Research article

Decoding the nucleoid organisation of Bacillus subtilis and Escherichia coli through gene expression data

Anne-Sophie Carpentier¹ , Bruno Torrésani² , Alex Grossmann¹ and Alain Hénaut¹

¹  Laboratoire Génome et Informatique, CNRS UMR 8116, Tour Evry2, 523 Place des Terrasses, 91034 Evry Cedex, France

²  CMI, Université de Provence, 39 rue Joliot-Curie, 13453 Marseille cedex 13, France

author email corresponding author email

BMC Genomics 2005, 6:84doi:10.1186/1471-2164-6-84

Published:	6 June 2005

Abstract

Background

Although the organisation of the bacterial chromosome is an area of active research, little is known yet on that subject. The difficulty lies in the fact that the system is dynamic and difficult to observe directly. The advent of massive hybridisation techniques opens the way to further studies of the chromosomal structure because the genes that are co-expressed, as identified by microarray experiments, probably share some spatial relationship. The use of several independent sets of gene expression data should make it possible to obtain an exhaustive view of the genes co-expression and thus a more accurate image of the structure of the chromosome.

Results

For both Bacillus subtilis and Escherichia coli the co-expression of genes varies as a function of the distance between the genes along the chromosome. The long-range correlations are surprising: the changes in the level of expression of any gene are correlated (positively or negatively) to the changes in the expression level of other genes located at well-defined long-range distances. This property is true for all the genes, regardless of their localisation on the chromosome.

We also found short-range correlations, which suggest that the location of these co-expressed genes corresponds to DNA turns on the nucleoid surface (14–16 genes).

Conclusion

The long-range correlations do not correspond to the domains so far identified in the nucleoid. We explain our results by a model of the nucleoid solenoid structure based on two types of spirals (short and long). The long spirals are uncoiled expressed DNA while the short ones correspond to coiled unexpressed DNA.