Figure 3: Chromatin accessibility is modulated through DNA protection by histone and non-histone factors. | Nature Communications

Figure 3: Chromatin accessibility is modulated through DNA protection by histone and non-histone factors.

From: MNase titration reveals differences between nucleosome occupancy and chromatin accessibility

Figure 3

(a,b) Comparison of h-MACC (based on histone enrichment data) and c-MACC (based on whole-chromatin digestion data). (a) Scatterplot showing h- and c-MACC values in all analysed bins. Ovals indicate the sets of genomic loci characterized by either high values of c-MACC and low values of h-MACC (group 1) or by high values of both h- and c-MACC (group 2). (b) A genome browser screenshot featuring a 2.5 Mb region from chromosome 2 L. (c) Overlap of the MACC peaks from group 1 or group 2 (blue and orange lines respectively) with protein binding. The results for two proteins are shown as examples (see Supplementary Figs 7–9 for a more comprehensive analysis). (d) Distributions of DHS and H3 signals around the MACC peaks from groups 1 or 2. (e) Distribution of the H3 enrichment levels at the sites associated with group 1 (blue), group 2 (orange) and all genomic bins (grey). The dashed vertical line provides reference of no ‘enrichment’. (f) An example of the protein binding reflected in the MACC profiles, featuring protein binding with (blue rectangle) and without (orange rectangle) nucleosome displacement. (g) Genomic distribution of the MACC peaks from groups 1 and 2. The enrichments were computed relative to the expected values for each type of genomic regions. See Methods for region definitions. The horizontal red lines provide reference of 1 (‘no enrichment’).

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