David Ussery Anders Gorm Pedersen Lars Juhl Jensen Carsten Friis Hans Henrik Stærfeldt Søren Brunak
Center for Biological Sequence Analysis
Institute of Biotechnology
Technical University of Denmark
The "DNA GenomeAtlas" homepage
An "Electronic Poster" for the 3rd Annual TIGR conference on "Comparative Microbial Genomics", at the Renaissance Harborplace Hotel in Baltimore, Maryland, USA (18 - 21 November, 1999).
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.
Background - What is a "DNA Structural Atlas"?
Three Views of Escherichia coli:The DNA Structural AtlasThe Genome Atlas (combined view)
The Base-Composition Atlas
The DNA Repeat Atlas
DNA Structural Analysis of Promoters Escherichia coli
Cluster Analysis of E. coli Genes
Gene Expression in E. coli
Analysis of Chromatin-Protein Binding Sites
DNA Periodicity in E. coli and other bacterial genomes
Analysis of Pathogenicity Islands and Plasmids
Link to electronic poster on DNA Periodicity Analysis, also for this conference.
Link to last year's "DNA Structural Atlas" electronic poster. (For the 2nd Annual Conference on Computational Genomics, held at the Hyatt Regency Reston Town Center, in Reston, Virginia, 31 October - 3 November, 1998)
Link to the E. coli GenomeAtlas page
Homepage for the Bioinformatics 2000 conference, to be held at Hotel Marienlyst, in Elsinore, Denmark, 27 - 30 April, 2000
Last modified on Tuesday, 2 November, 1999, by Dave Ussery