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Fig. 5 | Genome Biology

Fig. 5

From: Quantitative MNase-seq accurately maps nucleosome occupancy levels

Fig. 5

Normalized coverage (apparent occupancy) profiles confirm the prediction of the theoretical model. Apparent occupancy profiles for six regions of the genome (left panels) and the corresponding quantification of the average occupancy for the nucleosomes in the center of each panel (the corresponding right panels, blue circles). The occupancy levels for all six nucleosomes (blue circles) vary during the digestion as predicted by Eq. (2). Using the predicted analytical behavior given by Eq. (2), we can fit the experimental data very well, and we obtain the corresponding three parameters that characterize the digestion kinetics of each genomic locus: nucleosome occupancy O and the two rate constants k1 and k2, corresponding to the nucleosome release and decay processes, respectively. The fitted parameters are displayed above the right-hand plots, and the predicted dependence of the apparent nucleosome occupancy (fraction of nucleosomes present in the sample at each time point) on the level of digestion is shown with red dashed lines. The example nucleosomes shown in the figure occupy the following positions (centers of the 1-kb windows): (top row) chr2L:19,509,018 and chr2R:22,605,540; (middle row) chr3R:24,050,605 and chr2R:11,303,325; (bottom row) chr2L:1,732,199 and chr3R:27,301,872. These six examples were chosen such that the top two cases correspond to the regions for which the corresponding nucleosome counts have maxima after 2 min of digestion, the next two cases correspond to the regions that are digested more slowly, and the corresponding maxima are observed after 5 min of digestion, and the bottom panels correspond to the regions that are digested at an even slower rate, with the corresponding maxima obtained only after 15 min of digestion

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