Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in Xenopus egg extracts
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It is shown that few-piconewton tensions comparable to those generated by polymerases and helicases drastically affect nucleosomes positions in a sequence-dependent manner and that there is a long-lived structural “memory” of force-driven nucleosome rearrangement events.Abstract:
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.read more
Citations
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References
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Journal Article
The Genomic Code for Nucleosome Positioning
TL;DR: In this article, a nucleosome-DNA interaction model was proposed to predict the genome-wide organization of nucleosomes, and it was shown that genomes encode an intrinsic nucleosomal organization and that this intrinsic organization can explain ∼50% of the in-vivo positions.
Journal ArticleDOI
A genomic code for nucleosome positioning
Eran Segal,Yvonne N. Fondufe-Mittendorf,Lingyi Chen,Annchristine Thåström,Yair Field,Irene K. Moore,Ji Ping Wang,Jonathan Widom +7 more
TL;DR: This work isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosom–DNA interaction model, and to predict the genome-wide organization of nucleosomes.
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