ArticleProceedings of the National Academy of Sciences of the United States of America2009
Nucleosome positioning by genomic excluding-energy barriers.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 59 citations in OpenAlex.
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- Consecutive low-frequency shifts in A/T content denote nucleosome positions across microeukaryotes.iScience · 2025Article
- Review
- Effects of size, cooperativity, and competitive binding on protein positioning on DNA.Biophysical journal · 2021Article
- The implication of DNA bending energy for nucleosome positioning and sliding.Scientific reports · 2018Article
- Coupling of replisome movement with nucleosome dynamics can contribute to the parent-daughter information transfer.Nucleic acids research · 2018Article
- Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates.Biophysical journal · 2018Article
- Evidence of selection for an accessible nucleosomal array in human.BMC genomics · 2016Article
- A deformation energy-based model for predicting nucleosome dyads and occupancy.Scientific reports · 2016Article
- Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics.Nucleic acids research · 2016Article
- Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster.Nucleic acids research · 2016Article
- Global mapping of DNA conformational flexibility on Saccharomyces cerevisiae.PLoS computational biology · 2015Article
- Intasome architecture and chromatin density modulate retroviral integration into nucleosome.Retrovirology · 2015Article
- Embryonic stem cell specific "master" replication origins at the heart of the loss of pluripotency.PLoS computational biology · 2015Article
- DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity.PloS one · 2015Article
- Quantifying the role of steric constraints in nucleosome positioning.Nucleic acids research · 2014Article
- Nucleosome positioning and kinetics near transcription-start-site barriers are controlled by interplay between active remodeling and DNA sequence.Nucleic acids research · 2014Article
- Fitness landscape for nucleosome positioning.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Gene promoters show chromosome-specificity and reveal chromosome territories in humans.BMC genomics · 2013Article
- Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent genome-wide nucleosome mappings along with bioinformatics studies have confirmed that the DNA sequence plays a more important role in the collective organization of nucleosomes in vivo than previously thought. Yet in living cells, this organization also results from the action of various external factors like DNA-binding proteins and chromatin remodelers. To decipher the code for intrinsic chromatin organization, there is thus a need for in vitro experiments to bridge the gap between computational models of nucleosome sequence preferences and in vivo nucleosome occupancy data. Here we combine atomic force microscopy in liquid and theoretical modeling to demonstrate that a major sequence signaling in vivo are high-energy barriers that locally inhibit nucleosome formation rather than favorable positioning motifs. We show that these genomic excluding-energy barriers condition the collective assembly of neighboring nucleosomes consistently with equilibrium statistical ordering principles. The analysis of two gene promoter regions in Saccharomyces cerevisiae and the human genome indicates that these genomic barriers direct the intrinsic nucleosome occupancy of regulatory sites, thereby contributing to gene expression regulation.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.