Extended Data Fig. 2: Remodeling of oxidized nucleosomes is slowed specifically due to disulfide bond formation and is robust to remodeling conditions. | Nature Structural & Molecular Biology

Extended Data Fig. 2: Remodeling of oxidized nucleosomes is slowed specifically due to disulfide bond formation and is robust to remodeling conditions.

From: Histone dynamics play a critical role in SNF2h-mediated nucleosome sliding

Extended Data Fig. 2

(a) Left. Native gel remodeling assay with saturating SNF2h (1 μM), saturating ATP, and 15 nM cy3-nucleosomes as in Fig. 1. Middle. Quantification of the experiment at the left including a plot of all time points; and for ease of comparison a plot of the first 15 minutes of the reaction normalized to the best-fit parameters for Y0 and plateau. This experiment was performed 3 times with similar results. Right. Mean observed rate constants (kobs) from 3 independent experiments. Error bars reflect the standard error of the mean (SEM). (b) Left. Native gel remodeling assay with sub-saturating SNF2h (50 nM), saturating ATP, and 15 nM cy3-nucleosomes as in Fig. 1. Middle. Quantification of the experiment on the left. This experiment was performed 3 times with similar results. Right. Mean and SEM of the observed rate constants (kobs) from 3 independent experiments. The asterisk denotes that the rate constant for the oxidized reaction condition was too slow to reliably quantify with the time points taken. (C) Left. Native gel remodeling assay under the conditions of Yan et al. 2 using 50 nM SNF2h, saturating ATP, and 15 nM cy3-nucleosomes. Remodeling overall is substantially faster likely because of the different conditions used (higher temperature, lower salt concentration, the absence of .02% (v/v) NP40, and the presence of 0.1 mg/mL BSA). Middle. Quantification of the gel on the left along with the indicated observed rate constants. This experiment was performed once. Right. Time courses shown in the middle panel normalized to the best fit parameters for Y0 and Plateau of the exponential decay and zoomed in to the first 10 minutes of the reaction to better evaluate the fits. Uncropped images for panels A-C are available in Source Data and values obtained in quantifications are in Supplementary Table 1.

Source data

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