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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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Sequence-dependent structural properties of B-DNA: what have we learned in 40 years? Biophys Rev 2021; 13:995-1005. [DOI: 10.1007/s12551-021-00893-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 11/01/2021] [Indexed: 11/27/2022] Open
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3
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Contessoto VG, Cheng RR, Hajitaheri A, Dodero-Rojas E, Mello MF, Lieberman-Aiden E, Wolynes P, Di Pierro M, Onuchic JN. The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome. Nucleic Acids Res 2021; 49:D172-D182. [PMID: 33021634 PMCID: PMC7778995 DOI: 10.1093/nar/gkaa818] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/05/2020] [Accepted: 10/02/2020] [Indexed: 11/30/2022] Open
Abstract
We introduce the Nucleome Data Bank (NDB), a web-based platform to simulate and analyze the three-dimensional (3D) organization of genomes. The NDB enables physics-based simulation of chromosomal structural dynamics through the MEGABASE + MiChroM computational pipeline. The input of the pipeline consists of epigenetic information sourced from the Encode database; the output consists of the trajectories of chromosomal motions that accurately predict Hi-C and fluorescence insitu hybridization data, as well as multiple observations of chromosomal dynamics in vivo. As an intermediate step, users can also generate chromosomal sub-compartment annotations directly from the same epigenetic input, without the use of any DNA-DNA proximity ligation data. Additionally, the NDB freely hosts both experimental and computational structural genomics data. Besides being able to perform their own genome simulations and download the hosted data, users can also analyze and visualize the same data through custom-designed web-based tools. In particular, the one-dimensional genetic and epigenetic data can be overlaid onto accurate 3D structures of chromosomes, to study the spatial distribution of genetic and epigenetic features. The NDB aims to be a shared resource to biologists, biophysicists and all genome scientists. The NDB is available at https://ndb.rice.edu.
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Affiliation(s)
- Vinícius G Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Brazilian Biorenewables National Laboratory-LNBR, Brazilian Center for Research in Energy and Materials-CNPEM, Campinas, SP 13083-100, Brazil
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
| | - Ryan R Cheng
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Arya Hajitaheri
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Computer Science, University of Houston, Houston, TX 77204, USA
| | - Esteban Dodero-Rojas
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Theoretical and Computational Physics Laboratory, University of Costa Rica, San José 5 11501, Costa Rica
| | - Matheus F Mello
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, RJ 22290-270, Brazil
| | - Erez Lieberman-Aiden
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics & Astronomy, Rice University, Houston, TX 77005, USA
- Department of Chemistry, Rice University, Houston, TX 77005, USA
- Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Michele Di Pierro
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics & Astronomy, Rice University, Houston, TX 77005, USA
- Department of Chemistry, Rice University, Houston, TX 77005, USA
- Department of Biosciences, Rice University, Houston, TX 77005, USA
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4
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Li Z, Sun R, Bishop TC. Genome Dashboards: Framework and Examples. Biophys J 2020; 118:2077-2085. [PMID: 32171420 PMCID: PMC7203004 DOI: 10.1016/j.bpj.2020.02.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 01/28/2020] [Accepted: 02/18/2020] [Indexed: 12/11/2022] Open
Abstract
Genomics is a sequence-based informatics science and a three-dimensional-structure-based material science. However, in practice, most genomics researchers utilize sequence-based informatics approaches or three-dimensional-structure-based material science techniques, not both. This division is, at least in part, the result of historical developments rather than a fundamental necessity. The underlying computational tools, experimental techniques, and theoretical models were developed independently. The primary result presented here is a framework for the unification of informatics- and physics-based data associated with DNA, nucleosomes, and chromatin. The framework is based on the mathematical representation of geometrically exact rods and the generalization of DNA basepair step parameters. Data unification enables researchers to integrate computational, experimental, and theoretical approaches for the study of chromatin biology. The framework can be implemented using model-view-controller design principles, existing genome browsers, and existing molecular visualization tools. We developed a minimal, web-based genome dashboard, G-Dash-min, and applied it to two simple examples to demonstrate the usefulness of data unification and proof of concept. Genome dashboards developed using the framework and design principles presented here are extensible and customizable and are therefore more broadly applicable than the examples presented. We expect a number of purpose-specific genome dashboards to emerge as a novel means of investigating structure-function relationships for genomes that range from basepairs to entire chromosomes and for generating, validating, and testing mechanistic hypotheses.
