI: 10.1080/21553769.2016.1249033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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6
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Abstract
We study the elasticity of DNA based on local principal axes of bending identified from over 0.9-μs all-atom molecular dynamics simulations of DNA oligos. The calculated order parameters describe motion of DNA as an elastic rod. In 10 possible dinucleotide steps, bending about the two principal axes is anisotropic yet linearly elastic. Twist about the centroid axis is largely decoupled from bending, but DNA tends to overtwist for unbending beyond the typical range of thermal motion, which is consistent with experimentally observed twist-stretch coupling. The calculated elastic stiffness of dinucleotide steps yield sequence-dependent persistence lengths consistent with previous single-molecule experiments, which is further analyzed by performing coarse-grained simulations of DNA. Flexibility maps of oligos constructed from simulation also match with those from the precalculated stiffness of dinucleotide steps. These support the premise that base pair interaction at the dinucleotide-level is mainly responsible for the elasticity of DNA. Furthermore, we analyze 1381 crystal structures of protein-DNA complexes. In most structures, DNAs are mildly deformed and twist takes the highest portion of the total elastic energy. By contrast, in structures with the elastic energy per dinucleotide step greater than about 4.16 kBT (kBT: thermal energy), the major bending becomes dominant. The extensional energy of dinucleotide steps takes at most 35% of the total elastic energy except for structures containing highly deformed DNAs where linear elasticity breaks down. Such partitioning between different deformational modes provides quantitative insights into the conformational dynamics of DNA as well as its interaction with other molecules and surfaces.
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Affiliation(s)
- Xiaojing Teng
- Department of Biomedical Engineering, Texas A&M University , College Station, Texas 77843, United States
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University , College Station, Texas 77843, United States
- Department of Materials Science and Engineering, Texas A&M University , College Station, Texas 77843, United States
- School of Computational Sciences, Korea Institute for Advanced Study , Seoul, Korea 02455
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7
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Nash JA, Singh A, Li NK, Yingling YG. Characterization of Nucleic Acid Compaction with Histone-Mimic Nanoparticles through All-Atom Molecular Dynamics. ACS NANO 2015; 9:12374-82. [PMID: 26522008 DOI: 10.1021/acsnano.5b05684] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The development of nucleic acid (NA) based nanotechnology applications rely on the efficient packaging of DNA and RNA. However, the atomic details of NA-nanoparticle binding remains to be comprehensively characterized. Here, we examined how nanoparticle and solvent properties affect NA compaction. Our large-scale, all-atom simulations of ligand-functionalized gold nanoparticle (NP) binding to double stranded NAs as a function of NP charge and solution salt concentration reveal different responses of RNA and DNA to cationic NPs. We demonstrate that the ability of a nanoparticle to bend DNA is directly correlated with the NPs charge and ligand corona shape, where more than 50% charge neutralization and spherical shape of the NP ligand corona ensured the DNA compaction. However, NP with 100% charge neutralization is needed to bend DNA almost as efficiently as the histone octamer. For RNA in 0.1 M NaCl, even the most highly charged nanoparticles are not capable of causing bending due to charged ligand end groups binding internally to the major groove of RNA. We show that RNA compaction can only be achieved through a combination of highly charged nanoparticles with low salt concentration. Upon interactions with highly charged NPs, DNA bends through periodic variation in groove widths and depths, whereas RNA bends through expansion of the major groove.
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Affiliation(s)
- Jessica A Nash
- Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27606, United States
| | - Abhishek Singh
- Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27606, United States
| | - Nan K Li
- Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27606, United States
| | - Yaroslava G Yingling
- Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27606, United States
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Martínez-Soto D, González-Prieto JM, Ruiz-Herrera J. Transcriptomic analysis of the GCN5 gene reveals mechanisms of the epigenetic regulation of virulence and morphogenesis in Ustilago maydis. FEMS Yeast Res 2015; 15:fov055. [PMID: 26126523 DOI: 10.1093/femsyr/fov055] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2015] [Indexed: 12/21/2022] Open
Abstract
Chromatin in the eukaryotic nucleus is highly organized in the form of nucleosomes where histones wrap DNA. This structure may be altered by some chemical modifications of histones, one of them, acetylation by histone acetyltransferases (HATs) that originates relaxation of the nucleosome structure, providing access to different transcription factors and other effectors. In this way, HATs regulate cellular processes including DNA replication, and gene transcription. Previously, we isolated Ustilago maydis mutants deficient in the GCN5 HAT that are avirulent, and grow constitutively as mycelium. In this work, we proceeded to identify the genes differentially regulated by GCN5, comparing the transcriptomes of the mutant and the wild type using microarrays, to analyse the epigenetic control of virulence and morphogenesis. We identified 1203 genes, 574 positively and 629 negatively regulated in the wild type. We found that genes belonging to different categories involved in pathogenesis were downregulated in the mutant, and that genes involved in mycelial growth were negatively regulated in the wild type, offering a working hypothesis on the epigenetic control of virulence and morphogenesis of U. maydis. Interestingly, several differentially regulated genes appeared in clusters, suggesting a common regulation. Some of these belonged to pathogenesis or secondary metabolism.
