Construction of 'Promoter Chip' for Microarray Analysis of Regulation Targets of Transcription Factors

Escherichia coli carries a sophisticated genetic system for adaptation to changes in external environment by selective transcription of a total of about 4,400 genes on its genome. Gene selection takes place at the step of promoter recognition by the RNA polymerase. The promoter selectivity of RNA polymerase is, however, modulated after interaction with DNA-binding transcription factors. In E. coli, a total of about 300 species of transcription factor have been predicted, even though the regulatory functions remain identified for about half of these factors. In order to understand the global regulation of genome expression in E. coli, it is essential to identify the regulatory functions of all 300 transcription factors. For quick search of the regulation targets by each transcription factor, we developed the genomic SELEX (see Ishihama et al., in this volume). In parallel, we have constructed a novel method for comprehensive search of the promoters under the control of each transcription factor. Here we have constructed a 'promoter chip', which contains more than 1,000 species of the E. coli promoters. The promoter microarray can be used for identification of target promoters regulated by each transcription factor.