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Chen K, Wang L, Yang M, Liu J, Xin C, Hu S, Yu J. Sequence signatures of nucleosome positioning in Caenorhabditis elegans. GENOMICS PROTEOMICS & BIOINFORMATICS 2010; 8:92-102. [PMID: 20691394 PMCID: PMC5054450 DOI: 10.1016/s1672-0229(10)60010-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Our recent investigation in the protist Trichomonas vaginalis suggested a DNA sequence periodicity with a unit length of 120.9 nt, which represents a sequence signature for nucleosome positioning. We now extended our observation in higher eukaryotes and identified a similar periodicity of 175 nt in length in Caenorhabditis elegans. In the process of defining the sequence compositional characteristics, we found that the 10.5-nt periodicity, the sequence signature of DNA double helix, may not be sufficient for cross-nucleosome positioning but provides essential guiding rails to facilitate positioning. We further dissected nucleosome-protected sequences and identified a strong positive purine (AG) gradient from the 5′-end to the 3′-end, and also learnt that the nucleosome-enriched regions are GC-rich as compared to the nucleosome-free sequences as purine content is positively correlated with GC content. Sequence characterization allowed us to develop a hidden Markov model (HMM) algorithm for decoding nucleosome positioning computationally, and based on a set of training data from the fifth chromosome of C. elegans, our algorithm predicted 60%-70% of the well-positioned nucleosomes, which is 15%-20% higher than random positioning. We concluded that nucleosomes are not randomly positioned on DNA sequences and yet bind to different genome regions with variable stability, well-positioned nucleosomes leave sequence signatures on DNA, and statistical positioning of nucleosomes across genome can be decoded computationally based on these sequence signatures.
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Affiliation(s)
- Kaifu Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
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2
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Moukhtar J, Faivre-Moskalenko C, Milani P, Audit B, Vaillant C, Fontaine E, Mongelard F, Lavorel G, St-Jean P, Bouvet P, Argoul F, Arneodo A. Effect of Genomic Long-Range Correlations on DNA Persistence Length: From Theory to Single Molecule Experiments. J Phys Chem B 2010; 114:5125-43. [DOI: 10.1021/jp911031y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Julien Moukhtar
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Cendrine Faivre-Moskalenko
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Pascale Milani
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Benjamin Audit
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Cedric Vaillant
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Emeline Fontaine
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Fabien Mongelard
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Guillaume Lavorel
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Philippe St-Jean
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Philippe Bouvet
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Françoise Argoul
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Alain Arneodo
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
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Xu X, Tsumagari K, Sowden J, Tawil R, Boyle AP, Song L, Furey TS, Crawford GE, Ehrlich M. DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2. Nucleic Acids Res 2010; 37:7381-93. [PMID: 19820107 PMCID: PMC2794184 DOI: 10.1093/nar/gkp833] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A subtelomeric region, 4q35.2, is implicated in facioscapulohumeral muscular dystrophy (FSHD), a dominant disease thought to involve local pathogenic changes in chromatin. FSHD patients have too few copies of a tandem 3.3-kb repeat (D4Z4) at 4q35.2. No phenotype is associated with having few copies of an almost identical repeat at 10q26.3. Standard expression analyses have not given definitive answers as to the genes involved. To investigate the pathogenic effects of short D4Z4 arrays on gene expression in the very gene-poor 4q35.2 and to find chromatin landmarks there for transcription control, unannotated genes and chromatin structure, we mapped DNaseI-hypersensitive (DH) sites in FSHD and control myoblasts. Using custom tiling arrays (DNase-chip), we found unexpectedly many DH sites in the two large gene deserts in this 4-Mb region. One site was seen preferentially in FSHD myoblasts. Several others were mapped >0.7 Mb from genes known to be active in the muscle lineage and were also observed in cultured fibroblasts, but not in lymphoid, myeloid or hepatic cells. Their selective occurrence in cells derived from mesoderm suggests functionality. Our findings indicate that the gene desert regions of 4q35.2 may have functional significance, possibly also to FSHD, despite their paucity of known genes.
