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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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Related in: MedlinePlus

Ψ0-dependent array conformations before twisting. (a) Proportions of negative (orange), open (green) and positive (blue) nucleosome states and (b) rate constants of transitions across the three states as a function of Ψ0. For all Ψ0, kPO are significantly larger than the axis limit and kOP are essentially zero within SD. (c) Proposed energy landscape showing the free energies of the three nucleosome states and the barriers in between for three different regimes of Ψ0 as a function of nucleosomal linking number. (d) Array writhe WrS (RH and LH refer to right- and left-handed arrays) and (e) extension z0 as a function of Ψ0. Error bars in all plots indicate SD.
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Figure 2: Ψ0-dependent array conformations before twisting. (a) Proportions of negative (orange), open (green) and positive (blue) nucleosome states and (b) rate constants of transitions across the three states as a function of Ψ0. For all Ψ0, kPO are significantly larger than the axis limit and kOP are essentially zero within SD. (c) Proposed energy landscape showing the free energies of the three nucleosome states and the barriers in between for three different regimes of Ψ0 as a function of nucleosomal linking number. (d) Array writhe WrS (RH and LH refer to right- and left-handed arrays) and (e) extension z0 as a function of Ψ0. Error bars in all plots indicate SD.

Mentions: Before applying twist, we obtain the 0.34 pN tension-equilibrated conformations of nucleosome arrays as a function of the phase angle Ψ0. We first determine, using the procedure described in Supplementary Text and Supplementary Figure S1c, the fractions fO, fN and fP of nucleosomes in the array with open, negatively- and positively-crossed linker DNAs, respectively (Figure 2a). We refer to these states as open, negative and positive. The arrays are composed of mostly negative and open nucleosomes for all Ψ0, but their relative population varies strongly with Ψ0. When Ψ0 = 0, the nucleosomes are distributed almost evenly between open and negative states, consistent with recent FRET measurements (35). The nucleosomal DNA entry/exit angle of 120°, fixed in our model according to the nucleosome crystal structure, along with electrostatic repulsion between the entering and exiting linker DNAs likely promotes such a distribution. When Ψ0 < 0, the open state becomes more prevalent. In this case, the DNA pitch increases as the DNA is undertwisted. Consequently, the ‘downstream’ nucleosomes are oriented anticlockwise relative to the ones ‘upstream’, causing the two linkers DNAs to diverge (Figure 1a). When Ψ0 > 0, the negatively-crossed state becomes dominant. Here, the DNA pitch decreases as the DNA is overtwisted, leading to clockwise rotation of the downstream nucleosome, and subsequent convergence of the linker DNAs (Figure 1c).


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

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

Ψ0-dependent array conformations before twisting. (a) Proportions of negative (orange), open (green) and positive (blue) nucleosome states and (b) rate constants of transitions across the three states as a function of Ψ0. For all Ψ0, kPO are significantly larger than the axis limit and kOP are essentially zero within SD. (c) Proposed energy landscape showing the free energies of the three nucleosome states and the barriers in between for three different regimes of Ψ0 as a function of nucleosomal linking number. (d) Array writhe WrS (RH and LH refer to right- and left-handed arrays) and (e) extension z0 as a function of Ψ0. Error bars in all plots indicate SD.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: Ψ0-dependent array conformations before twisting. (a) Proportions of negative (orange), open (green) and positive (blue) nucleosome states and (b) rate constants of transitions across the three states as a function of Ψ0. For all Ψ0, kPO are significantly larger than the axis limit and kOP are essentially zero within SD. (c) Proposed energy landscape showing the free energies of the three nucleosome states and the barriers in between for three different regimes of Ψ0 as a function of nucleosomal linking number. (d) Array writhe WrS (RH and LH refer to right- and left-handed arrays) and (e) extension z0 as a function of Ψ0. Error bars in all plots indicate SD.
Mentions: Before applying twist, we obtain the 0.34 pN tension-equilibrated conformations of nucleosome arrays as a function of the phase angle Ψ0. We first determine, using the procedure described in Supplementary Text and Supplementary Figure S1c, the fractions fO, fN and fP of nucleosomes in the array with open, negatively- and positively-crossed linker DNAs, respectively (Figure 2a). We refer to these states as open, negative and positive. The arrays are composed of mostly negative and open nucleosomes for all Ψ0, but their relative population varies strongly with Ψ0. When Ψ0 = 0, the nucleosomes are distributed almost evenly between open and negative states, consistent with recent FRET measurements (35). The nucleosomal DNA entry/exit angle of 120°, fixed in our model according to the nucleosome crystal structure, along with electrostatic repulsion between the entering and exiting linker DNAs likely promotes such a distribution. When Ψ0 < 0, the open state becomes more prevalent. In this case, the DNA pitch increases as the DNA is undertwisted. Consequently, the ‘downstream’ nucleosomes are oriented anticlockwise relative to the ones ‘upstream’, causing the two linkers DNAs to diverge (Figure 1a). When Ψ0 > 0, the negatively-crossed state becomes dominant. Here, the DNA pitch decreases as the DNA is overtwisted, leading to clockwise rotation of the downstream nucleosome, and subsequent convergence of the linker DNAs (Figure 1c).

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