The sequencing of genomes has generated a huge amount of data still to be annotated. Computational methods are available to detect putative transcriptional promoter regions, but they are not 100% efficient and must be confirmed by experimentation. Unfortunately the wet-bench procedures that are currently available to study promoters are time-consuming, laborious, and can hardly be adapted to large numbers of promoters. New techniques for transcriptional studies are badly needed. We propose an array-based method for promoter detection and analysis. In our system, transcriptional products are tagged as they are synthesized, in such a way that one specific transcript is labeled with only one type of tag, and one tag labels only one type of transcript. All promoter candidates are analyzed simultaneously in one reaction vial. The transcriptional output is analyzed on conventional arrays and can be detected with procedures that do not require expensive instrumentation. Our system will strongly reduce the labor and therefore the costs associated with promoter studies, and if successful, will allow the detection of promoter regions from genomic libraries. In Phase I we plan (1) to assemble the components of the system and (2) validate the method at small scale. If Phase I milestones are reached, we will demonstrate in Phase II the usefulness of our system for highthroughput studies, including the detection and analysis of promoters from genomic libraries, detection of tissue-specific promoters, and construction of artificial promoters. Because our method is not restricted to the analysis of the human genome but may be applied to all sequenced organisms, it is likely that it will generate a strong interest among researchers in various disciplines.
