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This article is part of the supplement: Selected articles from The 5th IEEE International Conference on Systems Biology (ISB 2011)

Open Access Open Badges Research

The preservation of bidirectional promoter architecture in eukaryotes: what is the driving force?

Chao Xu, Jiajia Chen and Bairong Shen*

Author Affiliations

Center for Systems Biology, Soochow University, Suzhou 215006, China

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BMC Systems Biology 2012, 6(Suppl 1):S21  doi:10.1186/1752-0509-6-S1-S21

Published: 16 July 2012



The bidirectional gene architecture has been studied in many organisms, and the conservation of bidirectional arrangement has received considerable attention. However, the explanation for the evolutionary conservation about this genomic structure is still insufficient. In this study the large scale identification and pathway enrichment analysis for bidirectional genes were performed in several eukaryotes and the comparative analysis of this arrangement between human and mouse were dissected for the purpose of discovering the driving force of the preservation of this genomic structure.


We identified the bidirectional gene pairs in eight different species and found this structure to be prevalent in eukaryotes. The pathway enrichment analysis indicated the bidirectional genes at the genome level are conserved in certain pathways, such as the DNA repair and some other fundamental cellular pathways. The comparative analysis about the gene expression, function, between human and mouse bidirectional genes were also performed and we observed that the selective force of this architecture doesn't derive from the co-regulation between paired genes, but the functional bias of bidirectional genes at whole genome level is observed strengthened during evolution.


Our result validated the coexpression of bidirectional genes; however failed to support their functional relevance. The conservation of bidirectional promoters seems not the result of functional connection between paired genes, but the functional bias at whole genome level, which imply that the genome-wide functional constraint is important for the conservation of bidirectional structure.