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Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes.

Nam GM, Arya G - Nucleic Acids Res. (2014)

Bottom Line: Torsionally stressed DNA plays a critical role in genome organization and regulation.While the effects of torsional stresses on naked DNA have been well studied, little is known about how these stresses propagate within chromatin and affect its organization.The observed behavior is shown to arise from an interplay between nucleosomal transitions into states with crossed and open linker DNAs and global supercoiling of arrays into left- and right-handed coils, where Ψ0 serves to modulate the energy landscape of nucleosomal states.

View Article: PubMed Central - PubMed

Affiliation: Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0448, USA.

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Ψ0-dependent torsional response of nucleosome arrays. (a) Time evolution of the linking number and (b) extension-rotation curves of arrays with different Ψ0. Shaded regions represent standard deviations. (c–h) Representative conformations of arrays during twisting for different Ψ0 values. Numbers at the bottom indicate the number of imposed turns n. SI movies provide a higher time resolution of these conformational changes.
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Figure 3: Ψ0-dependent torsional response of nucleosome arrays. (a) Time evolution of the linking number and (b) extension-rotation curves of arrays with different Ψ0. Shaded regions represent standard deviations. (c–h) Representative conformations of arrays during twisting for different Ψ0 values. Numbers at the bottom indicate the number of imposed turns n. SI movies provide a higher time resolution of these conformational changes.

Mentions: We next twist the arrays in the positive and negative directions, starting from the untwisted arrays equilibrated under the stretching force. The amount of twist introduced into the arrays is quantified in terms of the number of turns n by which the free end of the array is rotated. To verify that no twist is being lost through the ends, we measure the linking number Lk of the arrays as a function of time. Lk is computed as the sum of twist Tw and writhe Wr, as detailed in the Supplementary Text. Figure 3a displays the Lk profiles for all tested values of Ψ0. In general, Lk shows a step-wise increase after each end rotation, and the step size measures the linking number difference ΔLk given by the sum of the changes in the writhe and twist of the array ΔLk = ΔWr + ΔTw. For all Ψ0, the measured ΔLk fall in the range 0.1–0.13, which agrees well with the amount of twist ΔΩ/2π = 0.125 introduced into the arrays through each end-rotation step. These results confirm that the topology of the arrays is conserved during twisting. The negative values of Lk result from the ∼1.65 left-handed superhelical turns of DNA wrapped in nucleosomes. The separation between Lk profiles for different Ψ0 points to its effects on the array topology, as described earlier. Supplementary Table S2 lists the measured Lk for all Ψ0 and its partitioning into Tw and Wr at n = 0.


Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes.

Nam GM, Arya G - Nucleic Acids Res. (2014)

Ψ0-dependent torsional response of nucleosome arrays. (a) Time evolution of the linking number and (b) extension-rotation curves of arrays with different Ψ0. Shaded regions represent standard deviations. (c–h) Representative conformations of arrays during twisting for different Ψ0 values. Numbers at the bottom indicate the number of imposed turns n. SI movies provide a higher time resolution of these conformational changes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150795&req=5

Figure 3: Ψ0-dependent torsional response of nucleosome arrays. (a) Time evolution of the linking number and (b) extension-rotation curves of arrays with different Ψ0. Shaded regions represent standard deviations. (c–h) Representative conformations of arrays during twisting for different Ψ0 values. Numbers at the bottom indicate the number of imposed turns n. SI movies provide a higher time resolution of these conformational changes.
Mentions: We next twist the arrays in the positive and negative directions, starting from the untwisted arrays equilibrated under the stretching force. The amount of twist introduced into the arrays is quantified in terms of the number of turns n by which the free end of the array is rotated. To verify that no twist is being lost through the ends, we measure the linking number Lk of the arrays as a function of time. Lk is computed as the sum of twist Tw and writhe Wr, as detailed in the Supplementary Text. Figure 3a displays the Lk profiles for all tested values of Ψ0. In general, Lk shows a step-wise increase after each end rotation, and the step size measures the linking number difference ΔLk given by the sum of the changes in the writhe and twist of the array ΔLk = ΔWr + ΔTw. For all Ψ0, the measured ΔLk fall in the range 0.1–0.13, which agrees well with the amount of twist ΔΩ/2π = 0.125 introduced into the arrays through each end-rotation step. These results confirm that the topology of the arrays is conserved during twisting. The negative values of Lk result from the ∼1.65 left-handed superhelical turns of DNA wrapped in nucleosomes. The separation between Lk profiles for different Ψ0 points to its effects on the array topology, as described earlier. Supplementary Table S2 lists the measured Lk for all Ψ0 and its partitioning into Tw and Wr at n = 0.

Bottom Line: Torsionally stressed DNA plays a critical role in genome organization and regulation.While the effects of torsional stresses on naked DNA have been well studied, little is known about how these stresses propagate within chromatin and affect its organization.The observed behavior is shown to arise from an interplay between nucleosomal transitions into states with crossed and open linker DNAs and global supercoiling of arrays into left- and right-handed coils, where Ψ0 serves to modulate the energy landscape of nucleosomal states.

View Article: PubMed Central - PubMed

Affiliation: Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0448, USA.

Show MeSH
Related in: MedlinePlus