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Open Access Research article

Ranges of control in the transcriptional regulation of Escherichia coli

Nikolaus Sonnenschein1, Marc-Thorsten Hütt1*, Helga Stoyan2 and Dietrich Stoyan2

Author Affiliations

1 School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany

2 Institute of Statistics, TU Bergakademie Freiberg, Prüferstraße 9, 09596 Freiberg, Germany

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BMC Systems Biology 2009, 3:119  doi:10.1186/1752-0509-3-119

Published: 24 December 2009

Abstract

Background

The positioning of genes in the genome is an important evolutionary degree of freedom for organizing gene regulation. Statistical properties of these distributions have been studied particularly in relation to the transcriptional regulatory network. The systematics of gene-gene distances then become important sources of information on the control, which different biological mechanisms exert on gene expression.

Results

Here we study a set of categories, which has to our knowledge not been analyzed before. We distinguish between genes that do not participate in the transcriptional regulatory network (i.e. that are according to current knowledge not producing transcription factors and do not possess binding sites for transcription factors in their regulatory region), and genes that via transcription factors either are regulated by or regulate other genes. We find that the two types of genes ("isolated" and "regulatory" genes) show a clear statistical repulsion and have different ranges of correlations. In particular we find that isolated genes have a preference for shorter intergenic distances.

Conclusions

These findings support previous evidence from gene expression patterns for two distinct logical types of control, namely digital control (i.e. network-based control mediated by dedicated transcription factors) and analog control (i.e. control based on genome structure and mediated by neighborhood on the genome).