ArticleChromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology2012
Calculation of nucleosomal DNA deformation energy: its implication for nucleosome positioning.
Article in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 12 citations in OpenAlex.
- Contributions of DNA mechanics and trans-regulation to nucleosome positioning in Schizosaccharomyces pombe and its role in co-transcriptional splicing.Epigenetics & chromatin · 2026Article
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- DNA Sequence-Dependent Properties of Nucleosome Positioning in Regions of Distinct Chromatin States in Mouse Embryonic Stem Cells.International journal of molecular sciences · 2022Article
- The implication of DNA bending energy for nucleosome positioning and sliding.Scientific reports · 2018Article
- LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks.Bioinformatics (Oxford, England) · 2018Article
- A deformation energy-based model for predicting nucleosome dyads and occupancy.Scientific reports · 2016Article
- Nucleosome Organization around Pseudogenes in the Human Genome.BioMed research international · 2015Article
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3 authors at 1 institution in 1 country.
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Abstract
Nucleosome positioning plays an essential role in various fundamental cellular processes by modulating the accessibility of DNA to binding proteins. Understanding the mechanisms and precise recognition of nucleosome positioning along genomic sequences are substantially important for elucidating regulations of cellular processes such as DNA replication, recombination, and gene transcription. In this report, we present a knowledge-based model for calculation of deformational energy of nucleosomal DNA and apply the model to the prediction of nucleosome positioning along the genome of Saccharomyces cerevisiae accurately. The model successfully predicted genome-wide in vitro nucleosome positions. When combined with quadratic discriminant classifier, the model achieved an accuracy of 92.9 % in discriminating in vitro nucleosome forming sequences from nucleosome inhibiting sequences. Our result supports the debated notion that the nucleosome positioning in the genomic sequences is guided primarily by deformational properties of DNA.
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Registered trials
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