Genomic SELEX screening of regulatory targets of Escherichia coli transcription factors

Tomohiro Shimada, Hiroshi Ogasawara, Akira Ishihama

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

16 Citations (Scopus)


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.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages21
Publication statusPublished - 2018

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • DNA-protein interaction
  • Escherichia coli
  • Genomic SELEX
  • RNA polymerase
  • Regulatory target
  • Transcription factor: Sigma factor


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