MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers

Mol Cell. 2017 Feb 2;65(3):565-577.e3. doi: 10.1016/j.molcel.2016.12.009.


Micrococcal nuclease (MNase) is commonly used to map nucleosomes genome-wide, but nucleosome maps are affected by the degree of digestion. It has been proposed that many yeast promoters are not nucleosome-free but instead occupied by easily digested, unstable, "fragile" nucleosomes. We analyzed the histone content of all MNase-sensitive complexes by MNase-ChIP-seq and sonication-ChIP-seq. We find that yeast promoters are predominantly bound by non-histone protein complexes, with little evidence for fragile nucleosomes. We do detect MNase-sensitive nucleosomes elsewhere in the genome, including at transcription termination sites. However, they have high A/T content, suggesting that MNase sensitivity does not indicate instability, but rather the preference of MNase for A/T-rich DNA, such that A/T-rich nucleosomes are digested faster than G/C-rich nucleosomes. We confirm our observations by analyzing ChIP-exo, chemical mapping, and ATAC-seq data from other laboratories. Thus, histone ChIP-seq experiments are essential to distinguish nucleosomes from other DNA-binding proteins that protect against MNase.

Keywords: fragile nucleosomes; micrococcal nuclease bias; micrococcal nuclease-sensitive nucleosomes; non-histone barrier complex; yeast chromatin.

MeSH terms

  • Base Composition
  • Micrococcal Nuclease / metabolism*
  • Nucleosomes
  • Promoter Regions, Genetic
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae Proteins / genetics*


  • Nucleosomes
  • Saccharomyces cerevisiae Proteins
  • Micrococcal Nuclease