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Open Access Research article

A comparative analysis of divergently-paired genes (DPGs) among Drosophila and vertebrate genomes

Liang Yang1 and Jun Yu12*

Author Affiliations

1 James D. Watson Institute of Genome Sciences, College of Life Sciences, Zhejiang University, Hangzhou, PR China

2 CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China

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BMC Evolutionary Biology 2009, 9:55  doi:10.1186/1471-2148-9-55

Published: 11 March 2009

Abstract

Background

Divergently-paired genes (DPGs) are defined as two adjacent genes that are transcribed toward the opposite direction (or from different DNA strands) and shared their transcription start sites (TSSs) less than 1,000 base pairs apart. DPGs are products of a common organizational feature among eukaryotic genes yet to be surveyed across divergent genomes over well-defined evolutionary distances since mutations in the sequence between a pair of DPGs may result in alternations in shared promoters and thus affect the function of both genes. By sharing promoters, the gene pairs take the advantage of co-regulation albeit bearing doubled mutational burdens in maintaining their normal functions.

Results

Drosophila melanogaster has a significant fraction (31.6% of all genes) of DPGs which are remarkably conserved relative to its gene density as compared to other eukaryotes. Our survey and comparative analysis revealed different evolutionary patterns among DPGs between insect and vertebrate lineages. The conservation of DPGs in D. melanogaster is of significance as they are mostly housekeeping genes characterized by the absence of TATA box in their promoter sequences. The combination of Initiator and Downstream Promoter Element may play an important role in regulating DPGs in D. melanogaster, providing an excellent niche for studying the molecular details for transcription regulations.

Conclusion

DPGs appear to have arisen independently among different evolutionary lineages, such as the insect and vertebrate lineages, and exhibit variable degrees of conservation. Such architectural organizations, including convergently-paired genes (CPGs) may associate with transcriptional regulation and have significant functional relevance.