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Molecular cell
07 19, 2018;71 (2): 294-305.e4.

Systematic Study of Nucleosome-Displacing Factors in Budding Yeast.

Chao Yan, Hengye Chen, Lu Bai
Author Information
  1. Chao Yan: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA.
  2. Hengye Chen: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA.
  3. Lu Bai: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA; Department of Physics, The Pennsylvania State University, University Park, PA 16802, USA. Electronic address: lub15@psu.edu.
PMID: 30017582 DOI: 10.1016/j.molcel.2018.06.017

Abstract

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

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Grants

  1. R01 GM121858/NIGMS NIH HHS

MeSH Term

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

Chemicals

Chromatin
DNA, Fungal
DNA-Binding Proteins
Histones
Nucleosomes
Transcription Factors
Journal Article Research Support, N.I.H., Extramural
Article has an altmetric score of 82

Word Cloud

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