Transcription factor distribution in Escherichia coli: studies with FNR protein

David C Grainger, Hirofumi Aiba, Douglas Hurd, Douglas F Browning, Stephen J W Busby

Research output: Contribution to journalArticlepeer-review


Using chromatin immunoprecipitation (ChIP) and high-density microarrays, we have measured the distribution of the global transcription regulator protein, FNR, across the entire Escherichia coli chromosome in exponentially growing cells. Sixty-three binding targets, each located at the 5' end of a gene, were identified. Some targets are adjacent to poorly transcribed genes where FNR has little impact on transcription. In stationary phase, the distribution of FNR was largely unchanged. Control experiments showed that, like FNR, the distribution of the nucleoid-associated protein, IHF, is little altered when cells enter stationary phase, whilst RNA polymerase undergoes a complete redistribution.

Original languageEnglish
Pages (from-to)269-278
Number of pages10
JournalNucleic Acids Research
Issue number1
Publication statusPublished - 1 Jan 2007

Bibliographical note

© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.


  • Binding Sites
  • Chromatin Immunoprecipitation
  • Chromosomes, Bacterial
  • DNA, Bacterial/chemistry
  • Escherichia coli/genetics
  • Escherichia coli Proteins/analysis
  • Iron-Sulfur Proteins/analysis
  • Oligonucleotide Array Sequence Analysis
  • Regulatory Elements, Transcriptional
  • Sequence Analysis, DNA
  • Transcription Factors/analysis


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