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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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Torsional resilience of nucleosome arrays. (a) Total energy and (b) torque profiles of arrays with different Ψ0 as a function of the number of rotations. The insets show the energies for Ψ0 = 80° fitted to a harmonic function.
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Figure 6: Torsional resilience of nucleosome arrays. (a) Total energy and (b) torque profiles of arrays with different Ψ0 as a function of the number of rotations. The insets show the energies for Ψ0 = 80° fitted to a harmonic function.

Mentions: To obtain the torsional rigidity Carray of the arrays, we examine their total energy as a function of imposed rotations (Figure 6a). The energy profiles exhibit a minimum located at n ≈ 0 regardless of Ψ0. Fitting this energy profile to a harmonic function yields Carray = 0.3 kcal/mol nm for arrays with Ψ0 = −80° (Figure 6a; Supplementary Text). We also estimate the torque experienced by the arrays as a function of imposed rotations (see Supplementary Text) and find that it remains <5 pN nm/rad for a broad range of rotations (Figure 6b), i.e. slightly smaller than the torque exerted by the RNA polymerase enzyme (36) and much smaller than that required to denature DNA (17). The small torsional rigidity of the arrays as compared to that of naked DNA (CDNA = 57 kcal/mol nm (14)) and the small torques experienced by the arrays confirm the high torsional resilience of chromatin observed in experiments (21,22). We note that Carray is largely independent of Ψ0, but is likely affected by other properties like the length of the linker DNAs and their entry/exit angle at nucleosomes. Another important parameter is the number of nucleosomes in the array, as one expects longer arrays with more combinations of nucleosome states to accommodate larger amount of DNA twist.


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

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

Torsional resilience of nucleosome arrays. (a) Total energy and (b) torque profiles of arrays with different Ψ0 as a function of the number of rotations. The insets show the energies for Ψ0 = 80° fitted to a harmonic function.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 6: Torsional resilience of nucleosome arrays. (a) Total energy and (b) torque profiles of arrays with different Ψ0 as a function of the number of rotations. The insets show the energies for Ψ0 = 80° fitted to a harmonic function.
Mentions: To obtain the torsional rigidity Carray of the arrays, we examine their total energy as a function of imposed rotations (Figure 6a). The energy profiles exhibit a minimum located at n ≈ 0 regardless of Ψ0. Fitting this energy profile to a harmonic function yields Carray = 0.3 kcal/mol nm for arrays with Ψ0 = −80° (Figure 6a; Supplementary Text). We also estimate the torque experienced by the arrays as a function of imposed rotations (see Supplementary Text) and find that it remains <5 pN nm/rad for a broad range of rotations (Figure 6b), i.e. slightly smaller than the torque exerted by the RNA polymerase enzyme (36) and much smaller than that required to denature DNA (17). The small torsional rigidity of the arrays as compared to that of naked DNA (CDNA = 57 kcal/mol nm (14)) and the small torques experienced by the arrays confirm the high torsional resilience of chromatin observed in experiments (21,22). We note that Carray is largely independent of Ψ0, but is likely affected by other properties like the length of the linker DNAs and their entry/exit angle at nucleosomes. Another important parameter is the number of nucleosomes in the array, as one expects longer arrays with more combinations of nucleosome states to accommodate larger amount of DNA twist.

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