Effective dynamics of nucleosome configurations at the yeast PHO5 promoter

• Main Authors: Michael Roland Wolff, Andrea Schmid, Philipp Korber, Ulrich Gerland
• Format: Article
• Language: English
• Published: eLife Sciences Publications Ltd 2021-03-01
• Series: eLife
• Subjects: PHO5 promoter; nucleosome dynamics; nucleosome configurations; chromatin regulation; chromatin remodeling
• Online Access: https://elifesciences.org/articles/58394

Chromatin dynamics are mediated by remodeling enzymes and play crucial roles in gene regulation, as established in a paradigmatic model, the Saccharomyces cerevisiae PHO5 promoter. However, effective nucleosome dynamics, that is, 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 68,145 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.