(63c) Dynamics of Torsionally Stressed Chromatin Fiber

Torsional stresses serve critical functions for chromatin fiber to participate in biological activities such as transcription and replication of DNA. Despite the biological significance, most experimental and theoretical work so far has focused on understanding supercoiling in naked DNA, and little is known about how torsional forces are propagated, stored, and mitigated within chromatin fiber. In this work, we investigate the dynamic properties of nucleosome arrays subjected to torsional forces using the Brownian Dynamic simulations of a coarse-grained model of the chromatin fiber. By applying the twist to one end of array in stepwise manner, we monitor the conformational changes of array by measuring its vertical extension as a function of the number of turns. The obtained extension-rotations curve shows asymmetric shape with a shifted maximal extension toward negative rotations, which is in good qualitative agreement with the earlier experiments. These features imply that the nucleosome array exhibits different torsional behaviors in the two opposite directions of rotations: Negative rotations promote the linker DNA wrapping around nucleosome, promoting a one-start solenoidal structure while positive rotations cause the linker DNA to be bent in opposite direction to the handedness of nucleosome, leading to formation of a zig-zag structure. These higher-order structures are characterized by the two-angle model and their dynamical organization can be elucidated in terms of twist propagation. By means of rotational autocorrelation function for each segment along the array, we show that nonuniform twist profiles reflect the existence of geometrical barrier for twist propagation, which modulate the internal and global organization of array under torsional stresses.