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Affiliation(s)
- Xueqing Xu
- Human Genetics Program and Department of Biochemistry and Tulane Cancer Center, Tulane Medical School, New Orleans, LA 70112, USA
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4
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Structural Mechanics of DNA Wrapping in the Nucleosome. J Mol Biol 2010; 396:264-79. [DOI: 10.1016/j.jmb.2009.11.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 11/09/2009] [Accepted: 11/14/2009] [Indexed: 10/20/2022]
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Takasuka TE, Cioffi A, Stein A. Sequence information encoded in DNA that may influence long-range chromatin structure correlates with human chromosome functions. PLoS One 2008; 3:e2643. [PMID: 18612465 PMCID: PMC2440353 DOI: 10.1371/journal.pone.0002643] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Accepted: 06/11/2008] [Indexed: 11/18/2022] Open
Abstract
Little is known about the possible function of the bulk of the human genome. We have recently shown that long-range regular oscillation in the motif non-T, A/T, G (VWG) existing at ten-nucleotide multiples influences large-scale nucleosome array formation. In this work, we have determined the locations of all 100 kb regions that are predicted to form distinctive chromatin structures throughout each human chromosome (except Y). Using these data, we found that a significantly greater fraction of 300 kb sequences lacked annotated transcripts in genomic DNA regions > or = 300 kb that contained nearly continuous chromatin organizing signals than in control regions. We also found a relationship between the meiotic recombination frequency and the presence of strong VWG chromatin organizing signals. Large (> or = 300 kb) genomic DNA regions having low average recombination frequency are enriched in chromatin organizing signals. As additional controls, we show using chromosome 1 that the VWG motif signals are not enriched in randomly selected DNA regions having the mean size of the recombination coldspots, and that non-VWG motif sets do not generate signals that are enriched in recombination coldspots. We also show that tandemly repeated alpha satellite DNA contains strong VWG signals for the formation of distinctive nucleosome arrays, consistent with the low recombination activity of centromeres. Our correlations cannot be explained simply by variations in the GC content. Our findings suggest that a specific set of periodic DNA motifs encoded in genomic DNA, which provide signals for chromatin organization, influence human chromosome function.
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Affiliation(s)
- Taichi E. Takasuka
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Alfred Cioffi
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Arnold Stein
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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Hernandez-Romano J, Carlos-Rivera FJ, Salgado H, Lamadrid-Figueroa H, Valverde-Garduño V, Rodriguez MH, Martinez-Barnetche J. Immunity related genes in dipterans share common enrichment of AT-rich motifs in their 5' regulatory regions that are potentially involved in nucleosome formation. BMC Genomics 2008; 9:326. [PMID: 18613977 PMCID: PMC2491644 DOI: 10.1186/1471-2164-9-326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Accepted: 07/09/2008] [Indexed: 01/08/2023] Open
Abstract
Background Understanding the transcriptional regulation mechanisms in response to environmental challenges is of fundamental importance in biology. Transcription factors associated to response elements and the chromatin structure had proven to play important roles in gene expression regulation. We have analyzed promoter regions of dipteran genes induced in response to immune challenge, in search for particular sequence patterns involved in their transcriptional regulation. Results 5' upstream regions of D. melanogaster and A. gambiae immunity-induced genes and their corresponding orthologous genes in 11 non-melanogaster drosophilid species and Ae. aegypti share enrichment in AT-rich short motifs. AT-rich motifs are associated with nucleosome formation as predicted by two different algorithms. In A. gambiae and D. melanogaster, many immunity genes 5' upstream sequences also showed NFκB response elements, located within 500 bp from the transcription start site. In A. gambiae, the frequency of ATAA motif near the NFκB response elements was increased, suggesting a functional link between nucleosome formation/remodelling and NFκB regulation of transcription. Conclusion AT-rich motif enrichment in 5' upstream sequences in A. gambiae, Ae. aegypti and the Drosophila genus immunity genes suggests a particular pattern of nucleosome formation/chromatin organization. The co-occurrence of such motifs with the NFκB response elements suggests that these sequence signatures may be functionally involved in transcriptional activation during dipteran immune response. AT-rich motif enrichment in regulatory regions in this group of co-regulated genes could represent an evolutionary constrained signature in dipterans and perhaps other distantly species.
