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Open Access Research article

Analyzing stochastic transcription to elucidate the nucleoid's organization

Alessandra Riva12*, Anne-Sophie Carpentier2, Frédérique Barloy-Hubler3, Angélique Chéron3 and Alain Hénaut2

Author Affiliations

1 Soluscience, Biopôle Clermont-Limagne, 63360 Saint-Beauzire, France

2 Université Pierre & Marie Curie – Paris 6, UMR 7138 "SAE" CNRS UPMC MNHN ENS IRD, Case 05, 7 quai St Bernard, 75005 Paris, France

3 CNRS-UMR 6026-Interactions Cellulaires et Moléculaires, Groupe B@sic, Université de Rennes 1, Campus de Beaulieu, 35042 Rennes, France

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BMC Genomics 2008, 9:125  doi:10.1186/1471-2164-9-125

Published: 10 March 2008

Abstract

Background

The processes of gene transcription, translation, as well as the reactions taking place between gene products, are subject to stochastic fluctuations. These stochastic events are being increasingly examined as it emerges that they can be crucial in the cell's survival.

In a previous study we had examined the transcription patterns of two bacterial species (Escherichia coli and Bacillus subtilis) to elucidate the nucleoid's organization. The basic idea is that genes that share transcription patterns, must share some sort of spatial relationship, even if they are not close to each other on the chromosome. We had found that picking any gene at random, its transcription will be correlated with genes at well-defined short – as well as long-range distances, leaving the explanation of the latter an open question.

In this paper we study the transcription correlations when the only transcription taking place is stochastic, in other words, no active or "deterministic" transcription takes place. To this purpose we use transcription data of Sinorhizobium meliloti.

Results

Even when only stochastic transcription takes place, the co-expression of genes varies as a function of the distance between genes: we observe again the short-range as well as the regular, long-range correlation patterns.

Conclusion

We explain these latter with a model based on the physical constraints acting on the DNA, forcing it into a conformation of groups of a few successive large and transcribed loops, which are evenly spaced along the chromosome and separated by small, non-transcribed loops.

We discuss the question about the link between shared transcription patterns and physiological relationship and come to the conclusion that when genes are distantly placed along the chromosome, the transcription correlation does not imply a physiological relationship.