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<p>Abstract</p> <p>Background</p> <p>The <it>Saccharopolyspora erythraea </it>genome sequence, recently published, presents considerable divergence from those of streptomycetes in gene organization and function, confirming the remarkable potential of <it>S. erythraea </it>for producing many other secondary metabolites in addition to erythromycin. In order to investigate, at whole transcriptome level, how <it>S. erythraea </it>genes are modulated, a DNA microarray was specifically designed and constructed on the <it>S. erythraea </it>strain NRRL 2338 genome sequence, and the expression profiles of 6494 ORFs were monitored during growth in complex liquid medium.</p> <p>Results</p> <p>The transcriptional analysis identified a set of 404 genes, whose transcriptional signals vary during growth and characterize three distinct phases: a rapid growth until 32 h (Phase A); a growth slowdown until 52 h (Phase B); and another rapid growth phase from 56 h to 72 h (Phase C) before the cells enter the stationary phase. A non-parametric statistical method, that identifies chromosomal regions with transcriptional imbalances, determined regional organization of transcription along the chromosome, highlighting differences between core and non-core regions, and strand specific patterns of expression. Microarray data were used to characterize the temporal behaviour of major functional classes and of all the gene clusters for secondary metabolism. The results confirmed that the <it>ery </it>cluster is up-regulated during Phase A and identified six additional clusters (for terpenes and non-ribosomal peptides) that are clearly regulated in later phases.</p> <p>Conclusion</p> <p>The use of a <it>S. erythraea </it>DNA microarray improved specificity and sensitivity of gene expression analysis, allowing a global and at the same time detailed picture of how <it>S. erythraea </it>genes are modulated. This work underlines the importance of using DNA microarrays, coupled with an exhaustive statistical and bioinformatic analysis of the results, to understand the transcriptional organization of the chromosomes of micro-organisms producing natural products.</p>