Time resolved DNA occupancy dynamics during the respiratory oscillation uncover a global reset point in the yeast growth program

Cornelia Amariei, Rainer Machné, Viktor Stolc, Tomoyoshi Soga, Masaru Tomita, Douglas B. Murray

Research output: Contribution to journalArticle

5 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)279-288
Number of pages10
JournalMicrobial Cell
Volume1
Issue number9
DOIs
Publication statusPublished - 2014 Sep 1

Fingerprint

Nucleosomes
Yeast
Yeasts
Histones
Chromatin
DNA
Histone Code
Growth
Genes
Paint
Structural dynamics
Cell growth
Gene Expression Profiling
Transcription
Time measurement
DNA Replication
Genetic Promoter Regions
DNA Repair
Oxidation-Reduction
Repair

Keywords

  • Anabolism
  • Catabolism
  • Chromatin dynamics
  • Energetics
  • Histone modification
  • Respiratory oscillation
  • Transcription regulation

ASJC Scopus subject areas

  • Immunology and Microbiology (miscellaneous)
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)

Cite this

Time resolved DNA occupancy dynamics during the respiratory oscillation uncover a global reset point in the yeast growth program. / Amariei, Cornelia; Machné, Rainer; Stolc, Viktor; Soga, Tomoyoshi; Tomita, Masaru; Murray, Douglas B.

In: Microbial Cell, Vol. 1, No. 9, 01.09.2014, p. 279-288.

Research output: Contribution to journalArticle

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