Micrococal nuclease (MNase) is a nuclease derived from Staphylococcus aureus secretion that possesses both nucleic acid exonuclease and endonuclease activities. MNase acts both as a nucleic acid endonuclease to cleave inter-nucleosomal DNA and as an exonuclease to degrade fragmented DNA not protected by proteins. Given the central role of histones in regulating chromatin accessibility, Lifeasible will apply MNase-seq technology to perform nucleosome occupancy localization and accessibility assays.

MNase preferentially cleaves and digests naked DNA or DNA that acts as a linkage between nucleosomes. After endocytosis of both DNA strands in turn, double-stranded ends are formed. Base pairs are cut one by one from the ends toward the fragment's center until a blocker such as a nucleosome or DNA-binding protein is encountered. We use the endonuclease and exonuclease activities of MNase to cleave the DNA in the open chromatin region and digest the linker DNA simultaneously to construct nucleosome DNA libraries to detect the nucleosome occupancy and chromatin accessibility at the same time.

In the MNase-seq library construction experiment, the cellular chromatin was pre-fixed with formaldehyde and then treated with an excess of MNase to obtain the entangled DNA on a single nucleosome histone. Finally, second-generation sequencing analysis is performed. Standard MNase-seq is mainly used for sequencing nucleosome fragments (~147 bp), limiting the analysis of non-histone proteins outside nucleosomes at DNA binding sites.

MNase-seq uses restriction exonucleases to remove all unprotected regions, leaving only the DNA sequences wrapped around the nucleosome. This sequencing method is similar in principle to DNase-seq, which detects regional complementarity. However, a significant difference between MNase-seq, DNase-seq, and ATAC-seq is that neither of the latter two undergoes a nucleosome DNA cleavage event.

• MNase-seq is widely used in many species.
• MNase-seq has been applied to the study of chromatin structure.
• In combination with other methods, MNase-seq can probe regulatory factors associated with nucleosomes, such as ChIP-seq.
• A large number of cells are required as samples.
• MNase cleavage is also preferential, with regions of higher A and T content being cleaved more readily.
• MNase-seq is performed using different concentrations of nucleases to detect differential accessibility across the genome.

Lifeasible utilizes MNase-seq technology to help you detect genome-wide nucleosome distribution and assess transcription factor binding, which can be used in various cell types. However, MNase-seq requires many cells and stringent enzymatic conditions if good reproducibility and comparability across experiments are to be obtained. Therefore, please feel free to contact our staff for a customized protocol that suits your needs.

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For research or industrial use.

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