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Affiliation(s)
- Zilong Li
- Chemistry and Physics, Louisiana Tech University, Ruston, Louisiana
| | - Ran Sun
- Chemistry and Physics, Louisiana Tech University, Ruston, Louisiana
| | - Thomas C Bishop
- Chemistry and Physics, Louisiana Tech University, Ruston, Louisiana.
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Matsushima Y, Sakamoto N, Awazu A. Insulator Activities of Nucleosome-Excluding DNA Sequences without Bound Chromatin Looping Proteins. J Phys Chem B 2019; 123:1035-1043. [DOI: 10.1021/acs.jpcb.8b10518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Yuki Matsushima
- Department of Mathematical and Life Sciences, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Naoaki Sakamoto
- Department of Mathematical and Life Sciences, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
- Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Akinori Awazu
- Department of Mathematical and Life Sciences, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
- Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
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Tahir M, Hayat M, Khan SA. iNuc-ext-PseTNC: an efficient ensemble model for identification of nucleosome positioning by extending the concept of Chou's PseAAC to pseudo-tri-nucleotide composition. Mol Genet Genomics 2018; 294:199-210. [PMID: 30291426 DOI: 10.1007/s00438-018-1498-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/28/2018] [Indexed: 10/28/2022]
Abstract
Nucleosome is a central element of eukaryotic chromatin, which composes of histone proteins and DNA molecules. It performs vital roles in many eukaryotic intra-nuclear processes, for instance, chromatin structure and transcriptional regulation formation. Identification of nucleosome positioning via wet lab is difficult; so, the attention is diverted towards the accurate intelligent automated prediction. In this regard, a novel intelligent automated model "iNuc-ext-PseTNC" is developed to identify the nucleosome positioning in genomes accurately. In this predictor, the sequences of DNA are mathematically represented by two different discrete feature extraction techniques, namely pseudo-tri-nucleotide composition (PseTNC) and pseudo-di-nucleotide composition. Several contemporary machine learning algorithms were examined. Further, the predictions of individual classifiers were integrated through an evolutionary genetic algorithm. The success rates of the ensemble model are higher than individual classifiers. After analyzing the prediction results, it is noticed that iNuc-ext-PseTNC model has achieved better performance in combination with PseTNC feature space, which are 94.3%, 93.14%, and 88.60% of accuracies using six-fold cross-validation test for the three benchmark datasets S1, S2, and S3, respectively. The achieved outcomes exposed that the results of iNuc-ext-PseTNC model are prominent compared to the existing methods so far notifiable in the literature. It is ascertained that the proposed model might be more fruitful and a practical tool for rudimentary academia and research.
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Affiliation(s)
- Muhammad Tahir
- Department of Computer Science, Abdul Wali Khan University Mardan, Mardan, KP, Pakistan
| | - Maqsood Hayat
- Department of Computer Science, Abdul Wali Khan University Mardan, Mardan, KP, Pakistan.
