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,

The identification of promoters and their regulatory elements is one of the major challenges in bioinformatics and integrates comparative, structural, and functional genomics. Many different approaches have been developed to detect conserved motifs in a set of genes that are either coregulated or orthologous. However, although recent approaches seem promising, in general, unambiguous identification of regulatory elements is not straightforward. The delineation of promoters is even harder, due to its complex nature, and in silico promoter prediction is still in its infancy. Here, we review the different approaches that have been developed for identifying promoters and their regulatory elements. We discuss the detection of cis-acting regulatory elements using word-counting or probabilistic methods (so-called "search by signal" methods) and the delineation of promoters by considering both sequence content and structural features ("search by content" methods). As an example of search by content, we explored in greater detail the association of promoters with CpG islands. However, due to differences in sequence content, the parameters used to detect CpG islands in humans and other vertebrates cannot be used for plants. Therefore, a preliminary attempt was made to define parameters that could possibly define CpG and CpNpG islands in Arabidopsis, by exploring the compositional landscape around the transcriptional start site. To this end, a data set of more than 5,000 gene sequences was built, including the promoter region, the 5Ј-untranslated region, and the first introns and coding exons. Preliminary analysis shows that promoter location based on the detection of potential CpG/CpNpG islands in the Arabidopsis genome is not straightforward. Nevertheless, because the landscape of CpG/ CpNpG islands differs considerably between promoters and introns on the one side and exons (whether coding or not) on the other, more sophisticated approaches can probably be developed for the successful detection of "putative" CpG and CpNpG islands in plants.Arabidopsis, and probably most plants, encode an exceptionally large number of DNA-binding proteins, potentially acting as transcription factors (TFs). In fact, more than 3,000 genes have been anticipated to be involved in transcription, more than one-half of which were expected to encode TFs (Arabidopsis Genome Initiative, 2000), corresponding to more than 5% of the Arabidopsis genes, and approximately twice the ratio observed for yeast and animal genomes (Riechmann et al., 2000). These TFs bind to the DNA on specific cis-acting regulatory elements (CAREs) and orchestrate the initiation of transcription, which is one of the most important control points in the regulation of gene expression. CAREs are short conserved motifs of five up to 20 nucleotides usually found in the vicinity of the 5Ј end of genes in what is called the promoter. The promoter sequence is usually located upstream from the transcription start site (TSS), but regulatory elements can also be located downstream, for ...

DNA encodes at least two independent levels of functional information. The first level is for encoding proteins and sequence targets for DNA-binding factors, while the second one is contained in the physical and structural properties of the DNA molecule itself. Although the physical and structural properties are ultimately determined by the nucleotide sequence itself, the cell exploits these properties in a way in which the sequence itself plays no role other than to support or facilitate certain spatial structures. In this work, we focus on these structural properties, comparing them between different organisms and assessing their ability to describe the core promoter. We prove the existence of distinct types of core promoters, based on a clustering of their structural profiles. These results indicate that the structural profiles are much conserved within plants (Arabidopsis and rice) and animals (human and mouse), but differ considerably between plants and animals. Furthermore, we demonstrate that these structural profiles can be an alternative way of describing the core promoter, in addition to more classical motif or IUPAC-based approaches. Using the structural profiles as discriminatory elements to separate promoter regions from non-promoter regions, reliable models can be built to identify core-promoter regions using a strictly computational approach.