Genomic SELEX for the genome-wide search of regulation targets by transcription factors: SELEX-clos and SELEX-chip procedures

The pattern of genome transcription in prokaryotes is determined by selective distribution of RNA polymerase within the genome. The gene selectivity of RNA polymerase is modulated after interaction with DNA-binding transcription factors (TFs). Escherichia coli contains a total of about 300 TFs, but the regulatory function has not yet been identified for about one third. For quick and systematic search of the regulation target genes by TFs, we have developed a novel screening technology “Genomic SELEX”, in which the recognition DNA sequences by the test TF are isolated from a mixture of genome DNA fragments. The sequences were determined by either cloning-sequencing of SELX fragments (SELEX-clos) or high-density microarray (tilling array) analysis (SELEX-chip). Here we describe the application of these novel technologies for search of the whole set of regulation target genes on the E. coli genome by CRP (cAMP-binding protein).