ArticleNucleic acids research2023
The nucleosome unwrapping free energy landscape defines distinct regions of transcription factor accessibility and kinetics.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 21 citations in OpenAlex.
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- An Energy Model Based on Molecular Structure for Predicting Histone Modification Levels at lncRNA Promoter Regions in HepG2 Cells.International journal of molecular sciences · 2026Article
- Insights from single-molecule force spectroscopy into chromatin topology.Biophysical reviews · 2026Review
- Conformations of Linker Histone H1 Bound to Nucleosome Arrays.Journal of molecular biology · 2026Article
- Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs.bioRxiv : the preprint server for biology · 2025Article
- The ISW1 and CHD1 chromatin remodelers suppress global nucleosome dynamics in living yeast cells.Science advances · 2025Article
- Mechanisms for DNA Interplay in Eukaryotic Transcription Factors.Annual review of biophysics · 2025Review
- ATAC and SAGA histone acetyltransferase modules facilitate transcription factor binding to nucleosomes independent of their acetylation activity.Nucleic acids research · 2025Article
- Transcriptional silencing in Saccharomyces cerevisiae: known unknowns.Epigenetics & chromatin · 2024Review
- Nucleosome Dynamics Derived at the Single-Molecule Level Bridges Its Structures and Functions.JACS Au · 2024Review
- The Free Energy of Nucleosomal DNA Based on the Landau Model and Topology.Biomolecules · 2023Article
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4 authors at 1 institution in 1 country.
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Abstract
Transcription factors (TF) require access to target sites within nucleosomes to initiate transcription. The target site position within the nucleosome significantly influences TF occupancy, but how is not quantitatively understood. Using ensemble and single-molecule fluorescence measurements, we investigated the targeting and occupancy of the transcription factor, Gal4, at different positions within the nucleosome. We observe a dramatic decrease in TF occupancy to sites extending past 30 base pairs (bp) into the nucleosome which cannot be explained by changes in the TF dissociation rate or binding site orientation. Instead, the nucleosome unwrapping free energy landscape is the primary determinant of Gal4 occupancy by reducing the Gal4 binding rate. The unwrapping free energy landscape defines two distinct regions of accessibility and kinetics with a boundary at 30 bp into the nucleosome where the inner region is over 100-fold less accessible. The Gal4 binding rate in the inner region no longer depends on its concentration because it is limited by the nucleosome unwrapping rate, while the frequency of nucleosome rewrapping decreases because Gal4 exchanges multiple times before the nucleosome rewraps. Our findings highlight the importance of the nucleosome unwrapping free energy landscape on TF occupancy and dynamics that ultimately influences transcription initiation.
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