An abundance of bidirectional promoters in the human genome

The alignment of full-length human cDNA sequences to the finished sequence of the human genome provides a unique opportunity to study the distribution of genes throughout the genome. By analyzing the distances between 23,752 genes, we identified a class of divergently transcribed gene pairs, represe...

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Bibliographic Details
Published in:Genome research 2004-01, Vol.14 (1), p.62-66
Main Authors: Trinklein, Nathan D, Aldred, Shelley Force, Hartman, Sara J, Schroeder, Diane I, Otillar, Robert P, Myers, Richard M
Format: Article
Language:English
Subjects:
Animals
Cell Line
Cell Line, Tumor
DNA Repair - genetics
DNA Repair - physiology
Embryo, Mammalian
Fibroblasts - chemistry
Fibroblasts - metabolism
Gene Expression Regulation - genetics
Genes - genetics
Genes - physiology
Genome
Genome, Human
HeLa Cells
Humans
Letters
Mice
Promoter Regions, Genetic - genetics
Promoter Regions, Genetic - physiology
Sequence Analysis, DNA - methods
Transcription, Genetic - genetics
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Summary:The alignment of full-length human cDNA sequences to the finished sequence of the human genome provides a unique opportunity to study the distribution of genes throughout the genome. By analyzing the distances between 23,752 genes, we identified a class of divergently transcribed gene pairs, representing more than 10% of the genes in the genome, whose transcription start sites are separated by less than 1000 base pairs. Although this bidirectional arrangement has been previously described in humans and other species, the prevalence of bidirectional gene pairs in the human genome is striking, and the mechanisms of regulation of all but a few bidirectional genes are unknown. Our work shows that the transcripts of many bidirectional pairs are coexpressed, but some are antiregulated. Further, we show that many of the promoter segments between two bidirectional genes initiate transcription in both directions and contain shared elements that regulate both genes. We also show that the bidirectional arrangement is often conserved among mouse orthologs. These findings demonstrate that a bidirectional arrangement provides a unique mechanism of regulation for a significant number of mammalian genes.
ISSN:1088-9051
1054-9803
DOI:10.1101/gr.1982804