ArticlePLoS computational biology2021
Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 17 citations in OpenAlex.
- ATAC-seq and MNase-seq Detect Distinct Modes of Chromatin Accessibility.bioRxiv : the preprint server for biology · 2026Article
- Native nucleosome-positioning elements as alternatives to the 601 sequence for nucleosome repositioning studies.Nucleic acids research · 2025Article
- DNA methylation-based high-resolution mapping of long-distance chromosomal interactions in nucleosome-depleted regions.Nature communications · 2024Article
- Review
- Partitioned usage of chromatin remodelers by nucleosome-displacing factors.Cell reports · 2022Article
- Nucleosome-directed replication origin licensing independent of a consensus DNA sequence.Nature communications · 2022Article
- Superstructure Detection in Nucleosome Distribution Shows Common Pattern within a Chromosome and within the Genome.Life (Basel, Switzerland) · 2022Article
- The Active Mechanism of Nucleosome Depletion by Poly(dA:dT) Tracts In Vivo.International journal of molecular sciences · 2021Review
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Nucleosome positioning in the genome is essential for the regulation of many nuclear processes. We currently have limited capability to predict nucleosome positioning in vivo, especially the locations and sizes of nucleosome depleted regions (NDRs). Here, we present a thermodynamic model that incorporates the intrinsic affinity of histones, competitive binding of sequence-specific factors, and nucleosome remodeling to predict nucleosome positioning in budding yeast. The model shows that the intrinsic affinity of histones, at near-saturating histone concentration, is not sufficient in generating NDRs in the genome. However, the binding of a few factors, especially RSC towards GC-rich and poly(A/T) sequences, allows us to predict ~ 66% of genome-wide NDRs. The model also shows that nucleosome remodeling activity is required to predict the correct NDR sizes. The validity of the model was further supported by the agreement between the predicted and the measured nucleosome positioning upon factor deletion or on exogenous sequences introduced into yeast. Overall, our model quantitatively evaluated the impact of different genetic components on NDR formation and illustrated the vital roles of sequence-specific factors and nucleosome remodeling in this process.
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