ArticleNucleic acids research2016
Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 31 citations in OpenAlex.
- Impact of variability in cell generation times on cell-to-cell variability of protein concentrations.bioRxiv : the preprint server for biology · 2026Article
- Bubble Relaxation Dynamics in Homopolymer DNA Sequences.Molecules (Basel, Switzerland) · 2023Article
- Computational analysis of GAL pathway pinpoints mechanisms underlying natural variation.PLoS computational biology · 2021Article
- Precise sequencing of single protected-DNA fragment molecules for profiling of protein distribution and assembly on DNA.Chemical science · 2021Article
- The Accidental Ally: Nucleosome Barriers Can Accelerate Cohesin-Mediated Loop Formation in Chromatin.Biophysical journal · 2020Article
- A unified computational framework for modeling genome-wide nucleosome landscape.Physical biology · 2018Article
- Theory of Site-Specific DNA-Protein Interactions in the Presence of Nucleosome Roadblocks.Biophysical journal · 2018Article
- Coupling of replisome movement with nucleosome dynamics can contribute to the parent-daughter information transfer.Nucleic acids research · 2018Article
- Regulation of Sensing, Transportation, and Catabolism of Nitrogen Sources in Saccharomyces cerevisiae.Microbiology and molecular biology reviews : MMBR · 2018Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is being increasingly realized that nucleosome organization on DNA crucially regulates DNA-protein interactions and the resulting gene expression. While the spatial character of the nucleosome positioning on DNA has been experimentally and theoretically studied extensively, the temporal character is poorly understood. Accounting for ATPase activity and DNA-sequence effects on nucleosome kinetics, we develop a theoretical method to estimate the time of continuous exposure of binding sites of non-histone proteins (e.g. transcription factors and TATA binding proteins) along any genome. Applying the method to Saccharomyces cerevisiae, we show that the exposure timescales are determined by cooperative dynamics of multiple nucleosomes, and their behavior is often different from expectations based on static nucleosome occupancy. Examining exposure times in the promoters of GAL1 and PHO5, we show that our theoretical predictions are consistent with known experiments. We apply our method genome-wide and discover huge gene-to-gene variability of mean exposure times of TATA boxes and patches adjacent to TSS (+1 nucleosome region); the resulting timescale distributions have non-exponential tails.
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