| | - Sher Afzal Khan
- Department of Computer Science, Abdul Wali Khan University Mardan, Mardan, KP, Pakistan
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Grigoryev SA. Chromatin Higher-Order Folding: A Perspective with Linker DNA Angles. Biophys J 2018; 114:2290-2297. [PMID: 29628212 DOI: 10.1016/j.bpj.2018.03.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/03/2018] [Accepted: 03/09/2018] [Indexed: 01/24/2023] Open
Abstract
The mechanism by which the "beads-on-a-string" nucleosome chain folds into various higher-order chromatin structures in eukaryotic cell nuclei is still poorly understood. The various models depicting higher-order chromatin as regular helical fibers and the very opposite "polymer melt" theory imply that interactions between nucleosome "beads" make the main contribution to the chromatin compaction. Other models in which the geometry of linker DNA "strings" entering and exiting the nucleosome define the three-dimensional structure predict that small changes in the linker DNA configuration may strongly affect nucleosome chain folding and chromatin higher-order structure. Among those studies, the cross-disciplinary approach pioneered by Jörg Langowski that combines computational modeling with biophysical and biochemical experiments was most instrumental for understanding chromatin higher-order structure in vitro. Strikingly, many recent studies, including genome-wide nucleosome interaction mapping and chromatin imaging, show an excellent agreement with the results of three-dimensional computational modeling based on the primary role of linker DNA geometry in chromatin compaction. This perspective relates nucleosome array models with experimental studies of nucleosome array folding in vitro and in situ. I argue that linker DNA configuration plays a key role in determining nucleosome chain flexibility, topology, and propensity for self-association, thus providing new implications for regulation of chromatin accessibility to DNA binding factors and RNA transcription machinery as well as long-range communications between distant genomic sites.
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Affiliation(s)
- Sergei A Grigoryev
- Department of Biochemistry & Molecular Biology, H171, Milton S. Hershey Medical Center, Penn State University College of Medicine, Hershey, Pennsylvania.
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Dzialo M, Szopa J, Czuj T, Zuk M. Oligodeoxynucleotides Can Transiently Up- and Downregulate CHS Gene Expression in Flax by Changing DNA Methylation in a Sequence-Specific Manner. FRONTIERS IN PLANT SCIENCE 2017; 8:755. [PMID: 28555142 PMCID: PMC5430052 DOI: 10.3389/fpls.2017.00755] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
Chalcone synthase (CHS) has been recognized as an essential enzyme in the phenylpropanoid biosynthesis pathway. Apart from the leading role in the production of phenolic compounds with many valuable biological activities beneficial to biomedicine, CHS is well appreciated in science. Genetic engineering greatly facilitates expanding knowledge on the function and genetics of CHS in plants. The CHS gene is one of the most intensively studied genes in flax. In our study, we investigated engineering of the CHS gene through genetic and epigenetic approaches. Considering the numerous restrictions concerning the application of genetically modified (GM) crops, the main purpose of this research was optimization of the plant's modulation via epigenetics. In our study, plants modified through two methods were compared: a widely popular agrotransformation and a relatively recent oligodeoxynucleotide (ODN) strategy. It was recently highlighted that the ODN technique can be a rapid and time-serving antecedent in quick analysis of gene function before taking vector-mediated transformation. In order to understand the molecular background of epigenetic variation in more detail and evaluate the use of ODNs as a tool for predictable and stable gene engineering, we concentrated on the integration of gene expression and gene-body methylation. The treatment of flax with a series of short oligonucleotides homologous to a different part of CHS gene isoforms revealed that those directed to regulatory gene regions (5'- and 3'-UTR) activated gene expression, directed to non-coding region (introns) caused gen activity reduction, while those homologous to a coding region may have a variable influence on its activity. Gene expression changes were accompanied by changes in its methylation status. However, only certain (CCGG) motifs along the gene sequence were affected. The analyzed DNA motifs of the CHS flax gene are more accessible for methylation when located within a CpG island. The methylation motifs also led to rearrangement of the nucleosome location. The obtained results suggest high specificity of ODN action and establish a potential valuable alternative for improvement of crops.