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Affiliation(s)
- Domingo Martínez-Soto
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36500 Irapuato, Gto., México
| | - Juan Manuel González-Prieto
- Biotecnología Vegetal, Centro de Biotecnologia Genómica, Instituto Politécnico Nacional, 88710 Reynosa, Tam., México
| | - José Ruiz-Herrera
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36500 Irapuato, Gto., México
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González-Prieto JM, Rosas-Quijano R, Domínguez A, Ruiz-Herrera J. The UmGcn5 gene encoding histone acetyltransferase from Ustilago maydis is involved in dimorphism and virulence. Fungal Genet Biol 2014; 71:86-95. [PMID: 25242418 DOI: 10.1016/j.fgb.2014.09.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 09/09/2014] [Accepted: 09/11/2014] [Indexed: 10/24/2022]
Abstract
We isolated a gene encoding a histone acetyltransferase from Ustilago maydis (DC.) Cda., which is orthologous to the Saccharomyces cerevisiae GCN5 gene. The gene was isolated from genomic clones identified by their specific hybridization to a gene fragment obtained by the polymerase chain reaction (PCR). This gene (Umgcn5; um05168) contains an open reading frame (ORF) of 1421bp that encodes a putative protein of 473 amino acids with a Mr. of 52.6kDa. The protein exhibits a high degree of homology with histone acetyltransferases from different organisms. Null a2b2 ΔUmgcn5 mutants were constructed by substitution of the region encoding the catalytic site with a hygromycin B resistance cassette. Null a1b1 ΔUmgcn5 mutants were isolated from genetic crosses of a2b2 ΔUmgcn5 and a1b1 wild-type strains in maize. Mutants displayed a slight reduction in growth rate under different conditions, and were more sensitive than the wild type to stress conditions, but more important, they grew as long mycelial cells, and formed fuzz-like colonies under all conditions where wild-type strains grew in the yeast-like morphology and formed smooth colonies. This phenotype was not reverted by cAMP addition. Mutants were not virulent to maize plants, and were unable to form teliospores. These phenotypic alterations of the mutants were reverted by their transformation with the wild-type gene.
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Affiliation(s)
- Juan Manuel González-Prieto
- Biotecnología Vegetal, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tam. 88710, Mexico; Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del I.P.N, Unidad Irapuato, Irapuato, Gto. 36500, Mexico
| | - Raymundo Rosas-Quijano
- Biotecnología Vegetal, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tam. 88710, Mexico; Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del I.P.N, Unidad Irapuato, Irapuato, Gto. 36500, Mexico
| | - Angel Domínguez
- Departamento de Microbiología y Genética, CIETUS, IBSAL, Universidad de Salamanca, 37007 Salamanca, Spain
| | - José Ruiz-Herrera
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del I.P.N, Unidad Irapuato, Irapuato, Gto. 36500, Mexico.
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Tasoulas J, Giaginis C, Patsouris E, Manolis E, Theocharis S. Histone deacetylase inhibitors in oral squamous cell carcinoma treatment. Expert Opin Investig Drugs 2014; 24:69-78. [PMID: 25216628 DOI: 10.1517/13543784.2014.952368] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Introduction: The involvement of the histone deacetylases (HDACs) family in tumor development and progression is well demonstrated. HDAC inhibitors (HDACis) constitute a novel, heterogeneous family of highly selective anticancer agents that inhibit HDACs and present significant antitumor activity in several human malignancies, including oral squamous cell carcinoma (OSCC). Areas covered: This review summarizes the current research on the anticancer activity of HDACis against OSCC. The review also presents the molecular mechanisms of HDACis action and the existing studies evaluating their utilization in combined therapies of OSCC. Expert opinion: The currently available data support evidence that HDACis may provide new therapeutic options against OSCC, decreasing treatment side effects and allowing a more conservative therapeutic approach. Future research should be focused on in vivo and clinical evaluation of their utilization as combined therapies or monotherapies. Before HDACis can be brought into clinical practice as treatment options for OSCC, further evaluation is needed to determine their optimal dosage, the appropriate duration of treatment and whether they should be used in combination or as stand-alone therapeutics.
