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Biophys J. 2014 Jul 15;107(2):384-392. doi: 10.1016/j.bpj.2014.05.042.

Routes to DNA accessibility: alternative pathways for nucleosome unwinding.

Author information

1
Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.
2
Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut; Department of Applied Physics, Yale University, New Haven, Connecticut.
3
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut; Department of Physics, Yale University, New Haven, Connecticut.
4
Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut; Department of Applied Physics, Yale University, New Haven, Connecticut; Department of Physics, Yale University, New Haven, Connecticut.
5
Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut; Department of Chemistry, Yale University, New Haven, Connecticut. Electronic address: lynne.regan@yale.edu.

Abstract

The dynamic packaging of DNA into chromatin is a key determinant of eukaryotic gene regulation and epigenetic inheritance. Nucleosomes are the basic unit of chromatin, and therefore the accessible states of the nucleosome must be the starting point for mechanistic models regarding these essential processes. Although the existence of different unwound nucleosome states has been hypothesized, there have been few studies of these states. The consequences of multiple states are far reaching. These states will behave differently in all aspects, including their interactions with chromatin remodelers, histone variant exchange, and kinetic properties. Here, we demonstrate the existence of two distinct states of the unwound nucleosome, which are accessible at physiological forces and ionic strengths. Using optical tweezers, we measure the rates of unwinding and rewinding for these two states and show that the rewinding rates from each state are different. In addition, we show that the probability of unwinding into each state is dependent on the applied force and ionic strength. Our results demonstrate not only that multiple unwound states exist but that their accessibility can be differentially perturbed, suggesting possible roles for these states in gene regulation. For example, different histone variants or modifications may facilitate or suppress access to DNA by promoting unwinding into one state or the other. We anticipate that the two unwound states reported here will be the basis for future models of eukaryotic transcriptional control.

PMID:
25028880
PMCID:
PMC4104035
DOI:
10.1016/j.bpj.2014.05.042
[Indexed for MEDLINE]
Free PMC Article

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