MNase is commonly reported as a single-strand-specific endo-exonuclease, although its exonuclease activity appears to be limited to only a few nucleotides on a single strand before cleavage of the antiparallel strand occurs [34–36]. Since the early 1970s MNase digestion has been applied to study chromatin structure in a low-throughput manner [37–40] and later in combination with tiled microarrays [41–44]. Currently, MNase digestion is used with NGS (MNase-seq or MAINE-seq [45]) for genome-wide characterization of average nucleosome occupancy and positioning in a qualitative and quantitative manner. In a typical MNase-seq experiment, mononucleosomes are extracted by extensive MNase treatment of chromatin that has been crosslinked with formaldehyde (Figure 1) [46]. The nucleosomal population is subsequently submitted to single-end (identifies one end of template) or paired-end (identifies both ends of template) NGS with a varying level of coverage depending on the exact goal of the experiment [31].
