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Proc Natl Acad Sci U S A
2007 Aug 21;10434:13649-54. doi: 10.1073/pnas.0701459104.
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Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in Xenopus egg extracts.
Ranjith P, Yan J, Marko JF.
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Chromatin function in vivo is intimately connected with changes in its structure: a prime example is occlusion or exposure of regulatory sequences via repositioning of nucleosomes. Cell extracts used in concert with single-DNA micromanipulation can control and monitor these dynamics under in vivo-like conditions. We analyze a theory of the assembly-disassembly dynamics of chromatin fiber in such experiments, including effects of lateral nucleosome diffusion ("sliding") and sequence positioning. Experimental data determine the force-dependent on- and off-rates as well as the nucleosome sliding diffusion rate. The resulting theory simply explains the very different nucleosome displacement kinetics observed in constant-force and constant-pulling velocity experiments. We also show that few-piconewton tensions comparable to those generated by polymerases and helicases drastically affect nucleosome positions in a sequence-dependent manner and that there is a long-lived structural "memory" of force-driven nucleosome rearrangement events.
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