ArticlePloS one2016
Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Contributions of Local Structural and Energetic Features of DNA to Large-scale Genomic Organization.Journal of molecular biology · 2026Review
- Nucleosome wrapping energy in CpG islands and the role of epigenetic base modifications.eLife · 2025Article
- The effects of DMSO on DNA conformations and mechanics.Biophysical journal · 2025Article
- The Avoidance of Purine Stretches by Cancer Mutations.International journal of molecular sciences · 2024Article
- The role of transcript regions and amino acid choice in nucleosome positioning.NAR genomics and bioinformatics · 2023Article
- Multiplexing mechanical and translational cues on genes.Biophysical journal · 2022Article
- DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles.Nucleic acids research · 2021Article
- The lane-switch mechanism for nucleosome repositioning by DNA translocase.Nucleic acids research · 2021Article
- Surprising Twists in Nucleosomal DNA with Implication for Higher-order Folding.Journal of molecular biology · 2021Article
- Review
- Asymmetry in histone rotation in forced unwrapping and force quench rewrapping in a nucleosome.Nucleic acids research · 2021Article
- A critical role for linker DNA in higher-order folding of chromatin fibers.Nucleic acids research · 2021Article
- Ensembles of Breathing Nucleosomes: A Computational Study.Biophysical journal · 2020Article
- Article
- Article
- The Latest Twists in Chromatin Remodeling.Biophysical journal · 2018Review
- The biology and polymer physics underlying large-scale chromosome organization.Traffic (Copenhagen, Denmark) · 2018Review
- The role of DNA sequence in nucleosome breathing.The European physical journal. E, Soft matter · 2017Article
- A single-molecule assessment of the protective effect of DMSO against DNA double-strand breaks induced by photo-and γ-ray-irradiation, and freezing.Scientific reports · 2017Article
- Benchmarking and refining probability-based models for nucleosome-DNA interaction.BMC bioinformatics · 2017Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Eukaryotic DNA is strongly bent inside fundamental packaging units: the nucleosomes. It is known that their positions are strongly influenced by the mechanical properties of the underlying DNA sequence. Here we discuss the possibility that these mechanical properties and the concomitant nucleosome positions are not just a side product of the given DNA sequence, e.g. that of the genes, but that a mechanical evolution of DNA molecules might have taken place. We first demonstrate the possibility of multiplexing classical and mechanical genetic information using a computational nucleosome model. In a second step we give evidence for genome-wide multiplexing in Saccharomyces cerevisiae and Schizosacharomyces pombe. This suggests that the exact positions of nucleosomes play crucial roles in chromatin function.
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