Genomic SELEX Screening of Regulatory Targets of Escherichia coli Transcription Factors.

The genome of Escherichia coli K-12 is transcribed by a single species of RNA polymerase. The selectivity of its transcriptional targets is modulated via two-steps of protein-protein interaction: at the first step, seven species of the sigma subunit are involved, at the second step, a total of approximately 300 species of transcription factor (TFs). For the identification of the regulatory targets of these two groups of regulatory proteins, we developed two in vitro approaches, "Genomic SELEX" (currently designated as gSELEX) and "PS (promoter-specific)-TF" screenings. Here, we describe a detailed protocol of the genomic SELEX screening system which uses purified regulatory proteins and fragments of genomic DNA from E. coli.