1. Chromosomes and Gene Expression
  2. Structural Biology and Molecular Biophysics
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Dissociation rate compensation mechanism for budding yeast pioneer transcription factors

  1. Benjamin T Donovan
  2. Hengye Chen
  3. Caroline Jipa
  4. Lu Bai
  5. Michael G Poirier  Is a corresponding author
  1. Ohio State University, United States
  2. The Pennsylvania State University, United States
Research Article
  • Cited 19
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Cite this article as: eLife 2019;8:e43008 doi: 10.7554/eLife.43008

Abstract

Nucleosomes restrict the occupancy of most transcription factors (TF) by reducing binding and accelerating dissociation, while a small group of TFs have high affinities to nucleosome-embedded sites and facilitate nucleosome displacement. To mechanistically understand this process, we investigated two S. cerevisiae TFs, Reb1 and Cbf1. We show these factors bind their sites within nucleosomes with similar affinities to naked DNA, trapping a partially unwrapped nucleosome without histone eviction. Both the binding and dissociation rates of Reb1 and Cbf1 are significantly slower at the nucleosomal sites relative to DNA, demonstrating that the high affinities are achieved by increasing the dwell time on nucleosomes to compensate for reduced binding. Reb1 also shows slow migration rate in the yeast nuclei. These properties are similar to human pioneer factors (PFs), suggesting the mechanism of nucleosome targeting is conserved from yeast to human.

Data availability

All analyzed data generated is included in the manuscript. In supplementary file 1, we include 6 supplementary tables. Table S1 documents all binding affinity measurements from this study. Table S2 documents measured binding rates from single molecule experiments. Table S3 documents relative binding affinities (Nuc/DNA) for ensemble and single molecule experiments. Table S4 documents the primers for in vitro experiments. Table S5 documents quality control information from single molecule experiments. Table S6 documents the primers used for FRAP experiments. Videos supporting this study have been deposited to Zenodo and are available under the doi:10.5281/zenodo.2595208

The following data sets were generated

Article and author information

Author details

  1. Benjamin T Donovan

    Biophysics Graduate Program, Ohio State University, Columbus, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Hengye Chen

    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Caroline Jipa

    Department of Physics, Ohio State University, Columbus, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Lu Bai

    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Michael G Poirier

    Department of Physics, Ohio State University, Columbus, United States
    For correspondence
    poirier.18@osu.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1563-5792

Funding

National Institutes of Health (R01 GM121858)

  • Lu Bai
  • Michael G Poirier

National Institutes of Health (R01 GM121966)

  • Michael G Poirier

National Institutes of Health (T32 GM086252)

  • Benjamin T Donovan

National Science Foundation (1516979)

  • Michael G Poirier

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Tim Formosa, University of Utah School of Medicine, United States

Publication history

  1. Received: October 19, 2018
  2. Accepted: March 14, 2019
  3. Accepted Manuscript published: March 19, 2019 (version 1)
  4. Version of Record published: April 4, 2019 (version 2)

Copyright

© 2019, Donovan et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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