Genome organisation and chromatin structure in Escherichia coli

We have analysed the complete sequence of the Escherichia coli K12 isolate MG1655 genome for chromatin-associated protein binding sites, and compared the predicted location of predicted sites with experimental expression data from ‘DNA chip’ experiments. Of the dozen proteins associated with chromat...

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Bibliographic Details
Published in:	Biochimie Vol. 83; no. 2; pp. 201 - 212
Main Authors:	Ussery, David, Schou Larsen, Thomas, Trevor Wilkes, K, Friis, Carsten, Worning, Peder, Krogh, Anders, Brunak, Søren
Format:	Journal Article
Language:	English
Published:	France Elsevier Masson SAS 01-02-2001
Subjects:	bacterial chromatin Bacterial Proteins - genetics Binding Sites Carrier Proteins - metabolism Chromatin - genetics DNA curvature DNA Replication DNA, Bacterial - genetics DNA-Binding Proteins - genetics Escherichia coli Escherichia coli - genetics Escherichia coli Proteins Factor For Inversion Stimulation Protein FIS Genome, Bacterial H-NS IHF Integration Host Factors Oligonucleotide Array Sequence Analysis - methods Operon Plasmids repetitive DNA Repetitive Sequences, Nucleic Acid IHF, integration host factor FIS H-NS, high molecular mass native subunit IHF Escherichia coli FIS, factor for inversion stimulation repetitive DNA H-NS DNA curvature bacterial chromatin
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Summary:	We have analysed the complete sequence of the Escherichia coli K12 isolate MG1655 genome for chromatin-associated protein binding sites, and compared the predicted location of predicted sites with experimental expression data from ‘DNA chip’ experiments. Of the dozen proteins associated with chromatin in E. coli, only three have been shown to have significant binding preferences: integration host factor (IHF) has the strongest binding site preference, and FIS sites show a weak consensus, and there is no clear consensus site for binding of the H-NS protein. Using hidden Markov models (HMMs), we predict the location of 608 IHF sites, scattered throughout the genome. A subset of the IHF sites associated with repeats tends to be clustered around the origin of replication. We estimate there could be roughly 6000 FIS sites in E. coli, and the sites tend to be localised in two regions flanking the replication termini. We also show that the regions upstream of genes regulated by H-NS are more curved and have a higher AT content than regions upstream of other genes. These regions in general would also be localised near the replication terminus.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0300-9084 1638-6183
DOI:	10.1016/S0300-9084(00)01225-6