Abstract：
: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.
journal_name
Biochimiejournal_title
Biochimieauthors
Ussery D,Larsen TS,Wilkes KT,Friis C,Worning P,Krogh A,Brunak Sdoi
10.1016/s0300-9084(00)01225-6keywords:
subject
Has Abstractpub_date
2001-02-01 00:00:00pages
201-12issue
2eissn
0300-9084issn
1638-6183pii
S0300908400012256journal_volume
83pub_type
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