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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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Local and global conformational changes in arrays under external twisting. (Top panel) Dynamic proportions of negative (orange), open (green) and positive (blue) nucleosomal states as a function of imposed rotations n for four different Ψ0 values. (Bottom panel) Corresponding plots of the extension (black) and WrS (red) of arrays.
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Figure 4: Local and global conformational changes in arrays under external twisting. (Top panel) Dynamic proportions of negative (orange), open (green) and positive (blue) nucleosomal states as a function of imposed rotations n for four different Ψ0 values. (Bottom panel) Corresponding plots of the extension (black) and WrS (red) of arrays.

Mentions: To uncover the underlying mechanism behind this unique Ψ0-dependent extension-rotation behavior, we trace the proportions fO, fN and fP of nucleosomes in the open, negative and positive states, and also compute the writhe WrS of the arrays as a function of n (Figure 4), which quantify respective changes in the nucleosomal and global writhe of the arrays. One expects negative twisting (n < 0) to favor nucleosomal states and array conformations that possess the most negative writhe, i.e., negative state and left-handed arrays, while positive twisting (n > 0) is expected to favor states and conformations with the most positive or least negative writhe, i.e., positive state and right-handed arrays (Supplementary Figure S6).


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

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

Local and global conformational changes in arrays under external twisting. (Top panel) Dynamic proportions of negative (orange), open (green) and positive (blue) nucleosomal states as a function of imposed rotations n for four different Ψ0 values. (Bottom panel) Corresponding plots of the extension (black) and WrS (red) of arrays.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 4: Local and global conformational changes in arrays under external twisting. (Top panel) Dynamic proportions of negative (orange), open (green) and positive (blue) nucleosomal states as a function of imposed rotations n for four different Ψ0 values. (Bottom panel) Corresponding plots of the extension (black) and WrS (red) of arrays.
Mentions: To uncover the underlying mechanism behind this unique Ψ0-dependent extension-rotation behavior, we trace the proportions fO, fN and fP of nucleosomes in the open, negative and positive states, and also compute the writhe WrS of the arrays as a function of n (Figure 4), which quantify respective changes in the nucleosomal and global writhe of the arrays. One expects negative twisting (n < 0) to favor nucleosomal states and array conformations that possess the most negative writhe, i.e., negative state and left-handed arrays, while positive twisting (n > 0) is expected to favor states and conformations with the most positive or least negative writhe, i.e., positive state and right-handed arrays (Supplementary Figure S6).

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