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

BMC Bioinformatics. 2010 Dec 14;11 Suppl 11(Suppl 11):S16. doi: 10.1186/1471-2105-11-S11-S16.


Background: 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.

Results: 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.

Conclusions: 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Evolution, Molecular*
  • Gene Expression Regulation
  • Genetic Loci
  • Humans
  • Phylogeny
  • Promoter Regions, Genetic
  • Transcription Factors / metabolism
  • Transcription Initiation Site
  • Transcription, Genetic*


  • Transcription Factors