Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome.
The Escherichia coli chromosome is condensed into an ill-defined structure known as the nucleoid. Nucleoid-associated DNA-binding proteins are involved in maintaining this structure and in mediating chromosome compaction. We have exploited chromatin immunoprecipitation and high-density microarrays to study the binding of three such proteins, FIS, H-NS and IHF, across the E.coli genome in vivo. Our results show that the distribution of these proteins is biased to intergenic parts of the genome, and that the binding profiles overlap. Hence some targets are associated with combinations of bound FIS, H-NS and IHF. In addition, many regions associated with FIS and H-NS are also associated with RNA polymerase.
Grainger
David C
DC
School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
Hurd
Douglas
D
Goldberg
Martin D
MD
Busby
Stephen J W
SJ
D001426:Bacterial Proteins / Q000378:metabolism; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D002876:Chromosomes, Bacterial; D004269:DNA, Bacterial / Q000378:metabolism*; D021901:DNA, Intergenic / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000302:isolation & purification / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000302:isolation & purification / Q000378:metabolism*; D035021:Factor For Inversion Stimulation Protein; D016680:Genome, Bacterial; D034982:Integration Host Factors / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D021901:DNA, Intergenic; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D035021:Factor For Inversion Stimulation Protein; C501034:Fis protein, E coli; C031908:H-NS protein, bacteria; D034982:Integration Host Factors; D014157:Transcription Factors; C440502:integration host factor, E coli; D012321:DNA-Directed RNA Polymerases