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Volume 156, Issue 6

Genome-wide analysis of DNA turnover and gene expression in stationary-phase Free

Abstract

Exponential-phase yeast cells readily enter stationary phase when transferred to fresh, carbon-deficient medium, and can remain fully viable for up to several months. It is known that stationary-phase prokaryotic cells may still synthesize substantial amounts of DNA. Although the basis of this phenomenon remains unclear, this DNA synthesis may be the result of DNA maintenance and repair, recombination, and stress-induced transposition of mobile elements, which may occur in the absence of DNA replication. To the best of our knowledge, the existence of DNA turnover in stationary-phase unicellular eukaryotes remains largely unstudied. By performing cDNA-spotted (i.e. ORF) microarray analysis of stationary cultures of a haploid strain, we demonstrated on a genomic scale the localization of a DNA-turnover marker [5-bromo-2′-deoxyuridine (BrdU); an analogue of thymidine], indicative of DNA synthesis in discrete, multiple sites across the genome. Exponential-phase cells on the other hand, exhibited a uniform, total genomic DNA synthesis pattern, possibly the result of DNA replication. Interestingly, BrdU-labelled sites exhibited a significant overlap with highly expressed features. We also found that the distribution among chromosomes of BrdU-labelled and expressed features deviates from random distribution; this was also observed for the overlapping set. Ty retrotransposon genes were also found to be labelled with BrdU, evidence for transposition during stationary phase; however, they were not significantly expressed. We discuss the relevance and possible connection of these results to DNA repair, mutation and related phenomena in higher eukaryotes.

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Keyword(s): ARS, autonomously replicating sequence(s) , BrdU, 5-bromo-2′-deoxyuridine , E, expressed , FDR, false discovery rate , GO, gene ontology , IP, immunoprecipitation , L, labelled , LE, labelled–expressed and SMM, supplemented minimal medium
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2010-06-01
2024-04-19
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Genome-wide analysis of DNA turnover and gene expression in stationary-phase Saccharomyces cerevisiae
Microbiology 156, 1758 (2010); https://doi.org/10.1099/mic.0.035519-0
/content/journal/micro/10.1099/mic.0.035519-0
/content/journal/micro/10.1099/mic.0.035519-0
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