MNase

Micrococcal nuclease (MNase) is a calcium-dependent nuclease derived from Staphylococcus aureus that cleaves DNA and, to a lesser extent, RNA. It is widely used in chromatin studies because it preferentially digests the linker DNA between nucleosomes, leaving DNA protected by histone cores.

MNase activity requires Ca2+ and is inhibited by chelating agents such as EDTA or EGTA. The extent of digestion depends on enzyme concentration, temperature, and incubation time; when digestion is limited, chromatin yields fragments corresponding to mono-, di-, and oligonucleosomes, with mononucleosome DNA around 147 bp in length. Over-digestion can dismantle nucleosomes and generate subnucleosomal or naked DNA, while under-digestion preserves longer, multi-nucleosome fragments.

Applications include MNase-seq, a technique to map nucleosome positions genome-wide by sequencing DNA released from mono- or oligonucleosomes; MNase protection assays used to infer protein-DNA footprints and chromatin accessibility; and preparation of mono- or oligonucleosome DNA for structural and biochemical studies of chromatin.

Practical considerations are important: precise control of digestion is essential to avoid bias introduced by over- or under-digestion; MNase can exhibit sequence- and chromatin-context biases, and results can be influenced by cell type, fixation, and extraction methods. Typical workflows involve partial MNase digestion of isolated nuclei or chromatin, followed by size selection and sequencing or analysis of the protected DNA fragments.

See also: MNase-seq, chromatin footprinting, nucleosome positioning.