An abundance of bidirectional promoters in the human genome.

By N. Trinklein, S. Aldred, S. J. Hartman, D. I. Schroeder, Robert Otillar, Richard M. Myers. Genome Research, 2003

631 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/2fa9c22878a6a905cb0363e6c7961065a29d1319

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Citations in the corpus

The Genetic Signatures of Noncoding RNAs (2009, neutral): “Conservation of genomic position [31,33,34]”
Genome-wide analysis of mammalian promoter architecture and evolution (2006, background): “CpG island promoter regions are also commonly associated with bidirectional promoter activit”
Genome-wide transcription and the implications for genomic organization (2007, background): “Consistent with these recent observations, 10% of all human genes lie 'head-to-head' (that is, they are transcribed in opposite directions, with their promoters being closest to each other), less than 1,000 bp apart, and are regulated by the same genomic sequenc”
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. (2008, result): “2006), the observed prevalence of positional equivalents is similar to that seen in previous studies (Trinklein et al. 2004; Engstrom et al. 2006) and supports the significance of the association between some ncRNAs and their adjacent protein-coding genes.”
Genome-wide computational identification and manual annotation of human long noncoding RNA genes. (2010, background): “…divergent over convergent gene pairs may merely reflect the known genomic excess of adjacent gene pairs driven by putative bidirectional promoters (Trinklein et al. 2004), and may in part reflect specifically the incidence of lncRNA gene-coding gene bidirectional pairs in mammalian genomes…”
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers (2014, neutral): “…of a pair, 3) are separated by 110bp on average, 4) are bound by central transcription activators, 5) are flanked on both sides by positioned nucleosomes, and 6) have histone modifications typically associated with transcription initiation, present in proportion to the amount of transcription.”
The Major Architects of Chromatin: Architectural Proteins in Bacteria, Archaea and Eukaryotes (2008, background): “Moreover, the gene products of many of these divergent promoters are often co-expressed (Trinklein et al., 2004).”