Dissociation rate compensation mechanism for budding yeast pioneer transcription factors
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
Publication 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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Further reading
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An evolutionary perspective enhances our understanding of biological mechanisms. Comparison of sex determination and X-chromosome dosage compensation mechanisms between the closely related nematode species C. briggsae (Cbr) and C. elegans (Cel) revealed that the genetic regulatory hierarchy controlling both processes is conserved, but the X-chromosome target specificity and mode of binding for the specialized condensin dosage compensation complex (DCC) controlling X expression have diverged. We identified two motifs within Cbr DCC recruitment sites that are highly enriched on X: 13-bp MEX and 30-bp MEX II. Mutating either MEX or MEX II in an endogenous recruitment site with multiple copies of one or both motifs reduced binding, but only removing all motifs eliminated binding in vivo. Hence, DCC binding to Cbr recruitment sites appears additive. In contrast, DCC binding to Cel recruitment sites is synergistic: mutating even one motif in vivo eliminated binding. Although all X-chromosome motifs share the sequence CAGGG, they have otherwise diverged so that a motif from one species cannot function in the other. Functional divergence was demonstrated in vivo and in vitro. A single nucleotide position in Cbr MEX can determine whether Cel DCC binds. This rapid divergence of DCC target specificity could have been an important factor in establishing reproductive isolation between nematode species and contrasts dramatically with conservation of target specificity for X-chromosome dosage compensation across Drosophila species and for transcription factors controlling developmental processes such as body-plan specification from fruit flies to mice.