Figure 1
From: Standardized collection of MNase-seq experiments enables unbiased dataset comparisons
Sampling of different nucleosome configurations changes with extent of MNase digestion. Computer simulation of an MNase digestion titration depicting different technical preparations of chromatin including under-digested samples (15% and 50% Monos), normal-digested samples (75% Monos), and complete-digested samples (100% Monos). Graphs illustrate the normalized count (# sequence reads) of mono-nucleosome fragments aligned to the original template sequence after a simulated digestion and size selection (115–195 bp). All simulations were conducted on an identical template population with each template containing 6 equally sized nucleosomes (147-bp) with 100% occupancy. Each nucleosome was spaced 15-bp apart except for a central 142-bp linker and a larger upstream linker (30-bp). Nucleosomal protection of DNA is modeled to range from 50x to 1000x greater than naked (linker) DNA and relates to a base-pair’s location within a nucleosome, based on the in vivo work of Widom and colleagues (see Additional file 2: Figure S5) [20].