Time resolved DNA occupancy dynamics during the respiratory oscillation uncover a global reset point in the yeast growth program
Authors:Cornelia Amariei, Rainer Machné, Viktor Stolc, Tomoyoshi Soga, Masaru Tomita and Douglas B. Murray
doi: 10.15698/mic2014.09.166
Volume 1, pp. 279 to 288, published 01/09/2014.
1 Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan.
2 Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan.
3 Institute for Theoretical Biology, Humboldt University, Berlin, Invalidenstrasse 43, D-10115, Berlin, Germany.
4 Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090, Vienna, Austria.
5 NASA Ames Research Center, Moffett Field, California, United States of America.
Keywords:
Keywords: respiratory oscillation, chromatin dynamics, transcription regulation, histone modification, anabolism, catabolism, energetics.
Abbreviations: AU = arbitrary units, bp = base pair, DO = dissolved oxygen, gDNA = genomic DNA, GB = gene body, NDR = nucleosome-depleted region, pDNA = protein-bound DNA, PolII = RNA Polymerase II, TSS = transcription start site.
Corresponding Author(s):
Conflict of interest statement:
The authors declare no conflict of interest.
Please cite this article as:
Cornelia Amariei, Rainer Machné, Viktor Stolc, Tomoyoshi Soga, Masaru Tomita and Douglas B. Murray (2014). Time resolved DNA occupancy dynamics during the respiratory oscillation uncover a global reset point in the yeast growth program. Microbial Cell 1(9): 279-288.
© 2014 Amariei et al. This is an open-access article released under the terms of the Creative Commons Attribution (CC BY) license, which allows the unrestricted use, distribution, and reproduction in any medium, provided the original author and source are acknowledged.
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.