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Affiliation(s)
- Magdalena Dzialo
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of WrocławWroclaw, Poland
| | - Jan Szopa
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of WrocławWroclaw, Poland
- Linum FoundationWroclaw, Poland
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life SciencesWroclaw, Poland
| | - Tadeusz Czuj
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life SciencesWroclaw, Poland
| | - Magdalena Zuk
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of WrocławWroclaw, Poland
- Linum FoundationWroclaw, Poland
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Awazu A. Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition. Bioinformatics 2016; 33:42-48. [PMID: 27563027 PMCID: PMC5860184 DOI: 10.1093/bioinformatics/btw562] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/02/2016] [Accepted: 08/19/2016] [Indexed: 11/13/2022] Open
Abstract
Motivation Nucleosome positioning plays important roles in many eukaryotic intranuclear processes, such as transcriptional regulation and chromatin structure formation. The investigations of nucleosome positioning rules provide a deeper understanding of these intracellular processes. Results Nucleosome positioning prediction was performed using a model consisting of three types of variables characterizing a DNA sequence—the number of five-nucleotide sequences, the number of three-nucleotide combinations in one period of a helix, and mono- and di-nucleotide distributions in DNA fragments. Using recently proposed stringent benchmark datasets with low biases for Saccharomyces cerevisiae, Homo sapiens, Caenorhabditis elegans and Drosophila melanogaster, the present model was shown to have a better prediction performance than the recently proposed predictors. This model was able to display the common and organism-dependent factors that affect nucleosome forming and inhibiting sequences as well. Therefore, the predictors developed here can accurately predict nucleosome positioning and help determine the key factors influencing this process. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Akinori Awazu
- Department of Mathematical and Life Sciences.,Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima, 739-8526, Japan
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Veith N, Ziehr H, MacLeod RAF, Reamon-Buettner SM. Mechanisms underlying epigenetic and transcriptional heterogeneity in Chinese hamster ovary (CHO) cell lines. BMC Biotechnol 2016; 16:6. [PMID: 26800878 PMCID: PMC4722726 DOI: 10.1186/s12896-016-0238-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/15/2016] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Recombinant cell lines developed for therapeutic antibody production often suffer instability or lose recombinant protein expression during long-term culture. Heterogeneous gene expression among cell line subclones may result from epigenetic modifications of DNA or histones, the protein component of chromatin. We thus investigated in such cell lines, DNA methylation and the chromatin environment along the human eukaryotic translation elongation factor 1 alpha 1 (EEF1A1) promoter in an antibody protein-expression vector which was integrated into the Chinese hamster ovary (CHO) cell line genome. RESULTS We analyzed four PT1-CHO cell lines which exhibited losses of protein expression at advanced passage number (>P35) growing in adherent conditions and in culture medium with 10 % FCS. These cell lines exhibited different integration sites and transgene copy numbers as determined by fluorescence in situ hybridization (FISH) and quantitative PCR (qPCR), respectively. By qRT-PCR, we analyzed the recombinant mRNA expression and correlated it with DNA methylation and with results from various approaches interrogating the chromatin landscape along the EEF1A1 promoter region. Each PT1-CHO cell line displayed specific epigenetic signatures or chromatin marks correlating with recombinant mRNA expression. The cell line with the lowest recombinant mRNA expression (PT1-1) was characterized by the highest nucleosome occupancy and displayed the lowest enrichment for histone marks associated with active transcription. In contrast, the cell line with the highest recombinant mRNA expression (PT1-55) exhibited the highest numbers of formaldehyde-assisted isolation of regulatory elements (FAIRE)-enriched regions, and was marked by enrichment for histone modifications H3K9ac and H3K9me3. Another cell line with the second highest recombinant mRNA transcription and the most stable protein expression (PT1-7) had the highest enrichments of the histone variants H3.3 and H2A.Z, and the histone modification H3K9ac. A further cell line (PT1-30) scored the highest enrichments for the bivalent marks H3K4me3 and H3K27me3. Finally, DNA methylation made a contribution, but only in the culture medium with reduced FCS or in a different expression vector. CONCLUSIONS Our results suggest that the chromatin state along the EEF1A1 promoter region can help predict recombinant mRNA expression, and thus may assist in selecting desirable clones during cell line development for protein production.
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Affiliation(s)
- Nathalie Veith
- Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
| | - Holger Ziehr
- Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
| | - Roderick A F MacLeod
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124, Braunschweig, Germany.
| | - Stella Marie Reamon-Buettner
- Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Nikolai-Fuchs Strasse 1, 30625, Hannover, Germany.
