title: Time resolved DNA occupancy dynamics during the respiratory oscillation uncover a global reset point in the yeast growth program.
abstract: The structural dynamics of chromatin have been implicated in the regulation of fundamental eukaryotic processes, such as DNA transcription, replication and repair. Although previous studies have revealed that the chromatin landscape, nucleosome remodeling and histone modification events are intimately tied into cellular energetics and redox state, few studies undertake defined time-resolved measurements of these state variables. Here, we use metabolically synchronous, continuously-grown yeast cultures to measure DNA occupancy and track global patterns with respect to the metabolic state of the culture. Combined with transcriptome analyses and ChIP-qPCR experiments, these paint an intriguing picture where genome-wide nucleosome focusing occurs during the recovery of energy charge, followed by clearance of the promoter regions and global transcriptional slow-down, thus indicating a nucleosome-mediated "reset point" for the cycle. The reset begins at the end of the catabolic and stress-response transcriptional programs and ends prior to the start of the anabolic and cell-growth transcriptional program, and the histones on genes from both the catabolic and anabolic superclusters are deacetylated.
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan. ; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan.
authors.forename: Cornelia
authors.initials: C
authors.lastname: Amariei
authors.affiliation: Institute for Theoretical Biology, Humboldt University, Berlin, Invalidenstrasse 43, D-10115, Berlin, Germany. ; Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090, Vienna, Austria.
authors.forename: Rainer
authors.initials: R
authors.lastname: Machné
authors.affiliation: NASA Ames Research Center, Moffett Field, California, United States of America.
authors.forename: Viktor
authors.initials: V
authors.lastname: Stolc
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan. ; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan.
authors.forename: Tomoyoshi
authors.initials: T
authors.lastname: Soga
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan. ; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan.
authors.forename: Masaru
authors.initials: M
authors.lastname: Tomita
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan.
authors.forename: Douglas B
authors.initials: DB
authors.lastname: Murray
keywords: anabolism; catabolism; chromatin dynamics; energetics; histone modification; respiratory oscillation; transcription regulation