Relevant bibliographies by topics / Nucleosome positioning prediction

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'Nucleosome positioning prediction'

Author: Grafiati
Published: 4 June 2021
Last updated: 2 February 2022

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Journal articles on the topic "Nucleosome positioning prediction"

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van der Heijden, Thijn, Joke J. F. A. van Vugt, Colin Logie, and John van Noort. "Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy." Proceedings of the National Academy of Sciences 109, no. 38 (August 20, 2012): E2514—E2522. http://dx.doi.org/10.1073/pnas.1205659109.

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Nucleosome positioning dictates eukaryotic DNA compaction and access. To predict nucleosome positions in a statistical mechanics model, we exploited the knowledge that nucleosomes favor DNA sequences with specific periodically occurring dinucleotides. Our model is the first to capture both dyad position within a few base pairs, and free binding energy within 2 kBT, for all the known nucleosome positioning sequences. By applying Percus’s equation to the derived energy landscape, we isolate sequence effects on genome-wide nucleosome occupancy from other factors that may influence nucleosome positioning. For both in vitro and in vivo systems, three parameters suffice to predict nucleosome occupancy with correlation coefficients of respectively 0.74 and 0.66. As predicted, we find the largest deviations in vivo around transcription start sites. This relatively simple algorithm can be used to guide future studies on the influence of DNA sequence on chromatin organization.
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Saxton, Daniel S., and Jasper Rine. "Nucleosome Positioning Regulates the Establishment, Stability, and Inheritance of Heterochromatin inSaccharomyces cerevisiae." Proceedings of the National Academy of Sciences 117, no. 44 (October 19, 2020): 27493–501. http://dx.doi.org/10.1073/pnas.2004111117.

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Heterochromatic domains are complex structures composed of nucleosome arrays that are bound by silencing factors. This composition raises the possibility that certain configurations of nucleosome arrays facilitate heterochromatic silencing. We tested this possibility inSaccharomyces cerevisiaeby systematically altering the distance between heterochromatic nucleosome-depleted regions (NDRs), which is predicted to affect local nucleosome positioning by limiting how nucleosomes can be packed between NDRs. Consistent with this prediction, serial deletions that altered the distance between heterochromatic NDRs revealed a striking oscillatory relationship between inter-NDR distance and defects in nucleosome positioning. Furthermore, conditions that caused poor nucleosome positioning also led to defects in both heterochromatin stability and the ability of cells to generate and inherit epigenetic transcriptional states. These findings strongly suggest that nucleosome positioning can contribute to formation and maintenance of functional heterochromatin and point to previously unappreciated roles of NDR positioning within heterochromatic domains.
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Widom, J. "Role of DNA sequence in nucleosome stability and dynamics." Quarterly Reviews of Biophysics 34, no. 3 (August 2001): 269–324. http://dx.doi.org/10.1017/s0033583501003699.

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1. Introduction 2701.1 Overview of nucleosome structure 2712. Relative equilibrium stability (affinity) of histone–DNA interactions in nucleosomes 2722.1 Relative affinity equals relative equilibrium stability 2722.2 Competition assays for relative free-energy measurements 2732.3 Technical issues in relative free-energy measurements 2752.4 Range of affinities 2783. Relation of nucleosome stability to nucleosome positioning 2793.1 Translational nucleosome positioning 2793.2 Rotational positioning 2803.3 Unfavorable positioning 2813.4 Experiments 2814. Physical basis of DNA sequence preferences 2824.1 Free-energy cost of DNA bending 2834.2 Molecular mechanics of DNA bending and bendability 2844.3 Bent and bendable DNA sequences 2864.4 Parameter sets for prediction of DNA bending and bendability 2884.5 DNA twisting 2904.6 Energetics of nucleosomal DNA packaging 2915. DNA sequence motifs for nucleosome packaging 2925.1 Natural and designed nucleosomal DNAs 2935.2 New rules and reagents from physical selection studies 2945.3 Molecular basis of DNA sequence preferences 2995.4 Special properties of the TA step 3005.5 Unfavorable sequences 3025.6 Natural genomes 3035.7 Evolutionary approach toward an optimal sequence 3055.8 Optimization by design 3056. Dynamic nucleosome instability 3086.1 Site-exposure equilibria 3086.2 DNA sequence-dependence to site-exposure equilibria 3126.3 Nucleosome translocation 3156.4 Action of processive enzymes 3197. Conclusions 3198. Acknowledgements 3209. References 320The nucleosome core particle is the fundamental repeating subunit of chromatin. It consists of two molecules each of the four ‘core histone’ proteins, H2A, H2B, H3 and H4, and a 147 bp stretch of DNA. The lowest level of chromatin organization consists of a repeated array of nucleosome core particles separated by variable lengths of ‘linker DNA’. In many, but not all, cases, each core particle plus its linker DNA is associated with one molecule of a fifth ‘linker’ histone protein, H1. The complex of the core particle plus its linker DNA and H1 (when present) is called a ‘nucleosome’.
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Fulnecek, Jaroslav, Roman Matyasek, and Ales Kovarik. "Plant 5S rDNA has multiple alternative nucleosome positions." Genome 49, no. 7 (July 1, 2006): 840–50. http://dx.doi.org/10.1139/g06-039.

