ArticleBiophysical journal2021
Kinetic origin of nucleosome invasion by pioneer transcription factors.
Article in Biophysical journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- An experimentally-informed polymer model reveals high resolution organization of genomic loci.Nature communications · 2026Article
- Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells.Nature structural & molecular biology · 2025Article
- Modeling Facilitated Diffusion of Proteins in Crowded Environment.Sub-cellular biochemistry · 2025Review
- Molecular Mechanism of Nucleosome Recognition by the Pioneer Transcription Factor Sox.Journal of chemical information and modeling · 2023Article
- Nucleosome breathing facilitates cooperative binding of pluripotency factors Sox2 and Oct4 to DNA.Biophysical journal · 2022Article
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Authors and funding
3 authors.
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Abstract
Recently, a cryo-electron microscopy study has captured different stages of nucleosome breathing dynamics that show partial unwrapping of DNA from histone core to permit transient access to the DNA sites by transcription factors. In practice, however, only a subset of transcription factors named pioneer factors can invade nucleosomes and bind to specific DNA sites to trigger essential DNA metabolic processes. We propose a discrete-state stochastic model that considers the interplay of nucleosome breathing and protein dynamics explicitly and estimate the mean time to search the target DNA sites. It is found that the molecular principle governing the search process on nucleosome is very different compared to that on naked DNA. The pioneer factors minimize their search times on nucleosomal DNA by compensating their nucleosome association rates by dissociation rates. A fine balance between the two presents a tradeoff between their nuclear mobility and error associated with the search process.
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