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Affiliation(s)
- Jason Tasoulas
- National and Kapodistrian University of Athens, Medical School, First Department of Pathology , Athens , Greece
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11
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LeGresley SE, Wilt J, Antonik M. DNA damage may drive nucleosomal reorganization to facilitate damage detection. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:032708. [PMID: 24730875 DOI: 10.1103/physreve.89.032708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Indexed: 06/03/2023]
Abstract
One issue in genome maintenance is how DNA repair proteins find lesions at rates that seem to exceed diffusion-limited search rates. We propose a phenomenon where DNA damage induces nucleosomal rearrangements which move lesions to potential rendezvous points in the chromatin structure. These rendezvous points are the dyad and the linker DNA between histones, positions in the chromatin which are more likely to be accessible by repair proteins engaged in a random search. The feasibility of this mechanism is tested by considering the statistical mechanics of DNA containing a single lesion wrapped onto the nucleosome. We consider lesions which make the DNA either more flexible or more rigid by modeling the lesion as either a decrease or an increase in the bending energy. We include this energy in a partition function model of nucleosome breathing. Our results indicate that the steady state for a breathing nucleosome will most likely position the lesion at the dyad or in the linker, depending on the energy of the lesion. A role for DNA binding proteins and chromatin remodelers is suggested based on their ability to alter the mechanical properties of the DNA and DNA-histone binding, respectively. We speculate that these positions around the nucleosome potentially serve as rendezvous points where DNA lesions may be encountered by repair proteins which may be sterically hindered from searching the rest of the nucleosomal DNA. The strength of the repositioning is strongly dependent on the structural details of the DNA lesion and the wrapping and breathing of the nucleosome. A more sophisticated evaluation of this proposed mechanism will require detailed information about breathing dynamics, the structure of partially wrapped nucleosomes, and the structural properties of damaged DNA.
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Affiliation(s)
- Sarah E LeGresley
- Department of Physics and Astronomy, University of Kansas, Lawrence, Kansas 66045, USA
| | - Jamie Wilt
- Department of Physics and Astronomy, University of Kansas, Lawrence, Kansas 66045, USA
| | - Matthew Antonik
- Department of Physics and Astronomy, University of Kansas, Lawrence, Kansas 66045, USA
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Čech P, Kukal J, Černý J, Schneider B, Svozil D. Automatic workflow for the classification of local DNA conformations. BMC Bioinformatics 2013; 14:205. [PMID: 23800225 PMCID: PMC3694522 DOI: 10.1186/1471-2105-14-205] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 05/28/2013] [Indexed: 12/03/2022] Open
Abstract
Background A growing number of crystal and NMR structures reveals a considerable structural polymorphism of DNA architecture going well beyond the usual image of a double helical molecule. DNA is highly variable with dinucleotide steps exhibiting a substantial flexibility in a sequence-dependent manner. An analysis of the conformational space of the DNA backbone and the enhancement of our understanding of the conformational dependencies in DNA are therefore important for full comprehension of DNA structural polymorphism. Results A detailed classification of local DNA conformations based on the technique of Fourier averaging was published in our previous work. However, this procedure requires a considerable amount of manual work. To overcome this limitation we developed an automatic classification method consisting of the combination of supervised and unsupervised approaches. A proposed workflow is composed of k-NN method followed by a non-hierarchical single-pass clustering algorithm. We applied this workflow to analyze 816 X-ray and 664 NMR DNA structures released till February 2013. We identified and annotated six new conformers, and we assigned four of these conformers to two structurally important DNA families: guanine quadruplexes and Holliday (four-way) junctions. We also compared populations of the assigned conformers in the dataset of X-ray and NMR structures. Conclusions In the present work we developed a machine learning workflow for the automatic classification of dinucleotide conformations. Dinucleotides with unassigned conformations can be either classified into one of already known 24 classes or they can be flagged as unclassifiable. The proposed machine learning workflow permits identification of new classes among so far unclassifiable data, and we identified and annotated six new conformations in the X-ray structures released since our previous analysis. The results illustrate the utility of machine learning approaches in the classification of local DNA conformations.
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Affiliation(s)
- Petr Čech
- Laboratory of Informatics and Chemistry, ICT Prague, Technická 5, Prague 6, 166 28, Czech Republic
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Norouzi D, Mohammad-Rafiee F. DNA conformation and energy in nucleosome core: a theoretical approach. J Biomol Struct Dyn 2013; 32:104-14. [PMID: 23384279 DOI: 10.1080/07391102.2012.755134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
DNA conformation in complex with proteins is far from its canonical B-form. The affinity of complex formation and structure of DNA depend on its attachment configuration and sequence. In this article, we develop a mechanical model to address the problem of DNA structure and energy under deformation. DNA in nucleosome core particle is described as an example. The structure and energy of nucleosomal DNA is calculated based on its sequence and positioning state. The inferred structure has remarkable similarity with X-ray data. Although there is no sequence-specific interaction of bases and the histone core, we found considerable sequence dependency for the nucleosomal DNA positioning. The affinity of nucleosome formation for several sequences is examined and the differences are compatible with observations. We argue that structural energy determines the natural state of nucleosomal DNA and is the main reason for affinity differences in vitro. This theory can be utilized for the DNA structure and energy determination in protein-DNA complexes in general. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:17.
