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MBE Advance Access published online on December 5, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msh040
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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Accepted October 9, 2003
© 2003 Society for Molecular Biology and Evolution

Original Articles

The Origins of Bi-Directional Promoters: Computational Analyses of Intergenic Distance in the Human Genome

Daiya Takai 1* and Peter A. Jones 1

1 Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, 1441 Eastlake Avenue, Los Angeles, California 90033, USA

* To whom correspondence should be addressed. E-mail: dtakai-ind{at}umin.u-tokyo.ac.jp.


  Abstract

We have analyzed intergenic distances and searched for the presence of bi-directional genes using the complete sequences and mapping information of human chromosomes 20, 21 and 22 which contain 2,122 known and predicted genes. Intergenic distances between genes with divergent transcripts were distributed in a biphasic manner with a strong peak of 25 kb and a weak peak of 0.3 kb between the divergent transcripts suggesting that the genes might share a common promoter. The weak peak was not observed at the transcriptional ends of genes. Seventy three percent (55/75 pairs of genes, from a total of 150 genes) of these divergent transcripts located within 1kb of one another were CpG islands. Expression of the divergent transcript genes was not concordant in various human tissues suggesting that they were independently regulated. Analyses of the frequency of occurrence of interspersed repeats in the intergenic sequences suggested that these repeats are strongly excluded from the regions of transcriptional starts. This exclusion might be responsible for the existence of these divergent transcript.

Key Words: Promoter, human genome, intergenic distance, bi-directional, head-to-head, overlapping promoters


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