title: An abundance of bidirectional promoters in the human genome.
abstract: 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.
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA.
authors.forename: Nathan D
authors.initials: ND
authors.lastname: Trinklein
authors.forename: Shelley Force
authors.initials: SF
authors.lastname: Aldred
authors.forename: Sara J
authors.initials: SJ
authors.lastname: Hartman
authors.forename: Diane I
authors.initials: DI
authors.lastname: Schroeder
authors.forename: Robert P
authors.initials: RP
authors.lastname: Otillar
authors.forename: Richard M
authors.initials: RM
authors.lastname: Myers
mesh_terms: D000818:Animals; D002460:Cell Line; D045744:Cell Line, Tumor; D004260:DNA Repair / Q000235:genetics / Q000502:physiology; D004622:Embryo, Mammalian; D005347:Fibroblasts / Q000737:chemistry / Q000378:metabolism; D005786:Gene Expression Regulation / Q000235:genetics; D005796:Genes / Q000235:genetics / Q000502:physiology; D016678:Genome; D015894:Genome, Human; D006367:HeLa Cells; D006801:Humans; D051379:Mice; D011401:Promoter Regions, Genetic / Q000235:genetics* / Q000502:physiology; D017422:Sequence Analysis, DNA / Q000379:methods; D014158:Transcription, Genetic / Q000235:genetics