ArticleProceedings of the National Academy of Sciences of the United States of America2012
Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- Cold-induced nucleosome dynamics linked to silencing of Arabidopsis FLC.Nature communications · 2025Article
- Promoter-pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt.The EMBO journal · 2023Article
- Specific DNA binding of archaeal histones HMfA and HMfB.Frontiers in microbiology · 2023Article
- Comprehensive computational analysis of epigenetic descriptors affecting CRISPR-Cas9 off-target activity.BMC genomics · 2022Article
- Reconstituted TAD-size chromatin fibers feature heterogeneous nucleosome clusters.Scientific reports · 2022Article
- The lane-switch mechanism for nucleosome repositioning by DNA translocase.Nucleic acids research · 2021Article
- Comparative analysis and prediction of nucleosome positioning using integrative feature representation and machine learning algorithms.BMC bioinformatics · 2021Article
- Nucleosome-induced homology recognition in chromatin.Journal of the Royal Society, Interface · 2021Article
- A deformation energy model reveals sequence-dependent property of nucleosome positioning.Chromosoma · 2021Article
- On the role of transcription in positioning nucleosomes.PLoS computational biology · 2021Article
- Q-Nuc: a bioinformatics pipeline for the quantitative analysis of nucleosomal profiles.Interdisciplinary sciences, computational life sciences · 2020Article
- Article
- DNA Sequence Is a Major Determinant of Tetrasome Dynamics.Biophysical journal · 2019Article
- Theory of Active Chromatin Remodeling.Physical review letters · 2019Article
- Deep learning architectures for prediction of nucleosome positioning from sequences data.BMC bioinformatics · 2018Article
- Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA.PLoS computational biology · 2018Article
- A unified computational framework for modeling genome-wide nucleosome landscape.Physical biology · 2018Article
- Inference of the human polyadenylation code.Bioinformatics (Oxford, England) · 2018Article
- MTF2 recruits Polycomb Repressive Complex 2 by helical-shape-selective DNA binding.Nature genetics · 2018Article
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4 authors.
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Abstract
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 k(B)T, 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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