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Cell reports
08 23, 2022;40 (8): 111250.

Partitioned usage of chromatin remodelers by nucleosome-displacing factors.

Hengye Chen, Hungyo Kharerin, Archana Dhasarathy, Michael Kladde, Lu Bai
Author Information
  1. 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.
  2. Hungyo Kharerin: 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. Archana Dhasarathy: Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58201, USA.
  4. Michael Kladde: Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA.
  5. 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: 36001970 DOI: 10.1016/j.celrep.2022.111250

Abstract

Nucleosome-displacing-factors (NDFs) in yeast, similar to pioneer factors in higher eukaryotes, can open closed chromatin and generate nucleosome-depleted regions (NDRs). NDRs in yeast are also affected by ATP-dependent chromatin remodelers (CRs). However, how NDFs and CRs coordinate in nucleosome invasion and NDR formation is still unclear. Here, we design a high-throughput method to systematically study the interplay between NDFs and CRs. By combining an integrated synthetic oligonucleotide library with DNA methyltransferase-based, single-molecule nucleosome mapping, we measure the impact of CRs on NDRs generated by individual NDFs. We find that CRs are dispensable for nucleosome invasion by NDFs, and they function downstream of NDF binding to modulate the NDR length. A few CRs show high specificity toward certain NDFs; however, in most cases, CRs are recruited in a factor-nonspecific and NDR length-dependent manner. Overall, our study provides a framework to investigate how NDFs and CRs cooperate to regulate chromatin opening.

Keywords

CP: Molecular biology binding specificity chromatin opening chromatin remodeler nucleosome invasion nucleosome positioning nucleosome remodeling nucleosome-depleted regions nucleosome-displacing factor pioneer factor synthetic oligonucleotide library transcription factor

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Grants

  1. R35 GM139654/NIGMS NIH HHS

MeSH Term

Chromatin
Chromatin Assembly and Disassembly
Nucleosomes
Saccharomyces cerevisiae
Saccharomyces cerevisiae Proteins

Chemicals

Chromatin
Nucleosomes
Saccharomyces cerevisiae Proteins
Journal Article Research Support, N.I.H., Extramural
Article has an altmetric score of 12

Word Cloud

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