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Affiliation(s)
- Jesus Hernandez-Romano
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av, Universidad 655, Col Sta Maria Ahuacatitlan, CP 62508, Cuernavaca, Morelos, México.
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7
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Song JS, Liu X, Liu XS, He X. A high-resolution map of nucleosome positioning on a fission yeast centromere. Genes Dev 2008; 18:1064-72. [PMID: 18411404 PMCID: PMC2493395 DOI: 10.1101/gr.075374.107] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Accepted: 04/03/2008] [Indexed: 11/25/2022]
Abstract
A key element for defining the centromere identity is the incorporation of a specific histone H3, CENPA, known as Cnp1p in Schizosaccharomyces pombe. Previous studies have suggested that functional S. pombe centromeres lack regularly positioned nucleosomes and may involve chromatin remodeling as a key step of kinetochore assembly. We used tiling microarrays to show that nucleosomes are, in fact, positioned in regular intervals in the core of centromere 2, providing the first high-resolution map of regional centromere chromatin. Nucleosome locations are not disrupted by mutations in kinetochore protein genes cnp1, mis18, mis12, nuf2, mal2; overexpression of cnp1; or the deletion of ams2, which encodes a GATA-like factor participating in CENPA incorporation. Bioinformatics analysis of the centromere sequence indicates certain enriched motifs in linker regions between nucleosomes and reveals a sequence bias in nucleosome positioning. In addition, sequence analysis of nucleosome-free regions identifies novel binding sites of Ams2p. We conclude that centromeric nucleosome positions are stable and may be derived from the underlying DNA sequence.
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Affiliation(s)
- Jun S. Song
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey 08540, USA
| | - Xingkun Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - X. Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Xiangwei He
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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Babbitt GA, Kim Y. Inferring natural selection on fine-scale chromatin organization in yeast. Mol Biol Evol 2008; 25:1714-27. [PMID: 18515262 DOI: 10.1093/molbev/msn127] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Despite its potential role in the evolution of complex phenotypes, the detection of negative (purifying) and positive selection on noncoding regulatory sequence has been elusive because of the inherent difficulty in predicting the functional consequences of mutations on noncoding sequence. Because the functioning of regulatory sequence depends upon both chromatin configuration and cis-regulatory factor binding, we investigate the idea that the functional conservation of regulatory regions should be associated with the conservation of sequence-dependent bending properties of DNA that determine its affinity for the nucleosome. Recent advances in the computational prediction of sequence-dependent affinity to nucleosomes provide an opportunity to distinguish between neutral and nonneutral evolution of fine-scale chromatin organization. Here, a statistical test is presented for detecting evolutionary conservation and/or adaptive evolution of nucleosome affinity from interspecies comparisons of DNA sequences. Local nucleosome affinities of homologous sequences were calculated using 2 recently published methods. A randomization test was applied to sites of mutation to evaluate the similarity of DNA-nucleosome affinity between several closely related species of Saccharomyces yeast. For most of the genes we analyzed, the conservation of local nucleosome affinity was detected at a few distinct locations in the upstream noncoding region. Our results also demonstrate that different patterns of chromatin evolution have shaped DNA-nucleosome interaction at the core promoters of TATA-containing and TATA-less genes and that elevated purifying selection has maintained low affinity for nucleosome in the core promoters of the latter group. Across the entire yeast genome, DNA-nucleosome interaction was also discovered to be significantly more conserved in TATA-less genes compared with TATA-containing genes.
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Affiliation(s)
- G A Babbitt
- Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, USA.
