Chromatin Dynamics: Nucleosomes go Mobile through Twist Defects

We study the spontaneous “sliding” of histone spools (nucleosomes) along DNA as a result of thermally activated single base pair twist defects. To this end we map the system onto a suitably extended Frenkel-Kontorova model. Combining results from several recent experiments we are able to estimate the nucleosome mobility without adjustable parameters. Our model shows also how the local mobility is intimately linked to the underlying base pair sequence.

Figure 1

The twist-diffusion mechanism for nucleosome repositioning. (a) A concerted translational and rotational motion of DNA leads to injection of twist defects (kinks) which migrate between the octamer adsorption sites (black triangles) leading to a ”creep” motion of DNA. (b) The corresponding Frenkel-Kontorova model for twist diffusion and its characteristic parameters (see text for details).

Figure 2

The extended Frenkel-Kontorova model includes effects from anisotropic bp sequences. (a) DNA sequences couple additionally to an octamer-fixed “bending field” through the anisotropic bending parameters $q_i$ (“bending charge”). (b) Two sequences with extremely different mobilities. S1: highly anisotropic, 10 bp phased (“TG”-like) sequence with $D_{\mathrm{s}\mathrm{d}}\approx {10}^{-4}–{10}^{-5}{\mathrm{b}\mathrm{p}}^2/\mathrm{s}$. S2: random sequence corresponding to $>95\%$ of the genome with $D_{\mathrm{s}\mathrm{d}}\approx {10}^2{\mathrm{b}\mathrm{p}}^2/\mathrm{s}$.