ArticleNucleic acids research2014
Nucleosome positioning and kinetics near transcription-start-site barriers are controlled by interplay between active remodeling and DNA sequence.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 42 citations in OpenAlex.
- Consecutive low-frequency shifts in A/T content denote nucleosome positions across microeukaryotes.iScience · 2025Article
- Stochastic nucleosome disassembly mediated by remodelers and histone fragmentation.The Journal of chemical physics · 2023Article
- The role of transcript regions and amino acid choice in nucleosome positioning.NAR genomics and bioinformatics · 2023Article
- Superstructure Detection in Nucleosome Distribution Shows Common Pattern within a Chromosome and within the Genome.Life (Basel, Switzerland) · 2022Article
- Review
- Effects of size, cooperativity, and competitive binding on protein positioning on DNA.Biophysical journal · 2021Article
- On the role of transcription in positioning nucleosomes.PLoS computational biology · 2021Article
- Article
- Theory of Active Chromatin Remodeling.Physical review letters · 2019Article
- ChIPulate: A comprehensive ChIP-seq simulation pipeline.PLoS computational biology · 2019Article
- 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
- Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters.PLoS computational biology · 2016Article
- Linking Core Promoter Classes to Circadian Transcription.PLoS genetics · 2016Article
- Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics.Nucleic acids research · 2016Article
- Role of transcription factor-mediated nucleosome disassembly in PHO5 gene expression.Scientific reports · 2016Article
- Replication-guided nucleosome packing and nucleosome breathing expedite the formation of dense arrays.Nucleic acids research · 2014Article
- Changing chromatin fiber conformation by nucleosome repositioning.Biophysical journal · 2014Article
- Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions.PLoS computational biology · 2014Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 2 countries.
Funding
Abstract
We investigate how DNA sequence, ATP-dependent chromatin remodeling and nucleosome-depleted 'barriers' co-operate to determine the kinetics of nucleosome organization, in a stochastic model of nucleosome positioning and dynamics. We find that 'statistical' positioning of nucleosomes against 'barriers', hypothesized to control chromatin structure near transcription start sites, requires active remodeling and therefore cannot be described using equilibrium statistical mechanics. We show that, unlike steady-state occupancy, DNA site exposure kinetics near a barrier is dominated by DNA sequence rather than by proximity to the barrier itself. The timescale for formation of positioning patterns near barriers is proportional to the timescale for active nucleosome eviction. We also show that there are strong gene-to-gene variations in nucleosome positioning near barriers, which are eliminated by averaging over many genes. Our results suggest that measurement of nucleosome kinetics can reveal information about sequence-dependent regulation that is not apparent in steady-state nucleosome occupancy.
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