2004/01/01 by Nathan D. Trinklein, Shelley Force Aldred, Sara J. Hartman +3 · 8 citations
Biochemistry, Genetics and Molecular Biology · Agricultural and Biological Sciences · #Genomics and Chromatin Dynamics #Chromosomal and Genetic Variations #Genetic Mapping and Diversity in Plants and Animals
paper · pdf · doi:10.1101/gr.1982804
openalex publication_date 2004/01/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
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.