MNase-seq thus probes chromatin accessibility indirectly by unveiling the areas of the genome occupied by nucleosomes and other regulatory factors. Commonly referred to as a nucleosome occupancy assay, it shares same principal mode of action (enzymatic cleavage) and can provide information on TF occupancy as other chromatin accessibility assays. MNase-seq has been implemented in a number of organisms, ranging from yeast to humans, for the mapping of chromatin structure [47–49]. In addition, MNase digestion has been successfully combined with ChIP-seq for enrichment of regulatory factors or histone-tail modifications and variants. Henikoff et al. [50] have also introduced a modified MNase-seq protocol for library preparation of fragments down to 25 bp, allowing the mapping of both nucleosomes and non-histone proteins with high resolution.
