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This article is part of the supplement: Proceedings of the 21st International Conference on Genome Informatics (GIW2010)

Open Access Research

Sorting out inherent features of head-to-head gene pairs by evolutionary conservation

Yun-Qin Chen13, Hui Yu23, Yi-Xue Li123* and Yuan-Yuan Li23*

Author Affiliations

1 School of Life Science and Technology, Tongji University, Shanghai 200092, P.R. China

2 Bioinformatics Center, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, P.R. China

3 Shanghai Center for Bioinformation Technology, Shanghai 200235, P.R. China

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BMC Bioinformatics 2010, 11(Suppl 11):S16  doi:10.1186/1471-2105-11-S11-S16

Published: 14 December 2010



A ‘head-to-head’ (h2h) gene pair is defined as a genomic locus in which two adjacent genes are divergently transcribed from opposite strands of DNA. In our previous work, this gene organization was found to be ancient and conserved, which subjects functionally related genes to transcriptional co-regulation. However, some of the biological features of h2h pairs still need further clarification.


In this work, we assorted human h2h pairs into four sequentially inclusive sets of gradually incremental conservation, and examined whether those previously asserted features were conserved or sharpened in the more conserved h2h pair sets in order to identify the inherent features of the h2h gene organization. The features of TSS distance, expression correlation within h2h pairs and among h2h genes, transcription factor association and functional similarities of h2h genes were examined. Our conservation-based analyses found that the bi-directional promoters of h2h gene pairs are most likely shorter than 100 bp; h2h gene pairs generally have only significant positive expression correlation but not negative correlation, and remarkably high positive expression correlations exist among h2h genes, as well as between h2h pairs observed in our previous study; h2h paired genes tend to share transcription factors. In addition, expression correlation of h2h pairs is positively related with the TF-sharing and functional coordination, while not related with TSS distance.


Our findings remove the uncertainties of h2h genes about TSS distance, expression correlation and functional coordination, which provide insights into the study on the molecular mechanisms and functional consequences of the transcriptional regulation based on this special gene organization.