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Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS, Struhl K, Weng Z. Nucleosome positioning signals in genomic DNA. Genome Res 2007; 17:1170-7. [PMID: 17620451 PMCID: PMC1933512 DOI: 10.1101/gr.6101007] [Citation(s) in RCA: 245] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Although histones can form nucleosomes on virtually any genomic sequence, DNA sequences show considerable variability in their binding affinity. We have used DNA sequences of Saccharomyces cerevisiae whose nucleosome binding affinities have been experimentally determined (Yuan et al. 2005) to train a support vector machine to identify the nucleosome formation potential of any given sequence of DNA. The DNA sequences whose nucleosome formation potential are most accurately predicted are those that contain strong nucleosome forming or inhibiting signals and are found within nucleosome length stretches of genomic DNA with continuous nucleosome formation or inhibition signals. We have accurately predicted the experimentally determined nucleosome positions across a well-characterized promoter region of S. cerevisiae and identified strong periodicity within 199 center-aligned mononucleosomes studied recently (Segal et al. 2006) despite there being no periodicity information used to train the support vector machine. Our analysis suggests that only a subset of nucleosomes are likely to be positioned by intrinsic sequence signals. This observation is consistent with the available experimental data and is inconsistent with the proposal of a nucleosome positioning code. Finally, we show that intrinsic nucleosome positioning signals are both more inhibitory and more variable in promoter regions than in open reading frames in S. cerevisiae.
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Affiliation(s)
- Heather E. Peckham
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Robert E. Thurman
- Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Yutao Fu
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
| | | | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
- Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Zhiping Weng
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
- Corresponding author.E-mail ; fax (617) 353-6766
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Fedoseyeva VB, Alexandrov AA. Analysis and development of the computer methods of nucleosome localization on DNA fragments with different AT-content. J Biomol Struct Dyn 2007; 24:481-8. [PMID: 17313193 DOI: 10.1080/07391102.2007.10507136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Trinucleotide parameter sets published previously were used for the development of the predictive method for the determining the nucleosome positions along the DNA. The choice of the type of parameter sets used depends upon AT-content of the fragment. Some limitations are imposed on these predictions due to the presence of A(n), T(n) tracts (in our case n>5 or =5) within the 145 bp fragment leading to the displacement or even the prohibition for the corresponding site to be occupied by nucleosomes. The predicted nucleosome positioning site with the large potential may influence on the choice of the proximal nucleosome positions with the weaker bending potentials as is revealed by the comparison with the micrococcal nuclease digestion map. Trinucleotide methods may be considered as advantageous in the comparison with the dinucleotide ones.
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Affiliation(s)
- V B Fedoseyeva
- Institute of Molecular Genetics, RAS, Kurchatov sq.2, Moscow 123182, Russia.
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Fraser RM, Allan J, Simmen MW. In silico approaches reveal the potential for DNA sequence-dependent histone octamer affinity to influence chromatin structure in vivo. J Mol Biol 2006; 364:582-98. [PMID: 17027853 DOI: 10.1016/j.jmb.2006.08.092] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Revised: 08/29/2006] [Accepted: 08/31/2006] [Indexed: 11/30/2022]
Abstract
Nucleosome positioning signals embedded within the DNA sequence have the potential to influence the detailed structure of the higher-order chromatin fibre. In two previous studies of long stretches of DNA, encompassing the chicken beta-globin and ovine beta-lactoglobulin genes, respectively, we mapped the relative affinity of every site for the core histone octamer. In both cases a periodic arrangement of the in vitro positioning sites suggests that they might influence the folding of a nucleosome chain into higher-order structure; this hypothesis was borne out in the case of the beta-lactoglobulin gene, where the distribution of the in vitro positioning sites is related to the positions nucleosomes actually occupy in sheep liver cells. Here, we have exploited the in vitro nucleosome positioning datasets to simulate nucleosomal organisation using in silico approaches. We use the high-resolution, quantitative positioning maps to define a one-dimensional positioning energy lattice, which can be populated with a defined number of nucleosomes. Monte Carlo techniques are employed to simulate the behaviour of the model at equilibrium to produce a set of configurations, which provide a probability-based occupancy map. Employing a variety of techniques we show that the occupancy maps are a sensitive function of the histone octamer density (nucleosome repeat length) and find that a minimal change in this property can produce dramatic localised changes in structure. Although simulations generally give rise to regular periodic nucleosomal arrangements, they often show octamer density-dependent discontinuities, which tend to co-localise with sequences that adopt distinctive chromatin structure in vivo. Furthermore, the overall organisation of simulated chromatin structures are more closely related to the situation in vivo than is the original in vitro positioning data, particularly at a nucleosome density corresponding to the in vivo state. Although our model is simplified, we argue that it provides a unique insight into the influence that DNA sequence can have in determining chromatin structure and could serve as a useful basis for the incorporation of other parameters.
