Abstract
Patterns of transcriptional activity along circular prokaryotic chromosomes such as Escherichia coli and Bacillus subtilis have previously been characterized through microarray-based analysis of gene expression. However, patterns across linear prokaryotic chromosomes are yet to be investigated. Given the different topological constraints (to circular DNA) imposed upon the linear chromosome the derived transcriptional patterns would be expected to be different. Here we explore transcriptional activity along the linear chromosome of Streptomyces coelicolor using expression data from 139 microarrays and genomic features. Representing total chromosomal expression as a spatial series of transcript abundances we observe both short and long range periodicities of transcription along the S. coelicolor chromosome with data derived from different microarray technologies (spotted and ink jet in situ-synthesized). Application of the autocorrelation function confirmed these periodicities as significant both in two and single channel analyses and allowed further analysis of chromosomal properties: Codon adaptation index, GC content, secondary structure and gene length. Another signal processing technique, namely wavelet analysis, has aided the visualization of the periodic signals along the chromosome, identifying ‘hot-spots’ of activity related to specific responses. The ranges of periodicity we observe for the linear chromosome of S. coelicolor indicate a different chromosomal organization than circular chromosomes; the short periodicity of 5 genes we observe cannot be accounted for by the currently proposed E. coli and B. subtilis models. We suggest a chromosome organization/transcriptional model that takes into consideration the transcriptional and genomic organization trends we observe.