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Background  Transcription is the first step in cellular information processing. It is regulated by  cis -acting elements such as promoters and operators in the DNA, and  trans -acting elements such as transcription factors and sigma factors. Identification of  cis -acting regulatory elements on a genomic scale requires computational analysis.    Results  We have used oligonucleotide profiling to predict regulatory regions in a bacterial genome. The method has been applied to the  Escherichia coli  K12 genome and the results analyzed. The information content of the putative regulatory oligonucleotides so predicted is validated through intra-genomic analyses, correlations with experimental data and inter-genome comparisons. Based on the results we have proposed a model for the bacterial promoter. The results show that the method is capable of identifying, in the  E.coli  genome,  cis -acting elements such as TATAAT (sigma70 binding site), CCCTAT (1 base relative of sigma32 binding site), CTATNN (LexA binding site), AGGA-containing hexanucleotides (Shine Dalgarno consensus) and CTAG-containing hexanucleotides (core binding sites for Trp and Met repressors).    Conclusion  The method adopted is simple yet effective in predicting upstream regulatory elements in bacteria. It does not need any prior experimental data except the sequence itself. This method should be applicable to most known genomes. Profiling, as applied to the  E.coli  genome, picks up known  cis -acting and regulatory elements. Based on the profile results, we propose a model for the bacterial promoter that is extensible even to eukaryotes. The model is that the core promoter lies within a plateau of bent AT-rich DNA. This bent DNA acts as a homing segment for the sigma factor to recognize the promoter. The model thus suggests an important role for local landscapes in prokaryotic and eukaryotic gene regulation.

Promoter addresses: revelations from oligonucleotide profiling applied to the Escherichia coli genome