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In plants, 5S ribosomal DNA (5S rDNA) is typically found in hundreds of copies of tandemly arranged units. Nucleotide database searches revealed that the majority of 5S genes (>90%) have repeat lengths that are not simple multiples of a plant nucleosomal unit, ranging in plants from 175–185 bp. To get insight into the chromatin structure, we have determined positions of nucleosomes in the Nicotiana sylvestris and Nicotiana tomentosiformis 5S rDNA units with repeat lengths of about 430 and 645 bp, respectively. Mapping experiments carried out on isolated nucleo somal DNA revealed many (>50) micrococcal nuclease cleavage sites in each class of repeats. Permutation analysis and theoretical computer prediction showed multiple DNA bend sites, mostly located in the nontranscribed spacer region. The distance between bend sites, however, did not correspond to the average spacing of nucleosomes in 5S chromatin (~180 bp). These data indicate that 5S rDNA does not have fixed nucleosomal positioning sites and that units can be wrapped in a number of alternative nucleosome frames. Consequently, accessibility of transcription factors to cognate motifs might vary across the tandem array, potentially influencing gene expression.Key words: Nicotiana, 5S rDNA, heterochromatin, tandem repeats, nucleosomes, DNA curvature.
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胡, 世赛. "Prediction of Nucleosome Positioning Sequence for Yeast Genome." Biophysics 06, no. 01 (2018): 1–6. http://dx.doi.org/10.12677/biphy.2018.61001.

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Boffelli, D., P. De Santis, A. Palleschi, and M. Savino. "The curvature vector in nucleosomal DNAs and theoretical prediction of nucleosome positioning." Biophysical Chemistry 39, no. 2 (February 1991): 127–36. http://dx.doi.org/10.1016/0301-4622(91)85014-h.

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Wang, Jia, Shuai Liu, and Weina Fu. "Nucleosome Positioning with Set of Key Positions and Nucleosome Affinity." Open Biomedical Engineering Journal 8, no. 1 (December 31, 2014): 166–70. http://dx.doi.org/10.2174/1874120701408010166.

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The formation and precise positioning of nucleosome in chromatin occupies a very important role in studying life process. Today, there are many researchers who discovered that the positioning where the location of a DNA sequence fragment wraps around a histone octamer in genome is not random but regular. However, the positioning is closely relevant to the concrete sequence of core DNA. So in this paper, we analyzed the relation between the affinity and sequence structure of core DNA, and extracted the set of key positions. In these positions, the nucleotide sequences probably occupy mainly action in the binding. First, we simplified and formatted the experimental data with the affinity. Then, to find the key positions in the wrapping, we used neural network to analyze the positive and negative effects of nucleosome generation for each position in core DNA sequences. However, we reached a class of weights with every position to describe this effect. Finally, based on the positions with high weights, we analyzed the reason why the chosen positions are key positions, and used these positions to construct a model for nucleosome positioning prediction. Experimental results show the effectiveness of our method.
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Liu, H., R. Zhang, W. Xiong, J. Guan, Z. Zhuang, and S. Zhou. "A comparative evaluation on prediction methods of nucleosome positioning." Briefings in Bioinformatics 15, no. 6 (September 10, 2013): 1014–27. http://dx.doi.org/10.1093/bib/bbt062.

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Liu, Guoqing, Fen Feng, Xiujuan Zhao, and Lu Cai. "Nucleosome Organization around Pseudogenes in the Human Genome." BioMed Research International 2015 (2015): 1–7. http://dx.doi.org/10.1155/2015/821596.

