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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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Different fibers show a large variation in condensation. (A) Ten chromatin fibers reconstituted on a 15*197 NRL DNA template. The high-force transitions align well with states that describe the last unfolding transition, plotted in gray dashed lines. All curves have a force plateau at 3 pN, but the size of the force plateau and the extension at lower forces varies significantly. Black lines represent fits to Equation (8). (B) Distribution of fit parameters obtained from (A). The stepsizes in the top histogram were determined independently using a t-test step finding algorithm. Except for the number of nucleosomes in the fiber, all parameters show a narrow distribution.
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Figure 4: Different fibers show a large variation in condensation. (A) Ten chromatin fibers reconstituted on a 15*197 NRL DNA template. The high-force transitions align well with states that describe the last unfolding transition, plotted in gray dashed lines. All curves have a force plateau at 3 pN, but the size of the force plateau and the extension at lower forces varies significantly. Black lines represent fits to Equation (8). (B) Distribution of fit parameters obtained from (A). The stepsizes in the top histogram were determined independently using a t-test step finding algorithm. Except for the number of nucleosomes in the fiber, all parameters show a narrow distribution.

Mentions: Whereas all chromatin fibers feature similar unfolding characteristics, we observed a rather large variation in the force-extension behavior between fibers. Figure 4 shows the force-extension curves of 10 different fibers. Because the last unfolding transition is not in thermodynamic equilibrium, the rupture forces for this transition are distributed stochastically. Nevertheless, all curves align well with the set of unfolding states that contain extended and fully unwrapped nucleosomes, indicated with the gray dashed lines. The first two transitions at forces below 7 pN on the other hand are fully reversible, resulting in overlapping pull and release curves (Figure 1A, inset). Despite the highly reproducible curves that we obtain from individual fibers, we observe large variations in extension between fibers in this low-force range. We attribute these differences to the variations in the composition of the fiber.


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

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

Different fibers show a large variation in condensation. (A) Ten chromatin fibers reconstituted on a 15*197 NRL DNA template. The high-force transitions align well with states that describe the last unfolding transition, plotted in gray dashed lines. All curves have a force plateau at 3 pN, but the size of the force plateau and the extension at lower forces varies significantly. Black lines represent fits to Equation (8). (B) Distribution of fit parameters obtained from (A). The stepsizes in the top histogram were determined independently using a t-test step finding algorithm. Except for the number of nucleosomes in the fiber, all parameters show a narrow distribution.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 4: Different fibers show a large variation in condensation. (A) Ten chromatin fibers reconstituted on a 15*197 NRL DNA template. The high-force transitions align well with states that describe the last unfolding transition, plotted in gray dashed lines. All curves have a force plateau at 3 pN, but the size of the force plateau and the extension at lower forces varies significantly. Black lines represent fits to Equation (8). (B) Distribution of fit parameters obtained from (A). The stepsizes in the top histogram were determined independently using a t-test step finding algorithm. Except for the number of nucleosomes in the fiber, all parameters show a narrow distribution.
Mentions: Whereas all chromatin fibers feature similar unfolding characteristics, we observed a rather large variation in the force-extension behavior between fibers. Figure 4 shows the force-extension curves of 10 different fibers. Because the last unfolding transition is not in thermodynamic equilibrium, the rupture forces for this transition are distributed stochastically. Nevertheless, all curves align well with the set of unfolding states that contain extended and fully unwrapped nucleosomes, indicated with the gray dashed lines. The first two transitions at forces below 7 pN on the other hand are fully reversible, resulting in overlapping pull and release curves (Figure 1A, inset). Despite the highly reproducible curves that we obtain from individual fibers, we observe large variations in extension between fibers in this low-force range. We attribute these differences to the variations in the composition of the fiber.

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