Dissociation rate compensation mechanism for budding yeast pioneer transcription factors

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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

1. Donovan B
2. Chen H
3. Jipa C
4. Poirier M
(2019) Dissociation rate compensation mechanism for budding yeast pioneer transcription factors
Zenodo, doi:10.5281/zenodo.2595208.

https://doi.org/10.5281/zenodo.2595208

Article and author information

Author details

Benjamin T Donovan

Biophysics Graduate Program, Ohio State University, Columbus, United States

Competing interests
The authors declare that no competing interests exist.
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.
Caroline Jipa

Department of Physics, Ohio State University, Columbus, United States

Competing interests
The authors declare that no competing interests exist.
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.
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.

"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.

Copyright

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.