Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in Xenopus egg extracts.
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.
Ranjith
Padinhateeri
P
Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA. ranjith@uic.edu
Yan
Jie
J
Marko
John F
JF
D000818:Animals; D002457:Cell Extracts; D002843:Chromatin / Q000737:chemistry* / Q000235:genetics*; D007700:Kinetics; D008954:Models, Biological; D009707:Nucleosomes / Q000737:chemistry* / Q000235:genetics*; D009865:Oocytes / Q000737:chemistry* / Q000378:metabolism*; D014981:Xenopus / Q000235:genetics*
D002457:Cell Extracts; D002843:Chromatin; D009707:Nucleosomes
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