Although it is easy to understand that changes in the place or time of gene expression can create new or alternative molecular interactions, little information about the organization and evolution of transcriptional regulation in plants is known. However, this knowledge is essential because each gene is flanked by regulatory sequences which, together with the expression and activity of other proteins, determine the amount, place, and timing of expression. Therefore, characterizing these regulatory motifs is required in order to understand the regulatory interactions between trans-acting proteins and the promoters of thousands of genes within a eukaryotic genome. This information is also essential when studying biological processes from a holistic point of view by integrating complementary functional data sets. We are studying the architecture of plant promoter sequences and try to identify cis-regulatory elements (or TFBS), which play an important role in transcriptional regulation. Fully sequenced plant genomes, together with extensive expression data sets are used to characterize the basic composition of plant promoters (e.g. TFBS, cis-regulatory modules) and to study their evolution within the green plant lineage.
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