Limits...
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.

Show MeSH

Related in: MedlinePlus

DNA twist propagation along arrays. C(t,i) landscape of arrays with (a) Ψ0 = −400°, (b) −80°, (c) 80° and (d) 200°. The location of each nucleosome in the array is marked on the y-axis; the end linker DNA being twisted is attached to the last nucleosome 12, and t = 0 corresponds to arrays at the onset of twisting. Sixteen microsecond represents 1 rotation.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4150795&req=5

Figure 5: DNA twist propagation along arrays. C(t,i) landscape of arrays with (a) Ψ0 = −400°, (b) −80°, (c) 80° and (d) 200°. The location of each nucleosome in the array is marked on the y-axis; the end linker DNA being twisted is attached to the last nucleosome 12, and t = 0 corresponds to arrays at the onset of twisting. Sixteen microsecond represents 1 rotation.

Mentions: Figure 5 displays the C(t,i) landscape for arrays with different Ψ0. The last few DNA segments in all arrays exhibit oscillations in C(t,i) between values of 1 and −1, indicative of the continuous twisting of the terminal linker DNA. The DNA twist ‘front’ is observed as the boundary of the blue region encompassing the t = 0 line. The left- and right-hand boundaries represent front propagation during negative and positive twisting, respectively, and their slopes represent speeds of twist propagation. We observe a dramatic effect of Ψ0 on twist propagation. Extreme values of Ψ0 lead to fast but abrupt propagation of DNA twist, which occurs in sharp bursts interspersed with long pauses (Figure 5a and d). The fast bursts arise from strongly correlated flipping of nucleosomes, allowing quick propagation of DNA twist from one linker DNA to the next, while the long pauses occur due to global coiling of arrays when nucleosomes are unable to flip due to steric constraints. Also, the speed of twist propagation differs for positive versus negative twisting, with higher speeds occurring during positive twisting for Ψ0 = −400°, and vice versa for Ψ0 = 200°. Moderate Ψ0, on the other hand, lead to slow but uniform twist propagation as well as similar speeds of propagation during positive and negative twisting (Figure 5b and c). The slower speeds likely occur due to transitions between open and negative nucleosomes. We also note a step-like propagation of twist across linker DNAs, indicating the existence of energy barriers during flipping of nucleosomes. Interestingly, the speed of twist propagation of ∼10 Mbp/s, even for the slowest scenario (Ψ0 = −80°), is quite rapid.


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

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

DNA twist propagation along arrays. C(t,i) landscape of arrays with (a) Ψ0 = −400°, (b) −80°, (c) 80° and (d) 200°. The location of each nucleosome in the array is marked on the y-axis; the end linker DNA being twisted is attached to the last nucleosome 12, and t = 0 corresponds to arrays at the onset of twisting. Sixteen microsecond represents 1 rotation.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 5: DNA twist propagation along arrays. C(t,i) landscape of arrays with (a) Ψ0 = −400°, (b) −80°, (c) 80° and (d) 200°. The location of each nucleosome in the array is marked on the y-axis; the end linker DNA being twisted is attached to the last nucleosome 12, and t = 0 corresponds to arrays at the onset of twisting. Sixteen microsecond represents 1 rotation.
Mentions: Figure 5 displays the C(t,i) landscape for arrays with different Ψ0. The last few DNA segments in all arrays exhibit oscillations in C(t,i) between values of 1 and −1, indicative of the continuous twisting of the terminal linker DNA. The DNA twist ‘front’ is observed as the boundary of the blue region encompassing the t = 0 line. The left- and right-hand boundaries represent front propagation during negative and positive twisting, respectively, and their slopes represent speeds of twist propagation. We observe a dramatic effect of Ψ0 on twist propagation. Extreme values of Ψ0 lead to fast but abrupt propagation of DNA twist, which occurs in sharp bursts interspersed with long pauses (Figure 5a and d). The fast bursts arise from strongly correlated flipping of nucleosomes, allowing quick propagation of DNA twist from one linker DNA to the next, while the long pauses occur due to global coiling of arrays when nucleosomes are unable to flip due to steric constraints. Also, the speed of twist propagation differs for positive versus negative twisting, with higher speeds occurring during positive twisting for Ψ0 = −400°, and vice versa for Ψ0 = 200°. Moderate Ψ0, on the other hand, lead to slow but uniform twist propagation as well as similar speeds of propagation during positive and negative twisting (Figure 5b and c). The slower speeds likely occur due to transitions between open and negative nucleosomes. We also note a step-like propagation of twist across linker DNAs, indicating the existence of energy barriers during flipping of nucleosomes. Interestingly, the speed of twist propagation of ∼10 Mbp/s, even for the slowest scenario (Ψ0 = −80°), is quite rapid.

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