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Affiliation(s)
- Davood Norouzi
- a Department of Physics and Department of Biological Sciences , Institute for Advanced Studies in Basic Sciences (IASBS) , Gava Zang road, 45137-66731 , Zanjan , Iran
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14
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Calculation of nucleosomal DNA deformation energy: its implication for nucleosome positioning. Chromosome Res 2012; 20:889-902. [DOI: 10.1007/s10577-012-9328-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 11/09/2012] [Accepted: 11/15/2012] [Indexed: 10/27/2022]
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15
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Battistini F, Hunter CA, Moore IK, Widom J. Structure-based identification of new high-affinity nucleosome binding sequences. J Mol Biol 2012; 420:8-16. [PMID: 22472421 DOI: 10.1016/j.jmb.2012.03.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 03/20/2012] [Accepted: 03/28/2012] [Indexed: 10/28/2022]
Abstract
The substrate for the proteins that express genetic information in the cell is not naked DNA but an assembly of nucleosomes, where the DNA is wrapped around histone proteins. The organization of these nucleosomes on genomic DNA is influenced by the DNA sequence. Here, we present a structure-based computational approach that translates sequence information into the energy required to bend DNA into a nucleosome-bound conformation. The calculations establish the relationship between DNA sequence and histone octamer binding affinity. In silico selection using this model identified several new DNA sequences, which were experimentally found to have histone octamer affinities comparable to the highest-affinity sequences known. The results provide insights into the molecular mechanism through which DNA sequence information encodes its organization. A quantitative appreciation of the thermodynamics of nucleosome positioning and rearrangement will be one of the key factors in understanding the regulation of transcription and in the design of new promoter architectures for the purposes of tuning gene expression dynamics.
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16
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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17
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Chekmeneva E, Hunter CA, Misuraca MC, Turega SM. Steric desolvation enhances the effective molarities of intramolecular H-bonding interactions. Org Biomol Chem 2012; 10:6022-31. [DOI: 10.1039/c2ob25372k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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18
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Kepper N, Ettig R, Stehr R, Marnach S, Wedemann G, Rippe K. Force spectroscopy of chromatin fibers: Extracting energetics and structural information from Monte Carlo simulations. Biopolymers 2011; 95:435-47. [DOI: 10.1002/bip.21598] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 01/18/2011] [Accepted: 01/18/2011] [Indexed: 11/09/2022]
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19
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Nikolaou C, Althammer S, Beato M, Guigó R. Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae. Epigenetics Chromatin 2010; 3:20. [PMID: 21073701 PMCID: PMC2994855 DOI: 10.1186/1756-8935-3-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 11/12/2010] [Indexed: 11/15/2022] Open
Abstract
Background Recent advances in the field of high-throughput genomics have rendered possible the performance of genome-scale studies to define the nucleosomal landscapes of eukaryote genomes. Such analyses are aimed towards providing a better understanding of the process of nucleosome positioning, for which several models have been suggested. Nevertheless, questions regarding the sequence constraints of nucleosomal DNA and how they may have been shaped through evolution remain open. In this paper, we analyze in detail different experimental nucleosome datasets with the aim of providing a hypothesis for the emergence of nucleosome-forming sequences. Results We compared the complete sets of nucleosome positions for the budding yeast (Saccharomyces cerevisiae) as defined in the output of two independent experiments with the use of two different experimental techniques. We found that < 10% of the experimentally defined nucleosome positions were consistently positioned in both datasets. This subset of well-positioned nucleosomes, when compared with the bulk, was shown to have particular properties at both sequence and structural levels. Consistently positioned nucleosomes were also shown to occur preferentially in pairs of dinucleosomes, and to be surprisingly less conserved compared with their adjacent nucleosome-free linkers. Conclusion Our findings may be combined into a hypothesis for the emergence of a weak nucleosome-positioning code. According to this hypothesis, consistent nucleosomes may be partly guided by nearby nucleosome-free regions through statistical positioning. Once established, a set of well-positioned consistent nucleosomes may impose secondary constraints that further shape the structure of the underlying DNA. We were able to capture these constraints through the application of a recently introduced structural property that is related to the symmetry of DNA curvature. Furthermore, we found that both consistently positioned nucleosomes and their adjacent nucleosome-free regions show an increased tendency towards conservation of this structural feature.
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Affiliation(s)
- Christoforos Nikolaou
- Bioinformatics and Genomics Group, Centre for Genomic Regulation (CRG), Biomedical Research Park of Barcelona (PRBB), Barcelona, 08003, Catalunya, Spain.
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