Effective dynamics of nucleosome configurations at the yeast PHO5 promoter
- Technical University of Munich, Germany
- Ludwig-Maximilians-Universität München, Germany
Abstract
Chromatin dynamics are mediated by remodeling enzymes and play crucial roles in gene regulation, as established in a paradigmatic model, the S. cerevisiae PHO5 promoter. However, effective nucleosome dynamics, i.e. trajectories of promoter nucleosome configurations, remain elusive. Here, we infer such dynamics from the integration of published single-molecule data capturing multi-nucleosome configurations for repressed to fully active PHO5 promoter states with other existing histone turnover and new chromatin accessibility data. We devised and systematically investigated a new class of 'regulated on-off-slide' models simulating global and local nucleosome (dis)assembly and sliding. Only seven of 68145 models agreed well with all data. All seven models involve sliding and the known central role of the N-2 nucleosome, but regulate promoter state transitions by modulating just one assembly rather than disassembly process. This is consistent with but challenges common interpretations of previous observations at the PHO5 promoter and suggests chromatin opening by binding competition.
Data availability
All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Figure 1,Table 1 and Figure 4. Program code has been uploaded to github (link in Methods).
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Dynamics of Replication-Independent Histone Turnover in Budding YeastNCBI Gene Expression Omnibus, GSE6666.
Article and author information
Author details
Michael Roland Wolff
Funding
Deutsche Forschungsgemeinschaft (SFB863)
- Ulrich Gerland
Deutsche Forschungsgemeinschaft (SFB1064)
- Philipp Korber
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2021, Wolff 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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Effective dynamics of nucleosome configurations at the yeast PHO5 promoter
eLife 10:e58394.
https://doi.org/10.7554/eLife.58394
Further reading
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