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11
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Isami S, Sakamoto N, Nishimori H, Awazu A. Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence. PLoS One 2015; 10:e0143760. [PMID: 26624614 PMCID: PMC4666469 DOI: 10.1371/journal.pone.0143760] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/09/2015] [Indexed: 11/19/2022] Open
Abstract
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of temperature factors for several crystal structures of DNA. Second, we propose a coarse-grained elastic network model of DNA, where each nucleotide is described only by one node. This model could effectively reproduce the detailed dynamics obtained with the all-atom elastic network model according to the sequence-dependent geometry. Through normal-mode analysis for the coarse-grained elastic network model, we exhaustively analyzed the dynamic features of a large number of long DNA sequences, approximately ∼150 bp in length. These analyses revealed positive correlations between the nucleosome-forming abilities and the inter-strand fluctuation strength of double-stranded DNA for several DNA sequences.
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Affiliation(s)
- Shuhei Isami
- Department of Mathematical and Life Sciences, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan
| | - Naoaki Sakamoto
- Department of Mathematical and Life Sciences, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan
- Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan
| | - Hiraku Nishimori
- Department of Mathematical and Life Sciences, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan
- Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan
| | - Akinori Awazu
- Department of Mathematical and Life Sciences, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan
- Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan
- * E-mail:
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Abstract
Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this review is to cover a practical aspect of this field, namely, to provide a guide to the multitude of nucleosome positioning resources available online. These include almost 300 experimental datasets of genome-wide nucleosome occupancy profiles determined in different cell types and more than 40 computational tools for the analysis of experimental nucleosome positioning data and prediction of intrinsic nucleosome formation probabilities from the DNA sequence. A manually curated, up to date list of these resources will be maintained at http://generegulation.info.
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Alharbi BA, Alshammari TH, Felton NL, Zhurkin VB, Cui F. nuMap: a web platform for accurate prediction of nucleosome positioning. GENOMICS PROTEOMICS & BIOINFORMATICS 2014; 12:249-53. [PMID: 25220945 PMCID: PMC4411418 DOI: 10.1016/j.gpb.2014.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 08/03/2014] [Accepted: 08/05/2014] [Indexed: 11/27/2022]
Abstract
Nucleosome positioning is critical for gene expression and of major biological interest. The high cost of experimentally mapping nucleosomal arrangement signifies the need for computational approaches to predict nucleosome positions at high resolution. Here, we present a web-based application to fulfill this need by implementing two models, YR and W/S schemes, for the translational and rotational positioning of nucleosomes, respectively. Our methods are based on sequence-dependent anisotropic bending that dictates how DNA is wrapped around a histone octamer. This application allows users to specify a number of options such as schemes and parameters for threading calculation and provides multiple layout formats. The nuMap is implemented in Java/Perl/MySQL and is freely available for public use at http://numap.rit.edu. The user manual, implementation notes, description of the methodology and examples are available at the site.
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Affiliation(s)
- Bader A Alharbi
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Thamir H Alshammari
- B. Thomas Golisano College of Computing & Information Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Nathan L Felton
- Information Technology Services, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Victor B Zhurkin
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Feng Cui
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA.
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14
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Cherstvy AG, Teif VB. Structure-driven homology pairing of chromatin fibers: the role of electrostatics and protein-induced bridging. J Biol Phys 2013; 39:363-85. [PMID: 23860914 PMCID: PMC3689366 DOI: 10.1007/s10867-012-9294-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 11/11/2012] [Indexed: 11/26/2022] Open
Abstract
Chromatin domains formed in vivo are characterized by different types of 3D organization of interconnected nucleosomes and architectural proteins. Here, we quantitatively test a hypothesis that the similarities in the structure of chromatin fibers (which we call "structural homology") can affect their mutual electrostatic and protein-mediated bridging interactions. For example, highly repetitive DNA sequences in heterochromatic regions can position nucleosomes so that preferred inter-nucleosomal distances are preserved on the surfaces of neighboring fibers. On the contrary, the segments of chromatin fiber formed on unrelated DNA sequences have different geometrical parameters and lack structural complementarity pivotal for stable association and cohesion. Furthermore, specific functional elements such as insulator regions, transcription start and termination sites, and replication origins are characterized by strong nucleosome ordering that might induce structure-driven iterations of chromatin fibers. We propose that shape-specific protein-bridging interactions facilitate long-range pairing of chromatin fragments, while for closely-juxtaposed fibers electrostatic forces can in addition yield fine-tuned structure-specific recognition and pairing. These pairing effects can account for some features observed for mitotic and inter-phase chromatins.
