ArticleNucleic acids research2015
Nucleosomes undergo slow spontaneous gaping.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Direct visualization and tracing of chromatin folding in the Drosophila embryo.The EMBO journal · 2026Article
- Base excision repair in chromatin: A tug-of-war for DNA damage.DNA repair · 2025Review
- Disentangling Timescales of Molecular Kinetics with spFRET using ALEX-FCS.Journal of fluorescence · 2025Article
- Poly(ADP-ribose)polymerase 2 is zinc-dependent enzyme and nucleosome reorganizer.Cellular and molecular life sciences : CMLS · 2025Article
- Mechanisms of DNA Damage Recognition by UDG and PARP1 in the Nucleosome.Biomolecules · 2025Article
- Structural basis of gap-filling DNA synthesis in the nucleosome by DNA Polymerase β.Nature communications · 2025Article
- Dynamics of nucleosomes and chromatin fibers revealed by single-molecule measurements.BMB reports · 2025Review
- Nanoscale Characterization of Interaction of Nucleosomes with H1 Linker Histone.International journal of molecular sciences · 2024Article
- Nucleosome Dynamics Derived at the Single-Molecule Level Bridges Its Structures and Functions.JACS Au · 2024Review
- Ionic strength modulates excision of uracil by SMUG1 from nucleosome core particles.DNA repair · 2023Article
- Histone variant H2A.Z modulates nucleosome dynamics to promote DNA accessibility.Nature communications · 2023Article
- Assignment of structural transitions during mechanical unwrapping of nucleosomes and their disassembly products.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Quantifying epigenetic modulation of nucleosome breathing by high-throughput AFM imaging.Biophysical journal · 2022Article
- Zero-mode waveguides and nanopore-based sequencing technologies accelerate single-molecule studies.Biophysics and physicobiology · 2022Article
- Histone Modifications, Internucleosome Dynamics, and DNA Stresses: How They Cooperate to "Functionalize" Nucleosomes.Frontiers in genetics · 2022Article
- Surprising Twists in Nucleosomal DNA with Implication for Higher-order Folding.Journal of molecular biology · 2021Article
- Structural basis of nucleosome dynamics modulation by histone variants H2A.B and H2A.Z.2.2.The EMBO journal · 2021Article
- Nucleosome allostery in pioneer transcription factor binding.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Ensembles of Breathing Nucleosomes: A Computational Study.Biophysical journal · 2020Article
- DNA Sequence Is a Major Determinant of Tetrasome Dynamics.Biophysical journal · 2019Article
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Authors and funding
2 authors.
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Abstract
In eukaryotes, DNA is packaged into a basic unit, the nucleosome which consists of 147 bp of DNA wrapped around a histone octamer composed of two copies each of the histones H2A, H2B, H3 and H4. Nucleosome structures are diverse not only by histone variants, histone modifications, histone composition but also through accommodating different conformational states such as DNA breathing and dimer splitting. Variation in nucleosome structures allows it to perform a variety of cellular functions. Here, we identified a novel spontaneous conformational switching of nucleosomes under physiological conditions using single-molecule FRET. Using FRET probes placed at various positions on the nucleosomal DNA to monitor conformation of the nucleosome over a long period of time (30-60 min) at various ionic conditions, we identified conformational changes we refer to as nucleosome gaping. Gaping transitions are distinct from nucleosome breathing, sliding or tightening. Gaping modes switch along the direction normal to the DNA plane through about 5-10 angstroms and at minutes (1-10 min) time scale. This conformational transition, which has not been observed previously, may be potentially important for enzymatic reactions/transactions on nucleosomal substrate and the formation of multiple compression forms of chromatin fibers.
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