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Quantitative analysis of single-molecule force spectroscopy on folded chromatin fibers.

Meng H, Andresen K, van Noort J - Nucleic Acids Res. (2015)

Bottom Line: Comparison of force-extension curves between single nucleosomes and chromatin fibers shows that embedding nucleosomes in a fiber stabilizes the nucleosome by 10 kBT.Chromatin fibers with 20- and 50-bp linker DNA follow a different unfolding pathway.These results have implications for accessibility of DNA in fully folded and partially unwrapped chromatin fibers and are vital for understanding force unfolding experiments on nucleosome arrays.

View Article: PubMed Central - PubMed

Affiliation: Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, The Netherlands.

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Schematic representation of the transitions between all metastable conformations of the nucleosomes. The double-headed arrows depict the extension per nucleosome for each conformation. As force increases, a nucleosome unwraps part of its DNA until a single full turn of DNA remains wrapped around the histone core. The next conformation is slightly extended, which may be due to further unwrapping of the DNA, conformational changes within the nucleosome and/or deformation of the linker DNA. We propose the extended conformation may involve dissociation of H2A/H2B dimers from histone core (see the Discussion section). In the last conformation all histone proteins remain attached to the DNA, but the DNA can stretch fully. When a nucleosome is embedded in a chromatin fiber and interactions between nucleosomes fold the fiber into a dense structure, the extension per nucleosome is further reduced, tentatively depicted as a stack of nucleosomes in the bottom left. After the first transition, involving a change in free energy of ΔG1, which may be different for a mono nucleosome and a nucleosome embedded in a fiber, all transitions will follow the same free energy landscape as schematically plotted in the inset.
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Figure 2: Schematic representation of the transitions between all metastable conformations of the nucleosomes. The double-headed arrows depict the extension per nucleosome for each conformation. As force increases, a nucleosome unwraps part of its DNA until a single full turn of DNA remains wrapped around the histone core. The next conformation is slightly extended, which may be due to further unwrapping of the DNA, conformational changes within the nucleosome and/or deformation of the linker DNA. We propose the extended conformation may involve dissociation of H2A/H2B dimers from histone core (see the Discussion section). In the last conformation all histone proteins remain attached to the DNA, but the DNA can stretch fully. When a nucleosome is embedded in a chromatin fiber and interactions between nucleosomes fold the fiber into a dense structure, the extension per nucleosome is further reduced, tentatively depicted as a stack of nucleosomes in the bottom left. After the first transition, involving a change in free energy of ΔG1, which may be different for a mono nucleosome and a nucleosome embedded in a fiber, all transitions will follow the same free energy landscape as schematically plotted in the inset.

Mentions: Comparison between force-extension curves of (A) a chromatin fiber and (B) a mononucleosome. Dark circles represent the pulling trace, light gray circles represent the release trace. All force-extension measurements are reversible, but a significant hysteresis is observed when the the force exceeds 6 pN. The inset in (A) shows a force-extension experiment in which the force was limited to 6 pN; no hysteresis is observed. Light gray dashed lines represent WLC descriptions of the bare DNA and the state in which all nucleosomes are in the extended conformation (see Figure 2). A third dashed line in (B) represents a WLC with a contour length 147 bp shorter than the bare DNA. Black lines are fits to Equation (8) yielding for (A) nfiber = 13, nunfolded = 4, k = 0.28 pN/nm, ext = 4.6 nm, ΔG1 = 20.6 kBT and ΔG2 = 5.5 kBT. For (B): ext = 6.5 nm, ΔG1 = 8.8 kBT and ΔG2 = 3.5 kBT.


Quantitative analysis of single-molecule force spectroscopy on folded chromatin fibers.

Meng H, Andresen K, van Noort J - Nucleic Acids Res. (2015)

Schematic representation of the transitions between all metastable conformations of the nucleosomes. The double-headed arrows depict the extension per nucleosome for each conformation. As force increases, a nucleosome unwraps part of its DNA until a single full turn of DNA remains wrapped around the histone core. The next conformation is slightly extended, which may be due to further unwrapping of the DNA, conformational changes within the nucleosome and/or deformation of the linker DNA. We propose the extended conformation may involve dissociation of H2A/H2B dimers from histone core (see the Discussion section). In the last conformation all histone proteins remain attached to the DNA, but the DNA can stretch fully. When a nucleosome is embedded in a chromatin fiber and interactions between nucleosomes fold the fiber into a dense structure, the extension per nucleosome is further reduced, tentatively depicted as a stack of nucleosomes in the bottom left. After the first transition, involving a change in free energy of ΔG1, which may be different for a mono nucleosome and a nucleosome embedded in a fiber, all transitions will follow the same free energy landscape as schematically plotted in the inset.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4402534&req=5

Figure 2: Schematic representation of the transitions between all metastable conformations of the nucleosomes. The double-headed arrows depict the extension per nucleosome for each conformation. As force increases, a nucleosome unwraps part of its DNA until a single full turn of DNA remains wrapped around the histone core. The next conformation is slightly extended, which may be due to further unwrapping of the DNA, conformational changes within the nucleosome and/or deformation of the linker DNA. We propose the extended conformation may involve dissociation of H2A/H2B dimers from histone core (see the Discussion section). In the last conformation all histone proteins remain attached to the DNA, but the DNA can stretch fully. When a nucleosome is embedded in a chromatin fiber and interactions between nucleosomes fold the fiber into a dense structure, the extension per nucleosome is further reduced, tentatively depicted as a stack of nucleosomes in the bottom left. After the first transition, involving a change in free energy of ΔG1, which may be different for a mono nucleosome and a nucleosome embedded in a fiber, all transitions will follow the same free energy landscape as schematically plotted in the inset.
Mentions: Comparison between force-extension curves of (A) a chromatin fiber and (B) a mononucleosome. Dark circles represent the pulling trace, light gray circles represent the release trace. All force-extension measurements are reversible, but a significant hysteresis is observed when the the force exceeds 6 pN. The inset in (A) shows a force-extension experiment in which the force was limited to 6 pN; no hysteresis is observed. Light gray dashed lines represent WLC descriptions of the bare DNA and the state in which all nucleosomes are in the extended conformation (see Figure 2). A third dashed line in (B) represents a WLC with a contour length 147 bp shorter than the bare DNA. Black lines are fits to Equation (8) yielding for (A) nfiber = 13, nunfolded = 4, k = 0.28 pN/nm, ext = 4.6 nm, ΔG1 = 20.6 kBT and ΔG2 = 5.5 kBT. For (B): ext = 6.5 nm, ΔG1 = 8.8 kBT and ΔG2 = 3.5 kBT.

Bottom Line: Comparison of force-extension curves between single nucleosomes and chromatin fibers shows that embedding nucleosomes in a fiber stabilizes the nucleosome by 10 kBT.Chromatin fibers with 20- and 50-bp linker DNA follow a different unfolding pathway.These results have implications for accessibility of DNA in fully folded and partially unwrapped chromatin fibers and are vital for understanding force unfolding experiments on nucleosome arrays.

View Article: PubMed Central - PubMed

Affiliation: Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, The Netherlands.

Show MeSH
Related in: MedlinePlus