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Affiliation(s)
- A G Cherstvy
- Institute for Physics and Astronomy, University of Potsdam, 14476, Potsdam-Golm, Germany.
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Bamburg V, Johnston W, Liman J, Solow J, Bishop TC. 57 Nucleosome [mis]positioning, chromatin folding, and a computational karyotype. J Biomol Struct Dyn 2013. [DOI: 10.1080/07391102.2013.786491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Reamon-Buettner SM, Borlak J. Dissecting epigenetic silencing complexity in the mouse lung cancer suppressor gene Cadm1. PLoS One 2012; 7:e38531. [PMID: 22701659 PMCID: PMC3368868 DOI: 10.1371/journal.pone.0038531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 05/07/2012] [Indexed: 11/19/2022] Open
Abstract
Disease-oriented functional analysis of epigenetic factors and their regulatory mechanisms in aberrant silencing is a prerequisite for better diagnostics and therapy. Yet, the precise mechanisms are still unclear and complex, involving the interplay of several effectors including nucleosome positioning, DNA methylation, histone variants and histone modifications. We investigated the epigenetic silencing complexity in the tumor suppressor gene Cadm1 in mouse lung cancer progenitor cell lines, exhibiting promoter hypermethylation associated with transcriptional repression, but mostly unresponsive to demethylating drug treatments. After predicting nucleosome positions and transcription factor binding sites along the Cadm1 promoter, we carried out single-molecule mapping with DNA methyltransferase M.SssI, which revealed in silent promoters high nucleosome occupancy and occlusion of transcription factor binding sites. Furthermore, M.SssI maps of promoters varied within and among the different lung cancer cell lines. Chromatin analysis with micrococcal nuclease also indicated variations in nucleosome positioning to have implications in the binding of transcription factors near nucleosome borders. Chromatin immunoprecipitation showed that histone variants (H2A.Z and H3.3), and opposing histone modification marks (H3K4me3 and H3K27me3) all colocalized in the same nucleosome positions that is reminiscent of epigenetic plasticity in embryonic stem cells. Altogether, epigenetic silencing complexity in the promoter region of Cadm1 is not only defined by DNA hypermethylation, but high nucleosome occupancy, altered nucleosome positioning, and ‘bivalent’ histone modifications, also likely contributed in the transcriptional repression of this gene in the lung cancer cells. Our results will help define therapeutic intervention strategies using epigenetic drugs in lung cancer.
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Affiliation(s)
- Stella Marie Reamon-Buettner
- Toxicology and Environmental Hygiene, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany.
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Khandelwal G, Jayaram B. DNA-water interactions distinguish messenger RNA genes from transfer RNA genes. J Am Chem Soc 2012; 134:8814-6. [PMID: 22551381 DOI: 10.1021/ja3020956] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Physicochemical properties of DNA sequences as a guide to developing insights into genome organization has received little attention. Here, we utilize the energetics of DNA to further advance the knowledge on its language at a molecular level. Specifically, we ask the question whether physicochemical properties of different functional units on genomes differ. We extract intramolecular and solvation energies of different DNA base pair steps from a comprehensive set of molecular dynamics simulations. We then investigate the solvation behavior of DNA sequences coding for mRNAs and tRNAs. Distinguishing mRNA genes from tRNA genes is a tricky problem in genome annotation without assumptions on length of DNA and secondary structure of the product of transcription. We find that solvation energetics of DNA behaves as an extremely efficient property in discriminating 2,063,537 genes coding for mRNAs from 56,251 genes coding for tRNAs in all (~1500) completely sequenced prokaryotic genomes.
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Affiliation(s)
- Garima Khandelwal
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India
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