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Affiliation(s)
- Ross M Fraser
- School of Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
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Li W, Miramontes P. Large-scale oscillation of structure-related DNA sequence features in human chromosome 21. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 74:021912. [PMID: 17025477 DOI: 10.1103/physreve.74.021912] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2006] [Indexed: 05/12/2023]
Abstract
Human chromosome 21 is the only chromosome in the human genome that exhibits oscillation of the (G+C) content of a cycle length of hundreds kilobases (kb) ( 500 kb near the right telomere). We aim at establishing the existence of a similar periodicity in structure-related sequence features in order to relate this (G+C)% oscillation to other biological phenomena. The following quantities are shown to oscillate with the same 500 kb periodicity in human chromosome 21: binding energy calculated by two sets of dinucleotide-based thermodynamic parameters, AA/TT and AAA/TTT bi- and tri-nucleotide density, 5'-TA-3' dinucleotide density, and signal for 10- or 11-base periodicity of AA/TT or AAA/TTT. These intrinsic quantities are related to structural features of the double helix of DNA molecules, such as base-pair binding, untwisting or unwinding, stiffness, and a putative tendency for nucleosome formation.
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Affiliation(s)
- Wentian Li
- The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore LIJ Health System, 350 Community Drive, Manhasset, New York 11030, USA.
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Cioffi A, Fleury TJ, Stein A. Aspects of large-scale chromatin structures in mouse liver nuclei can be predicted from the DNA sequence. Nucleic Acids Res 2006; 34:1974-81. [PMID: 16614447 PMCID: PMC1435979 DOI: 10.1093/nar/gkl078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The large amount of non-coding DNA present in mammalian genomes suggests that some of it may play a structural or functional role. We provide evidence that it is possible to predict computationally, from the DNA sequence, loci in mouse liver nuclei that possess distinctive nucleosome arrays. We tested the hypothesis that a 100 kb region of DNA possessing a strong, in-phase, dinucleosome period oscillation in the motif period-10 non-T, A/T, G, should generate a nucleosome array with a nucleosome repeat that is one-half of the dinucleosome oscillation period value, as computed by Fourier analysis of the sequence. Ten loci with short repeats, that would be readily distinguishable from the pervasive bulk repeat, were predicted computationally and then tested experimentally. We estimated experimentally that less than 20% of the chromatin in mouse liver nuclei has a nucleosome repeat length that is 15 bp, or more, shorter than the bulk repeat value of 195 +/- bp. All 10 computational predictions were confirmed experimentally with high statistical significance. Nucleosome repeats as short as 172 +/- 5 bp were observed for the first time in mouse liver chromatin. These findings may be useful for identifying distinctive chromatin structures computationally from the DNA sequence.
