Micrococcal nuclease (MNase) is derived from Staphylococcus aureus, and its first use to determine chromatin structure dates back to 1975, when the method was called, variously, staphylococcal nuclease or micrococcal nuclease digestion of nuclei or chromatin.1, 2 With the advent of NGS, MNase digestion3 became more popular and the term MNase-Seq was coined finally4. The terms MNase-assisted isolation of nucleosomes sequencing (MAINE-seq)5, 6 Nucleo-Seq7, and Nuc-seq8 are not commonly used. MNase, fused to the protein of interest, has been also been used for calcium-dependent cleavage to study specific genomic loci in vivo (ChEC-seq)9.

In MNase-Seq, gDNA is treated with MNase. Sequences bound by chromatin proteins are protected from MNase digestion. Next, the DNA from the DNA-protein complexes is extracted and used to prepare a sequencing library. Deep sequencing provides accurate representation of the location of regulatory DNA-binding proteins in the genome10.

  • Can map nucleosomes and other DNA-binding proteins11
  • Can footprint subnucleosomal particles protecting as little as ~25 bp12
  • Identifies location of various regulatory proteins in the genome
  • Covers a broad range of regulatory sites
  • MNase sites might not account for the entire genome
  • AT-dependent sequence bias13
  • Integration of MNase with ChIP data is necessary to identify and differentiate similar protein-binding sites
  1. Yan H., Tian S., Slager S. L., Sun Z. and Ordog T. Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. Am J Epidemiol. 2016;183:96-109
  1. Lavender C. A., Cannady K. R., Hoffman J. A., et al. Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters. PLoS Genet. 2016;12:e1006224
  2. Rube H. T., Lee W., Hejna M., et al. Sequence features accurately predict genome-wide MeCP2 binding in vivo. Nat Commun. 2016;7:11025
  3. de Dieuleveult M., Yen K., Hmitou I., et al. Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Nature. 2016;530:113-116
  4. Cole H. A., Cui F., Ocampo J., et al. Novel nucleosomal particles containing core histones and linker DNA but no histone H1. Nucleic Acids Res. 2016;44:573-581
  5. Deniz O., Flores O., Aldea M., Soler-Lopez M. and Orozco M. Nucleosome architecture throughout the cell cycle. Sci Rep. 2016;6:19729
  6. Devaiah B. N., Case-Borden C., Gegonne A., et al. BRD4 is a histone acetyltransferase that evicts nucleosomes from chromatin. Nat Struct Mol Biol. 2016;23:540-548
  7. Johnson G. D., Jodar M., Pique-Regi R. and Krawetz S. A. Nuclease Footprints in Sperm Project Past and Future Chromatin Regulatory Events. Sci Rep. 2016;6:25864
  8. Kensche P. R., Hoeijmakers W. A., Toenhake C. G., et al. The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences. Nucleic Acids Res. 2016;44:2110-2124
  9. Lombrana R., Alvarez A., Fernandez-Justel J. M., et al. Transcriptionally Driven DNA Replication Program of the Human Parasite Leishmania major. Cell Rep. 2016;16:1774-1786
  10. Maehara K. and Ohkawa Y. Exploration of nucleosome positioning patterns in transcription factor function. Sci Rep. 2016;6:19620
  11. Matveeva E., Maiorano J., Zhang Q., et al. Involvement of PARP1 in the regulation of alternative splicing. Cell Discov. 2016;2:15046
  12. Mieczkowski J., Cook A., Bowman S. K., et al. MNase titration reveals differences between nucleosome occupancy and chromatin accessibility. Nat Commun. 2016;7:11485
  13. Ramakrishnan S., Pokhrel S., Palani S., et al. Counteracting H3K4 methylation modulators Set1 and Jhd2 co-regulate chromatin dynamics and gene transcription. Nat Commun. 2016;7:11949
  14. Wang M., Wang P., Tu L., et al. Multi-omics maps of cotton fibre reveal epigenetic basis for staged single-cell differentiation. Nucleic Acids Res. 2016;44:4067-4079