Cell cycle population effects in perturbation studies

Eoghan O'Duibhir, Philip Lijnzaad, Joris J. Benschop, Tineke L. Lenstra, Dik van Leenen, Marian J. A. Groot Koerkamp, Thanasis Margaritis, Mariel O. Brok, Patrick Kemmeren, Frank C. P. Holstege*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Growth condition perturbation or gene function disruption are commonly used strategies to study cellular systems. Although it is widely appreciated that such experiments may involve indirect effects, these frequently remain uncharacterized. Here, analysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common gene expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. The slow growth signature is highly similar to the environmental stress response (ESR), an expression response common to diverse environmental perturbations. Both environmental and genetic perturbations result in growth rate changes. These are accompanied by a change in the distribution of cells over different cell cycle phases. Rather than representing a direct expression response in single cells, both the slow growth signature and ESR mainly reflect a redistribution of cells over different cell cycle phases, primarily characterized by an increase in the G1 population. The findings have implications for any study of perturbation that is accompanied by growth rate changes. Strategies to counter these effects are presented and discussed.

Original languageEnglish
Article number732
Number of pages14
JournalMolecular Systems Biology
Volume10
Issue number6
DOIs
Publication statusPublished - Jun 2014

Keywords / Materials (for Non-textual outputs)

  • environmental stress response
  • gene deletion
  • gene expression
  • genome-wide transcription
  • growth rate
  • YEAST SACCHAROMYCES-CEREVISIAE
  • GENE-EXPRESSION
  • BUDDING YEAST
  • HEAT-SHOCK
  • ENVIRONMENTAL-CHANGES
  • TRANSCRIPTION FACTORS
  • REGULATORY NETWORKS
  • METABOLIC CYCLE
  • MICROARRAY DATA
  • GROWTH-RATE

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