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Pseudogene, disabled copy of functional gene, plays a subtle role in gene expression and genome evolution. The first step in deciphering RNA-level regulation of pseudogenes is to understand their transcriptional activity. So far, there has been no report on possible roles of nucleosome organization in pseudogene transcription. In this paper, we investigated the effect of nucleosome positioning on pseudogene transcription. For transcribed pseudogenes, the experimental nucleosome occupancy shows a prominent depletion at the regions both upstream of pseudogene start positions and downstream of pseudogene end positions. Intriguingly, the same depletion is also observed for nontranscribed pseudogenes, which is unexpected since nucleosome depletion in those regions is thought to be unnecessary in light of the nontranscriptional property of those pseudogenes. The sequence-dependent prediction of nucleosome occupancy shows a consistent pattern with the experimental data-based analysis. Our results indicate that nucleosome positioning may play important roles in both the transcription initiation and termination of pseudogenes.
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Yi, Xianfu, Yu-Dong Cai, Zhisong He, WeiRen Cui, and Xiangyin Kong. "Prediction of Nucleosome Positioning Based on Transcription Factor Binding Sites." PLoS ONE 5, no. 9 (September 1, 2010): e12495. http://dx.doi.org/10.1371/journal.pone.0012495.

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Dissertations / Theses on the topic "Nucleosome positioning prediction"

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Hasan, S. "Prediction and analysis of nucleosome positioning in genomic sequences." Thesis, University of Cambridge, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.603834.

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One theory suggests that DNA sequences, which are intrinsically “curved”, can position nucleosomes. In a previous study, using “cyclical” hidden-markov models, it had been suggested that a 10 periodic occurrence of the [VWG] motif could have such an effect and could help nucleosomes to be positioned in human exons. This work was extended in this thesis. 60% of human genomic sequences were seen to be covered in apparently weak 9-10 bp periodic patches of [CWG]. [CWG]-dense regions were seen to alternate with regions which were rich in [W] motifs in human. However, the pattern was not the same in mouse. Another theory suggests that highly flexible or highly rigid DNA sequences may favour or disfavour nucleosome formation respectively. The locations of such patterns were investigated in human sequences using the wavelet technique. This approach identified confined periodic patterns (in the range of 80-200 bp) of rigidity in human genomic sequences; the patterns themselves were, however, mainly consequences of alu repeat-clustering. However, the same analysis in the mouse genome indicated that such a mechanism for positioning nucleosomes was not conserved and therefore unlikely. A different approach to model nucleosomes was to train weighted DNA matrices from experimentally-mapped nucleosomes datasets. This technique gave some encouraging results (one model showing 100% accuracy at 40% coverage), but was restricted by the limited size of the datasets. Overall the conclusion is that there is some evidence for sequence specific nucleosome positioning, but that more experimental data is needed to build and evaluate practical and predictive computational models.
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Višňovský, Marek. "Prediction and Analysis of Nucleosome Positions in DNA." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2013. http://www.nusl.cz/ntk/nusl-412874.

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Eukaryotní DNA se váže kolem nukleozomů, čím ovplyvnuje vyšši strukturu DNA a přístup k vazebním mistům pro všeobecní transkripční faktory a oblasti genů. Je proto důležité vědet, kde se nukleozomy vážou na DNA, a jak silná tato vazba je, abychom mohli porozumět mechanizmům regulace genů. V rámci projektu byla implementována nová metoda pro predikci nukleozomů založená na rozšíření Skrytých Markovových modelů, kde jako trénovací a testovací sada posloužila publikována data z Brogaard et al. (Brogaard K, Wang J-P, Widom, J. Nature 486(7404), 496-501 (2012). doi:10.1038/nature11142). Správne predikováno bylo zhruba 50% nukleozomů, co je porovnatenlný výsledek s existujícimi metodami. Okrem toho byla provedena řada experimentů popisující vlastnosti sekvencí nukleozomů a ich organizace.
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Book chapters on the topic "Nucleosome positioning prediction"

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Reynolds, Sheila M., Zhiping Weng, Jeff A. Bilmes, and William Stafford Noble. "Predicting Nucleosome Positioning Using Multiple Evidence Tracks." In Lecture Notes in Computer Science, 441–55. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-12683-3_29.

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Conference papers on the topic "Nucleosome positioning prediction"

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TANAKA, YOSHIAKI, and KENTA NAKAI. "AN ASSESSMENT OF PREDICTION ALGORITHMS FOR NUCLEOSOME POSITIONING." In Proceedings of the 20th International Conference. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2009. http://dx.doi.org/10.1142/9781848165632_0016.

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Xiujuan Zhao, Zhiyong Pe, Jia Liu, Songye Ren, and Lu Cai. "Nucleosome positioning prediction in C. elegans based on increment of diversity combined with quadratic discriminant analysis." In 2010 3rd International Conference on Advanced Computer Theory and Engineering (ICACTE 2010). IEEE, 2010. http://dx.doi.org/10.1109/icacte.2010.5579020.

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Zhang, Wei, Haiying Zheng, and Juhua Zhang. "Nucleosome positioning plays an important role in predicting the methylation status of CpG islands." In 2011 4th International Conference on Biomedical Engineering and Informatics (BMEI). IEEE, 2011. http://dx.doi.org/10.1109/bmei.2011.6098535.

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