A DNA Structural Atlas for E. coli

We have constructed a "DNA Structural Atlas" as a method of visualising structural features of DNA in complete genomes. We use this method to examine mechanical properties of the DNA helix, various types of repeats, and base composition, and produce a detailed analysis of the Escherichia coli genome in terms of DNA structures in highly expressed genes, transposable elements, and promoters for four different sigma factors. On a global scale, one can observe large regions of the E. coli genome which could act as organisational determinants of chromosome architecture; an example of this is the rhs gene family of repetitive elements. Cluster analysis of the E. coli genes, based on their DNA structural properties, resulted in five classes of genes, with highly expressed genes, viruses, and transposable elements grouping in distinct classes. At the level of individual genes, the structural atlas indicates a preferential localisation of sequences prone towards specific structures within intergenic regions. Structural profiles for aligned promoter regions reveal that the helix tends to be more rigid within about a hundred bp upstream of the transcription start sites and are more deformable immediately downstream of the transcript start sites. Each of four different classes of promoter binding sites are statistically distinct from each other, in terms of DNA structural profiles. In general, promoters are more rigid, curved, easily melted, and AT rich than coding regions. We also include a comparative analysis of 30 other sequenced microbial genomes.

A DNA Structural Atlas of Escherichia coli