Genome-Wide Identification of Potential Plant E2F Target Genes

Abstract

Entry into the S phase of the cell cycle is controlled by E2F transcription factors that induce the transcription of genes required for cell cycle progression and DNA replication. Although the E2F pathway is highly conserved in higher eukaryotes, only a few E2F target genes have been experimentally validated in plants. We have combined microarray analysis and bioinformatics tools to identify plant E2F-responsive genes. Promoter regions of genes that were induced at the transcriptional level in Arabidopsis (Arabidopsis thaliana) seedlings ectopically expressing genes for the E2Fa and DPa transcription factors were searched for the presence of E2F-binding sites, resulting in the identification of 181 putative E2F target genes. In most cases, the E2F-binding element was located close to the transcription start site, but occasionally could also be localized in the 5# untranslated region. Comparison of our results with available microarray data sets from synchronized cell suspensions revealed that the E2F target genes were expressed almost exclusively during G1 and S phases and activated upon reentry of quiescent cells into the cell cycle. To test the robustness of the data for the Arabidopsis E2F target genes, we also searched for the presence of E2F-cis-acting elements in the promoters of the putative orthologous rice (Oryza sativa) genes. Using this approach, we identified 70 potential conserved plant E2F target genes. These genes encode proteins involved in cell cycle regulation, DNA replication, and chromatin dynamics. In addition, we identified several genes for potentially novel S phase regulatory proteins.The heterodimeric E2F-DP transcription factors control the cell cycle by regulating transcription of genes required for DNA replication and cell cycle (Helin, 1998;Lavia and Jansen-Dü rr, 1999). In mammals, eight E2Fs have been cloned and characterized (Trimarchi and Lees, 2002;de Bruin et al., 2003;Di Stefano et al., 2003;Maiti et al., 2005). E2F1, E2F2, and E2F3 function as potent transcriptional activators of E2F-responsive genes, and the overproduction of one of them is sufficient to drive serum-starved cells into the cell cycle. In contrast, E2F4 and E2F5 are mainly found in quiescent cells and are believed to control cell cycle exit and the onset of terminal differentiation. The physiological role of the E2F6, E2F7, and E2F8 proteins is less well understood, but the lack of a clear trans-activation domain suggests that they may function as repressors of E2F-dependent transcription (Mü ller and Helin,

ANTI-SILENCING FUNCTION1 Proteins Are Involved in Ultraviolet-Induced DNA Damage Repair and Are Cell Cycle Regulated by E2F Transcription Factors in Arabidopsis

“…In humans, ASF1B is regulated by E2F transcription factors during cell cycle progression (Hayashi et al, 2007). Moreover, in plants, Vandepoele et al (2005) were able to identify that ASF1A and ASF1B are among the 181 putative E2Fa-DPa target genes. To validate these observations, we investigated the regulation of ASF1A and ASF1B genes by the E2F family.…”

Dynamic Localization of the DNA Replication Proteins MCM5 and MCM7 in Plants

“…Arabidopsis MCM2 to MCM5 and MCM7 genes contain E2F consensus sites in their promoters, and their transcripts are elevated in plants ectopically expressing E2FA/DPA (Stevens et al, 2002;Vandepoele et al, 2005). We found an E2F consensus motif in the Arabidopsis MCM6 promoter (R.W.…”

E2F RegulatesFASCIATA1, a Chromatin Assembly Gene Whose Loss Switches on the Endocycle and Activates Gene Expression by Changing the Epigenetic Status

“…This suggests a complex regulatory network in which different combinations of E2F may affect FAS1 expression, possibly in a cell type-dependent manner. This idea of complexity in E2F regulation has a precedent in the data obtained in mRNA-profiling experiments of plants with increased levels of E2Fa, considered a typical activator (Vlieghe et al, 2003;Vandepoele et al, 2005). These studies identified genes whose expression was activated as well as genes whose expression was repressed, although, in both cases, some of them contain E2F binding sites in their promoters.…”