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Affiliation(s)
| | | | - Arnold Stein
- To whom correspondence should be addressed. Tel: +1 765 494 6546; Fax: +1 765 494 0876;
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14
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Dalal Y, Fleury TJ, Cioffi A, Stein A. Long-range oscillation in a periodic DNA sequence motif may influence nucleosome array formation. Nucleic Acids Res 2005; 33:934-45. [PMID: 15716311 PMCID: PMC549395 DOI: 10.1093/nar/gki224] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
We have experimentally examined the characteristics of nucleosome array formation in different regions of mouse liver chromatin, and have computationally analyzed the corresponding genomic DNA sequences. We have shown that the mouse adenosine deaminase (MADA) gene locus is packaged into an exceptionally regular nucleosome array with a shortened repeat, consistent with our computational prediction based on the DNA sequence. A survey of the mouse genome indicates that <10% of 70 kb windows possess a nucleosome-ordering signal, consisting of regular long-range oscillations in the period-10 triplet motif non-T, A/T, G (VWG), which is as strong as the signal in the MADA locus. A strong signal in the center of this locus, confirmed by in vitro chromatin assembly experiments, appears to cooperate with weaker, in-phase signals throughout the locus. In contrast, the mouse odorant receptor (MOR) locus, which lacks locus-wide signals, was representative of ∼40% of the mouse genomic DNA surveyed. Within this locus, nucleosome arrays were similar to those of bulk chromatin. Genomic DNA sequences which were computationally similar to MADA or MOR resulted in MADA- or MOR-like nucleosome ladders experimentally. Overall, we provide evidence that computationally predictable information in the DNA sequence may affect nucleosome array formation in animal tissue.
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Affiliation(s)
| | | | | | - Arnold Stein
- To whom correspondence should be addressed. Tel: +1 765 494 6546; Fax: +1 765 494 0876;
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Audit B, Vaillant C, Arnéodo A, d'Aubenton-Carafa Y, Thermes C. Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences. J Biol Phys 2004; 30:33-81. [PMID: 23345861 PMCID: PMC3456503 DOI: 10.1023/b:jobp.0000016438.86794.8e] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Analyses of genomic DNA sequences have shown in previous works that base pairs are correlated at large distances with scale-invariant statistical properties. We show in the present study that these correlations between nucleotides (letters) result in fact from long-range correlations (LRC) between sequence-dependent DNA structural elements (words) involved in the packaging of DNA in chromatin. Using the wavelet transform technique, we perform a comparative analysis of the DNA text and of the corresponding bending profiles generated with curvature tables based on nucleosome positioning data. This exploration through the optics of the so-called `wavelet transform microscope' reveals a characteristic scale of 100-200 bp that separates two regimes of different LRC. We focus here on the existence of LRC in the small-scale regime (≲ 200 bp). Analysis of genomes in the three kingdoms reveals that this regime is specifically associated to the presence of nucleosomes. Indeed, small scale LRC are observed in eukaryotic genomes and to a less extent in archaeal genomes, in contrast with their absence in eubacterial genomes. Similarly, this regime is observed in eukaryotic but not in bacterial viral DNA genomes. There is one exception for genomes of Poxviruses, the only animal DNA viruses that do not replicate in the cell nucleus and do not present small scale LRC. Furthermore, no small scale LRC are detected in the genomes of all examined RNA viruses, with one exception in the case of retroviruses. Altogether, these results strongly suggest that small-scale LRC are a signature of the nucleosomal structure. Finally, we discuss possible interpretations of these small-scale LRC in terms of the mechanisms that govern the positioning, the stability and the dynamics of the nucleosomes along the DNA chain. This paper is maily devoted to a pedagogical presentation of the theoretical concepts and physical methods which are well suited to perform a statistical analysis of genomic sequences. We review the results obtained with the so-called wavelet-based multifractal analysis when investigating the DNA sequences of various organisms in the three kingdoms. Some of these results have been announced in B. Audit et al. [1, 2].
