ArticleJournal of molecular biology2012
Kinetics and thermodynamics of phenotype: unwinding and rewinding the nucleosome.
Article in Journal of molecular biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 49 citations in OpenAlex.
- Autoregressive HMM resolves biomolecular transitions from passive optical tweezer force measurements.Biophysical journal · 2025Article
- Single gene analysis in yeast suggests nonequilibrium regulatory dynamics for transcription.Nature communications · 2024Article
- The Histone Chaperones SET/TAF-1β and NPM1 Exhibit Conserved Functionality in Nucleosome Remodeling and Histone Eviction in a Cytochrome c-Dependent Manner.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- High-yield ligation-free assembly of DNA constructs with nucleosome positioning sequence repeats for single-molecule manipulation assays.The Journal of biological chemistry · 2023Article
- PICH acts as a force-dependent nucleosome remodeler.Nature communications · 2022Article
- A Horizontal Magnetic Tweezers for Studying Single DNA Molecules and DNA-Binding Proteins.Molecules (Basel, Switzerland) · 2021Article
- Asymmetry in histone rotation in forced unwrapping and force quench rewrapping in a nucleosome.Nucleic acids research · 2021Article
- Ensembles of Breathing Nucleosomes: A Computational Study.Biophysical journal · 2020Article
- Article
- Single and double box HMGB proteins differentially destabilize nucleosomes.Nucleic acids research · 2019Article
- Mechanical evolution of DNA double-strand breaks in the nucleosome.PLoS computational biology · 2018Article
- Multiplexed fluctuation-dissipation-theorem calibration of optical tweezers inside living cells.The Review of scientific instruments · 2017Article
- Tension-Dependent Free Energies of Nucleosome Unwrapping.ACS central science · 2016Article
- H2A.Z controls the stability and mobility of nucleosomes to regulate expression of the LH genes.Nature communications · 2016Article
- Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics.Nucleic acids research · 2016Article
- Recent insights from in vitro single-molecule studies into nucleosome structure and dynamics.Biophysical reviews · 2016Review
- Nucleosomes undergo slow spontaneous gaping.Nucleic acids research · 2015Article
- Quantitative analysis of single-molecule force spectroscopy on folded chromatin fibers.Nucleic acids research · 2015Article
- Article
- Crop epigenetics and the molecular hardware of genotype × environment interactions.Frontiers in plant science · 2015Review
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Chromatin "remodeling" is widely accepted as the mechanism that permits access to DNA by the transcription machinery. To date, however, there has been no experimental measurement of the changes in the kinetics and thermodynamics of the DNA-histone octamer association that are required to remodel chromatin so that transcription may occur. Here, we present the results of optical tweezer measurements that compare the kinetic and thermodynamic properties of nucleosomes composed of unmodified histones with those of nucleosomes that contain a mutant histone H4 (H4-R45H), which has been shown to allow SWI/SNF remodeling factor-independent transcription from the yeast HO promoter in vivo. Our measurements, carried out in a force-clamp mode, determine the force-dependent unwinding and rewinding rates of the nucleosome inner turn. At each force studied, nucleosomes containing H4-R45H unwind more rapidly and rewind more slowly than nucleosomes containing unmodified H4, indicating that the latter are the more stable. Extrapolation to forces at which the winding and unwinding rates are equal determines the absolute free energy of the nucleosome inner turn to be -32k(B)T for nucleosomes containing unmodified H4 and -27k(B)T for nucleosomes containing H4-R45H. Thus, the "loosening" or "remodeling" caused by this point mutation, which is demonstrated to be sufficient to allow transcriptional machinery access to the HO promoter (in the absence of other remodeling factors), is 5k(B)T. The correlation between the free energy of the nucleosome inner turn and the sin (SWI/SNF-independent) transcription suggests that, beyond partial unwinding, complete histone unwinding may play a role in transcriptional activation.
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Registered trials
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.