1887

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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2010-06-01
2019-10-23
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GO ToolBox analysis of the L, E and LE sets, indicating enrichment and depletion of GO terms in GO root terms 'Biological process' and 'Molecular function'. [Excel file](101 KB)

EXCEL

A table listing all 728 features that exhibited significant BrdU labelling (synthesized features, 'L' set). A table of features expressed during the entire 6 days of the stationary-phase time-course ('E' set). A table listing labelled–expressed features. [PDF of Tables S2–S4](241 KB)

PDF

Raw and normalized microarray expression data. Column labels are as follows: c1t10_C_lnS2, natural logarithm (ln) of S2 channel (Cy3, green) of the third replicate hybridization (C) at time point t10; c1t13_A_lnS1, natural logarithm (ln) of S1 channel (Cy5, red) of the first replicate hybridization (A) at time point t13; D, Cy3/Cy5 differentials; Tt, -values for Cy3/Cy5 differentials; Av, averages of differentials for replicates; LnP, natural logarithm of -values. [Excel file](11.7 MB)

EXCEL

All real-time PCR data, including reaction charts, melt curves and standard curves. Calculated replicate concentrations are geometric means of individual reaction concentrations. Column descriptions and abbreviations are as follows: Ct, threshold cycle; Conc., concentration; Nor., normalizer; Var., variance; Std. Dev., standard deviation; Rep., replicate; Calc., calculated; CI, confidence interval; NTC, non-template control. [Excel file](351 KB)

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