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The modulation of gene selectivity of RNA polymerase is the key step in the bacterial response to environmental changes. The gene selectivity of RNA polymerase is modulated after interaction with seven species of sigma factor, the promoter recognition subunit, and a total of about 300 DNA-binding transcription factors in the second step. In order to get insights into the molecular mechanisms underlying the global regulation of genome expression, our effort has been focused on the identification of genes and promoters under the control of each transcription factor. For this purpose, we have developed the 'Genomic SELEX' system, which allows the quick identification of DNA sequences recognized in vitro by transcription factors. Regulation in vivo of the target genes predicted after the 'Genomic SELEX' was examined by analysis of individual transcripts in the presence and absence of the test transcription factors. The regulated promoter activity was also examined using the newly constructed two-fluorescent-protein promoter assay vector pGRP. Results altogether indicate the involvement of complex networks between transcription factors and promoters in the global regulation of genome transcription.