Role for E2F in Control of Both DNA Replication and Mitotic Functions as Revealed from DNA Microarray Analysis

Abstract

We have used high-density DNA microarrays to provide an analysis of gene regulation during the mammalian cell cycle and the role of E2F in this process. Cell cycle analysis was facilitated by a combined examination of gene control in serum-stimulated fibroblasts and cells synchronized at G₁/S by hydroxyurea block that were then released to proceed through the cell cycle. The latter approach (G₁/S synchronization) is critical for rigorously maintaining cell synchrony for unambiguous analysis of gene regulation in later stages of the cell cycle. Analysis of these samples identified seven distinct clusters of genes that exhibit unique patterns of expression. Genes tend to cluster within these groups based on common function and the time during the cell cycle that the activity is required. Placed in this context, the analysis of genes induced by E2F proteins identified genes or expressed sequence tags not previously described as regulated by E2F proteins; surprisingly, many of these encode proteins known to function during mitosis. A comparison of the E2F-induced genes with the patterns of cell growth-regulated gene expression revealed that virtually all of the E2F-induced genes are found in only two of the cell cycle clusters; one group was regulated at G₁/S, and the second group, which included the mitotic activities, was regulated at G₂. The activation of the G₂ genes suggests a broader role for E2F in the control of both DNA replication and mitotic activities.

ACKNOWLEDGMENTS

We thank Kaye Culler for help with preparation of the manuscript and Helena Abushamma for performing the Affymetrix GeneChip analyses.

J.R.N. is an Investigator in the Howard Hughes Medical Institute.