Microarray analysis of gene expression during the cell cycle

Abstract

Microarrays have been applied to the determination of genome-wide expression patterns during the cell cycle of a number of different cells. Both eukaryotic and prokaryotic cells have been studied using whole-culture and selective synchronization methods. The published microarray data on yeast, mammalian, and bacterial cells have been uniformly interpreted as indicating that a large number of genes are expressed in a cell-cycle-dependent manner. These conclusions are reconsidered using explicit criteria for synchronization and precise criteria for identifying gene expression patterns during the cell cycle. The conclusions regarding cell-cycle-dependent gene expression based on microarray analysis are weakened by arguably problematic choices for synchronization methodology (e.g., whole-culture methods that do not synchronize cells) and questionable statistical rigor for identifying cell-cycle-dependent gene expression. Because of the uncertainties in synchrony methodology, as well as uncertainties in microarray analysis, one should be somewhat skeptical of claims that there are a large number of genes expressed in a cell-cycle-dependent manner.

Figure 1

Illustration of places for application of criteria for synchronization. Numbers refer to criteria in list in Appendix 1 [see additional file 1]. The top box is an activity/cell graph, the lower box is a synchrony curve, and below the synchrony curve are DNA content (left) and size analyses (right) of synchronized cells. Note that the expression of a cycle-dependent gene should peak at the same part of the cell cycle in successive cell cycles. Also, the DNA content should progress as expected through the cell cycle and repeat in the second cycle. The cell size of synchronized cells should have a distribution that is significantly narrower than the unsynchronized, original culture.