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Open Access Research article

Co-expression of adjacent genes in yeast cannot be simply attributed to shared regulatory system

Huai-Kuang Tsai12, Cindy PC Su3, Mei-Yeh J Lu4, Ching-Hua Shih15 and Daryi Wang3*

Author Affiliations

1 Institute of Information Science, Academia Sinica, Taipei 115, Taiwan

2 Research Center for Information Technology Innovation, Academia Sinica, Taipei 115, Taiwan

3 Research Center for Biodiversity, Academia Sinica, Taipei 115, Taiwan

4 Genomics Research Center, Academia Sinica, Taipei 115, Taiwan

5 Department of Ecology and Evolutionary Biology, Rice University, Houston, TX 77005, USA

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BMC Genomics 2007, 8:352  doi:10.1186/1471-2164-8-352

Published: 3 October 2007

Abstract

Background

Adjacent gene pairs in the yeast genome have a tendency to express concurrently. Sharing of regulatory elements within the intergenic region of those adjacent gene pairs was often considered the major mechanism responsible for such co-expression. However, it is still in debate to what extent that common transcription factors (TFs) contribute to the co-expression of adjacent genes. In order to resolve the evolutionary aspect of this issue, we investigated the conservation of adjacent pairs in five yeast species. By using the information for TF binding sites in promoter regions available from the MYBS database http://cg1.iis.sinica.edu.tw/~mybs/ webcite, the ratios of TF-sharing pairs among all the adjacent pairs in yeast genomes were analyzed. The levels of co-expression in different adjacent patterns were also compared.

Results

Our analyses showed that the proportion of adjacent pairs conserved in five yeast species is relatively low compared to that in the mammalian lineage. The proportion was also low for adjacent gene pairs with shared TFs. Particularly, the statistical analysis suggested that co-expression of adjacent gene pairs was not noticeably associated with the sharing of TFs in these pairs. We further proposed a case of the PAC (polymerase A and C) and RRPE (rRNA processing element) motifs which co-regulate divergent/bidirectional pairs, and found that the shared TFs were not significantly relevant to co-expression of divergent promoters among adjacent genes.

Conclusion

Our findings suggested that the commonly shared cis-regulatory system does not solely contribute to the co-expression of adjacent gene pairs in yeast genome. Therefore we believe that during evolution yeasts have developed a sophisticated regulatory system that integrates both TF-based and non-TF based mechanisms(s) for concurrent regulation of neighboring genes in response to various environmental changes.