Dissociation rate compensation mechanism for budding yeast pioneer transcription factors
- Ohio State University, United States
- The Pennsylvania State University, United States
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
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Dissociation rate compensation mechanism for budding yeast pioneer transcription factorsZenodo, doi:10.5281/zenodo.2595208.
Article and author information
Author details
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
- Tim Formosa, University of Utah School of Medicine, United States
Version history
- Received: October 19, 2018
- Accepted: March 14, 2019
- Accepted Manuscript published: March 19, 2019 (version 1)
- 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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Dissociation rate compensation mechanism for budding yeast pioneer transcription factors
eLife 8:e43008.
https://doi.org/10.7554/eLife.43008
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