Characterization of the Nucleosome Landscape by Micrococcal Nuclease-Sequencing (MNase-seq)

Methods Mol Biol. 2018:1689:83-101. doi: 10.1007/978-1-4939-7380-4_8.


MNase-seq allows the genome-wide examination of the nucleosome landscape by determination of nucleosome positioning and occupancy. Typically, native or formaldehyde fixed chromatin is subjected to digestion by micrococcal nuclease (MNase), which degrades linker DNA and yields mainly mono-nucleosomes. The resulting material can be processed directly or can be subjected to an optional chromatin immunoprecipitation step (MNase-ChIP-seq). De-crosslinked and purified DNA is then subjected to next-generation sequencing. The protocol presented here has been tailored for the analysis of nucleosome landscape in the malaria parasite, Plasmodium falciparum, but most steps are directly applicable to other cell types. We also discuss general considerations for experimental design and computational analysis, which are crucial for accurate investigation of the nucleosome landscape.

Keywords: AT-rich DNA; MNase-ChIP-seq; MNase-seq; Micrococcal nuclease (MNase); Nucleosome landscape; Nucleosome occupancy; Nucleosome positioning; Plasmodium falciparum.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Chromatin / genetics
  • Chromatin / metabolism
  • Chromatin Immunoprecipitation* / methods
  • DNA / genetics
  • DNA / metabolism
  • DNA Cleavage
  • Gene Library
  • High-Throughput Nucleotide Sequencing* / methods
  • Micrococcal Nuclease / metabolism*
  • Nucleosomes / metabolism*
  • Plasmodium falciparum / genetics
  • Plasmodium falciparum / metabolism
  • Quality Control


  • Chromatin
  • Nucleosomes
  • DNA
  • Micrococcal Nuclease