Systematic Study of Nucleosome-Displacing Factors in Budding Yeast

Mol Cell. 2018 Jul 19;71(2):294-305.e4. doi: 10.1016/j.molcel.2018.06.017. Epub 2018 Jul 12.


Nucleosomes present a barrier for the binding of most transcription factors (TFs). However, special TFs known as nucleosome-displacing factors (NDFs) can access embedded sites and cause the depletion of the local nucleosomes as well as repositioning of the neighboring nucleosomes. Here, we developed a novel high-throughput method in yeast to identify NDFs among 104 TFs and systematically characterized the impact of orientation, affinity, location, and copy number of their binding motifs on the nucleosome occupancy. Using this assay, we identified 29 NDF motifs and divided the nuclear TFs into three groups with strong, weak, and no nucleosome-displacing activities. Further studies revealed that tight DNA binding is the key property that underlies NDF activity, and the NDFs may partially rely on the DNA replication to compete with nucleosome. Overall, our study presents a framework to functionally characterize NDFs and elucidate the mechanism of nucleosome invasion.

Keywords: Abf1; Reb1; chromatin opening; nucleosome; oligo biology; pioneer factor; synthetic biology; transcription factor.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Chromatin / metabolism
  • DNA Replication
  • DNA, Fungal / metabolism
  • DNA-Binding Proteins / metabolism
  • High-Throughput Screening Assays / methods
  • Histones / metabolism
  • Humans
  • Models, Molecular
  • Nucleosomes / genetics
  • Nucleosomes / metabolism*
  • Promoter Regions, Genetic
  • Protein Binding
  • Protein Multimerization
  • Saccharomycetales / genetics
  • Saccharomycetales / metabolism*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism


  • Chromatin
  • DNA, Fungal
  • DNA-Binding Proteins
  • Histones
  • Nucleosomes
  • Transcription Factors