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Affiliation(s)
- Benjamin Audit
- Centre de Recherche Paul Pascal, avenue Schweitzer, 33600 Pessac, France
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Stein A, Dalal Y, Fleury TJ. Circle ligation of in vitro assembled chromatin indicates a highly flexible structure. Nucleic Acids Res 2002; 30:5103-9. [PMID: 12466533 PMCID: PMC137980 DOI: 10.1093/nar/gkf671] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Evidence is provided that some condensed linker histone-containing chromatin structures are highly flexible in solutions containing 2 mM Mg2+. Chromatin assembled in vitro +/- histone H5 on a 6.3 kb linear DNA fragment in 90 mM NaCl using the polyglutamic acid method sedimented fairly homogeneously. The H5-containing sample had s(20, w) values that were 58-69% greater than the sample lacking H5. Chromatin assembled on linear pUC19 plasmid DNA was treated with T4 DNA ligase in solutions containing 2 mM Mg2+ over a range of DNA concentrations. It was found that the intramolecular DNA ends of the chromatin could be joined together more efficiently than the intramolecular ends of the naked DNA at the higher DNA concentrations. This result could not be attributed to the effective reduction in DNA length by nucleosome formation. The chromatin structures formed did not have naked DNA tails extending from the ends as assessed by exonuclease III digestion. Chromatin assembled on DNA shortened by up to 420 bp gave very similar results, suggesting that the structure was a flexible one, rather than a rigid one having DNA ends that were fortuitously juxtaposed.
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Affiliation(s)
- A Stein
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
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17
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Abstract
Here we propose a new determinant for localization of nucleosomes along genomic DNA, in addition to sequence-dependent features. The new specific class of chromatin scaling signals involves curved DNA. According to the observed positional distribution of DNA curvature, the new synchronizing signal occurs once per four nucleosomes on average. This new factor in nucleosome positioning should substantially influence the efficiency of biological reactions through regulatory factors microscopically and the entire chromatin structure through the 30 nm fiber structure macroscopically. Allocation of the new type of signals is found to be fixed evolutionarily although they could be shifted in accordance with the hierarchy of functional genomic structures.
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Affiliation(s)
- Ryoiti Kiyama
- Research Center for Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Ibaraki, Japan.
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Audit B, Vaillant C, Arneodo A, d'Aubenton-Carafa Y, Thermes C. Long-range correlations between DNA bending sites: relation to the structure and dynamics of nucleosomes. J Mol Biol 2002; 316:903-18. [PMID: 11884131 DOI: 10.1006/jmbi.2001.5363] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
It has been established that the precise positioning of nucleosomes on genomic DNA can be achieved, at least for a minority of them, through sequence-dependent processes. However, to what extent DNA sequences play a role in the positioning of the major part of nucleosomes is still debated. The aim of the present study is to examine to what extent long-range correlations (LRC) are related to the presence of nucleosomes. Using the wavelet transform technique, we perform a comparative analysis of the DNA text and of the corresponding bending profiles generated with curvature tables based on nucleosome positioning data. The exploration of a number of eukaryotic and bacterial genomes through the optics of the so-called "wavelet transform microscope" reveals a characteristic scale of 100-200 bp that separates two regimes of different LRC. Here, we focus on the existence of LRC in the small-scale regime (10-200 bp) which are actually observed in eukaryotic genomes, in contrast to their absence in eubacterial genomes. Analysis of viral DNA genomes shows that, like their host's genomes, eukaryotic viruses present LRC but eubacterial viruses do not. There is one exception for genomes of poxviruses (Vaccinia and Melamoplus sanguinipes) which do not replicate in the cell nucleus and do not exhibit LRC. No small-scale LRC are detected in the genomes of all examined RNA viruses, with the exception of retroviruses. These results together with the observation of LRC between particular sequence motifs known to participate in the formation of nucleosomes (e.g. AA dinucleotides) strongly suggest that the 10-200 bp LRC are a signature of the sequence-dependence of nucleosome positioning. Finally, we discuss possible interpretations of these LRC in terms of the physical mechanisms that might govern the positioning and the dynamics of the nucleosomes along the DNA chain through cooperative processes.
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Abstract
In studies of both short and relatively long human genomic DNA, we found a clustering of the consensus site for the transcription factor GCF at the 5' boundary of a subset of human genes. In studies of promoter regions with known transcription initiation site, the cluster of consensus GCF site appeared near the transcription initiation site and in some sequences it extended into the transcribed region defining the leader mRNA. We also found a detectable correlation between the 5' boundary of human genes and recognition motifs for other transcription factors that bind to GC-rich sequences. But in these cases, the correlation was not as general as the correlation observed for the consensus GCF site.
