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Analysis of cell-cycle gene expression in Saccharomyces cerevisiae using microarrays and multiple synchronization
Kerby Shedden1, Stephen Cooper
1Department of Statistics, University of Michigan, Ann Arbor, MI 48109-1285, USA. kshedden@umich.edu
Nucleic Acids Research
|June 28, 2002
Summary
Gene expression in yeast Saccharomyces cerevisiae shows cell-cycle specificity, but results vary significantly between synchronization methods. Elutriation may offer the most accurate view of the unperturbed cell cycle.
Area of Science:
- Molecular Biology
- Genetics
- Cell Biology
Background:
- Microarray analysis suggests many genes in Saccharomyces cerevisiae exhibit cell-cycle-specific expression.
- Understanding cell cycle regulation is crucial for comprehending fundamental biological processes.
Purpose of the Study:
- To investigate the reproducibility of cell-cycle-specific gene expression patterns in yeast.
- To compare different synchronization methods for their impact on gene expression analysis.
Main Methods:
- Utilized microarray analysis to measure gene expression during the yeast cell cycle.
- Employed four distinct synchronization methods: alpha-factor, CDC28, CDC15, and elutriation.
- Analyzed periodicity and phase timing of gene expression across experiments.
Main Results:
- Cyclic patterns in gene expression were statistically significant and not due to random noise.
- High variability in gene cyclicity and phase timing was observed between different synchronization methods.
- Elutriation synchronization yielded distinct patterns compared to arrest-release methods (alpha-factor, CDC28, CDC15).
Conclusions:
- Synchronization methods can introduce artifacts, leading to non-reproducible gene expression patterns.
- The elutriation method, potentially less perturbing, may provide a more accurate representation of the unperturbed yeast cell cycle.
- Observed cyclicities in other methods might reflect a stress response rather than true cell-cycle-dependent regulation.