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Affiliation(s)
- M Bina
- Department of Chemistry, Purdue University, W. Lafayette, IN 47907-1393, USA.
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Begusova M, Sy D, Charlier M, Spotheim-Maurizot M. Radiolysis of nucleosome core DNA: a modelling approach. Int J Radiat Biol 2000; 76:1063-73. [PMID: 10947119 DOI: 10.1080/09553000050111532] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
PURPOSE To calculate the expected pattern of frank strand breaks (FSB) induced in the DNA of a nucleosome core particle (NCP) by the attack of radiolytic OH* radicals and to compare this with the experimental pattern of FSB induced by the in vitro irradiation of chicken NCP. MATERIALS AND METHODS The structure of NCP was obtained from the PDB databank. Using molecular modelling, the structure of a linear DNA fragment with the central 60 bp sequence of NCP-DNA was determined. The accessibility of the sugar attack sites to OH* radicals at each nucleotide of the linear fragment or of the NCP-DNA was calculated. The probability of reaction of OH* with each sugar reactive site was calculated using a Monte-Carlo method-based stochastic model. RESULTS The accessibility of attack sites in the NCP-DNA and the calculated probabilities of sugar attack are mainly modulated through masking by histones, and only slightly through bending. The periodicity of the calculated FSB probabilities is identical to that of the experimental FSB probabilities in chicken NCP (period 10.4 +/- 0.1 bp). CONCLUSIONS The good agreement between the calculated and experimental results recommends the presented modelling procedure as a tool in predicting the radiosensitivity of DNA in DNA-ligand complexes of known structure.
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Affiliation(s)
- M Begusova
- Nuclear Physics Institute, Radiation Protection Department, Praha, Czech Republic
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Bina M, Demmon S, Pares-Matos EI. Syndromes associated with Homo sapiens pol II regulatory genes. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2000; 64:171-219. [PMID: 10697410 DOI: 10.1016/s0079-6603(00)64005-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
The molecular basis of human characteristics is an intriguing but an unresolved problem. Human characteristics cover a broad spectrum, from the obvious to the abstract. Obvious characteristics may include morphological features such as height, shape, and facial form. Abstract characteristics may be hidden in processes that are controlled by hormones and the human brain. In this review we examine exaggerated characteristics presented as syndromes. Specifically, we focus on human genes that encode transcription factors to examine morphological, immunological, and hormonal anomalies that result from deletion, insertion, or mutation of genes that regulate transcription by RNA polymerase II (the Pol II genes). A close analysis of abnormal phenotypes can give clues into how sequence variations in regulatory genes and changes in transcriptional control may give rise to characteristics defined as complex traits.
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Affiliation(s)
- M Bina
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47097, USA
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Packer MJ, Dauncey MP, Hunter CA. Sequence-dependent DNA structure: dinucleotide conformational maps. J Mol Biol 2000; 295:71-83. [PMID: 10623509 DOI: 10.1006/jmbi.1999.3236] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have used a computational model to calculate the potential energy surface for dinucleotide steps in double helical DNA as a function of the two principal degrees of freedom, slide and shift. By using a virtual bond to model the constraints imposed by the sugar-phosphate backbone, twist, roll, tilt and rise can be simultaneously optimised for any given values of slide and shift. Thus we have been able to construct complete conformational maps for all step types. For some steps, the maps agree well with experimental data from X-ray crystal structures, but other steps appear to be strongly perturbed by the effects of context (conformational coupling with the neighbouring steps). The optimised values of twist and roll show sequence-dependent variations consistent with the crystal structure data. The conformational maps allow us to construct adiabatic paths, and hence calculate the flexibility of each step with respect to slide and shift. Again the results agree well with the available experimental assignments of flexibility: YR steps, CA/TG and CG, are the most flexible and RR steps, such as AA, the least flexible.
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Affiliation(s)
- M J Packer
- University of Sheffield, Sheffield, S3 7HF, England.
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